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Entries in "Science"

January 08, 2012

Guess I won't be invited to write for The Huffington Post

They have started a new science section and Arianna Huffington says this of her hopes for it:

I'm particularly looking forward to HuffPost Science's coverage of one of my longtime passions: the intersection of science and religion, two fields often seen as contradictory -- or at least presented that way by those waging The War on Science. A key part of HuffPost Science's mission will be to cut through the divisions that have resulted from that false war.

Rather than taking up arms in those misguided, outdated battles, HuffPost Science will work in the tradition of inquisitive minds that can accommodate both logic and mystery. It's a tradition exemplified by Brown University biology professor Kenneth Miller, who, when I visited with him last year, told me that he sees Darwin not as an obstacle to faith but as "the key to understanding our relationship with God."

Ah, yes, the old "accommodate both logic and mystery" ploy, as Inspector Clousseau would say. Expect to see full-bore accommodationism that tells you that magical thinking is perfectly compatible with science, as long as you throw in sexy sciency words such as 'quantum' and 'indeterminancy' to mask the woo that lurks beneath. I don't know why they don't call it the 'Deepak Chopra section' and be done with it.

January 06, 2012

My brain is already falling apart

A new study says that people start losing their brain powers as early as 45 years of age.

The results of the tests show that cognitive scores declined in all categories except vocabulary - and there was a faster decline in older people.

The study found a 9.6% decline in mental reasoning in men aged 65-70 and a 7.4% decline for women of the same age.

For men and women aged 45-49, there was a 3.6% decline.

Since my work involves mainly words, the lack of decline in vocabulary skills may be masking my decrepitude.

The study can be read here.

January 04, 2012

The wonder of science

One of the common criticisms that one hears against us science-based atheists is that our search for naturalistic explanations of hitherto mysterious phenomena, coupled with a relentless assault on irrational and unscientific thinking, results in all the wonder being drained from life. We are told, for example, that to explain that the rainbow is the product of multiple scattering of light by water droplets in the air is to somehow detract from its beauty or that when gazing at the billions of twinkling stars on a beautifully clear cloudless night, to be aware that they are the products of nuclear fusion reactions that took place billions of years ago is to reduce their grandeur.

I must say that I don't understand the criticism. For me at least, understanding how these things come about actually enhances my sense of wonder about the universe. The more I learn about how the universe works and how the impersonal forces of nature created everything around us, the more I am impressed.

To illustrate my point, I am now going to show you something that I think is incredibly beautiful. It is the equation:

T = 2tanh^-1(√Ω_Λ)/(3H₀√Ω_Λ)

So what is so great about this equation? It is the equation that tells us the age of the universe. Note that the age T depends on just two quantities H₀ and the square root of Ω_Λ, both of which are measured quantities. H₀ is the value of the Hubble constant at the present time and is given by the slope of the straight line obtained when one plots the speed of distant galaxies (on the y-axis) versus the distance to those galaxies (on the x-axis). Ω_Λ is the ratio of the density of dark energy in the universe to the total energy density of the universe.

As with all scientific results, there are some basic theoretical assumptions that go into obtaining them. This particular one requires that the universe be governed by Einstein's equations of general relativity and that its current state is 'matter dominated' (i.e., the energy contribution of pure radiation is negligible) and 'flat' (i.e., the total density of the universe is at its critical value so that the curvature of space is neither convex nor concave). These 'assumptions' are supported by other measurements, so they are not arbitrary.

The values of H₀ and Ω_Λ are obtained using satellite probes that collect a vast body of data from stars and galaxies and scientists then do a best fit to those data for multiple parameters, of which these are just two. The current values were obtained in 2009 by the WMAP (Wilkinson Microwave Satellite Probe) satellite launched in 2001, and are given by H₀=70.5 km/s/Mpc and Ω_Λ=0.726. Insert these values into the above equation (with the appropriate units) and you get that the age of the universe is 13.7 billion years.

Why do I think this equation is a thing of extraordinary beauty? Just think about the implications of that equation for a moment. We humans have been around for just an infinitesimally small period of time in history and occupy an infinitesimally small part of the universe. And yet we have been able, using pure ingenuity and by steadily building upon the scientific achievements of our predecessors, to not only figure out the large-scale structure of the vast universe we happen to occupy but to determine, in a simple equation, its actual age! That is truly incredible. If that does not strike you with wonder, then I don't know what will.

Furthermore, note how simple the equation is. The tanh^-1 function (which represents the inverse of the hyperbolic tangent) may be intimidating for some but it is such a standard mathematical function that it can be found on any scientific hand calculator. If a news report states that new satellite data have given revised best fit values for by H₀ and Ω_Λ, anyone can calculate the revised age of the universe themselves in a few minutes.

But as this xkcd cartoon captures accurately, it is not that scientists lose their sense of wonder but that they find wonder in learning about the universe, and do not need to invoke mystery to sense it.

December 31, 2011

Antonio Damasio on the quest to understand consciousness

December 26, 2011

New particle state discovered at CERN

While a lot of the science media attention has focused on the search for the Higgs boson, we should not forget that that is not sole purpose of the Large Hadron Collider at CERN. Its high energies allow it to do more conventional work and there is now a report of the discovery of an excited state of the bottom quark-antiquark, a consequence of the standard model of particle physics. The preprint of the paper can be read here.

December 07, 2011

The factors that drive obedience and conformity

There was an old TV program called Candid Camera that used hidden cameras to capture what people did when confronted with awkward or unexpected situations. While the aim of the program was humorous, usually at the expense of the hapless person who happened to be caught on camera, some of the episodes serve as useful experiments on human behavior.

One particularly revealing one involved the desire of people to conform to powerful norms of behavior that we all follow without even thinking about it. For example, when people get into an elevator, they space themselves as far as possible from others, immediately turn around and face the front, and not make eye contact or speak, apart from sometimes a quick nod of greeting upon entering. But in this episode, the camera noted what happens when the norms seem to suddenly change.

Although the above experiment is amusing, psychologist Philip Zimbardo, the person behind the famous Stanford Prison Experiment (SPE) , reflects on it and the Milgram obedience study, and says that the Candid Camera elevator experiment reveals how the strong desire to conform to the norms of the people around us can lead to behaviors that are evil, something he calls 'the Lucifer effect'. (Zimbardo has written a book titled The Lucifer Effect: Understanding How Good People Turn Evil that I have bought and plan to read and write about soon.)

Zimbardo points an interesting feature in the Milgram obedience and the SPE studies about the role that religion plays in the willingness to obey authority and inflict pain on others even when one's own moral instincts are repulsed by the idea.

The large, diverse cast of ordinary characters in the obedience studies and the normal, healthy, intelligent cast in the prison study also serve to make vivid the tragic conclusion that we all hate to acknowledge: The goodness of Everyman and of Everywoman can be transformed and overwhelmed by the an accumulation of small forces of evil. The character transformation seen in many of the participants in both studies represents "The Lucifer Effect" in action. Both studies teach us lessons about authority; the obedience research teaches us to question authority when it is excessive and unjust, while the SPE teaches us the dangers of too little responsible authority when it is needed to perform oversight of the behavior of individuals within its agency.
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Religious upbringing also comes to play in a complex way, leading both to unquestioning obedience to doctrinal beliefs as well as a profound caring for one's fellows. The first values should lead to greater obedience to authority in the Milgram paradigm, while the second should lead to less obedience to such authority. Support for the first prediction comes from a Milgram-like study that compared participants with various measured levels religious orientation in the extent to which they obeyed one of three authority figures: neutral, scientific, or religious. The results reveal that the shock scores elicited in this experiment were highest for the most religious participants, less for those moderately religious, and lowest for the least religious. Among those highly and moderately religious, the scientific and religious authorities were more effective than the neutral authority in eliciting the most obedience. Those who scored lowest on the religious measures, that centered around beliefs that one's life is under divine control, tended to reject any authority, be it religious or scientific. [My emphasis]

There is no question that scientific figures carry authority which is why scientific malpractice or fraud is taken so seriously. It is perhaps not hard to see why being religious or having a religious authority figure makes people more likely to be persuaded to go along with cruel acts. Religious people have usually been indoctrinated from childhood to believe that god is the ultimate authority figure and that unquestioning obedience to god's commands constitutes a virtue that will be rewarded. Their religious texts also have countless examples of the most appalling atrocities that their god has done or commanded people to do and which are supposed to serve a greater good. The appalling doctrine known as 'divine command theory' justifies such actions by saying that whatever god commands has to be good, even if it goes against every norm of humane behavior. Such beliefs can be a powerful force that can overcome the scruples that come with normal feelings of empathy towards other living things.

As a side note, a few months ago, I wrote about people who get lost in Death Valley and have even died because they followed the instructions of their GPS system even when it erroneously instructed them to take roads that barely existed. I wonder if that is another symptom of this phenomenon. After all, an assured and confident disembodied voice telling them what to do is somewhat like what they imagine some god-like authority figure would do, and they follow blindly.

December 05, 2011

Sleep

I like to sleep. I need a minimum of eight hours a night. But it is not just the good feeling that comes with resting that I find attractive. I really enjoy sleeping, the sensation of drowsing off, and usually have no difficulty doing so anywhere at any time, even on cramped airline seats on long flights. On weekends, I take a long nap after lunch and sometimes take a short nap seated up at my desk during the weekday.

I used to worry that this was a sign that I was lazy but learned later that most people don't get enough sleep and that this can really be harmful.

Here is a 60 Minutes report on the importance of getting enough sleep every day.

Now comes a new study that suggests that the variations in sleep needs can be traced to the influence of a specific gene.

I learned from the news report that Einstein needed 11 hours of sleep per night, which makes me a real slacker in the sleep department.

November 30, 2011

Inequality makes us less happy

Via reader Norm, I learned about a new study using brains scans that suggest that people are aren't nearly as self-interested as some might think and that inequality makes people unhappy. "The scientists speculate that people have a natural dislike of inequality. In fact, our desire for equal outcomes is often more powerful (at least in the brain) than our desire for a little extra cash. It's not that money doesn't make us feel good — it's that sharing the wealth can make us feel even better."

November 29, 2011

Curiosity landing

The Mars explorer named Curiosity was launched successfully on Saturday and is expected to land on the planet on August 6, 2012. Because Curiosity is a much larger object than previous explorers, engineers needed to develop a new way of giving it a soft landing and this new technique is causing some anxiety to mission scientists about whether the rover can survive the landing. Some of them refer to the final stages of the landing as 'six minutes of terror'.

You can see an animation (made back in 2005) of what the landing should look like.

Here is a test run of the final stage done in the laboratory.

November 17, 2011

Where does our morality come from?

For reasons that are not clear to me, some religious people seem to think that the moral sense that we possess is evidence for god. In fact, some of them (such as Francis Collins in his book The Language of God) go so far as to claim that this is a really powerful argument for god. They point to the fact that there are quite a few moral impulses that seem to be universal and claim that this must mean that they were implanted in us by god.

This is a specious argument. In my series of posts on the biological basis for justice and altruism (part 1, part 2, part 3, and part 4), I discussed how our ideas of justice and our altruistic impulses can be traced to biological origins. What science is making abundantly clear is that the foundation of our moral senses also are evolutionary in origin and that culture builds on those basic biological impulses to create moral system of increasing generality.

Paul Bloom has studied this question by looking at what we can learn about the moral thinking of babies and in his article The Moral Life of Babies in the New York Times issue on May 5, 2010 writes:

The notion at the core of any mature morality is that of impartiality. If you are asked to justify your actions, and you say, "Because I wanted to," this is just an expression of selfish desire. But explanations like "It was my turn" or "It's my fair share" are potentially moral, because they imply that anyone else in the same situation could have done the same. This is the sort of argument that could be convincing to a neutral observer and is at the foundation of standards of justice and law. The philosopher Peter Singer has pointed out that this notion of impartiality can be found in religious and philosophical systems of morality, from the golden rule in Christianity to the teachings of Confucius to the political philosopher John Rawls's landmark theory of justice. This is an insight that emerges within communities of intelligent, deliberating and negotiating beings, and it can override our parochial impulses.

The aspect of morality that we truly marvel at — its generality and universality — is the product of culture, not of biology. There is no need to posit divine intervention. A fully developed morality is the product of cultural development, of the accumulation of rational insight and hard-earned innovations. The morality we start off with is primitive, not merely in the obvious sense that it's incomplete, but in the deeper sense that when individuals and societies aspire toward an enlightened morality — one in which all beings capable of reason and suffering are on an equal footing, where all people are equal — they are fighting with what children have from the get-go.
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Babies possess certain moral foundations — the capacity and willingness to judge the actions of others, some sense of justice, gut responses to altruism and nastiness. Regardless of how smart we are, if we didn't start with this basic apparatus, we would be nothing more than amoral agents, ruthlessly driven to pursue our self-interest. But our capacities as babies are sharply limited. It is the insights of rational individuals that make a truly universal and unselfish morality something that our species can aspire to.

There is a nice video of the experiments that Bloom has done with babies.

This is why science and religion are at loggerheads. As science advances, religion simply has less room to exist. This is true in all areas of knowledge and, in particular, in the area of morality. We now realize that evolution has given us two great gifts: basic moral instincts and the capacity to reason. The latter has enabled us to build on the former and create the complex moral systems that currently exist. God is entirely superfluous.

November 16, 2011

General relativity versus modified Newton theories of gravity

In the case of the large-scale structure of the universe, the dominant paradigm is that the dynamics of the universe are governed by the theory of general relativity, augmented by the postulation of the existence of dark matter and dark energy. Classical Newtonian theory of gravity was not believed to hold, because it could not explain many features of galaxies.

But in science, one can always come up with alternative theories to the dominant paradigm to explain any phenomenon and there have been efforts to develop what are known as MOND theories (standing for MOdified Newtonian Dynamics) to explain the properties of the universe that would dispense with general relativity and revert to Newtonian gravity with slight modifications. Via blog reader Hunter, I came across this article that says that they have tested one form of the MOND hypothesis and found that it cannot explain the measured gravitational redshift of galaxy clusters, while general relativity and dark matter can.

This does not definitely rule out MOND theories since any theory can always be tweaked to accommodate any experimental result. But such negative results do make them less plausible to scientists.

November 02, 2011

Richard Feynman on science

He makes a good analogy for how scientists go about their work.

October 30, 2011

What use is half a wing?

Creationists like to challenge the theory of evolution by asking how it can be that things can evolve incrementally since in its early stages the new feature seems to lack its final functionality. They pose questions like "What is the use of half an eye or half a wing?" Of course, scientists have long explained this. They have shown how the eye could have evolved by tiny changes and in fact even right now almost the full spectrum of differential eye development can be seen in existing species.

They have also pointed out that it is a mistake to assume that the final functionality of a feature was the only functionality all along, and that features may have had other functions in the early stages and only later became adapted to its final use.

Carl Zimmer had a nice article earlier this year in National Geographic about the evidence that feathers might have evolved for a different purpose long before flight occurred. More recently, he reports on new research results that add to our knowledge of what purpose those non-flying feathers in primitive wing forms might have served.

October 25, 2011

Climate change skeptic changes mind

Global-warming deniers eagerly embrace anyone who supports their cause, however much of a crank that person may be. So any respectable scientist who expresses skepticism about global warming or who criticizes the work of those scientists who have warned us about it is makes them delirious with joy.

They were particularly pleased when Richard Muller did so because he is a physicist at the University of California-Berkeley and thus comes with good credentials. Based on preliminary work he had done, Muller had said that he thought the previous studies that said global warming was happening were wrong. Republicans invited him to testify to Congress and in 2010 many right wing groups, including the Koch brothers, were willing to fund his Berkeley Earth Surface Temperature (BEST) project, which aimed to do a new and independent study as a check on all the other global warming studies, no doubt expecting him to contradict them.

But things didn't go quite according to plan. In a press release announcing the first set of four papers that they have submitted to journals, Muller says, "Our biggest surprise was that the new results agreed so closely with the warming values published previously by other teams in the US and the UK." In an op-ed in the Wall Street Journal titled The Case Against Global-Warming Skepticism: There were good reasons for doubt, until now, Muller reinforced that message, adding:

When we began our study, we felt that skeptics had raised legitimate issues, and we didn't know what we'd find. Our results turned out to be close to those published by prior groups. We think that means that those groups had truly been very careful in their work, despite their inability to convince some skeptics of that. They managed to avoid bias in their data selection, homogenization and other corrections.

Global warming is real. Perhaps our results will help cool this portion of the climate debate.

One has to be a bit concerned that Muller announced his results in a press release and in a newspaper op-ed and not after the papers had undergone peer review. Bypassing the normal processes of science and going straight to the public tends not to have good results.

The problem for climate change skeptics when they try to co-opt real scientists to their cause is that real scientists deal with the data they have and not the data they wish they had. Whatever the private beliefs of scientists, they cannot go outside the bounds allowed them by the data, unless they are dishonest and suppress or fabricate them.

As Kevin Drum comments:

The BEST report is purely an estimate of planetary warming, and it makes no estimate of how much this warming is due to human activity. So in one sense, its impact is limited since the smarter skeptics have already abandoned the idea that warming is a hoax and now focus their fire solely on the contention that it's man-made. (And the even smarter ones have given up on that, too, and now merely argue that it's economically pointless to try to stop it.) Still, the fact that climate scientists turned out to be careful and thorough in their basic estimates of temperature rise surely enhances their credibility in general. Climategate was always a ridiculous sideshow, and this is just one more nail in its coffin. Climate scientists got the basic data right, and they've almost certainly gotten the human causes right too.

Those deniers, like James M. Taylor of the Heartland Institute who had earlier embraced Muller as one of them are now disowning him, calling these new results "meaningless" and attacking his credibility, saying that he might be having the "intent of deceiving casual observers about the true nature of the global warming debate." Other deniers are also edging away from their earlier embrace of Muller.

Global warming deniers will probably still give a platform to people like the Briton Lord Monckton, who has made quite a name for himself talking about this subject even though he has no expertise whatsoever in this area and makes outrageous statements such as calling an Australian government climate adviser a Nazi. The Australian comedy show The Chasers interviews Monckton and he clearly has no suspicions until the very end that his leg is being pulled and that he is being made to look a fool.

October 23, 2011

Siri and the Turing test

I don't have an iPhone of any kind but was intrigued by the reports of the latest one that had the voice recognition software known as Siri that seems to have a conversational ability reminiscent of HAL in 2001: A Space Odyssey, as can be seen from this compilation of a conversation.

I am not sure if this is a hoax but the person who put up the video assures skeptics that this is real and says that anyone can test it by getting hold of a Siri-enabled iPhone. I am curious if any blog reader who has it can confirm.

As an aside, I am a bit bothered by Siri referring to the user as 'Master'. I know it is not a real person but the feudal overtone is jarring.

Taking his claims at face, it seems as if Siri is able to pass at least a low-level Turing test.

October 21, 2011

When did humans arrive in the Americas?

It used to be thought that they came 13,000 years ago across the then-existing land bridge connecting Siberia and Alaska, during what is known as the 'Clovis' period.

A paper published today in the journal Science has measured with high precision (with new techniques) the age of a mastodon fossil bone with a weapon point embedded in it that was found in 1970. It found that it is 13,800 years ago, with an uncertainty of only 20 years, suggesting that humans were here earlier than thought, supporting other evidence that there was human hunter activity here as early as 15,000-16,000 years ago.

A large number of mammals (mastodons, woolly mammoths, sabre-toothed cats, giant sloths, camels) disappeared rapidly around 12,700 years ago and it was thought that this must have been due to rapid climate change as the Ice Age ended, since Clovis hunters were not thought to have been around for that long.

But the new earlier date for humans in the Americas suggests that mammal extinction may have been accelerated by humans hunting them with weapons.

October 18, 2011

Scientific responsibility

Science has a unique role in the growing recognition that it is the source of authoritative and reliable knowledge. But that carries with it a great burden to make sure that the public's trust is not abused. Via Machines Like Us, I learned about the General Assembly of the International Council for Science (ICSU) issuing a statement last month on "The Principle of Universality (freedom and responsibility) of Science" that spelled out what the responsibilities of scientists are.

The free and responsible practice of science is fundamental to scientific advancement and human and environmental well-being. Such practice, in all its aspects, requires freedom of movement, association, expression and communication for scientists, as well as equitable access to data, information, and other resources for research. It requires responsibility at all levels to carry out and communicate scientific work with integrity, respect, fairness, trustworthiness, and transparency, recognising its benefits and possible harms.

This followed up on the second World Conference on Research Integrity held in Singapore in July 2010 that issued a statement that "emphasizes the need for honesty in all aspects of research, accountability in the conduct of scientific research, professional courtesy and fairness in working with others, and good stewardship of research on behalf of others."

Scientists have to be vigilant in maintaining these standards.

October 01, 2011

Carl Sagan

I never met Carl Sagan but in addition to being a good scientist, prolific writer, great popularizer and advocate for science, he had the reputation of being a really nice person, which is probably why so many of us mean and nasty new atheists are urged to be more like him.

Neil deGrasse Tyson relates an anecdote that reinforces that last characteristic.

The true character of a person is revealed in the way they treat people who, by the usual standards of society, are of no importance to them whatsoever.

September 29, 2011

Lioness saves her cub

I am a sucker for animal stories that have happy endings.

Another example of altruism in the animal kingdom.

September 28, 2011

Reading your brains

A new study reports that fMRI machines can roughly reconstruct the images of film clips that test subjects have been viewing.

What I found interesting was that the reconstructed images, while retaining the general shape of the original, seemed to replace the details with what to me seemed like the details of another image.

September 26, 2011

Narrowing the search for the Higgs particle

It looks like the search for the elusive Higgs particle is getting close. The so-called Standard Model of particle led to the existence of the Higgs being proposed 1964 as an explanation of how elementary particles get their mass and it is the final particle of the model to be yet directly detected. If it is not found, that would require us to re-think some important theories of particle physics.

They are hoping for something definite to emerge within the next year. But if the Higgs is not found by then, the search may drag on longer because concluding that something is not there is more difficult than concluding that it is.

September 23, 2011

Faster-than-light neutrinos?

I came across this BBC report about some observations at CERN that suggested that neutrinos may be traveling faster than the speed of light. If this is true, it would mean that one of the pillars of modern science, the theory of special relativity, would have to undergo serious scrutiny.

I personally was not too excited by the news and was not even planning to comment on it but it seems to be causing a media sensation and several blog readers sent me clippings from various sources and asked for my opinion, so here it is.

I think that this result is unlikely to hold up and so am not too excited. The reason that I am underwhelmed is that I have been around long enough to recall many previous sightings of tachyons (the technical term for faster-than-light particles) that turned out to be false alarms. They are like Elvis sightings in that there is an initial flurry of excitement that then fades under closer scrutiny. The scientists who reported the recent events are aware of this history and are understandably cautious about making any grandiose claims. They can depend on the media to do that. If other research groups study this is some detail and the results hold up, then there will be cause for excitement. This will likely take a couple of years. Until then, I treat this with considerable skepticism.

So my present attitude is captured in this xkcd cartoon that I saw via Jeff at Have Coffee Will Write.

Sorry to be such a downer but if the history of science teaches us anything it is that the great and enduring theories of physics are never overthrown on the basis of a single experiment.

September 22, 2011

The scientific basis for justice and altruism-part 4

(An expanded version of a talk given at CWRU's Share the Vision program, Severance Hall, Friday, August 26, 2011 1:00 pm. This program is to welcome all incoming first year students. My comments centered on the ideas in the common reading book selection Justice: What's the right thing to do? by Michael Sandel. See part 1, part 2, and part 3.)

In the previous post, I pointed out that experiments with babies suggested that although the theory of evolution supports the idea that the desire for justice and fairness is part of our genetic makeup, it is also limited in that seems to stop with our relatives and immediate community or nation. It is not entirely limited, though. There are many examples in evolution of characteristics that evolved to serve one purpose but then get used for other purposes. Sex is a good example. The pleasure it gives served the purpose of encouraging procreation but now people indulge in it for pleasure alone. Similarly, although the desire for justice my have evolved within the domain of kin and the immediate community to benefit the propagation of genes, it can still drive our relationships with the broader community even when there is no genetic benefit.

But there is another important evolutionary development that extends the drive for justice and fairness. What ethicist Peter Singer points out in an excellent book titled The Expanding Circle (2009) is that evolution has also given us the power of reasoning and it is the use of this power that has enabled us to build upon our biological sense of justice to encompass more and more people within our sphere of concern. In other words, our reasoning power has enabled us to go far beyond the initial biological impulse to seek justice only for our relatives and local community and has helped us to develop the idea of impartiality, which is a core feature of the desire for justice.

The way this happens is that while biology might instill in us a desire to treat just our own relatives fairly, our sense of reason tells us that there is nothing particularly special about our families, that ours is just one among many families and that all of them are equally worthy of being treated as fairly as our own. It is then a natural extension to realize that our own community or nation is also just one among many communities and nations and that they deserve fairness and justice too. Once we start reasoning along those lines, the advance is inexorable and we start increasing the size of the circle that encompasses our concern. Reason can overcome parochialism.

As a result of this process, over time we can see that the circle of concern has expanded greatly. We now think that discrimination towards anyone based on gender, race, ethnicity, national origin, sexuality, etc. is wrong. We are also expanding the circle to include non-human animals, with the realization that they too should have many of the rights that we take for granted. As a result we see the rise of animal rights movements, the increased adoption of vegan and vegetarian diets, the drive to eliminate factory farming to ensure that animals are treated humanely, much stricter controls on animal research, and so on.

So while the basic drive for justice and fairness is innate in us, in the sense that it is hardwired into our genetic makeup as a result of our evolutionary history, it required the further evolutionary development of the sense of reason to bring it to fruition, where we seek to maximize justice for everyone, not just our own group.

In his essay Morals Without God?, primatologist Frans de Waal said that Charles Darwin foresaw that this expanded concept of morality would follow naturally in any species that developed social instincts along with sophisticated intellectual powers:

Charles Darwin was interested in how morality fits the human-animal continuum, proposing in The Descent of Man: "Any animal whatever, endowed with well-marked social instincts … would inevitably acquire a moral sense or conscience, as soon as its intellectual powers had become as well developed … as in man."

As Sandel makes clear in the book, it is not always clear or obvious how to decide what is just in any given situation. What is clear is the importance of developing our ability to reason, so that we can break free of, and rise above, our tribal instincts that makes us want to give special privileges and favors to our own group that we deny to others.

This is where all of you are particularly fortunate. For the next four years, you will be in an environment at Case Western Reserve University that is dedicated almost exclusively to helping you develop your sense of reason and all the other critical thinking skills. During this period of your education you will have access to the finest teachers and scholars, incredible knowledge resources in the library, and most importantly, like-minded and concerned fellow students. You should take maximum advantage of this opportunity to equip yourself with the knowledge and reasoning powers to overcome the challenges you will undoubtedly face in your lifetime.

Such a deep education will also enable you to better judge what is the right thing to do. It is important to do so because the quality of our entire civic life depends on having people work for justice. The writer H. L. Mencken put it well when he said, "If you want peace, work for justice."

September 21, 2011

Earth seen from the ISS

This time-lapse film of the Earth as viewed from the International Space Station is nice to see.

It also shows that the ISS and the shuttles did not fly as far out in space as people often think, being on average just about 225 miles up. So they are quite close to the Earth.

The scientific basis for justice and altruism-part 3

(An expanded version of a talk given at CWRU's Share the Vision program, Severance Hall, Friday, August 26, 2011 1:00 pm. This program is to welcome all incoming first year students. My comments centered on the ideas in the common reading book selection Justice: What's the right thing to do? by Michael Sandel. See part 1 and part 2.)

There is considerable evidence that the desire for justice and fairness is innate in us. In an article titled The Moral Life of Babies (New York Times, May 5, 2010) child development psychologist Paul Bloom describes how very young children have a strong sense of justice.

A growing body of evidence, though, suggests that humans do have a rudimentary moral sense from the very start of life. With the help of well-designed experiments, you can see glimmers of moral thought, moral judgment and moral feeling even in the first year of life. Some sense of good and evil seems to be bred in the bone.

He reports on experiments in which babies were presented with puppets who either helped or hindered other puppets.

In the end, we found that 6- and 10-month-old infants overwhelmingly preferred the helpful individual to the hindering individual. This wasn’t a subtle statistical trend; just about all the babies reached for the good guy.
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We found that, given a choice, infants prefer a helpful character to a neutral one; and prefer a neutral character to one who hinders. This finding indicates that both inclinations are at work — babies are drawn to the nice guy and repelled by the mean guy. Again, these results were not subtle; babies almost always showed this pattern of response.

Sometimes the babies were quite emphatic about their preferences.

Not long ago, a team of researchers watched a 1-year-old boy take justice into his own hands. The boy had just seen a puppet show in which one puppet played with a ball while interacting with two other puppets. The center puppet would slide the ball to the puppet on the right, who would pass it back. And the center puppet would slide the ball to the puppet on the left . . . who would run away with it. Then the two puppets on the ends were brought down from the stage and set before the toddler. Each was placed next to a pile of treats. At this point, the toddler was asked to take a treat away from one puppet. Like most children in this situation, the boy took it from the pile of the "naughty" one. But this punishment wasn’t enough — he then leaned over and smacked the puppet in the head.

The toddlers also watched pairs of puppets in which one puppet did a good or bad thing and the other puppet rewarded or punished the first. Of the four possible combinations of actions and consequences, toddlers overwhelmingly preferred the puppets that rewarded good acts and punished bad acts over puppets that rewarded bad acts and punished good acts. This showed that the babies were not basing their preferences on what they perceived as good or bad actions but viewed the actions in the context of the purpose they served. This is pretty sophisticated thinking about crime and punishment and justice.

The desire for justice is strong and biological but is limited. For example, toddlers tend to prefer people of their own races, who speak their own language and share their taste in food. Bloom writes that:

3-month-olds prefer the faces of the race that is most familiar to them to those of other races; 11-month-olds prefer individuals who share their own taste in food and expect these individuals to be nicer than those with different tastes; 12-month-olds prefer to learn from someone who speaks their own language over someone who speaks a foreign language. And studies with young children have found that once they are segregated into different groups — even under the most arbitrary of schemes, like wearing different colored T-shirts — they eagerly favor their own groups in their attitudes and their actions.

So are babies and little children racists? If you waggle your finger and go "kitchy-coo" at a baby of a different racial group, will it bite you? It might, but the babies are not making conscious decisions to prefer their own, which is the real mark of racism. They are simply reacting instinctively based on their biology. So biology seems to strongly suggest that our desire for justice, though it is biologically based on our long history of evolution, is also limited to our in-group. This difference in the way we treat in-group members versus the way we view those who are 'out-group' members can and does lead to all manner of strife and tribal behavior between communities, religions, castes, and nations.

So does the theory of evolution say that our biological desire for justice stops with our relatives and immediate community or nation? In the next and final post in this series, I will look at how we overcome that kind of parochialism.

September 20, 2011

The biological basis for justice and altruism-part 2

(An expanded version of a talk given at CWRU's Share the Vision program, Severance Hall, Friday, August 26, 2011 1:00 pm. This program is to welcome all incoming first year students. My comments centered on the ideas in the common reading book selection Justice: What's the right thing to do? by Michael Sandel. See part 1 here.)

The primatologist Frans de Waal in his excellent book The Age of Empathy (2009) provides case study after case study of animals displaying a keen sense of justice and fairness, providing convincing evidence that these impulses are innate in us and arise from our common evolutionary history with other animals. In a newspaper article titled Morals Without God? he writes about his observations:

Chimpanzees and bonobos will voluntarily open a door to offer a companion access to food, even if they lose part of it in the process. And capuchin monkeys are prepared to seek rewards for others, such as when we place two of them side by side, while one of them barters with us with differently colored tokens. One token is "selfish," and the other "prosocial." If the bartering monkey selects the selfish token, it receives a small piece of apple for returning it, but its partner gets nothing. The prosocial token, on the other hand, rewards both monkeys. Most monkeys develop an overwhelming preference for the prosocial token, which preference is not due to fear of repercussions, because dominant monkeys (who have least to fear) are the most generous.
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It is not only humans who are capable of genuine altruism; other animals are, too. I see it every day. An old female, Peony, spends her days outdoors with other chimpanzees at the Yerkes Primate Center's Field Station. On bad days, when her arthritis is flaring up, she has trouble walking and climbing, but other females help her out. For example, Peony is huffing and puffing to get up into the climbing frame in which several apes have gathered for a grooming session. An unrelated younger female moves behind her, placing both hands on her ample behind and pushes her up with quite a bit of effort, until Peony has joined the rest.

We have also seen Peony getting up and slowly move towards the water spigot, which is at quite a distance. Younger females sometimes run ahead of her, take in some water, then return to Peony and give it to her. At first, we had no idea what was going on, since all we saw was one female placing her mouth close to Peony's, but after a while the pattern became clear: Peony would open her mouth wide, and the younger female would spit a jet of water into it.

Such observations fit the emerging field of animal empathy, which deals not only with primates, but also with canines, elephants, even rodents. A typical example is how chimpanzees console distressed parties, hugging and kissing them, which behavior is so predictable that scientists have analyzed thousands of cases. Mammals are sensitive to each other's emotions, and react to others in need.
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A few years ago Sarah Brosnan and I demonstrated that primates will happily perform a task for cucumber slices until they see others getting grapes, which taste so much better. The cucumber-eaters become agitated, throw down their measly veggies and go on strike. A perfectly fine food has become unpalatable as a result of seeing a companion with something better.

We called it inequity aversion, a topic since investigated in other animals, including dogs. A dog will repeatedly perform a trick without rewards, but refuse as soon as another dog gets pieces of sausage for the same trick. Recently, Sarah reported an unexpected twist to the inequity issue, however. While testing pairs of chimps, she found that also the one who gets the better deal occasionally refuses. It is as if they are satisfied only if both get the same. We seem to be getting close to a sense of fairness.

Can we assume that the human species has also inherited this biological predisposition to justice? Yes, because we are all linked by the great tree of life to all other species. If we go back far enough in our lineages, we will find a common ancestor for all of use, which makes us all effectively cousins, and so you can treat this occasion, where all of us have gathered together in this magnificent concert hall, as a family reunion where you are meeting long-lost relatives. In fact, if you and your pet dog or cat trace your lineages back about a hundred million years, you will find that you have a common ancestor, which is a nice thing to realize.

So given that the desire for justice is so widespread among so many different species, it is very likely that we have inherited the desire for justice from deep evolutionary times. In his book, de Waal concludes that studies in the fields of anthropology, psychology, biology, and neuroscience reveal that we are essentially group animals: "highly cooperative, sensitive to injustice, sometimes warmongering, but mostly peace-loving. A society that ignores these tendencies cannot be optimal." (p. 5)

But is there any direct evidence that humans have a biological predisposition that makes them favor justice and fairness? Yes there is, and I will explore that in the next (and last) post of this series.

September 19, 2011

The biological basis for justice and altruism-part 1

(An expanded version of a talk given at CWRU's Share the Vision program, Severance Hall, Friday, August 26, 2011 1:00 pm. This program is to welcome all incoming first year students. My comments centered on the ideas in the common reading book selection Justice: What's the right thing to do? by Michael Sandel.)

This year's common reading book assumes that there is something fundamental about justice that makes its desirability self-evident. What the book discusses are three approaches to justice: the first based on the greatest happiness for the greatest number, the second on respect for the freedom of choice of individuals, and the third on the cultivation of virtue and the common good.

In this talk, I want to examine the very premise that justice is something desirable. What makes us think that people want or seek justice as an end in itself and that the only problem is how to implement that ideal in specific situations? For example, John Rawls's model of justice (as elucidated in his book The Theory of Justice) assumes that when people are given the opportunity to design a society under the veil of ignorance so that no one knows what situation in life they personally will be placed in, they will create one that is based on the idea of 'justice as fairness'. Is Rawls justified in assuming that? Is it self-evident that justice is such an obvious good thing that people will want to use it as a central organizing principle?

We may think that it is obvious but one of the characteristics of academia is to not accept things just because they seem obvious and instead look for underlying reasons.

It turns out that there is a solid scientific basis for the desire that humans have for justice and it arises from the theory of evolution. This may come as a surprise to those who think of evolution as based on fierce competition for survival in which justice and fairness plays no role. But in fact, not just justice but also altruism, which can be roughly defined as an act that benefits someone else at a personal cost to us, has been studied extensively and we think we know how it originated biologically.

In his landmark book On the Origin of Species, Charles Darwin carefully avoided all discussions of human evolution, limiting it to just one statement near the end: "Light will be thrown on the origin of man and his history." That has to rank as one of the greatest understatements ever. It turns out that the theory of evolution, in addition to providing explanations for the physical features of all life, is increasingly explaining our morality as well. The basic desire for justice is ingrained in us as a result of biological evolution.

The reason for this, as was developed over fifty years ago and summarized by Richard Dawkins in his classic book The Selfish Gene (1989), is that while natural selection acts on the whole organism (whether human or fish or snake), the fundamental unit of evolution is not the whole organism but the individual gene, and evolution can be understood as the means by which individual genes try to maximally propagate themselves. But while organisms are unique in the particular combination of genes they possess, each individual gene is shared by many people, with the closer the relationship, the greater the number of genes being shared. So each one of us shares exactly half our genes with our parents and (on average) half with our siblings, one-eighth of them with our first cousins, and so on, with the fraction shared becoming lower the more distant the kin. As biologist W. D. Hamilton showed, as a result there are circumstances in which can be beneficial for a gene if the organism in which it exists sacrifices its own needs to benefit its relatives. When the eminent population geneticist J. B. S. Haldane, who pioneered a lot of the mathematical studies in this area, was asked if he would give his life to save his brother, he jokingly replied, "No, but I would to save two brothers or eight cousins." In short, the mathematics of genes can favor a limited form of self-sacrifice among relatives and so we should not be surprised if that gene is widely present.

But this kind of altruism, known as kin altruism, is just one form of it. Another important form that was shown by Robert Trivers to be biologically based is reciprocal altruism whereby an organism will do a favor for another that is not a relation in the expectation that in its own time of need the favor will be returned. Take vampires, which seem to have grabbed the public's imagination for some reason and are now all over popular culture. Vampire bats need to drink some blood every day or they will die. But in bat colonies it has been observed that those who return after having obtained a good meal will regurgitate some of the blood to a less fortunate unrelated bat and in return will receive blood from that bat on the days that they are unlucky.

This kind of behavior has been observed in a wide range of animals, and is another source of the idea that our desire for justice has biological roots. Reciprocal altruism only works if people carry out their obligation to return favors. If cheating or other forms of selfishness occur, the system breaks down and so it should not be surprising that quite elaborate structures have evolved in the animal kingdom, of which we are a part, to monitor behavior so as to reward good citizens and punish cheaters, so that the community as a whole benefits.

This sense of fairness and justice even extends to larger groups. For example, there is a remarkable video of penguins in the Antarctic, where temperatures can reach minus 50 degrees Fahrenheit with wind speeds greater than 100 miles per hour. How do they survive in such bitter conditions? They do so by large groups of thousands of them huddling together very closely at a density of about 2 animals per square foot. The temperatures in the inner regions of the group can rise up to our human body temperatures, which is nice and pleasant. Of course, the penguins on the outer rim of the group will be cold but what the video shows is that the density is just sufficient to provide warmth while at the same time allowing for a constant shuffling around. The penguins all face in roughly the same direction and penguins enter at the rear and then slowly work their way to the front and then return to the rear. As a result, each penguin spends a small time on the cold outer rim in return for much longer times in the warmth inside and thus everyone benefits.

Similar cooperative behavior is seen in locusts and fish schools. It is quite remarkable how widespread such practices are in nature.

Next: More evidence from nature

August 30, 2011

A national weight problem?

A new study suggests that obesity is increasing in the US:

Currently, figures from the U.S. Centers for Disease Control and Prevention put the prevalence of overweight and obesity in adults at about 66 percent. But lead study author Dr. Youfa Wang of the Johns Hopkins Bloomberg School of Public Health in Baltimore says that if current overweight and obesity trends continue, 86 percent of Americans could be overweight or obese by the year 2030.

The standard measure used is the body mass index (BMI) that is obtained by diving your mass (measured in kilograms) by the square of your height (measured in meters). This website calculates it for those who use pounds and feet and inches. A BMI of 30 or over indicates obesity while 25 or over means overweight. The 'normal' (i.e., supposedly desirable) range lies between 18.5 and 25

The study's authors also say that, "By 2048, all American adults would become overweight or obese." I tend to be wary of this kind of extrapolation, especially when it involves human behavior. A self-correction usually sets in at some point.

Another study released around the same time projects figures that are not quite as high:

If obesity rates continue to climb in the U.S. as they've done in the past, about half of all men and women could be obese in 20 years, adding an extra 65 million obese adults to the country's population.

The current figure of 66% of overweight and obese adults surprised me. Can it really be that two out of every three people are like that or is the cut-off for being overweight too low? One common comment I hear from overseas visitors is their initial surprise at the number of overweight people they see in the US. Have I simply got used to thinking of larger people as the norm after living in the US for so long?

One of the peculiar features of the coverage of people's weight in the media is the appearance of headless torsos accompanying the stories. News stories on obesity will be accompanied by photos and videos of people from the neck down, an indication of the stigma associated with being overweight. In fact, overweight people are often subjected to gratuitously rude comments and made to feel as if they have some kind of moral failing.

Some are fighting back, saying that they do not see obesity as a disease or even a problem, and definitely not anything to be ashamed of or have to apologize for. They say that that is simply who they are and the rest of the population simply has to deal with it. They have rejected the idea that the word fat is some kind of slur requiring the use of euphemisms to soften it, and have embraced it and made it their own, the way that the gay community did with the word queer. They are fat and proud of it.

The Daily Show had a segment on the coverage of obesity some time ago, and interviewed some who see the campaigns against obesity and the drive to eat healthier as a sign of creeping fascism.

The Daily Show With Jon Stewart	Mon - Thurs 11p / 10c
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August 29, 2011

Hurricane Irene

Cleveland was not in the path of Irene so we just observed it from afar but I am puzzled by those who now claim that it was over-hyped, merely because it caused less damage than expected.

It is quite extraordinary that the National Hurricane Center is able to predict the track and intensity of a swirling storm five days out with pretty good precision, enabling cities and people to take safety precautions. David Kurtz points out that there have been huge gains recently in the ability to predict the track of hurricanes, and less progress in our ability to predict the intensity, as was the case with Irene.

But it was still quite an impressive feat for which the people at the NHC deserve a lot of credit.

August 14, 2011

Tests of the existence of other universes

When Louis de Broglie first proposed in 1924 that particles had wavelike properties, the technological challenges to investigating the idea were so immense that the prospects for testing it seemed to lie very far into the distant future, if at all. But one of the features of science is that however incredible an idea may seem when it is first proposed, if it gains credibility and acceptance from the scientific community as a whole, it will only be a matter of time before someone finds an ingenious way to try and test it. So it was with de Broglie's idea. It was such so beautiful in the way that it unified waves and particles in a symmetric way in quantum mechanics, that it spurred creative thinking and within just three years C. J. Davisson and L. Germer were able to construct an experiment that confirmed it, resulting in de Broglie receiving the Nobel Prize in 1929, an incredibly rapid pace of advance.

So it is with the multiverse idea, that entire universes can be created spontaneously from the vacuum and thus our own universe may be just one of an enormous number (as many as 10⁵⁰⁰) of universes, each having their own laws and structure. This idea not only does not violate the laws of science, it is not even a new theory, being in fact a prediction of other theories.

As with de Broglie's hypothesis, when the multiverse idea was initially proposed there seemed to be no way to test it. But now people have come along with suggestions of how to do it, by looking for disk-like patterns in the cosmic microwave background that may be the telltale relics of collisions of other universes with our own.

Science is such fun.

August 13, 2011

Radioactive heating of the Earth

Recent measurements show that about half of the 40 trillion watts of heat radiated continuously by the Earth comes from radioactivity taking place in its mantle and crust, while the remainder is due to the primordial heat that was created at the formation of the Earth and is located mainly in the core.

Historians of science are aware of the importance of the discovery of the radioactivity as an ongoing source of the heating of the Earth. Before the immense amount of heat associated with radioactive decay was discovered around 1903, physicists like Lord Kelvin had calculated the age of the Earth by treating it as an initially hot body that was steadily cooling. They concluded that it could not be older than 100 million years and could be as low as 20 million years. This made it very difficult, if not impossible, for the theory of evolution by natural selection, because it was a slow process that required long time scales. This was seized upon by religious people to argue against the evolution and in favor of the special creation of species by god. (See my series on the age of the Earth for a more detailed discussion of this.)

The discovery of radioactivity had two revolutionary impacts. It created an awareness that radioactivity was an ongoing source of the heating of the Earth that undermined all the earlier calculations of Kelvin and others, and it provided an important new tool for measuring time that opened the gates to new discoveries that rapidly pushed the age of the Earth to more than four billion years, giving plenty of time for evolution to take place.

August 05, 2011

Is there anything that makes humans special?

Primatologist Frans de Waal's latest book The Age of Empathy (2009) argues against the idea that we humans have some special quality that separates us from all the other animals. Some people, especially those who are religious, seem to be very reluctant to accept that idea that other animal species share pretty much all the same basic physical and emotional characteristics that we humans have.

There is an interesting passage in the book (p. 206-208) where he says that this wrong idea in Christianity, Judaism, and Islam originated because the part of the world in which those religions originated were those that did not contain our closest non-human relatives.

For the Darwinist, there is nothing more logical than the assumption of emotional continuity. Ultimately, I believe that the reluctance to talk about animal emotions has less to do with science than religion. And not just any, religion, but particularly religions that arose in isolation from animals that look like us. With monkeys and apes around every corner, no rain forest culture has ever produced a religion that places humans outside of nature. Similarly, in the East-surrounded by native primates in India, China, and Japan-religions don't draw a sharp line between humans and other animals. Reincarnation occurs in many shapes and forms: A man may become a fish and a fish may become God. Monkey gods, such as Hanuman, are common. Only the Judeo-Christian religions place humans on a pedestal, making them the only species with a soul. It's not hard to see how desert nomads might have arrived at this view. Without animals to hold up a mirror to them, the notion that we're alone came naturally to them. They saw themselves as created in God's image and as the only intelligent life on earth. Even today, we're so convinced of this that we search for other such life by training powerful telescopes on distant galaxies.

It's extremely telling how Westerners reacted when they finally did get to see animals capable of challenging these notions. When the first live apes went on display, people couldn't believe their eyes. In 1835, a male chimpanzee arrived at London Zoo, clothed in a sailor's suit. He was followed by a female orangutan, who was put in a dress. Queen Victoria went to see the exhibit, and was appalled. She called the apes "frightful, and painfully and disagreeably human." This was a widespread sentiment, and even nowadays I occasionally meet people who call apes "disgusting." How can they feel like this unless apes are telling them something about themselves that they don't want to hear? When the same apes at the London Zoo were studied by the young Charles Darwin, he shared the queen's conclusion but without her revulsion. Darwin felt that anyone convinced of man's superiority ought to go take a look at these apes.

All of this occurred in the not too distant past, long after Western religion had spread its creed of human exceptionalism to all corners of knowledge. Philosophy inherited the creed when it blended with theology, and the social sciences inherited it when they emerged out of philosophy. After all, psychology was named after Psykhe, the Greek goddess of the soul. These religious roots are reflected in continued resistance to the second message of evolutionary theory. The first is that all plants and animals, including ourselves, are the product of a single process. This is now widely accepted: also outside biology. But the second message is that we are continuous with all other life forms, not only in body but also in mind. This remains hard to swallow. Even those who recognize humans as a product of evolution keep searching for that one divine spark, that one "huge anomaly" that sets us apart. The religious connection has long been pushed to the subconscious, yet science keeps looking for something special that we as a species can be proud of.

When it comes to characteristics that we don't like about ourselves, continuity is rarely an issue. As soon as people kill, abandon, rape, or otherwise mistreat one another we are quick to blame it on our genes. Warfare and aggression are widely recognized as biological traits, and no one thinks twice about pointing at ants or chimps for parallels. It's only with regard to noble characteristics that continuity is an issue, and empathy is a case in point. Toward the end of a long career, many a scientist cannot resist producing a synopsis of what distinguishes us from the brutes. American psychologist David Premack focused on causal reasoning, culture, and the taking of another's perspective, while his colleague Jerome Kagan mentioned language, morality, and yes, empathy. Kagan included consolation behavior, such as a child embracing his mother, who has hurt herself. This is indeed a great example, but of course hardly restricted to our species. My main point, however, is not whether the proposed distinctions are real or imagined, but why all of them need to be in our favor. Aren't humans at least equally special with respect to torture, genocide, deception, exploitation, indoctrination, and environmental destruction? Why does every list of human distinctiveness need to have the flavor of a feel-good note?

This is one of the fundamental reasons that the Abrahamic religions find it so hard to reconcile their beliefs with science. They have locked themselves into a dogma that human beings are special in some discontinuous way from all other animals, when science is increasingly revealing that all species lie on a continuum with no sharp boundaries. These religions simply cannot live with the idea that what makes us human is just that we have different amounts of same things that are possessed by other animal species.

Religious people keep searching for that one spark of divine fire that reassures them that they are unique and that their god really does care for them in a special way. But they keep repeatedly failing in their quest because the 'soul' (for want of a better term) is like the rainbow, an illusion that keeps receding. It is kind of sad that they never seem to be able to come to terms with their true place in the universe.

I myself find it enormously uplifting to think that I am part of all of life, that I can connect myself to every single thing that lives and has ever lived by tracing a path through the great tree of life. What could be more magnificent than that?

July 27, 2011

How yogis 'levitate'

Hindu mystics have long been claiming that they can, by sheer will and/or the intervention of god, levitate off the ground. Here is one way it is done.

A good rule of thumb is that if something violates the laws of science, it is not a miracle, it is not by 'harnessing the energy field' or some such Deepak Chopraesque mumbo-jumbo, and it is not due to a god. It is merely a trick. The only question to be explored is how the trick is carried out.

July 11, 2011

World Cup soccer final for robots

Exciting!

July 10, 2011

The 44 chromosome man

Almost all human beings have 46 chromosomes (23 pairs) and being born with an extra or missing one usually signifies that the person will have serious medical problems such as Down syndrome.

On the other hand, our close relatives the chimpanzees have 48 chromosomes (24 pairs). The chimps and us shared a common ancestor about 6-8 million years ago. So how did we end up with fewer? This is because about a million years ago, two of the 24 chromosomes in a human fused together end-to-end to form a single longer chromosome. Since the crucial genetic information in each chromosome was preserved by this fusion process, the organism could survive. The evidence suggests that it was chromosomes #12 and #13 that fused to form the present chromosome #2.

The interesting question is how that mutation might have occurred and why it took hold in the human population so that 46 chromosomes is now the standard.

In this fascinating article (sent to me by reader Fu DaYi), Barry Starr of Stanford University describes a recent discovery in China of a man who seems to have undergone a similar reduction process with chromosomes #14 and #15 becoming fused, and now has just 44 chromosomes (22 pairs). His case sheds light on how the chromosome reduction process might have occurred in our own ancestors.

July 08, 2011

Heart with no heartbeat

NPR had an interesting story on a new type of artificial heart. Older models had tried to replicate the human heart with its pumping mechanism but have been unable to create models that work without problems for a long time.

This new heart is radically different in that it foregoes the pumping action and has motors that continuously drive blood through the body. This makes for a much simpler design with less chance of breakdown. It seems as if the pumping action is not essential for the working of the body, though it is still early days and we do not have long-term data on the effects.

If the results hold up and a heart that beats is not really necessary, it means that the beating heart is a product of evolution that is functional but not optimal. This would illustrate once again that the processes of evolution do not necessarily produce the best design but merely a design that works. This will not be the first time that thinking that nature's design is the best and trying to copy it has sent us in the wrong direction. Early experiments with flight tried to emulate the flapping wing action of birds with little luck.

What is kind of weird is that with this new artificial heart, there will be no heartbeat, no pulse, and the EKG signal will be a flat line. So the most common markers we currently use to see if someone is dead or alive would indicate that the person is dead.

June 30, 2011

Early eyes

A new article published today in Nature finds fossil evidence that fairly sophisticated eyes had evolved as early as 515 millions years ago, around the time known as the Cambrian explosion.

There were no fossil bodies found attached to the eyes, but the eyes probably belonged to a shrimp-like creature.

June 21, 2011

Myths about the Golden Ratio

Take a straight line. How should one divide the length into two parts such that the ratio of the length of the whole line to the longer segment is equal to the ratio of the longer segment to the shorter one? A little algebra gives you the result that longer segment should be 0.618 times the length of the whole line and thus the ratio of the full line to the longer segment is 1.618 (=1/0.618).

The number 1.618 is known as the 'Golden Ratio' and folklore ascribes deep significance to it and claims a ubiquity for it that far exceeds the reality.

Mathematician Keith Devlin tries to set the record straight.

June 16, 2011

Who am I?

In yesterday's post, I wrote about the fact that different parts of our bodies keep regenerating themselves periodically. This fact alone should make nonsense of the belief of some religious people that our bodies become physically reconstituted after death in the afterlife, because if so, the resurrected body of a person who died at the age of 70 would be unrecognizably grotesque, consisting of around 70 livers and 7 full skeletons, all surrounded by hundreds, maybe thousands, of pounds of skin.

But leaving aside that, there is an interesting question raised by this constant regeneration of the body and that is how we retain a sense of having a single identity over our full life spans even as individual parts of us get replaced periodically. The average age of the molecules in my body is around 7 to 10 years and yet I have the strong sense of continuity, that I am in some fundamental sense the same person that I was as a child, even though almost none of those molecules have stayed with me over that time. How is it that we retain a strong sense of permanence in our identity while being so transient in our bodies?

The answer may lie in the fact that our brain seems to be the most permanent of our organs, undergoing little or no regeneration. In the same article in the New York Times that I referred to yesterday, Nicholas Wade says:

Dr. Frisen, a stem cell biologist at the Karolinska Institute in Stockholm, has also discovered a fact that explains why people behave their birth age, not the physical age of their cells: a few of the body's cell types endure from birth to death without renewal, and this special minority includes some or all of the cells of the cerebral cortex.

The cerebral cortex is the thin sheet that forms the outer layer of the brain and is divided up into several zones that have different functional roles. If the cortex were removed and smoothed out to eliminate all the creases and folds, it would look like a dinner napkin. It is gray in color, the origin of its popular euphemism of 'gray matter'. The network of nerve cells in the brain (called neurons) determines how the brain functions.

While the brain seems to be the most enduring part of the body, even here there is variation. The cerebellum seems to contain non-neuronal cells that are close to the birth age (within three years or so) while the cerebral cortex (which is responsible for our cognitive capabilities and is thus most closely identified with our sense of self) has a slightly greater turnover of non-neuronal cells. But the researchers do not turn up any evidence that there is neuronal generation after birth, at least in the region known as the occipital cortex.

It was long believed that the number of neuronal connections in the brain grew rapidly during the first year or two of life and then got pruned and this was how our lives shaped our brains without new neurons being created. In 1999, there was research that found that new neurons were being created in the cerebral cortex of adult monkeys, suggesting that it could happen in adult humans too. This would complicate things somewhat as to how we retain a permanent sense of self but also provide hope that brains could regenerate. But this summary of later research (much of it by the same Karolinka group that I referred to yesterday) that appeared in the Proceedings of the National Academy of Sciences says that this does not happen with the neurons in the human cerebral cortex. (The neocortex referred to in the paper is the most recently evolved part of the cortex that is defined as containing the 'higher' functions and are "arranged in six layers, within which different regions permit vision, hearing, touch, the sense of balance, movement, emotional responses and every other feat of cognition.")

The results show that the average age of the neurons (with respect to the age of the individual) is age 0.0 ± 0.4 years, i.e., the same as the age of the individual. In contrast, the nonneuronal cells have an average birth date of 4.9 ± 1.1 years after the birth of the individual.
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Both of the experiments of Bhardwaj et al. indicate that there are no new neurons, either long-lived or transient, produced in the adult human for the neocortex. Importantly, these experiments are quantitative and indicate a theoretical maximum limit of 1% on the proportion of new neurons made over a 50-year period.
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Bhardwaj et al. settle a hotly contested issue, unequivocally. The two-pronged experimental approach clearly establishes (i) that there is little or no continuous production of new neurons for long-term addition to the human neocortex and (ii) that there are few if any new neurons produced and existing transiently in the adult human neocortex. Importantly, the results are quantitatively presented, and a maximum limit to the amount of production of the new neurons can be established from the data presented. The data show that virtually all neurons (i.e., >99%) of the adult human neocortex are generated before the time of birth of the individual, exactly as suggested by Rakic, and the inescapable conclusion is that our neocortical neurons, the cell type that mediates much of our cognition, are produced prenatally and retained for our entire lifespan. [My italics]

So basically, even though every other part of us gets sloughed off and replaced at different points in time, for good or bad we are pretty much stuck with the brains that we have at birth. This may be crucial to our ability to retain a sense of a permanent identity that lasts all through our lives, although this is not yet established. Even if new research emerges that new neuronal cells could be generated over time replacing older ones, it may turn out to be able to do this seamlessly and provide cognitive continuity, just the way our other organs give us the illusion of being permanent even though they are not.

It seems like our brains are our essential selves with the rest of our bodies just superstructure. Rene Descartes famously said "I think, therefore I am." We could also say, "My brain is who I am."

June 15, 2011

Amazing robots

Now that computers have beaten us at chess, robots are turning their attention to pool.

(Via Machines Like Us.)

How old are you?

In an article in the New York Times, Nicholas Wade points out that our bodies are younger than we think, because there is a discrepancy between our birth age and the age of the cells that make up our bodies

Whatever your age, your body is many years younger. In fact, even if you're middle aged, most of you may be just 10 years old or less.

This heartening truth, which arises from the fact that most of the body's tissues are under constant renewal, has been underlined by a novel method of estimating the age of human cells. Its inventor, Jonas Frisen, believes the average age of all the cells in an adult's body may turn out to be as young as 7 to 10 years.

He quotes the work of Spalding, Bhardwaj, Buchhold, Druid, and Frisén of the Karolinska institute that uses the radioactive isotope carbon-14 to determine the age of the cells in bodies. Their paper appeared in the July 15, 2005 issue of Cell. They used carbon-14 dating to determine the age of cells. The carbon that forms organic matter is largely obtained from the atmosphere. Plants, for example, take in carbon dioxide from the air and exude oxygen as part of the process of photosynthesis. Hence the proportion of carbon-14 that is found in living organic matter is the same as that in the ambient atmosphere at the time it was absorbed. The level of the radioactive isotope carbon-14 that occurs in the atmosphere is fairly constant because its rate of production is balanced by the rate of decay. Once the plant dies, it does not take in any new carbon and the decay of the carbon-14 that it had at the moment of death results in a steadily smaller proportion of it and the difference can be used to measure how long it has been dead. The half-life of carbon-14 is 5,730 years and this method can be used to determine the age of dead organic matter up to about 50,000 years, which is a convenient range for archeological dating because it lies in the range required for those studies.

The way that Frisén and his co-workers used this knowledge to measure the age of cells in humans is quite clever. Carbon-14 is produced by cosmic rays and the level of carbon-14 in the atmosphere should be constant. This is why we can tell how long something has been dead but not when it was 'born', i.e., when the organic matter was created. But in the 1950s and 1960s, there was a sharp spike in carbon-14 levels because of the atmospheric testing of nuclear weapons. Once atmospheric test ban treaties came into came into being, the surge of carbon-14 that had been produced steadily became diffused in the atmosphere as it spread over the globe, and so there has been a steady decline in average carbon-14 levels over time. It is this that enables us to know when the carbon-14 was absorbed to create organic matter.

The amount of carbon-14 in the genomic DNA can thus be used to measure when the DNA in the cell was created. The technique was checked against the age of trees which can be measured by the amounts of carbon-14 found in the various rings as the isotope is absorbed during photosynthesis. Their results and those of others show that different parts of the body get replaced after different durations, whose approximate values are given below. (I have included results from both the Wade newspaper article and the Frisen paper.)

Stomach lining: five days
Surface layer of skin: two weeks
Red blood cells: three months
Liver: one year
Skeleton: 10 years
Intestine: 11 years
Rib muscles: 15 years

This explains why our bodies seem so durable and able to withstand considerable abuse.

So why do we die if parts of us keep getting regenerated? It seems as if the ability of stem cells to keep reproducing declines with age. In other words there seems to be a limit to the number of times that cells can reproduce and once we reach that limit, the ability of the body to regenerate itself ceases. What causes this limit is still an open question. As Wade writes:

Some experts believe the root cause is that the DNA accumulates mutations and its information is gradually degraded. Others blame the DNA of the mitochondria, which lack the repair mechanisms available for the chromosomes. A third theory is that the stem cells that are the source of new cells in each tissue eventually grow feeble with age.

Frisen thinks his research might be able to shed some light on this question, especially the third option, saying "The notion that stem cells themselves age and become less capable of generating progeny is gaining increasing support."

June 14, 2011

Patenting DNA and genetic tests

In an article titled Patently Unjust in the June 2010 issue of The Progressive (not available online), Kari Lydersen describes a similar issue to the one involving Henrietta Lacks, where private companies are making a bundle out of publicly funded research. In this case, the publicly funded Human Genome Project has made freely available the full human genome but some private companies have obtained patents over individual genes.

The particular case that Lydersen deals with involves the genes known as BRCA1 and BRCA2. Certain mutations in these genes are predictors of breast and ovarian cancer, since women with such mutations are five times more likely to develop breast cancer and ten to thirty times more likely to develop ovarian cancer. We are now able to test if a woman has these mutations in which case they have to make difficult decisions about whether to preemptively remove their breasts and ovaries. These genes were discovered as part of the genome project.

It turns out that a single company named Myriad Genetics holds several patents on the genes and as a result claims exclusive rights to the tests they developed to detect the mutations. They charge about $3,000 for the test, which prices many women out of the market. They claim that if companies could not make money, they would not have the incentive to develop the tests. There is some truth in this but it is also true that a huge amount of federal (i.e. public) research funding went into the research that provided the basis for the company's work, which should also be a factor. If the public funds something, the public should also benefit.

The reasons given by the company's founder for the high price they charge for the tests is revealing about the why medical costs are so high in the US. He says, "In the U.S. what you charge for a test is a complex equation of what it costs you to do it and what people will pay" (my italics). This is part of the problem in a system with employer-based private health insurance coupled with monopoly providers. Well-to-do groups with power can pressure their insurance companies to cover the costs of tests which enables the testing companies to charge higher prices than they need to merely cover costs and provide a reasonable profit. The price then becomes prohibitive for those without insurance and drives up the cost of health care. I have written about this before.

As Lydersen writes, this is a widespread problem.

Myriad is far from the only patent holder on human genes; about 20 percent of the human genome is patented. This basically means that only the patent holder can offer testing and other services related to a specific gene. Patents currently cover genes related to other diseases, including Alzheimer’s, asthma, colon cancer, muscular dystrophy, and spinal muscular atrophy, a hereditary disease that kills children at a young age.

What is worse, because the company claims exclusive rights to the genes, women cannot get a second opinion on such a major question. At a minimum, what is needed is at least for more than one company to be able to provide services so that they can compete with each other. Giving private companies monopoly power over the use of research results that were largely publicly funded seems wrong.

The intricacies of patent law are too subtle for me to get into but on the surface the U. S. Patent Office seems to have been too generous in allowing companies to patent genes. It is illegal to patent a product of nature but the US Patent Office has granted Myriad and similar outfits patents on the genes on the basis that they were able to isolate them from their natural state and purify them. But others argue that this is far too expansive a view. After all, just because you develop a technique to highly purify gold (say) should not enable you to claim the patent to gold. I can understand patents being awarded to the purifying process because that is something the company did develop. That would reward their intellectual contribution while yet preserving the right of other companies to invent alternative methods of purification of the same gene and thus develop competing tests.

The right of private companies to patent genes was litigated and Lydersen writes that in March of 2010 US District Judge judge Robert W. Sweet ruled that Myriad's claims did not meet the test of what makes something derived from nature patentable and invalidated the patents, saying in his ruling:

"The patents issued by the USPTO are directed to a law of nature and therefore were improperly granted," Sweet wrote. "DNA represents the physical embodiment of biological information, distinct in its essential characteristics from any other chemical found in nature…. DNAs existence in an 'isolated' form alters neither this fundamental quality of DNA as it exists in the body nor the information it encodes. Therefore, the patents at issue directed to 'isolated DNA containing sequences found in nature are unsustainable as a matter of law and are deemed unpatentable subject matter."

Patents are valuable things and protect the rights of inventors and other creative people but the Patent Office should be wary of taking the claims of private companies too much at face value, especially when it comes to patenting things in nature like bits of DNA.

Myriad has appealed the ruling to the US Court of Appeals and much hangs in the balance.

June 13, 2011

Who should own the rights to one's tissues?

People generally do not think about what happens to the blood and tissue samples they give as part of medical tests, assuming that they are eventually discarded in some way. Many are not aware that your samples may be retained for research or even commercial purposes. Once you give it away, you lose all rights to what is subsequently done with it, even if your body parts have some unique property that can be used to make drugs and other things that can be marketed commercially.

The most famous case of this is Henrietta Lacks, a poor black woman in Baltimore who died from cervical cancer in 1951. A researcher who had been trying unsuccessfully, like others, to have cells reproduce in the test tube, received a sample of hers too. It turned out that her cancer cells, unlike other cells, could reproduce endlessly in test tubes, providing a rich and inexhaustible source of cells for research and treatment. Her cells, called HeLa, have taken on a life of their own and have travelled the world long after she died. Her story is recounted in the book The Immortal Life of Henrietta Lacks by Rebecca Skloot.

The issue of whether one's cells should be used without one's permission and whether one should be able to retain the rights to one's tissues is a tricky one for law and ethics.

"Science is not the highest value in society," [Lori Andrews, director of the Institute for Science, Law, and Technology at the Illinois Institute of Technology] says, pointing instead to things like autonomy and personal freedom. "Think about it," she says. "I decide who gets my money after I die. It wouldn't harm me if I died and you gave all my money to someone else. But there is something psychologically beneficial to me as a living person to know I can give my money to whoever I want. No one can say, 'She shouldn't be allowed to do that with her money because that might not be most beneficial to society.' But replace the word money in that sentence with tissue, and you've got precisely the logic many people use against giving donors control over their tissues." (Skloot, p. 321)

It does seem wrong somehow for private companies to hugely profit from the lives and bodies of others without owing them anything. In the case of Henrietta Lacks, her family remained very poor and lacked health insurance and proper medical care even while her cells became famous and they bitterly resented this. They did not even know about the widespread use of her cells until two decades later.

On the other hand, it would put a real crimp on research if scientists had to keep track of whose tissues they were working on. Since we all benefit (or should benefit) from the results of scientific research, one can make the case that the tissues we give up are like the trash we throw away, things for which we have voluntarily given away our rights. If the tissues are used for medical research done by public institutions like the NIH or universities and the results are used not for profit but to benefit the general public, this would, I believe, remove many of the objections to the unaccredited use of tissues.

You can see why scientists would prefer to have the free use of tissues but what I don't understand are those scientists who go overboard in making special exceptions for religion.

David Korn, vice president for research at Harvard University says: "I think people are morally obligated to allow their bits and pieces to be used to advance knowledge to help others. Since everybody benefits, everybody can accept the small risks of having their tissue scraps used in research. "The only exception he would make is for people whose religious belief prohibit tissue donation. "If somebody says being buried without all their pieces will condemn them to wandering forever because they can't get salvation, that's legitimate, and people should respect it," Korn says. (Skloot, p. 321)

This is another case where religions try to claim special privileges denied to everyone else. Why is that particular claim legitimate? Why should religious superstitions get priority over other irrational beliefs? Our bodies are in a constant state of flux. It sheds cells all the time in the normal course of our daily lives, which is why DNA testing has become such a valuable forensic tool for solving crimes. Since we are losing old cells and gaining new cells all the time, it is a safe bet that hardly any of the cells that were part of me as a child are still in my body. So the whole idea that the afterlife consists of 'all of me' is absurd since that would require bringing together all the cells that I have shed during my life, resulting in me having multiple organs and limbs, like some horror fiction monster.

Rather than pandering to this fantasy, we should educate people that our bodies are in a constant state of flux, that our seemingly permanent bodies are actually transient entitites.

June 10, 2011

Atheism is a byproduct of science

Science is an atheistic enterprise. As the eminent population geneticist J. B. S. Haldane said:

My practice as a scientist is atheistic. That is to say, when I set up an experiment I assume that no god, angel or devil is going to interfere with its course; and this assumption has been justified by such success as I have achieved in my professional career. I should therefore be intellectually dishonest if I were not also atheistic in the affairs of the world.

While not every scientist would apply the highly successful atheistic methodology to every aspect of their lives as Haldane does, the fact that intellectual consistency requires it, coupled with the success of science, has persuaded most scientists that leaving god out of things is a good way to proceed and hence it should not be surprising that increasing awareness of science correlates with increased levels of atheism.

But it would be wrong to conclude that scientists have atheism as a driving concern in their work or that they actively seek out theories that deny the existence of god. God is simply irrelevant to their work. The negative implications for god of scientific theories is a byproduct of scientific research rather than the principle aim of it. Non-scientists may be surprised that discussions about god are almost nonexistent at scientific meetings and even in ordinary interactions among scientists. We simply take it for granted that god plays no role whatsoever.

For example, the idea of the multiverse has torpedoed the argument of religious people that the universe must have had a beginning or that its parameters seem to be fine-tuned for human life, which they argue are evidences for god. They seem suspicious that the multiverse idea was created simply to eliminate god from these two of the last three refuges in which he could be hiding. (The third refuge is the origin of a self-replicating molecule that was the precursor of life.) In his article titled Does the Universe Need God?, cosmologist Sean Carroll dismisses that idea.

The multiverse is not a theory; it is a prediction of a theory, namely the combination of inflationary cosmology and a landscape of vacuum states. Both of these ideas came about for other reasons, having nothing to do with the multiverse. If they are right, they predict the existence of a multiverse in a wide variety of circumstances. It's our job to take the predictions of our theories seriously, not to discount them because we end up with an uncomfortably large number of universes.

Carroll ends with a nice summary of what science is about and why god really has no reason to be postulated into existence. This is similar to the points I made in my series on why atheism is winning.

Over the past five hundred years, the progress of science has worked to strip away God's roles in the world. He isn't needed to keep things moving, or to develop the complexity of living creatures, or to account for the existence of the universe. Perhaps the greatest triumph of the scientific revolution has been in the realm of methodology. Control groups, double-blind experiments, an insistence on precise and testable predictions – a suite of techniques constructed to guard against the very human tendency to see things that aren't there. There is no control group for the universe, but in our attempts to explain it we should aim for a similar level of rigor. If and when cosmologists develop a successful scientific understanding of the origin of the universe, we will be left with a picture in which there is no place for God to act – if he does (e.g., through subtle influences on quantum-mechanical transitions or the progress of evolution), it is only in ways that are unnecessary and imperceptible. We can't be sure that a fully naturalist understanding of cosmology is forthcoming, but at the same time there is no reason to doubt it. Two thousand years ago, it was perfectly reasonable to invoke God as an explanation for natural phenomena; now, we can do much better.

None of this amounts to a "proof" that God doesn't exist, of course. Such a proof is not forthcoming; science isn't in the business of proving things. Rather, science judges the merits of competing models in terms of their simplicity, clarity, comprehensiveness, and fit to the data. Unsuccessful theories are never disproven, as we can always concoct elaborate schemes to save the phenomena; they just fade away as better theories gain acceptance. Attempting to explain the natural world by appealing to God is, by scientific standards, not a very successful theory. The fact that we humans have been able to understand so much about how the natural world works, in our incredibly limited region of space over a remarkably short period of time, is a triumph of the human spirit, one in which we can all be justifiably proud.

Religious believers misuse this fundamental nature of scientific inquiry, that all conclusions are tentative and that what we believe to be true is a collective judgment made by comparing theories and determining which one is best supported by evidence, to make the misleading case that unless we have proved one single theory to be true, other theories (especially the god theory) should merit serious consideration. This is wrong. While we may not be able to prove which theories are right and which are wrong, we do know how to judge which ones are good and which ones are bad.

God is a terrible theory. It fails utterly to deliver the goods, and so should be abandoned like all the other failed theories of the past. In the film Love and Death, Woody Allen's character says, "If it turns out that there is a god, I don't think that he's evil. I think that the worst you can say about him is that basically he's an underachiever." He is right.

June 09, 2011

God is not the 'simplest' explanation for the universe

Believers in god (especially of the intelligent design variety) like to argue that a god is a 'simpler' explanation than any of the alternatives for many natural phenomena. But they seem to equate simple with naïve, in the sense that what makes something simple is something that should be understandable by a child. For example, if a child asks you why the sun rises and sets every day, giving an explanation in terms of the laws of gravity, Newton's laws of motion, and the Earth's rotation about its own axis, is not 'simple'. A child would more likely understand an explanation in which there is a man whose job it was to push the sun around in its daily orbit. This is 'simpler' because the concepts of 'man' and 'push' are familiar ones to a child, requiring no further explication. But this apparent simplicity is an illusion because it ignores enormously complicating factors such as how the man got up there, how strong must he be, why don't we see him, and so on. It is because such issues are swept under the rug that this explanation appears to be simple.

In his article titled Does the Universe Need God?, cosmologist Sean Carroll points out that introducing a new ad hoc element like god into a theory actually makes things enormously complicated. The erroneous idea that simplicity is linked to the number of entities involved is based on a misconception of science.

All else being equal, a simpler scientific theory is preferred over a more complicated one. But how do we judge simplicity? It certainly doesn't mean "the sets involved in the mathematical description of the theory contain the smallest possible number of elements." In the Newtonian clockwork universe, every cubic centimeter contains an infinite number of points, and space contains an infinite number of cubic centimeters, all of which persist for an infinite number of separate moments each second, over an infinite number of seconds. Nobody ever claimed that all these infinities were a strike against the theory.
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The simplicity of a theory is a statement about how compactly we can describe the formal structure (the Kolmogorov complexity), not how many elements it contains. The set of real numbers consisting of "eleven, and thirteen times the square root of two, and pi to the twenty-eighth power, and all prime numbers between 4,982 and 34,950" is a more complicated set than "the integers," even though the latter set contains an infinitely larger number of elements. The physics of a universe containing 10⁸⁸ particles that all belong to just a handful of types, each particle behaving precisely according to the characteristics of its type, is much simpler than that of a universe containing only a thousand particles, each behaving completely differently.
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At first glance, the God hypothesis seems simple and precise – an omnipotent, omniscient, and omnibenevolent being. (There are other definitions, but they are usually comparably terse.) The apparent simplicity is somewhat misleading, however. In comparison to a purely naturalistic model, we're not simply adding a new element to an existing ontology (like a new field or particle), or even replacing one ontology with a more effective one at a similar level of complexity (like general relativity replacing Newtonian spacetime, or quantum mechanics replacing classical mechanics). We're adding an entirely new metaphysical category, whose relation to the observable world is unclear. This doesn't automatically disqualify God from consideration as a scientific theory, but it implies that, all else being equal, a purely naturalistic model will be preferred on the grounds of simplicity.

Religious people think that god is a 'simpler' theory because they give themselves the license to assign their god any property they wish in order to 'solve' any problem they encounter, without making the answer given in one area consistent with an answer given elsewhere. But the very fact that the god model is so malleable is what makes it so useless. For example, religious people will argue (as they must) that the way that the world currently exists, despite the suffering, disasters, and catastrophes that seem to afflict everyone indiscriminately, is evidence for a loving god. A colleague of mine who is a very thoughtful and sophisticated person told me recently that when he looks at the world, he sees one that is consistent with the existence of god.

This raises two questions. The first is whether the world that he sees also consistent with the non-existence of god. If yes, how does he decide which option to believe? If no, what exactly is the source of the inconsistency?

The second question is what the world would need to look like for him to conclude that the there is no god. Carroll gives a thought experiment that illustrates the shallowness of those who argue that the evils and misfortunes and calamities that bestride this world are actually evidence for god.

In numerous ways, the world around us is more like what we would expect from a dysteleological set of uncaring laws of nature than from a higher power with an interest in our welfare. As another thought experiment, imagine a hypothetical world in which there was no evil, people were invariably kind, fewer natural disasters occurred, and virtue was always rewarded. Would inhabitants of that world consider these features to be evidence against the existence of God? If not, why don't we consider the contrary conditions to be such evidence?

It is not hard to understand why the concept of god could only have arisen in primitive, or at least pre-modern, times.

Consider a hypothetical world in which science had developed to something like its current state of progress, but nobody had yet thought of God. It seems unlikely that an imaginative thinker in this world, upon proposing God as a solution to various cosmological puzzles, would be met with enthusiasm. All else being equal, science prefers its theories to be precise, predictive, and minimal – requiring the smallest possible amount of theoretical overhead. The God hypothesis is none of these. Indeed, in our actual world, God is essentially never invoked in scientific discussions. You can scour the tables of contents in major physics journals, or titles of seminars and colloquia in physics departments and conferences, looking in vain for any mention of possible supernatural intervention into the workings of the world.

The concept of god is a relic of our ancient history, like the vestigial elements of animal physiology such as the legs bones of some snakes, the small wings of flightless birds like the kiwi, the eyes of the blind mole rat, and the tailbone, ear muscles, and appendix of humans. It will, like them, eventually disappear for the same reason, because they have ceased to be of use.

June 08, 2011

The failure of fine-tuning arguments for god

When I ask people why they believe in god, their response almost invariably comes down to them being impressed with the complexity of the world and thinking that it could not have come about without some intelligent agent behind it. It is highly likely that this 'reason' is not the actual cause of their belief but a later rationalization for beliefs that they unthinkingly adopted as part of their childhood indoctrination into religion. When people become adults, they realize that saying they believe something because they were told it as children is likely to expose them to ridicule, and so they manufacture a superficially more rational answer.

The more sophisticated among them, who like to consider themselves as modernists who are accepting of science, argue that the properties of the laws of science and the inanimate matter that make up the universe seem to have just the right values to make life possible and that this implies that god must have chosen those values in order to enable the emergence of humans. This is what is known as the fine-tuning argument for god. (See also the discussion in the comments in yesterday's post .)

In his article titled Does the Universe Need God?, cosmologist Sean Carroll elaborates on it.

In recent years, a different aspect of our universe has been seized upon by natural theologians as evidence for God's handiwork – the purported fine-tuning of the physical and cosmological parameters that specify our particular universe among all possible ones. These parameters are to be found in the laws of physics – the mass of the electron, the value of the vacuum energy – as well as in the history of the universe – the amount of dark matter, the smoothness of the initial state. There's no question that the universe around us would look very different if some of these parameters were changed. The controversial claims are two: that intelligent life can only exist for a very small range of parameters, in which our universe just happens to find itself; and that the best explanation for this happy circumstance is that God arranged it that way.

I have argued before that this makes no logical sense. It seems to imply that god was somehow locked into a blue-print for what humans should be like, and then had to carefully retro-engineer the evolution of the entire universe in order that the humans determined by that blueprint could emerge and survive. But this seems pointlessly Rube Goldbergish. The simpler thing for an omnipotent designer god to do would be to first create the universe and then design humans to fit into whatever emerged. After all, a god can presumably do anything and could have designed us to live in the vacuum of deep space or in the Sun or on any planet in the universe under any conceivable conditions.

But even if we take the fine-tuning argument of religious people on their own terms, we are by no means forced to the conclusion that a god is necessary. In fact, Carroll lists other possible alternatives:

1. Life is extremely robust, and would be likely to arise even if the parameters were very different, whether or not we understand what form it would take.
   
2. There is only one universe, with randomly-chosen parameters, and we just got lucky that they are among the rare values that allow for the existence of life.
   
3. In different regions of the universe the parameters take on different values, and we are fooled by a selection effect: life will only arise in those regions compatible with the existence of life.
   
4. The parameters are not chosen randomly, but designed that way by a deity.

So postulating a god is only one of many options to explain fine-tuning and by no means the most plausible one. It is not even the most attractive one.

Carroll then addresses the position that religion supplies the answers to the 'why' questions that science cannot.

These ideas all arise from a conviction that, in various contexts, it is insufficient to fully understand what happens; we must also provide an explanation for why it happens – what might be called a "meta-explanatory" account.

It can be difficult to respond to this kind of argument. Not because the arguments are especially persuasive, but because the ultimate answer to "We need to understand why the universe exists/continues to exist/exhibits regularities/came to be" is essentially "No we don't." That is unlikely to be considered a worthwhile comeback to anyone who was persuaded by the need for a meta-explanatory understanding in the first place.

Granted, it is always nice to be able to provide reasons why something is the case. Most scientists, however, suspect that the search for ultimate explanations eventually terminates in some final theory of the world, along with the phrase "and that's just how it is." It is certainly conceivable that the ultimate explanation is to be found in God; but a compelling argument to that effect would consist of a demonstration that God provides a better explanation (for whatever reason) than a purely materialist picture, not an a priori insistence that a purely materialist picture is unsatisfying.
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There is no reason, within anything we currently understand about the ultimate structure of reality, to think of the existence and persistence and regularity of the universe as things that require external explanation. Indeed, for most scientists, adding on another layer of metaphysical structure in order to purportedly explain these nomological facts is an unnecessary complication.

It is hard for religious people to accept that there need not be an answer to every 'why' question. What is laughable is that after insisting that the why questions must have answers, religious people simply make up stuff, however preposterous or implausible it may be, without any evidence or even attempt at justification, and then proudly proclaim that they have solved the problem. It is better to accept that some things are just the way they are than make up an answer that has no evidence or reason behind it.

June 07, 2011

Why a god is not necessary to create the universe

In an article titled Does the Universe Need God?, cosmologist Sean Carroll provides a rejoinder to those who would try to squeeze god in as an answer to what they perceive as unexplained gaps in our knowledge. It is a long article that is worth reading in full but for those who lack the time, I will excerpt some of the key points.

He starts by making the same point that I made in the series Why atheism is winning, that the long-term outlook for religion is extremely bleak because science and its associated modernistic outlook is making it irrelevant in ways that are hard to ignore even by the most determined religionist.

Most modern cosmologists are convinced that conventional scientific progress will ultimately result in a self-contained understanding of the origin and evolution of the universe, without the need to invoke God or any other supernatural involvement. This conviction necessarily falls short of a proof, but it is backed up by good reasons. While we don't have the final answers, I will attempt to explain the rationale behind the belief that science will ultimately understand the universe without involving God in any way.

Those who want to insert god somewhere, to show that he/she/it is necessary in some way, need to realize that they have at most a window of one second just after the Big Bang to work with.

While we don't claim to understand the absolute beginning of the universe, by the time one second has elapsed we enter the realm of empirical testability. That's the era of primordial nucleosynthesis, when protons and neutrons were being converted into helium and other light elements. The theory of nucleosynthesis makes precise predictions for the relative abundance of these elements, which have passed observational muster with flying colors, providing impressive evidence in favor of the Big Bang model. Another important test comes from the cosmic microwave background (CMB), the relic radiation left over from the moment the primordial plasma cooled off and became transparent, about 380,000 years after the Big Bang. Together, observations of primordial element abundances and the CMB provide not only evidence in favor of the basic cosmological picture, but stringent constraints on the parameters describing the composition of our universe.

He then clarifies what it means to talk about the Big Bang event, a singular event in time, as distinct from the Big Bang model that is the working out of the aftermath of that event.

One sometimes hears the claim that the Big Bang was the beginning of both time and space; that to ask about spacetime "before the Big Bang" is like asking about land "north of the North Pole." This may turn out to be true, but it is not an established understanding. The singularity at the Big Bang doesn't indicate a beginning to the universe, only an end to our theoretical comprehension. It may be that this moment does indeed correspond to a beginning, and a complete theory of quantum gravity will eventually explain how the universe started at approximately this time. But it is equally plausible that what we think of as the Big Bang is merely a phase in the history of the universe, which stretches long before that time – perhaps infinitely far in the past. [My italics] The present state of the art is simply insufficient to decide between these alternatives; to do so, we will need to formulate and test a working theory of quantum gravity.
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The problem with "creation from nothing" is that it conjures an image of a pre-existing "nothingness" out of which the universe spontaneously appeared – not at all what is actually involved in this idea. Partly this is because, as human beings embedded in a universe with an arrow of time, we can't help but try to explain events in terms of earlier events, even when the event we are trying to explain is explicitly stated to be the earliest one. It would be more accurate to characterize these models by saying "there was a time such that there was no earlier time."

To make sense of this, it is helpful to think of the present state of the universe and work backwards, rather than succumbing to the temptation to place our imaginations "before" the universe came into being. The beginning cosmologies posit that our mental journey backwards in time will ultimately reach a point past which the concept of "time" is no longer applicable. Alternatively, imagine a universe that collapsed into a Big Crunch, so that there was a future end point to time. We aren't tempted to say that such a universe "transformed into nothing"; it simply has a final moment of its existence. What actually happens at such a boundary point depends, of course, on the correct quantum theory of gravity.

The important point is that we can easily imagine self-contained descriptions of the universe that have an earliest moment of time. There is no logical or metaphysical obstacle to completing the conventional temporal history of the universe by including an atemporal boundary condition at the beginning. Together with the successful post-Big-Bang cosmological model already in our possession, that would constitute a consistent and self-contained description of the history of the universe.

Nothing in the fact that there is a first moment of time, in other words, necessitates that an external something is required to bring the universe about at that moment. [My italics]

The Big Bang event itself does not necessarily imply that the universe had a beginning in time and even if it should turn out that it had, it does not imply a beginner. This strikes at the heart of the arguments of religious apologists who need a beginning to make their claim say that a beginning necessarily implies a beginner. That argument is weak to begin with, but is the main one they have for god.

Religious people know that this conclusion is a devastating one for them. After all, if no god is required to create the universe, then he is truly an unnecessary concept. So they will fight or ignore or obfuscate this point with theological jargon.

May 29, 2011

Inattentional deafness

I have long been intrigued by the fact that when I am absorbed in reading, I completely miss what people have said, even if they have been speaking directly to me. This can be embarrassing but in my case people tend to indulgently excuse it because of the stereotype of the 'absent minded professor'. Being a theoretical physicist also helps since we are considered to be a little weird anyway.

But since I have been in the same room as the speaker, the sound waves must have entered my ears and gone to my brain but I have absolutely no memory of hearing anything. It is like the sound never even entered my head. This article explains why.

The researchers believe this deafness when attention is fully taken by a purely visual task is the result of our senses of seeing and hearing sharing a limited processing capacity. It is already known that people similarly experience 'inattentional blindness' when engrossed in a task that takes up all of their attentional capacity – for example, the famous Invisible Gorilla Test, where observers engrossed in a basketball game fail to observe a man in a gorilla suit walk past. The new research now shows that being engrossed in a difficult task makes us blind and deaf to other sources of information.

So it seems like we never really 'hear' anything until the brain has actually processed the incoming sound waves to register as sound. If the part of my brain responsible for this task is otherwise occupied, I haven't really 'heard' it.

This has happened to me other than reading, when I am merely thinking about something and have tuned the speaker out. I am sure everyone has had the same experience of daydreaming and missing what was said. This adds to the evidence that certain kinds of multitasking are impossible at a basic cognitive level.

May 19, 2011

The McGurk effect

Blog reader Henry sent me the link to this clip from the BBC program Horizon of what is known as the McGurk effect, that shows that when the brain receives two different inputs, one aural and one visual, the brain forces you to register just one. Lawrence Rosenblum of the University of California, Riverside explains this effect and demonstrates how in this particular case the visual overrides the sound.

If we cannot do such a simple act of multitasking, imagine how unlikely it is that we can do more complex and challenging multitasking.

May 18, 2011

The motives of the Templeton Foundation

The June 21, 2010 issue The Nation has a good article by Nathan Schneider titled God, Science and Philanthropy that looks at the work of this wealthy foundation that dangles generous grants and a cash prize every year that is larger than the Nobel prize that goes, as Richard Dawkins says, "usually to a scientist who is prepared to say something nice about religion."

Along with providing support for politically right-wing organizations, the foundation's goal seems to be to lure scientists to sign on to the idea that science and religion are compatible. Nobel prize winning chemist Harold Kroto is one of those fighting back against it and says of the foundation that "They are involved in an exercise that endangers the fundamental credibility of the scientific community."

The myth of multitasking

Since I work at a university and am around young adults all the time, I have long been aware that young people today are avid consumers of multimedia, who are adept at emailing, texting, listening to mp3 players, surfing the web, checking up on Facebook, etc. It seems like they are quite proficient at multitasking.

I have always been a poor multitasker. I cannot read or do any work that requires serious thinking if I can hear conversation or loud noises in the background. I have found that I cannot even listen to music in the background when reading. But I know people who seem to thrive on that kind of ambient sound and even deliberately go to coffee shops to do work such as grading papers or writing, things that would be impossible for me.

I had thought that my lack of ability to multitask was partly due to being old and not acquiring these skills while young, similar to my slow reaction time when playing video games (which results in being destroyed when playing them with my children) and my inability to manipulate my thumbs dexterously enough to use the small keys on cell phones without making numerous mistakes.

I thought my poor multitasking skills may also be due to a cognitive disability, similar to the one that prevents me from ever seeing the hidden 3-D images in those so-called autostereogram ('Magic Eye') pictures that were such a rage a few years ago. The Sunday papers used to have one and my daughters would look briefly at it and say, "Oh, look at the dolphins" or whatever it was that day whereas, despite my strenuous efforts at staring using all the recommended tricks, all I saw were colored dots and wiggly lines. I later learned that some people never see the hidden image, due to some feature of their visual-cognitive brain function. It was not reassuring to discover that I have a defective brain, and that there is no warranty.

But a study by Stanford researchers Eyal Ophira, Clifford Nass, and Anthony D. Wagner titled Cognitive control in media multitaskers and published in 2009 the Proceedings of the National Academy of Sciences seems to indicate that hardly anyone can really multitask and they are only deluding themselves that they can.

In an interview with the PBS program Frontline, lead researcher Clifford Nass said that it is possible to multitask certain things if those require different parts of the brain. For example, one might be able to cook and keep an eye on the children, or do gardening while listening to music or drive while talking. But classical psychology says that when it comes to doing more than one task that requires similar cognitive abilities, the brain simply cannot do that. What people do is try to rapidly switch their attention from one task to the next.

Nass and his colleagues hypothesized that to carry out successful multitasking of this latter sort required three distinct skills. One is the ability to filter, to detect irrelevancy, to be able to quickly distinguish between those things that are important and those that are not important. The second is the rapidity with which they could switch from one task to the next. The third is a greater ability to sort and organize the information in the brain so as to keep track of the results of their different tasks.

The researchers expected to find that people who were 'high multitaskers', i.e., people who tend to do multiple things, would be very good at least in one of those areas when compared to the 'low multitaskers', i.e., people like me who have to do things sequentially. What they were surprised to find was that the high multitaskers were terrible in all three areas.

So we know, for example, that people's ability to ignore irrelevancy -- multitaskers love irrelevancy. They get distracted constantly. Multitaskers are very disorganized in keeping their memory going so that we think of them as filing cabinets in the brain where papers are flying everywhere and disorganized, much like my office.

And then we have them being worse at switching from one task to another. ... It's very troubling. And we have not yet found something that they're definitely better at than people who don't multitask.

There is a serious cost to this. The researchers say that trying to multitask leads to deficiencies in analytical reasoning because people don't stick to one thing long enough to think it through but instead shift to another task, thus thinking in fragments.

We worry about it, because as people become more and more multitaskers, as more and more people -- not just young kids, which we're seeing a great deal of, but even in the workplace, people being forced to multitask, we worry that it may be creating people who are unable to think well and clearly.

And it seems as if simply telling them that trying to multitask is bad does not have any effect.

One would think that if people were bad at multitasking, they would stop. However, when we talk with the multitaskers, they seem to think they're great at it and seem totally unfazed and totally able to do more and more and more.
…
[V]irtually all multitaskers think they are brilliant at multitasking. And one of the big new items here, and one of the big discoveries is, you know what? You're really lousy at it. And even though I'm at the university and tell my students this, they say: "Oh, yeah, yeah. But not me! I can handle it. I can manage all these".
…
One of the biggest delusions we hear from students is, "I do five things at once because I don't have time to do them one at a time." And that turns out to be false. That is to say, they would actually be quicker if they did one thing, then the next thing, then the next. It may not be as fun, but they'd be more efficient.

One interesting finding in the study was that there were no gender differences, which goes against the myth that women are either naturally good multitaskers or become so because of the multiple roles imposed on them by society, such as caregiver, housekeeper, breadwinner, etc. This may be an illusion that arose from the fact that the multiple tasks that they have traditionally had to do (keeping an eye on the children while cooking or cleaning the house and listening to the radio) largely involved different parts of the brain and thus did not pose any serious cognitive conflicts.

The big challenge will be how to wean people away from thinking they can multitask. We are not doing them any favors by letting them continue to delude themselves.

May 11, 2011

Living sculptures

These wind-powered sculptures by Theo Jansen are amazing to behold.

You can see more of Jansen's creations at his website.

(Via Why Evolution is True.)

May 10, 2011

Altruism

Jerry Coyne has a nice post about the various forms of altruism and what biology and genetics does, or does not, have to do with them.

May 08, 2011

How the face evolved

Your Inner Fish is a book by Neil Shubin, the leader of the team that in 2006 discovered Tiktaalik, the 375 million year old transitional fossil between fish and land animal. The book shows how the basic morphology (i.e., form and structure) of human bodies can be traced back to our fishy ancestors.

The BBC has nice report (with a short video) on how some of our features, especially the face, came about. In particular, it explains the presence of the philtrum, the little groove on our upper lip just below the nose that has no obvious function.

April 26, 2011

Participants needed for brain study on morality

A reader of this blog told me that he had participated in a study on morality and that they are looking for more people.

Study Name: Moral Boundaries
Location: CCIR at University Hospital (in Cleveland)
Researcher: Megan Norr

Detailed Description:

This study consists of a 2.5 hour research appointment which takes place at the Case Center for Imaging Research at University Hospital. This study seeks to define which brain areas are responsible for moral judgment processing and to determine how they are working with other parts of the brain when we make moral judgments. By using behavioral questionnaires to gather information about individual attitudes on morality and fMRI to examine brain activation in response to a variety of stimuli, we hope to shed some light on the neural representation of human morality. During the appointment, participants will complete a computer-based questionnaire which takes roughly 1 hour and participate in an MRI scan which will take 1 hour and 10 minutes. The MRI session consists of a variety of unique tasks, including viewing of photos and video, listening to stories, reading text, and responding to opinion questions. Some stimuli in this study may be morally challenging or alarming. All participants will have the opportunity to view sample stimuli prior to beginning the study. Participation is voluntary. Participants will be compensated a flat rate of $50. If you are a medical doctor, medical student, or professional in the fields of biology or medicine, you are ineligible for this study.

I believe they are looking for people in the 30-40 year old range but they may not be too rigid about the boundaries.

The blog reader who participated said this about his experience:

In short, It's a morality study that uses MRI and behavioral measures to examine human morality. They investigate brain areas responsible for moral judgment and moral attitudes. It was a fun experience, asked many thought-provoking questions that revealed many subtleties about myself after some self-reflection and makes for interesting conversation amongst friends over drinks. Would love to give examples, but I don't want to influence the test in any way if you participate. So neat!.. O and the frosting and cherry on top: they give you a 3D movie of your brain on CD when you are done!

If you are interested you can register and schedule an appointment online or contact Megan Norr at megan.norr@gmail.com.

April 15, 2011

How the eye evolved

Richard Dawkins gives a clear explanation

April 10, 2011

Prostate cancer tests

Older men like me are routinely given a PSA test for prostate cancer as part of our check-ups. My numbers fluctuated from year to year. Some years my number would rise slightly and my physician would alert me to it, but the next year it would drop. I never did anything about it since I was not convinced that the tests were conclusive enough. Now a new study seems to indicate that my skepticism was justified, since the PSA seems to have high levels of false negatives and even higher levels of false positives.

This latest study was carried out in Norrkoping in Sweden. It followed 9,026 men who were in their 50s or 60s in 1987.

Nearly 1,500 men were randomly chosen to be screened every three years between 1987 and 1996. The first two tests were performed by digital rectal examination and then by prostate specific antigen testing.

The report concludes: "After 20 years of follow-up, the rate of death from prostate cancer did not differ significantly between men in the screening group and those in the control group."

The favoured method of screening is the prostate specific antigen (PSA) test.

However, around 15% of men with normal PSA levels will have prostate cancer and two-thirds of men with high levels of PSA do not in fact have prostate cancer.

One study has suggested that to prevent one death from prostate cancer you would have to screen 1,410 men and treat 48 of them. (My italics)

April 06, 2011

Scientific American on evolution education

Five years after the Dover trial, Scientific American looks at the state of teaching evolution.

(via Machines Like Us.)

March 03, 2011

Ron Paul thinks that evolution is only a theory

February 27, 2011

A new planet in our Solar system?

I was stunned recently by this report that there may be a massive new planet that we did not know about in our very own Solar system. I thought this must be a hoax report but apparently it is being considered as a serious possibility.

The hunt is on for a gas giant up to four times the mass of Jupiter thought to be lurking in the outer Oort Cloud, the most remote region of the solar system. The orbit of Tyche (pronounced ty-kee), would be 15,000 times farther from the Sun than the Earth's, and 375 times farther than Pluto's, which is why it hasn't been seen so far.

But scientists now believe the proof of its existence has already been gathered by a Nasa space telescope, Wise, and is just waiting to be analysed.

You would have thought that our knowledge of our own stellar neighborhood was complete but apparently not. The suggestion that Tyche existed was first made as far back as 1999 but not everyone is persuaded that it exists.

We should know with greater certainty either way by 2012. This is what makes science so much fun. There are always new discoveries to look forward to.

February 11, 2011

Solar sail vessel unfurled

The idea that the electromagnetic radiation can exert pressure is an interesting idea that I taught in my physics courses. As an example, the idea of using the pressure from solar radiation to power a spacecraft has been around for a long time, and I used to give this as a homework problem.

It looks like it has finally come to fruition. Japan used one to fly by Venus in 2010 and now NASA has deployed one to orbit the Earth. Plans are underway to use one to fly to Jupiter later in the decade.

(via Machines Like Us.)

January 14, 2011

The story of life

(via Machines Like Us.)

January 06, 2011

How the case against the MMR vaccine was fixed

Some of you may be aware that many parents are not giving their children the MMR (measles, mumps, rubella) vaccine out of fears that it may cause autism. These fears were generated by a paper published in 1998 by the British medical journal Lancet by Andrew Wakefield and others suggesting such a link. The findings were challenged but the journal only withdrew the paper in 2010.

The British Medical Journal has now published a detailed investigation and concludes that all of the twelve original cases reported had had their data misreported or altered in order to make the link.

The Lancet paper was a case series of 12 child patients; it reported a proposed "new syndrome" of enterocolitis and regressive autism and associated this with MMR as an "apparent precipitating event." But in fact:

• Three of nine children reported with regressive autism did not have autism diagnosed at all. Only one child clearly had regressive autism
  
  
• Despite the paper claiming that all 12 children were "previously normal," five had documented pre-existing developmental concerns
  
  
• Some children were reported to have experienced first behavioural symptoms within days of MMR, but the records documented these as starting some months after vaccination
  
  
• In nine cases, unremarkable colonic histopathology results—noting no or minimal fluctuations in inflammatory cell populations—were changed after a medical school "research review" to "non-specific colitis"
  
  
• The parents of eight children were reported as blaming MMR, but 11 families made this allegation at the hospital. The exclusion of three allegations—all giving times to onset of problems in months—helped to create the appearance of a 14 day temporal link
  
  
• Patients were recruited through anti-MMR campaigners, and the study was commissioned and funded for planned litigation

None of the families of the children were aware that Wakefield was involved in a lawsuit that would benefit from showing the link he purportedly discovered..

As the editors of the BMJ say:

Who perpetrated this fraud? There is no doubt that it was Wakefield. Is it possible that he was wrong, but not dishonest: that he was so incompetent that he was unable to fairly describe the project, or to report even one of the 12 children's cases accurately? No. A great deal of thought and effort must have gone into drafting the paper to achieve the results he wanted: the discrepancies all led in one direction; misreporting was gross.
…
Meanwhile the damage to public health continues, fuelled by unbalanced media reporting and an ineffective response from government, researchers, journals, and the medical profession. Although vaccination rates in the United Kingdom have recovered slightly from their 80% low in 2003 they are still below the 95% level recommended by the World Health Organization to ensure herd immunity. In 2008, for the first time in 14 years, measles was declared endemic in England and Wales. Hundreds of thousands of children in the UK are currently unprotected as a result of the scare, and the battle to restore parents’ trust in the vaccine is ongoing.

What Wakefield set in motion was a monstrous crime, playing on the great fear of parents that some well-meaning action on their part may cause harm to their children and for which they will never forgive themselves. Fortunately for me, my own children were vaccinated well before this scare arose otherwise I too would have agonized over what to do.

Due to so many not giving their children the vaccines because of these fears, all children have been put at risk, while many have suffered from each of these diseases and some have died. Despite this new report, it will be hard to convince die-hard vaccine skeptics to change their minds.

(via Balloon-Juice)

January 02, 2011

The story of the whale

Of all the arguments that are used by religious people against evolution, the most fraudulent is that there are no transitional forms between species. People who say this either willfully ignore the evidence that does exist or think that a transitional form must be a hybrid between two currently existing species.

Do you think that no one could be that stupid? Behold the infamous crocoduck argument.

Yes, some creationists like Kirk Cameron are so ignorant of the theory of evolution that they will actually go on national TV and make fools of themselves in that way.

Fossilization can occur only under very special conditions which is why they occur so rarely and why the discovery of transitional forms like Tiktaalik are so notable.

But if someone should raise this argument with you, point them to whale evolution. Since 1978, we have pieced together in step-by-step form how a mammal that can live in the ocean came about and it is a truly remarkable and well evidenced story. The short video showing how the story was pieced together is fascinating.

It's the tale of an ancient land mammal making its way back to the sea, becoming the forerunner of today's whales. In doing so, it lost its legs, and all of its vital systems became adapted to a marine existence -- the reverse of what happened millions of years previously, when the first animals crawled out of the sea onto land.

Some details remain fuzzy and under investigation. But we know for certain that this back-to-the-water evolution did occur, thanks to a profusion of intermediate fossils that have been uncovered over the past two decades. (My italics)

Starting with wolf-sized carnivores that existed between 60 and 37 million years ago, we see in the fossil record the steady evolution of features that were once suitable for living on the land becoming adapted to water.

None of these animals is necessarily a direct ancestor of the whales we know today; they may be side branches of the family tree. But the important thing is that each fossil whale shares new, whale-like features with the whales we know today, and in the fossil record, we can observe the gradual accumulation of these aquatic adaptations in the lineage that led to modern whales.

The story of the whale likely will not convince your hardcore creationists because they have learned how not to see things they don't want to see. And the truly loony will say that god deliberately planted these fossils to give us the impression that evolution occurred.

But the story of the whale cannot fail to have an impact on those who are genuine seekers of truth.

December 17, 2010

Plenty of time for evolution to occur

Critics of evolution sometimes try to argue that the mechanism of natural selection works too slowly to produce the world we now have in the time that was available. P. Z. Myers shows why that argument is wrong.

December 11, 2010

How bacteria talk to each other...

... and can thus work together for good or bad. Fascinating.

November 02, 2010

Why do so many birds die by flying into power lines?

This was a puzzle and attempts to make the power lines more visible failed. Apparently the answer is that birds have blind spots in their field of vision that make the power lines 'invisible' to them, due to the way they have evolved to become successful foragers.

Although the heavy bustard differs greatly in general body shape from the delicate crane and stork, the birds share a foraging technique - visually guiding their bill to take food items.

This technique requires excellent vision at the end of the bill, resulting in a narrow field of vision and wide "blind spots".

"Once we saw the wisdom of looking at the problem through birds' eyes rather than human eyes, it all made sense," says Professor Graham Martin.

"These birds can see straight ahead in flight but they only need to pitch their heads forward by a small amount and they will be blind in the direction of travel."

Many species of bird have been observed looking down during flight, possibly to locate fellow birds and suitable foraging and nesting sites.

Narrow binocular fields combined with birds' tendencies to look down effectively means certain species cannot see power lines until it is too late.

It is sad that there seems to be nothing we can do about it.

November 01, 2010

Alcohol more harmful to society than heroin?

The former chief drug advisor to the UK government, who was sacked from that post in 2009, has published a study that examines the harm to the individual and to society of various drugs.

Heroin, crack cocaine, and crystal meth are the most harmful to individual users but the widespread use (and abuse) of alcohol is what makes it the most harmful to society, followed by heroin and crack cocaine.

October 21, 2010

Physicists and climate change

In 2007, the American Physical Society issued a short but strong statement stating that the evidence for global warming is incontrovertible. It is no secret that there is a very small but vocal minority within the APS membership that disputes the idea that global warming has a significant human-based cause and who were upset with the APS's strong stand. Because of the fuss they created, the APS issued a longer clarifying statement in 2010 providing some context and the basis of their reasoning. Both statements can be read here.

A minor kerfuffle has now broken out because a physicist named Hal Lewis has resigned from the American Physical Society in protest at its stance on climate change. (Thanks to Chaz for the link.)

I am not sure why it is significant when a retired 87-year old physicist whose work during his research career had nothing to do with climate change resigns from the APS in protest. He is not a 'top' physicist in that although I do not doubt that is competent in his specialized field and known within it, I would guess that most physicists have not heard of him. The claim in some global warming skeptic circles that Lewis's resignation letter is the equivalent of Martin Luther nailing his theses to the church door that sparked the Protestant reformation is laughable. I predict that it will not cause even a ripple within the physics community.

Lewis is not like Freeman Dyson, for example, another 87-year old physicist who is also a global warming skeptic. Although he too has no background in climate science, at least Dyson is very well known among physicists and any theoretical physicist in any field around the world would likely know his name and have some awareness of his work.

I agree with Lewis that money is having a negative effect in general in that it may be distorting the direction of research, but there is no evidence to support his charge that it has influenced the APS's stance on climate change.

The APS has issued a statement in response to the Lewis resignation.

October 17, 2010

Benoit Mandelbrot

The mathematician who founded the discipline of fractal geometry has died at the age of 85. To see some of the beautiful patterns generated by fractals, see here.

October 09, 2010

DNA coiling and replicating

Via Machines Like Us, here is a wonderful animation of DNA coiling and replicating.

October 06, 2010

The Sound of Science

(via Why Evolution is True.)

September 07, 2010

Stephen Hawking on the universe and god

Recently religious apologists have taken to harping on the question "How can something come from nothing?" because they think that science cannot explain how the universe came into existence. Of course, their own answer that "God must have done it!" is not an answer at all since it merely shifts the problem to that of how god could come into being from nothing.

Stephen Hawking has recently published a book that says that we can indeed understand how the universe came into being without invoking god. The idea itself has been known for sometime but when Hawking says it, it generates a lot of media attention. Cosmologist Sean Carroll explains Hawking's ideas in a three-minute video.

In short, science has not proved that there is no god (because such proofs are impossible) but has shown is there is no need for god.

November 18, 2009

Transitional forms

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here. You can also listen to the podcast of the interview on WCPN 90.3 about the book.)

In the previous post, I said that one thing that keeps creationists from 'seeing' the truth of evolution is that their teleological viewpoint makes them think that species in their current form are the aim of creation. If that is the case, why would god bother making anything else? Hence ancestral forms of current species that are unlike anything that currently exist simply have no place in their model.

Another mental block that prevents them from seeing transitional forms for what they are also arises due to this teleological viewpoint. Here they are misled by the very word 'transitional', which suggests something less that perfect and on the way to perfection.

In an online debate with Eugenie Scott, the head of the National Center for Science Education, Ray Comfort makes the following jaw-dropping statement where he illustrates this misconception by pointing to what he thinks is the weakness of the theory of evolution:

Nothing we have in creation is half evolved. The cow has a working udder to make drinkable milk. The bee has working apparatus to make edible honey. We don't find a half-evolved cow or bee. None of the 1.4 million species on the Earth has half an eye. All have the necessary functioning equipment, from the brain, to the teeth, to the eye, to limbs, to reproductive necessities. Everything that we see in creation is in full working order—from the sun, to the mixture of the air, to the seasons, to fruit trees and vegetables, to the animal kingdom—from the tiny ant right up to the massive elephant.

But not only do we see this mature completion in creation; we see it displayed in the fossil record. It reveals that each animal was complete.
…
I went to the Smithsonian to see the fossils galore, and they were there—millions of fossils that were evidence of special creation. The Smithsonian didn't have any transitional fossils that proved evolution (staunch believers claim that they have them, but not on display). I also visited the evolution museum in Paris (Grande Galerie de L'Evolution). I took a camera crew, and we spent an hour looking for the evolution exhibit. It didn't have one. All it had were millions of fossils of fully formed animals that God created (my italics).

This is a perfect example of creationists not 'seeing' the evidence for evolution that the rest of us see. It reveals the creationist teleological belief that everything we have now is in its final form and is functioning as designed. The very use of the phrase 'half evolved' reveals the deep misconceptions originating from a teleological viewpoint, because that phrase is meaningless unless one sees current species as being in their final, perfectly functioning forms.

In this view, a 'transitional' form must be something less than perfectly functioning. What Comfort thinks evolution predicts is that transitional forms should consist of animals malformed in weird ways, like cows with udders that do not produce milk or bees that have not figured out yet how to make honey or human beings with only one leg. This displays a staggering ignorance of the most basic elements of how evolution works. But because Comfort has a teleological view that starts from the end, he cannot see that all of us, even though we are fully functioning and adapted to our present environment, are also at the same time transitional forms even though we don't know how we will evolve in the future.

Evolution tells us what we evolved from, not what we are evolving to. Every species that lives now or has ever lived is both 'fully evolved' (in that it is the result of successful adaptations to its past environments) and a transitional form (in that it will evolve in the future as a result of new environmental pressures). There is no such thing as being 'fully evolved' in the Comfort sense of having reached unchanging perfection.

There are only three reasons I can think of for people making the kinds of extraordinary statements that Comfort makes above.

One is, of course, outright stupidity, coupled with ignorance. One should never rule that out.

Another reason is dishonesty, in that they know they are spreading falsehoods about what evolution is but think that saving souls for Jesus compensates for lying to them. One cannot rule that out either. The ranks of religious liars and charlatans are legion.

The third and most charitable explanation, which is what I am suggesting in this series of posts, is that that they simply haven't been able to make the Gestalt-type switch from the old teleological and Platonic worldview to the modern scientific one. While scientists can look at living organisms and fossils and see them as both fully functioning and transitional, creationists can see only a 'fully evolved' object. This is an almost perfect example of what happens when you cannot make the Gestalt switch to see two images while viewing a single object. While scientists can look at the image below and see both a duck and a rabbit, for creationists the duck is still only a duck, and as a consequence, the two pointy-things on the left can only be its bill.

It is quite sad.

POST SCRIPT: Here's a 'fully evolved' ape

From the BBC comedy show Not the Nine O'Clock News.

November 17, 2009

Why creationists do not 'see' evolution

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here. You can also listen to the podcast of the interview on WCPN 90.3 about the book.)

One specific creationist religious belief whose origins I have been curious about is the bizarre argument that is advanced by anti-evolution religious people about how the lack of transitional fossils is undermining the theory of evolution. This argument mystifies scientists because of course there are huge numbers of such fossils. The evidence is incontrovertible. In fact, every living or fossilized organism can also be considered a transitional form, since change is constant. It should also be borne in mind that Darwin arrived at his theory without having the wealth of fossils that are now available, basing his arguments largely on biogeography, the similarities in body patterns of animals, embryology, and the existence of vestigial organs. Nowadays, the fossils that keep being found and the relationships that have been discovered between the DNA molecules of species have sealed the case for evolution.

Fossils are extra evidence and the case for evolution would be strong even without them. So why do creationists keep harping on transitional fossils? One reason is because they think that that is their strongest point. They also know that fossils seem more persuasive to the general public because we can actually see them with the naked eye.

But it may be that they are possessed of a deep misconception (like those involving electric current) about how evolution works that prevents them from actually 'seeing' the evidence the way that scientists see it. Changing that deep misconception requires a Gestalt-type switch but may prove as hard as getting people to understand that electric current flows in closed loops and is not used up.

A few weeks ago, I had quite a bit of fun with Ray Comfort's banana argument and with Kirk Cameron's belief that a transitional fossil is a weird hybrid between two existing species, the latter giving as an example an animal with the head of a crocodile and the body of a duck, which he cleverly calls a 'crocoduck'. But it appears that I was wrong in crediting him with originating this inspired piece of idiocy. It apparently goes back much further to at least Duane Gish, one of the founders of 'modern creationism' (now there's an oxymoron for you). Biologist Jerry Coyne says he heard Gish give a talk where he showed a cartoon of what he expected a transitional form between a fish and a mammal to look like. It consisted of an animal whose front half was a cow and rear half was a fish. (Jerry Coyne, Why Evolution is True, 2009, p. 47.) Gish's message, like Kirk Cameron's, is "Ha! Ha! These wacky evolutionists may be willing believe such crazy things but we are too smart for that."

In this case, I think that these religious people have a wrong point of view of species that dooms them from the start. Like the pre-Galilean theorists of motion who thought that the end point of motion was what was important, or that of Platonic idealists who focused on the essential unchanging nature of things, they too make the mistake of starting from the end point.

In the case of biology, this translates into a teleological view that sees all the current species as the end point, the convergence if you will, of a grand plan. Hence the word 'transitional' does not mean to them an ancestor of a current species that looks different from anything that we currently see, because such things are inconceivable in their teleological model which sees everything as purpose-driven. For them, such an organism would be unnecessary, not serving any purpose. As long as they have a teleological view of the world with its current life forms being representatives of a Platonic ideal, the very word 'evolution' will mean something very different to them from what it means to the rest of us.

So what can a transitional form mean to people with that view? The only transitional forms that they can conceive of are the curious hybrids they keep coming up with, like the crocoduck and the cow-fish. Unfortunately, as I said yesterday, even some of the visual images that we have of the process of evolution, such as the one that draws it as fish→amphibian→monkey→human (with the drawing of each showing what a current typical specimen looks like), reinforce this misconception by suggesting that evolution consists of transitions between forms that currently exist.

When these creationists claim there is lack of fossil evidence of transitional forms, they mean the absence of fossils of these bizarre hybrids. It is clear that people like Gish, Comfort, and Cameron are 'seeing' the theory of evolution in a very different way from the way that scientists see it, and this explains why they will keep coming up with theories so outlandish that we are often at a loss to know how to even start to refute them.

Until they make that Gestalt switch and see evolution and transitional forms the way that scientists see it, they are hopelessly lost. The duck, for them, will remain a duck.

Another obstacle to creationists 'seeing' evolution will be discussed in the next post.

POST SCRIPT: Science vs. religion debate

Thanks to Machines Like Us, you can see the entire recent debate between Christopher Hitchens, Sam Harris, and Daniel Dennett on the one hand versus Dinesh D'Souza (Roman Catholic), Shmuley Boteach (Orthodox Jewish rabbi), and Robert Wright (whom I have labeled as a religious atheist) on the other. It was held at the La Ciudad de las Ideas in Mexico.

November 16, 2009

The power of subconscious theories

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here. You can also listen to the podcast of the interview on WCPN 90.3 about the book.)

The existence and history of religion tells us that people are willing to believe things for which there is no evidence and that they will fight to hold on to them even in the face of overwhelming evidence and arguments to the contrary. But when those beliefs collapse, as they sometimes do, the switch to disbelief can often be quite sudden. I know that in my case, I had been struggling (unsuccessfully) to reconcile my scientific ideas with that of a god for some time. The realization that everything made a lot more sense if there was no god hit me like a Gestalt switch.

One specific creationist religious belief whose origins I have been curious about is the bizarre argument that is advanced by anti-evolution religious people about how the lack of transitional fossils is undermining the theory of evolution. This argument mystifies scientists because it is so palpably wrong and the fossil evidence is so strong. So where does this weird idea come from? And why does it persist?

As much of research in science education has shown, robust misconceptions are often not simply bits of false knowledge (like thinking that Portland is the capital of the state of Maine) that can be easily corrected, but instead are the manifestations of elaborate theories that emerge from a deeply rooted but fundamentally flawed premise. As long as that flawed premise remains intact and unexamined, the misconceptions that flow from it will reappear even if countered in specific cases.

I have seen this phenomenon in my own teaching of electricity to people without a science background. One of the strong misconceptions that people have about electric current is that it emerges from a source (a battery or an electrical outlet), flows through the wire, and is then 'used up' by the radio or light or whatever device it is connected to. They also think that a battery always supplies the same amount of current. Based on this model of electricity, they will then make wrong predictions about how current will flow in more complicated circuits, say by connecting two or more devices to the same source of current.

In actuality, current is never used up. It just flows around in a circuit. Current flows out of one end of the battery (or other source), goes through one wire to the device, passes through the device, and then flows back through another wire into the other end of the battery. The amount of current flowing out of the battery at one end is exactly equal to the amount of current flowing into it at the other end. But it is extraordinarily hard to persuade novice learners of this model, even when they want to learn about electricity and have no reasons to resist it. After all, the Bible does not say anything about electricity. When I tell them how current really behaves, they believe me because I am an authority figure. But yet the misconceptions persist.

If you teach the right model of current to people and then ask them a direct question about how current flows, they will give back the right answer. But when they are asked something indirect, like giving them a circuit and asking them to predict how current will flow, very often they will come up with an answer that is at variance with how it really will behave. If you trace the reasoning of the wrong answer back to its source, you will find that it arises from their original misconception of current being used up and the battery producing a fixed amount of current, even though they consciously thought they had rejected that old way of thinking. When you point this out, they will think that this time they have definitely overcome the misconception. But when they are given a yet more complicated circuit, very often they will make a wrong prediction again, based on the same underlying misconception.

It is only after it has been repeatedly pointed out to them the important role that their basic deep misconception plays in their surface thinking that they switch to seeing the current flowing in a circuit. Once they make that switch in their basic misconception, there is no going back. They cannot imagine that they could have ever thought otherwise.

The reason this particular misconception about current is so deeply held is because people have constructed it on their own. Most of them are not even aware that they have this underlying theory of electricity because they have not consciously thought about it. The theory is built intuitively. Nobody taught it to them, they just 'picked it up' because it makes sense. After all, they know that appliances have a power cord that must be connected to an electrical supply system in order to work. They know that electrical devices 'use up' power because batteries eventually die. The power cord looks like a single tube, like a garden hose, and thus electricity seems like it can flow only in one direction. All these things make sense by assuming their simple model. Most people do not look more closely and wonder why the plug has two prongs and they do not break open the wires or their devices and find that there are incoming and outgoing pathways for the current.

The theories that people intuitively create for themselves are the hardest to refute because they are buried deeply in their thinking and are not consciously articulated by them. The consequences of these misconceptions are often erroneous but if we only correct the consequences without understanding and addressing the source, then we will find that same misconception rearing its head each time a novel situation is encountered.

The misconceptions about how evolution works are of the same kind. They are created deep in the minds of people at an early age, often by well meaning, science-supporting adults who tell their children that 'we evolved from monkeys' and by some of the visual images that we have of the process of evolution, such as the one that draws it as fish→amphibian→monkey→human (with the drawing of each showing what a current typical specimen looks like).

Once these misconceptions about evolution take root at an early age by a process of intuitive thinking, they become, just like the false electricity models, hard to dislodge in adulthood even by confronting people with the most clear reasoning.

As Jonathan Swift said, "You cannot reason a person out of a position he did not reason himself into in the first place."

Next: The role that deep misconceptions play in evolution

POST SCRIPT: How not to stalk off an interview

It is not uncommon for guests on TV or radio to get miffed about something, throw a fit, and stalk off the set. Some may even do it deliberately as a strategy, knowing it will get them publicity. But it sometimes doesn't work out well, with some forgetting to take off either the earpiece or the mike and getting yanked, resulting in a less-than-impressive exit.

But the award for the worst interview termination must surely go to Carrie Prejean. Remember her? Here are some keywords to jog your memory: Miss California who was stripped of her title, supporter of 'opposite marriage', breast implants, topless photos, Donald Trump, lawsuit against Miss USA pageant, sex video.

While on a tour promoting her book, she was irked by a question posed by Larry King of all people, who is notorious for his softball questions. So she removes her mike but instead of then walking off the set, she just sits there, talks to someone off-camera, and smiles at the camera as if she was competing in a pageant, leaving King baffled as to what is going on. Watch.

November 13, 2009

The key steps in adopting evolution

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here. You can also listen to the podcast of the interview on WCPN 90.3 about the book.)

Making a Gestalt-type switch is often aided by nudges from outside sources, and in the case of evolution, two such factors came into play: the age of the Earth and concerns about the effects of human population growth.

Darwin was fortunate that he lived in a time when advances in knowledge in other areas, such as the idea of uniformitarianism in geology, were coming along at the same time that he was pondering all the things he was observing on his voyage on the Beagle. The first edition of the first volume of Charles Lyell's highly influential book The Principles of Geology was published in 1830 and was given to Darwin to read on his voyage on the Beagle that began in 1831. Its argument that small changes (such as erosion) can accumulate over long periods of time to produce major geological features such as mountains and gorges had an impact on him.

By measuring the rates of erosion and sedimentation that were occurring in his own time and calculating how long it would take at that rate to produce the existing rivers and canyons, Lyell concluded that the Earth must be hundreds of millions of years old. Furthermore, Lyell's books discussed some of the fossil evidence that existed at that time because he used them as aids in arriving at the ages of rocks, although Lyell himself believed in special creation.

The fact that the Earth was now possibly hundreds of millions of years old, rather than merely thousands, created an intellectual environment that was more open to acceptance of the idea that new species can gradually evolve from old ones, because that needed long time spans too.

Darwin (and also Wallace) had a Gestalt-type switch when he was struggling to find the mechanism that causes species to evolve in a way that seemed to indicate directionality. The trigger was Thomas Malthus's Essay on the Principle of Population (1798) that argued that populations would grow exponentially, except for the fact that they encounter limited resources that restricts growth because of starvation and premature death. This gave Darwin the idea that natural selection could serve as the mechanism he was looking for. In The autobiography of Charles Darwin 1809-1882 (Nora Barlow (ed), 1958, page 120), he describes his epiphany in ways that suggest a Gestalt-type switch:

In October 1838, that is, fifteen months after I had begun my systematic enquiry, I happened to read for amusement Malthus on Population, and being well prepared to appreciate the struggle for existence which everywhere goes on from long-continued observation of the habits of animals and plants, it at once struck me that under these circumstances favourable variations would tend to be preserved, and unfavourable ones to be destroyed. The result of this would be the formation of new species. Here, then, I had at last got a theory by which to work. (my italics)

Darwin and Wallace saw that if there are variations, then it makes sense that some variations are more likely to survive to adulthood and produce more offspring than others. If this advantageous property is heritable and passed on to its offspring then, over time, that particular variation will dominate the population. And by a very long series of such small changes, new species would emerge.

Once Darwin saw the world in this new way, there was no going back. And the rest, as they say, is history.

I have argued that the kinds of switches in viewing the world that Darwin and Wallace experienced are like Gestalt switches in perception. When one changes one's perspective, suddenly things fall into place and new patterns emerge. What seemed inexplicable, mysterious, and even impossible before suddenly seems clear and even obvious. And once the new way of seeing things is pointed out to others, they immediately see it as obvious too. As Thomas Huxley said after learning how the theory of evolution worked, "How extremely stupid not to have thought of that!" As a result, the new view spreads like wildfire.

But even when told what to look for, not everyone makes the switch. There are some people who never see the new pattern, either because of a rigidity of attitude or, as we will see in the next posting in the case of evolution, because they do not want to see the new pattern because they cannot bear to give up the old one. For them the duck remains a duck and they never see a rabbit.

Next: The mental block of creationists

POST SCRIPT: Well, that didn't take long!

On Tuesday, I wrote about the atheist billboard campaign in Ohio, putting up three billboards near Cleveland, Columbus, and Cincinnati. Some godly people in the Cincinnati area have already taken offense and threatened violence, requiring the billboard to be moved to another location.

See here for more details.

November 12, 2009

Gestalt switches in evolution

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here. You can also listen to the podcast of the interview on WCPN 90.3 about the book.)

After Darwin published his book On the Origin of Species in 1859, large numbers of people were convinced in a very short time by his arguments, although full acceptance of the mechanism of natural selection took longer. But the idea of evolution had been in the air for some time. Why didn't people before him see what Darwin and his co-discoverer Alfred Russell Wallace saw, since they had access to much of the same evidence that he had?

A possible reason is because the theory of evolution also required a Gestalt-type switch. People had been viewing the world through a prism of Platonic ideal forms. In the Platonic view, real objects are approximations to their ideal forms and it is only the ideal forms that matter and from which we get true information. So for example, for any triangle that we draw on paper, the angles will not add up to exactly 180 degrees because of the inevitable imperfections of our drawing and the inaccuracies of our measuring instruments. But the angles of all ideal triangles (that we can only conceive of in our minds) will always add up to 180 degrees, and it is the properties of that ideal form that is important to understand, not our real-life approximations.

While this way of looking at things is perfectly suited for mathematics, it leads people hopelessly astray when applied to biology. In the case of biological organisms, the Platonic model translates into thinking of each species as having an ideal form and of real organisms as just approximations that can and do deviate from the ideal in unimportant ways. So real chickens, with all their variety, are just imperfect manifestations of the ideal, perfect chicken that we can only conceive of in our minds. It is this perfect chicken that we need to study to understand what makes a chicken a chicken, the essence of chickenhood.

But the problem is that the ideal perfect chicken will necessarily always remains the same and cannot evolve into anything else, just like a triangle will not become a square nor will the sum of its angles slowly change with time. Platonic thinking rules out change but is perfectly consistent with the idea of a god creating every species as perfect unchangeable beings and part of a grand plan.

Darwin and Wallace both realized that it is the real forms of organisms that are important, not its idealized version, and furthermore that there are no ideal forms in biology. There is no idealized chicken. The variations found in real chickens, rather than being a nuisance detracting from our understanding of the ideal chicken, actually contain the key to understanding the nature of chickens and how they and other things can change. This shift in perception made the variations in a species central to our understanding, and not peripheral.

The likely reason that Darwin and Wallace may have been able to make the switch is because they spent some time traveling to other parts of the world and saw much more of the variety of life than those who stayed pretty much in one locality. Darwin's voyage on the Beagle confronted him with so much new information about the diversity of life in so many new locations that it forced him into new ways of thinking. Alfred Russell Wallace also had his epiphany while travelling through Asia collecting biological specimens that were exotic and new to him.

Once Darwin and Wallace had made this switch, things started falling into place. They realized that if one adds up these small variations cumulatively over a long time, then even though each one is so small that it cannot be observed with the naked eye or even in one's lifetime, it can add up to huge changes, resulting in the emergence of new species, something that was ruled out by Platonic thinking.

Two things stood in the way of making such an idea workable. It seemed to require an inordinate amount of time, much longer than people at that time thought the Earth had existed, and it lacked a plausible mechanism for species change. An obvious objection to their model that they needed to find an answer for was why should the variations in organisms cumulatively add up to result in large changes? Why could they not simply vary randomly leaving, on average, no net change?

This is where other factors can play a role in making a Gestalt switch in perception.

Next: The key steps in 'seeing' evolution

POST SCRIPT: Jon Stewart parodies Glenn Beck

This clip has been all over the political blogs but it is well worth seeing. Utterly hilarious.

The Daily Show With Jon Stewart	Mon - Thurs 11p / 10c
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November 11, 2009

Perception changes in physics

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here. You can also listen to the podcast of the interview on WCPN 90.3 about the book.)

In an earlier post, I suggested (following Thomas Kuhn) that Gestalt-type switches can play an important role in the creation and adoption of new theories in science. Today I want to look at specific examples of such changes.

Take the case of a simple pendulum, made by hanging a small weight from a fixed point by a string and setting it in motion by pulling it back and releasing it. What had been observed from time immemorial is the weight swinging back and forth with decreasing amplitude before finally coming to rest at the lowest point in its trajectory. People used to interpret this motion as the pendulum weight, when released, 'seeking' (to use anthropomorphic language) to get to its final resting place at the lowest point in its trajectory, but initially overshooting the mark, trying again to get to the lowest point, overshooting again by a smaller amount, and so on, until it finally reaches its destination and stays there.

Viewed this way what the pendulum is 'trying' to do is to come to rest at the bottom but is prevented from doing so by overshooting it due to its motion. Hence the time taken from the instant of release to the final resting point would be the significant thing to measure to see if there are any patterns in this data. But we now know that the time taken to reach the lowest point in its trajectory is not a useful parameter and this is why this approach did not lead to any interesting results.

It took a Galileo to observe the same pendulum motion as everyone else but see it in a different way. He saw the fundamental aspect as an oscillation. In that view, what the pendulum is 'trying' to do is keep oscillating forever with the same amplitude but other factors prevent it from doing so, bringing it to rest. In this view, it makes sense to measure the period of oscillation (i.e. the time taken to go through one cycle) and this data does yield useful patterns, such as that the period is independent of the weight or the amplitude of motion (within certain limits), but does depend in a precise way on the length of the string.

The point is that how one views a phenomenon will determine what one chooses to measure. And what one measures determines what one will discover.

In the case of theories of motion in a straight line, the ancient Greeks saw the motion of bodies as headed towards something. In such a view, the key distance is the distance of the object from its final destination. It was only the reversal of worldview that saw the distance and elapsed time of the object from its starting point as the parameters worth measuring that yielded useful patterns of relationships that eventually culminated in Newton's laws of motion.

Once someone had made this Gestalt-type switch and were able to articulate the new view to others, others quickly started seeing the same thing. What had been seen as a duck was now a rabbit, what was as two faces was now a vase. But not everyone will see the world in the new way. Those who are strongly wedded to the old way of looking at the world will resist making the switch. It may not be that they see the duck and are consciously rejecting it in favor of the rabbit. It may actually be that they do not even 'see' the duck. For them, the rabbit remains a rabbit and never becomes a duck.

In the actual case of the rabbit and the duck image, it has been my experience everyone sees both shapes within moments of it being pointed out to them, although there are small differences in the time taken for the realization to hit. But there are other examples of switches where people struggle for a long time. (These are taken from this site where you can see even more examples.)

A popular one that some have a hard time seeing is the one below. People initially tend to see either one image or the other but not both. Once they have locked onto one image, they find it hard to switch until they are told what to look for and specific features are pointed out.

The next one is even harder. It is not two images but requires one to see a single image instead of seemingly randomly scattered blobs. I initially could not see anything. Even after I was told what to look for, I still did not see it for some time until it suddenly 'appeared'. Now that I have seen it, it seems obvious.

In both cases, most people do not see the picture on their own but need someone else to point out to them what they should be seeing before they suddenly see it for themselves. This was the particular genius of people like Copernicus, Galileo, Newton, Einstein, and (as I shall argue in the next post) Darwin. They looked at the same world that others did but saw it in a new way. And they were able to persuade others to see what they saw.

Next: Gestalt switches in evolution

POST SCRIPT: Buster Keaton film shorts

One of the funniest comics of the silent era was Buster Keaton. The Cleveland Cinematheque will show a series of his short films on Friday, November 13 at 7:30 pm. The films will be introduced by Robert Spadoni, professor of film studies at Case Western Reserve University. Accompanying the films will be live music, with pianist Shuai Bertalan-Wang playing the ragtime music of Scott Joplin.

For more details on location, admission prices, etc. see here. There is also a Facebook page about it.

November 09, 2009

Gestalt switches in science

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here.)

In the history of science, we have often seen a theory being accepted and used over a long period and then replaced with a new one, with the transition occurring over a relatively short time. Sometimes the new theory is fairly simple and we marvel as to why people did not think of it before. For example, the Copernican heliocentric model is not a complicated idea when compared to the previous geocentric model. Similarly Newtonian mechanics can be formulated in terms of laws that are very simple mathematically and easy to understand. The essential ideas of Darwin's theory of evolution by natural selection can also be stated in a few simple sentences.

All three of these major new theories are of the kind that, if we had lived in the times when their inventors articulated them, we would have reacted exactly like T. H. Huxley, an early convert to Darwin's theory of evolution, who once he understood how natural selection worked, said "How extremely stupid not to have thought of that!"

So why did it take so long for people like Copernicus, Newton, and Darwin to come along with these new ideas? After all, the ancient Greek and Arab and Chinese civilizations were scientifically advanced. Why did it take over a millenium for us to develop modern science, which can arguably said to begin with Galileo?

This is the topic of study of historians and philosophers of science and they have come up with many factors to explain this phenomenon.

One explanation is, of course, the appearance of new evidence and data. If the new evidence is hard to reconcile under the old paradigmatic theory and causes serious problems for it, that can create an openness to new ideas and trigger the search for new theories. People try to see things in new ways.

Then there are the influences of developments in other areas. Advances in technology often lead to new data that were inaccessible before. The invention of telescopes, for example, allowed for the detection by Galileo of the moons orbiting Jupiter and dealt a serious blow to the geocentric model that said that every celestial body orbited the Earth. It became clear that other celestial objects could be the center of an orbit and thus the heliocentric idea became less outlandish.

Similarly, changes in the political, social, and intellectual climate may makes communities more open to ideas that were unthinkable before. The period we know as the Enlightenment was more open to new ideas and less wedded to religious dogma. Societies that are repressive in general are unlikely to be sources of great new intellectual discoveries.

One has also to take into account individual genius to create the new theory, though the way they contributed is often misunderstood. These geniuses often did not come up with completely new ideas but were able to recognize that the same buzz swirling around them as around others actually fit into a new pattern. Once they articulated that new pattern, others could almost immediately identify it as the right way to see things. But what enabled the pioneers to make that particular leap that eluded others who had access to the same ideas and knowledge?

Thomas Kuhn has argued, especially in his classic work The Structure of Scientific Revolutions, that what happened with these people is similar to the phenomenon known as the Gestalt switch, familiar to all of us in those visual puzzles where we can look at a single image and see it switching between a duck and a rabbit, or between a vase and two people facing each other.

What happens with some scientific revolutions is that what everyone sees as a duck, one person suddenly sees as a rabbit. When they point out to others the new way of seeing the world, the reaction of others is similar to the reaction you get from people who initially saw only the duck (say) but now almost immediately see the rabbit. After the revelation, it is hard for people to imagine how they could not have seen it before because it seems so obvious.

Next: Specific examples of Gestalt-like switches in science

POST SCRIPT: Radio interview about my book

On Tuesday, November 10, I will be interviewed on the Cleveland NPR affiliate station WCPN 90.3 from 9:00-10:00 am on its program The Sound of Ideas. This was rescheduled from last Thursday.

The topic will be my latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom. You can listen online live on its webcast or listen to the podcast after the show.

It is a call-in show: local 216-578-0903 or toll-free 866-578-0903.

That same evening at 7:00 pm I will be speaking to the Center for Inquiry–Northeast Ohio in the second floor reading room of the Maple Heights library 5225 Library Lane, Maple Heights, OH 44137-1291. The event is open and free.

October 22, 2009

The interconnectedness of science

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here.)

Even the most die-hard religious person will concede that scientific knowledge is extremely powerful. In thinking about evolution alone and the arguments presented for evolution by natural selection in Richard Dawkins's new book The Greatest Show on Earth, questions that might occur to the reader are: Why is science so powerful? What is it about its structure that has made it so successful?

This is a question that people have been grappling with for a long time and the answer is surprisingly hard to come by. The facile answer that science works so well because it produces truth is not easy to justify because great scientific theories in the past that were thought to be true have fallen by the wayside and there is little reason to think that we are better judges of the truth of theories than our predecessors were.

As long ago as 1906, Pierre Duhem in his book The Aim and Structure of Physical Theory laid out the difficulties that a scientist face in determining if a particular theory is true, by drawing an analogy between how a watchmaker and a doctor go about diagnosing the source of a malfunction in their respective areas of expertise:

People generally think that each one of the hypotheses employed in physics can be taken in isolation, checked by experiment, and then, when many varied tests have established its validity, given a definitive place in the system of physics. In reality, this is not the case. Physics is not a machine which lets itself be taken apart; we cannot try each piece in isolation and, in order to adjust it, wait until its solidity has been carefully checked. Physical science is a system that must be taken as a whole; it is an organism in which one part cannot be made to function except when the parts that are most remote from it are called into play, some more so than others, but all to some degree. If something goes wrong, if some discomfort is felt in the functioning of the organism, the physicist will have to ferret out through its effect on the entire system which organ needs to be remedied or modified without the possibility of isolating this organ and examining it apart. The watchmaker to whom you give a watch that has stopped separates all the wheelworks and examines them one by one until he finds the part that is defective or broken. The doctor to whom a patient appears cannot dissect him in order to establish his diagnosis; he has to guess the seat and cause of the ailment solely by inspecting disorders affecting the whole body. Now, the physicist concerned with remedying a limping theory resembles the doctor and not the watchmaker.

All of science is an interconnected web if theories. It is not like a set of independent modules where you can pluck one out and replace it with another. It is more like the way that the box springs in a mattress are all linked together. This is why it is so hard to replace one theory with another. All the other theories to which it is linked work to prevent the change.

This is why people who think that they can replace just evolution with some creationist idea du jour stumble badly. The theory of evolution gets its strength from that fact that it meshes well (though not perfectly because while science progresses it is never perfect) with the other theories of biology and chemistry and physics and geology and astronomy, as Dawkins so tellingly demonstrates. Creationist ideas go against all these other theories to various degrees. So when you reject the theory of evolution, you are pretty much rejecting all of science. Trying to replace evolution with the theory of intelligent design in a few cases is like (to switch analogies for the moment) trying to replace just one of the fuel injectors in a modern car with a carburetor from an older car. It just will not work.

An obvious objection to the above description is that it implies that all theories are locked in place forever, which is obviously false since we know that scientific revolutions have occurred in the past in single areas of science. How could that have happened? If you examine closely the history of how scientific revolutions occur, you see that they are preceded by extended periods of crises, when theories come under increased critical scrutiny and suspicion because of perceived weaknesses. Those correspond to the weakening, and even the slow removal, of the links connecting the theory under question to the rest of science. The other theories slowly adapt to the fact that one of their theories is suspect. This enables the suspect theory to be decoupled from the rest and replaced by the new theory.

Initially the new theory will work somewhat imperfectly because it will have few connections to the rest of the scientific theory web. But if it is a good theory that performs its own functions well and has at least some good working connections to other theories, the other areas of science will adapt to the new theory and new links will be forged, so that the end result will once again be a strong interconnected web of theories, but a different one from what existed earlier.

What religious people do not realize is that the theory of evolution is nowhere close to being in crisis and is firmly embedded in the fabric of science. In attempting to discredit it, they are taking on all of science. This is why they have failed so far and will continue to fail.

POST SCRIPT: Stephen Colbert gets ready for the end times

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October 16, 2009

On quoting scientists-5: Religious scientists' beliefs about god

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here.)

When scientists who are also religious believers are quoted as to why they believe in god, their reasons almost always fall into one of two classes. (I am excluding those who believe in the literal truth of their religious texts and, in my opinion, have effectively rejected science altogether.)

One is the ever-popular Argument from Personal Incredulity. This goes as follows:

1. There is no positive evidence for god.
2. But X (insert your preferred natural phenomenon here) is amazing.
3. I don't understand how X could have come about by natural processes.
4. Hence god must have done it.
5. Hence god exists.

The other is a self-serving circular argument that is driven by emotional needs:

1. There is no positive evidence for god.
2. But I want/need to believe in god.
3. Hence god must be acting in ways that preclude leaving any evidence.
4. Hence the absence of credible evidence for god is evidence for my belief that god chooses to act in ways that do not leave any evidence.
5. Hence god exists.

New atheists suggest that the following reasoning is simpler and makes more sense:

1. There is no positive evidence for god.
2. Hence there is no reason to believe in god.

It is in essence the advice that Bertrand Russell gave in his book Skeptical Essays, vol. I (1928):

I wish to propose for the reader's favourable consideration a doctrine which may, I fear, appear wildly paradoxical and subversive. The doctrine in question is this: that it is undesirable to believe a proposition when there is no ground whatever for supposing it is true. I must, of course, admit that if such an opinion become common it would completely transform our social life and our political system; since both are at present faultless, this must weigh against it.

I must say that I find that I find the willingness of those few scientists to express belief in anything more than a Slacker God somewhat surprising because it so fundamentally contradicts the basic assumptions under which science operates. The population geneticist J.B.S. Haldane (1892-1964), who did so much to advance the theory of evolution by natural selection by placing it on a firm mathematical footing, explained that he was an atheist simply as a result of his desire for consistency:

My practice as a scientist is atheistic. That is to say, when I set up an experiment I assume that no god, angel or devil is going to interfere with its course; and this assumption has been justified by such success as I have achieved in my professional career. I should therefore be intellectually dishonest if I were not also atheistic in the affairs of the world.

But this kind of desire to have a unified and consistent worldview is surprisingly rare. What religious scientists do is tacitly compartmentalize their thinking into two worlds: their scientific world where god does not act, and their religious world where god lives and acts. The word 'tacitly' is important. As long as you do not specify how this two-world system actually operates, you can ignore the huge contradictions that exist.

What I would like to ask the scientists who believe in god is the following question: Are you an atheist when you do scientific experiments, not allowing the hypothesis of god's action entering at all? If so, why do you have one set of beliefs when doing science and another set for all the other areas of your life?

The only way to make sense of this double standard is to assume that god thinks as follows:

If I feel like it, I may once in a while cure a sick person, while most of the time letting them die, sometimes cruel and horrible deaths. Once in a while I may avert a hurricane or tsunami from a populated area though most of the time I will let it destroy thousands of homes and people. I may save a few people in a plane crash just for the hell of it while killing off the rest. I may allow one baby to live and be rescued days after an earthquake that killed of its entire family and town, because I know my followers get a kick out of things like that and will rejoice in the 'miracle'. I will let an insane killer mow down many people in a crowded building just so that those whom he misses think that I picked them out to save. I will allow child rapist-murderers to get away with these and other horrendous crimes. I will create diseases that kill millions of people.

But I will never, ever, interfere with a scientist's experiments and mess up their search for scientific laws.

Because that would be wrong.

A physicist colleague of mine, a well-regarded scientist, is also an observant Jew. I once asked him how he reconciled his scientific work, which excludes supernatural intervention and explanations, with his belief in the Bible with all its stories of god messing around with the laws of the universe. He suggested that he thought that god used to do miracles and then decided around 2,000 years ago to not do any more.

"Why?" I asked.
"He must be having his reasons" he replied.

By invoking that ad hoc strategem, he was able to believe in the truth of the Bible and also avoid having to deal with the god hypothesis in his research. I think all religious scientists in the end adopt similar self-serving views. They just compartmentalize things differently and idiosyncratically depending on their personal beliefs and needs and preferences.

This is why I think Oxford University scientist Peter Atkins was exactly right when he said: "You clearly can be a scientist and have religious beliefs. But I don't think you can be a real scientist in the deepest sense of the word because they are such alien categories of knowledge."

POST SCRIPT: Interview

I was interviewed recently about an article that I had published called Death to the Syllabus! where I argued that our classrooms and syllabi had become too authoritarian and controlling, and that we needed to try and create a more collegial atmosphere in out classes if we were to achieve true learning. You can find the 25-minute podcast of the interview here.

October 15, 2009

On quoting scientists-4: God as metaphor

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here.)

If one looks at the quotes of scientists used by religious believers, one sees that they fall into a familiar pattern. One is to take the metaphorical use of the word god by some scientists and imply that these imply belief in a real god. One of the most common examples is the popularity amongst religious people of a statement in Stephen Hawking's best-selling book A Brief History of Time that is often quoted this way: "[I]f we discover a complete theory…then we should know the mind of God". It has been seized upon by religious people to imply that Hawking believes in god, and is a prime example of this practice of 'quote mining'.

But Hawking, like Albert Einstein, is using god as a metaphor for complete knowledge, as can be seen in the full passage from which the quote is taken:

If we discover a complete theory, it should be understandable in broad principle by everyone, not just a few scientists. Then we shall all, philosophers, scientists and just ordinary people, be able to take part in the discussion of the question of why it is that we and the universe exist. If we find the answer to that, it would be the ultimate triumph of human reason-for then we would know the mind of God. (my emphasis)

In a BBC interview, he was asked to further clarify his statement that we might one day know the mind of god and his answer clearly indicates that his idea of god is nothing like the god that religious people believe in.

It seems that the universe is governed by a set of scientific laws. One might say that these laws were the work of god but it would be an impersonal god who did not intervene in the universe apart from setting the laws. What I meant when I said we would know the mind of god was that if we discovered the complete set of laws and understood why the universe existed we would be in the position of god… One could define god as the embodiment of the laws of nature. However, this is not what most people would think of as god. They mean a human-like being with whom one can have a personal relationship. When you look at the vast size of the universe and how insignificant and accidental human life is in it, that seems most implausible. (my emphasis)

Einstein was someone else who loved to use god as a metaphor in the same way as Hawking, and people have similarly seized on those quotes as evidence for at least a Slacker God. But Einstein viewed belief in god as a "childish superstition". In a letter written just a year before his death, he said:

The word god is for me nothing more than the expression and product of human weaknesses, the Bible a collection of honourable, but still primitive legends which are nevertheless pretty childish. No interpretation no matter how subtle can (for me) change this… For me the Jewish religion like all others is an incarnation of the most childish superstitions. And the Jewish people to whom I gladly belong and with whose mentality I have a deep affinity have no different quality for me than all other people.

Some scientists throw in god into their statements because it is a sure-fire way of drawing media interest. Physicists in particular seem to be prone to gratuitously using god as a metaphor. Leon Lederman gave his 1994 book the title The God Particle, which was his idea of a cute name for the Higgs boson, a particle that is predicted to play a crucial role in the standard model of particle physics but has not been detected as yet. Then there was this statement last week by two physicists speculating about why the Higgs boson (which is what the newly constructed massive Large Hadron Collider is designed to create) has been so hard to detect.

"It must be our prediction that all Higgs producing machines shall have bad luck," Dr. Nielsen said in an e-mail message. In an unpublished essay, Dr. Nielson said of the theory, "Well, one could even almost say that we have a model for God." It is their guess, he went on, "that He rather hates Higgs particles, and attempts to avoid them."

One can be sure that some religious people will seize on this statement as evidence for those scientists' belief in god.

But what Hawking or Einstein or Darwin or Dawkins or whomever believes about god is ultimately irrelevant. Unlike some religious people who unquestioningly accept what the Pope or other religious people or the authors of their religious texts say, atheists reject belief in god because there is no evidence for it and not because of any authority. That's it. Nothing more. If Richard Dawkins were to suddenly announce that he had had a vision of god and become a Christian, that would no doubt cause considerable surprise, shock even, but would not change anything about the existential status of god unless Dawkins could provide evidence that what he had experienced was not just a delusion or a psychotic episode but really was credible evidence of god's existence.

POST SCRIPT: Stephen Colbert on Democratic opponents of the public option

The Colbert Report	Mon - Thurs 11:30pm / 10:30c
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October 14, 2009

On quoting scientists-3: What about statements about god?

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here.)

I have said in the previous two posts that we should take scientists seriously when they talk about science (even outside their immediate fields of study) because they have their reputation for credibility at stake and they value that more than almost anything else professionally.

But what about when scientists go even farther afield and infer from that what they know about science to what they believe about god? Then the strength of their case rests only on the quality of the argument they make and the nature of the inferential reasoning they use. It does not rest on their scientific expertise except as far as the truth claims of the science on which they base their arguments is concerned. This affects the way we should use and evaluate the use of quotes.

The only purpose of using quotes in these cases is because the author has said something very succinctly or pithily and one wants to use their words in order to give them proper credit for expressing an idea. The quote by itself is never evidence either for or against the existence of god and the supernatural, but it is evidence as to the beliefs of the person who made the quote about the phenomenon. So a quote about what Darwin believed and said about god would not be evidence for or against god. But when it comes to the issue of Darwin's views on the existence of god, what he actually said would be relevant and well worth quoting.

Religious people tend to misunderstand this. They sometimes comb through the writings of famous dead scientists to find quotes that seem to suggest a belief in god, and use them as if it strengthens the case for god. This is a waste of time because it doesn't. For example, Charles Darwin died not believing in god. While there is no doubt whatsoever that his theory of evolution has made god increasingly redundant and strengthened the case for atheism, his disbelief by itself is not evidence against the existence of god.

Darwin's disbelief bothers some religious people and they think that if they could show that he was a believer in god, that discovery would undermine atheism. Such people sometimes even repeat the thoroughly debunked story of him having had a deathbed conversion to Christianity or make a big deal about the fact that Darwin explicitly rejected the label of atheist and embraced the term agnostic. They are misguided in their efforts. Neither of those things are relevant to the point that the theory of evolution seriously undermines belief in the existence of god.

Even if Darwin actually had made a deathbed conversion to Christianity, it would not prove anything about god either way. All it would have shed light on was about Darwin's state of mind as he lay dying. After all, his co-discoverer of the theory of natural selection Alfred Russell Wallace later in life seemed to embrace some forms of mysticism. Even the great scientist Isaac Newton believed in god in some form. But all that such stories tell us is what those people believed about those phenomena. By themselves they are not evidence for or against god or the supernatural.

One can sometimes use the consensus views of scientists about religion as evidence for some propositions about religion. As an example, suppose we take the new atheists' statement that science and religion are incompatible. The basis of this claim is that advances in science have made the god hypothesis increasingly redundant, that there is simply no need to believe in the existence of such an entity, and to invoke it is to turn one's back on methodological naturalism which is a foundational principle of modern science.

One consequence of this argument is that science as advanced even more, we would expect that the number of disbelieving scientists, especially those who are leaders in their fields and thus more intimately familiar with the frontiers of scientific research, should increase with time. As Oxford University scientist Peter Atkins said: "You clearly can be a scientist and have religious beliefs. But I don't think you can be a real scientist in the deepest sense of the word because they are such alien categories of knowledge."

As a result we might expect some circumstantial evidence in support of the claim that increasing depth of knowledge about science leads to greater disbelief. And there is. In medieval times or earlier there is no evidence that many scientists were disbelievers, unless they were keeping it secret. This is possible since death was a common punishment for heretics. But we have no way of really knowing the situation back then.

But with the enlightenment things began to change for the better. As Edward Larson and Larry Witham reported in a study published in Nature in 1998, at least in the 20th century there has been a steep drop from nearly 28% to 7% in the number of leading scientists who believe in a 'personal god', while the number of disbelievers and doubters rose from nearly 74% to 93%. If the numbers had gone the other way, that as science learned more and more about how the world worked that the number of religious scientists increased, then that would cast some doubt on the claim of the new atheists, although such data, depending as it does on people's beliefs, can never be conclusive about the truth or falsity of any proposition.

Next: God as metaphor

POST SCRIPT: No, let's not leave it there

Jon Stewart on the vapidity of the cable news shows.

The Daily Show With Jon Stewart	Mon - Thurs 11p / 10c
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October 13, 2009

On quoting scientists-2: When is a quote evidence, and for what?

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here.)

I myself use direct quotes quite often and attribute them to the source whenever I can. Why?

One reason is simply style. Using quotes make for livelier reading. Inserting quotes set off differently from the rest of the text breaks up the visual monotony of the page, the way that dialogue does in fiction, and introducing the different rhythm of a new writer keeps the reader on her toes.

Another reason is to acknowledge the source of an idea that I am using. In writing a scholarly paper, one is obliged to track down the original source of an idea, not merely the person who brought it to your attention, but in blog writing it is acceptable to quote secondary sources.

Another reason is to introduce readers to other writers whom they may not have heard of before.

A fourth reason is that there are a lot of good writers out there who often express what I want to say much better than I can, so I use their words. I prefer to give direct quotes whenever possible rather than paraphrase because that leaves less room for unintentionally distorting their views. I cite the source whenever I can so that readers can check for themselves the full context of the quote if they think I am misinterpreting the words.

Why is that famous people are quoted more often than unknown people? It may often seem as if the authors of the quotes are being used as authority figures merely because of their fame, and the quotes themselves are evidence for some point of view, as if the beliefs of famous people have more weight. This is not necessarily so. It is more likely that people who are prolific and/or well-known and/or good writers get quoted more often because they have written more and are read more than obscure or poor writers.

Does the fame of the author give them more credibility? Yes sometimes, but only so far as what they say reflects their detailed knowledge of their subject. For example, when I make assertions about fields about which I have no direct knowledge, I like to quote the words of scholars or people whom I have confidence have actually studied the issue and have a reputation for presenting their subject with appropriate scholarly caution. This naturally skews the quotes in favor of well-known scholars since then I do not have to go through the dreary exercise of first establishing the quoted person's credentials in the field. Quotes by Richard Dawkins on evolution and Albert Einstein on physics have to be taken very seriously. Dawkins on physics and Einstein on evolution, not so much. Sarah Palin on evolution or physics, not at all.

Why do we take the words of scientists and other academic scholars seriously when they are talking about their own fields? Because academia works by peer review. The peers of scientists who are in a position to independently check their work would strongly challenge them if they were saying wrong things about the science, and in the absence of such critiques one can assume that they are expressing the consensus views of their field, even if there are some scientists who disagree with them.

The fact that there are some scientists outside the consensus does not weaken the consensus claims unless the theory really is experiencing a crisis, and it is usually fairly obvious when that is the case. As an example, in physics there are still some scientists who dispute the theory of relativity or the big bang, but those theories remain the consensus views of the community. There is no crisis there. When the consensus view among physicists is that the structure of the entire physical universe has the potential to be explained and understood using mathematical laws without any supernatural intervention, one has to take this view seriously, unless one can provide evidence against those consensus views. Assertions by religious people and theologians of the existence of supernatural forces simply do not carry anywhere near the same weight.

So when Charles Darwin or Richard Dawkins or any working biologist describes biological phenomena and the science behind it, their words definitely have greater credibility than those of non-biologists. The consensus view amongst biologists is that all the biological complexity that we see around us could easily have come about mainly by natural selection without any hidden mechanisms or supernatural intervention. As physicist Sean Carroll says:

Go to a biology conference, read a biology journal, spend time in a biology department; nobody is arguing about the possibility that an ill-specified supernatural "designer" is interfering at whim with the course of evolution. It's not a serious idea. It may be out there in the public sphere as an idea that garners attention — but, as we all know, that holds true for all sorts of non-serious ideas.

It is because of this consensus amongst biologists that we take the idea of evolution seriously, and discount supernatural explanations.

But we take academic scholars somewhat seriously even when they venture a little further afield, outside their narrow fields of expertise. The reason for this is that the most important thing to a working scholar is his or her credibility in the eyes of other scientists, and the more well known they are, the more effort they put into protecting that. This makes most scientists cautious about saying things about any subject that will earn them the scorn of their peers.

So serious scientists who need to express an opinion in a field outside their own specialty will usually check with scientists in that field to make sure they are getting the science right. I am currently reading Richard Dawkins's latest book The Greatest Show on Earth where he marshalls all the evidence in favor of evolution. In the process he talks about radiometric dating and continental drift, which lie in the fields of physics and geology and are outside his range of direct expertise. But it was clear to me that he had consulted knowledgeable people in those fields before he had used those arguments as evidence because it would be embarrassing for a scientist to err about any area of science.

Next: What about when scientists talk about god?

POST SCRIPT: Jon Stewart of the Democrats messing up health care reform

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October 12, 2009

On quoting scientists-1: The numbers game

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here.)

I recently received an email the subject line of which said, "Some leading and Nobel prize winner scientists view [sic] on God." The contents of the email consisted solely of 25 brief quotes, all in support of the existence of god, with no further explanation.

I am not sure what the point of this kind of exercise is since the email author did not explain. Is it to show that there are scientists who are also religious? If so, there is no need to make the case because no atheist denies that fact, so producing such lists serves no purpose than identifying some of the religious scientists by name.

In fact, one should be able to find even more than 25. The National Academy of Science is widely recognized as constituting only the leading scientists. It currently has about 2100 members. In response to a survey, 7% of NAS members said they believe in a personal god defined by the statement "a God in intellectual and affirmative communication with man ... to whom one may pray in expectation of receiving an answer." This is a far more active deity than the Slacker God of some accommodationists, so the email writer should have been able to dig up about 150 members of the NAS who have nice things to say about god.

If the point of the exercise is to impress atheists with the number of scientists who are religious, then this is the wrong way to go, since there are far more skeptics than believers in the NAS. About 72% are outright nonbelievers and another 21% are doubtful or agnostic. So if it comes down to a numbers game, believers lose by a landslide.

This reminds me of the time when the Discovery Institute, the organization that was behind intelligent design, issued a list of 103 people with doctorates in any field who had signed on to the following statement: "We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged." They even placed an ad touting the list as an argument against the theory of evolution.

In response, the National Center for Science Education started Project Steve, consisting of a list of scientists who were willing to sign on to the following statement:

Evolution is a vital, well-supported, unifying principle of the biological sciences, and the scientific evidence is overwhelmingly in favor of the idea that all living things share a common ancestry. Although there are legitimate debates about the patterns and processes of evolution, there is no serious scientific doubt that evolution occurred or that natural selection is a major mechanism in its occurrence. It is scientifically inappropriate and pedagogically irresponsible for creationist pseudoscience, including but not limited to "intelligent design," to be introduced into the science curricula of our nation's public schools.

The gimmick was that the signatories were limited to scientists who had names that were variations on some form of Stephen, such as Steve, Stephanie, Stefan, and so on. They got 367 scientists (including Stephen Hawking) to sign which, since the name Steve only represents 1% of the population, can be extrapolated to suggest that 36,700 scientists support the statement.

The whole point of Project Steve was to make fun of the idea that numbers of scientists behind a proposition alone is an argument for anything and if someone should think so, it is going to be a definite loser for religious beliefs.

But the email made me think about the uses of quotes by scientists in general. I myself use direct quotes quite often and attribute them to the source whenever I can. Why do I use them? What purposes do they serve?

Next: When do quotes serve as evidence for anything?

POST SCRIPT: Tuesdays with Moron?

Bill Maher speculates on the other ghostwriters who were considered for Sarah Palin's book and the titles they suggested.

September 23, 2009

Using placebos as part of treatments

Nowadays, the testing of new drugs often involves comparisons not only with placebos but also with older established drugs in three-way double-blind tests. What is emerging from these trials is that the placebo effect seems to be getting stronger, which means that new drugs in clinical trials are having a harder time showing that they are better than the placebo. Another consequence of stronger placebo responses is that some well-known drugs used is the trials as the older standard (and that had beaten the placebo in earlier tests) seem not to be able to do so now.

As Steve Silberman in Wired Magazine says:

Some products that have been on the market for decades, like Prozac, are faltering in more recent follow-up tests. In many cases, these are the compounds that, in the late '90s, made Big Pharma more profitable than Big Oil. But if these same drugs were vetted now, the FDA might not approve some of them. Two comprehensive analyses of antidepressant trials have uncovered a dramatic increase in placebo response since the 1980s. One estimated that the so-called effect size (a measure of statistical significance) in placebo groups had nearly doubled over that time.

It's not that the old meds are getting weaker, drug developers say. It's as if the placebo effect is somehow getting stronger.

But why would the sugar pill placebos be having a stronger effect now? One possibility is that we are getting better at doing double-blind tests, thus eliminating spurious effects that escaped detection earlier. For example it is found that certain assumptions used in drug testing (that geography does not matter) are now found to be not valid. Not only does the placebo response of the patient vary from place to place, so do the ratings by trial observers, leading to the unfortunate possibility that drug companies may 'placebo-shop', choosing for their clinical tests those areas where the placebo response is low in order to have their drugs seem more effective.

But the more interesting thing that Silberman points out is that the rising strength of the placebo response may be telling us something valuable about the power of the brain to influence our biochemical processes. The placebo effect may be more of a physiological response than a psychological one, and something that can be harnessed in favor of better treatments. Many of these effects are related to pain-reducing compounds called opiods that are produced by the brain. Placebos can act like catalysts, triggering the release of these opiods.

Researcher Fabrizio Benedetti at the University of Turin finds that:

Placebo-activated opioids, for example, not only relieve pain; they also modulate heart rate and respiration. The neurotransmitter dopamine, when released by placebo treatment, helps improve motor function in Parkinson's patients. Mechanisms like these can elevate mood, sharpen cognitive ability, alleviate digestive disorders, relieve insomnia, and limit the secretion of stress-related hormones like insulin and cortisol.

What seems to be going on is that our expectations of what the future will be like seem to play a significant role in how our brain influences our body. If we feel that a good result will ensue from a treatment, the brain releases chemicals that assist in creating that result. What placebos seem to be doing is manipulating those expectations.

It also works in reverse. There are things called 'nocebos' that work opposite to placebos, suppressing the beneficial brain functioning. "Cancer patients undergoing rounds of chemotherapy often suffer from debilitating nocebo effects—such as anticipatory nausea—conditioned by their past experiences with the drugs."

This has led to a revision in attitudes towards placebos, shifting them from a problem to be overcome to viewing them as an additional form of treatment that should be better harnessed. Of course, there are limits to what placebos and the brain can do. As Silberman says, a placebo "can ease the discomfort of chemotherapy, but it won't stop the growth of tumors."

The success of modern medicine in treating many ailments may have strengthened the placebo effect by instilling greater confidence in patients that their treatment will work, triggering the release of opiods and dopamine. Furthermore, drug companies also advertise heavily these days, promoting the benefits of their products to relieve all manner of ailments and associating taking it with good things in life, such as beautiful sunsets, playing with children, enjoying the outdoors, sex, sports, etc. So placebos may be getting stronger because people believe that the drugs will give them a better future.

As a result, the very success of drugs in the past may be working against the drug companies now by increasing the expectations of drugs and thus creating a stronger placebo response. Furthermore,

Existing tests also may not be appropriate for diagnosing disorders like social anxiety and premenstrual dysphoria—the very types of chronic, fuzzily defined conditions that the drug industry started targeting in the '90s, when the placebo problem began escalating. The neurological foundation of these illnesses is still being debated, making it even harder for drug companies to come up with effective treatments.

What all of these disorders have in common, however, is that they engage the higher cortical centers that generate beliefs and expectations, interpret social cues, and anticipate rewards. So do chronic pain, sexual dysfunction, Parkinson's, and many other ailments that respond robustly to placebo treatment. To avoid investing in failure, researchers say, pharmaceutical companies will need to adopt new ways of vetting drugs that route around the brain's own centralized network for healing.

It seems like there need to be developments in two areas. One is to find better ways to test for the true effectiveness of drugs that go even beyond the current double-blind testing. What may be necessary is to incorporate 'open/hidden' tests where the test subjects don't know when they being given any treatment at all, whether it be placebo or drug. This will remove the placebo effect of expectations, giving a better measure for the effectiveness of the drugs.

The second development is to learn how to better use the brain-based nature of the placebo response as part of therapy. A judicious combination of truly effective drugs and the placebo response may be an important part of the future of medicine.

POST SCRIPT: This Modern World

Tom Tomorrow's comic strip imagines how the health insurance industry would have operated in medieval times if it behaved the way it does now.

September 22, 2009

The placebo effect

In the previous post, I described the practice of homeopathy and explained why it should no longer be taken seriously. Now that we know that its originator Samuel Hahnemann was basically treating his patients with water, what made him think his treatment was effective? There is no evidence that he was a fraud or charlatan, foisting on his patients something he knew was bogus in order to take their money. He was probably genuine in his belief in the efficacy of his treatment.

It is likely that he was misled by the placebo effect, where patients recover from an illness due to any number of factors that have nothing to do with treatment provided by the doctor. People who want to believe seize on these random events and see patterns that don't exist. For example, since colds get better after a few days, it is possible to get gullible people to believe that practically anything is a cure for cold since if you take it soon after the onset of symptoms, presto, the cold disappears in a couple of days.

Steve Silberman in Wired Magazine describes how the placebo effect was discovered.

The roots of the placebo problem can be traced to a lie told by an Army nurse during World War II as Allied forces stormed the beaches of southern Italy. The nurse was assisting an anesthetist named Henry Beecher, who was tending to US troops under heavy German bombardment. When the morphine supply ran low, the nurse assured a wounded soldier that he was getting a shot of potent painkiller, though her syringe contained only salt water. Amazingly, the bogus injection relieved the soldier's agony and prevented the onset of shock.

Returning to his post at Harvard after the war, Beecher became one of the nation's leading medical reformers. Inspired by the nurse's healing act of deception, he launched a crusade to promote a method of testing new medicines to find out whether they were truly effective.
…
In a 1955 paper titled "The Powerful Placebo," published in The Journal of the American Medical Association, Beecher described how the placebo effect had undermined the results of more than a dozen trials by causing improvement that was mistakenly attributed to the drugs being tested. He demonstrated that trial volunteers who got real medication were also subject to placebo effects; the act of taking a pill was itself somehow therapeutic, boosting the curative power of the medicine. Only by subtracting the improvement in a placebo control group could the actual value of the drug be calculated.

The placebo explains why so many medical procedures that are now viewed with horror were standard treatments in the past. Bloodletting, bleeding with leeches, attaching maggots, dousing with cold water, were among the treatments once recommended. Charles Darwin suffered from all manner of undiagnosed ailments that included frequent vomiting and he subjected himself to various uncomfortable water treatments in the belief that they helped him. His beloved daughter Annie died of an unknown illness after receiving similar water treatments.

In my own building on the third floor is a small museum of medical history that contains all manner of gruesome-looking medical devices that no one thinks of using today but once were believed to be effective, even state-of-the-art. As long as the physician and patient had confidence in the treatment, it must have seemed to work.

Because of the repeated discrediting of medical treatments that were once considered effective, it has been suggested that the history of medicine is actually the history of the placebo effect, with new placebos replacing the old, leading to the uncomfortable suggestion that our current treatments, however sophisticated they may seem, are merely the latest placebos.

But there is reason to think that we now have a much better idea of what really works and what is a placebo because Beecher's work led to the invention of the practice of double-blind experimental testing, where neither the patient nor the researcher collecting the data and doing the analyses knows who is receiving the experimental treatment and who is receiving the placebo.

By 1962, the government had started requiring drug companies to perform clinical tests with placebos in order to get approval and this has led to the elimination of outright quackery in medicine. Without such precautions, people can, even with the best of intentions, subtly distort the results to get the result they want or expect.

As a result of the widespread adoption of double-blind testing, there is good reason to think that our current practices are significantly better than those of the past, and that we are no longer so easily fooled by placebos.

Next: Using placebos as part of treatment.

POST SCRIPT: How double blind tests work

Double-blind tests are useful not only in medicine. Richard Dawkins shows what happens when it is used to test the claims of people who think they can detect the presence of water by dowsing.

It is interesting that when the tests show the dowsers that the "powers" they thought they had is non-existent, they make up stuff to enable them to continue believing. Does that remind you of anything?

April 03, 2009

The stem cell issue-2: The ethics

Yesterday, I discussed the science involved in stem cell research. Today I want to discuss the ethics.

The ethical problems associated with stem cell research occur because although the fertilized eggs were not created for the purposes of research but to help infertile couples, since the method of in vitro fertilization for the treatment of infertility has not been perfected, more fertilized eggs are created than can be used to actually generate pregnancies, and the question of what to do with these extra frozen stored embryos is problematic.

If the extra ones are not needed for future implantation in a womb, then the options are to destroy them, preserve them forever, or use them for research. Those favoring stem cell research argue that preserving them forever is not realistic, that they will have to be thrown away eventually, and that using them for research is better than destroying them without any benefit being obtained, even though the resulting blastocyst must be destroyed in order to produce the stem cell lines,

Those opposed to stem cell research (and abortion) have a simple and clear argument: Life begins at the instant when an egg is fertilized, and no human action is permissible thereafter to prevent that egg from being eventually born. So once an egg is fertilized, whether in the uterus or outside, then we have a human life and using a blastocyst for research is effectively destroying life. This is a secular argument, even though many, or even the majority, of those who support it may have religious reasons for their stand, such as the idea that god inserts the soul at the moment of conception when the egg is fertilized. They argue that if such a position requires the preservation of unused embryos indefinitely, then we should do so, however impractical that might be.

Those who support a woman's right to terminate a pregnancy and/or the use of embryonic stem cells for research have more difficulty in justifying their position because drawing a clear line as to when 'life' begins or a clump of cells becomes 'human' is hard. One thing they are agreed upon is that a human being is much more than a fertilized egg or a bunch of cells such as a blastocyst. But where does one draw the line?

One line is that until such time as the fetus can exist independently outside the womb, it is not a human being. Right now that time corresponds roughly to the third trimester of the pregnancy. But as technology improves, that is likely to shift to earlier times. Others argue that any organism (human or otherwise) must have some higher level of capacity, such as a brain, before its life becomes worthy of protection from harm. After all, when it comes to question of death, society seems to have decided that when the brain stops functioning one is effectively dead and one no longer needs to take steps to keep the body alive. And as the Terry Schiavo case tragically illustrated, what we mean by a functioning brain is more than just brain stem functions that maintain basic body processes and some reflexes. It means that the part of the brain, such as memory and cognition, that gives us our personality and makes us who we are must be functioning. Once a person has reached the stage of being in what is known as a 'persistent vegetative state', that person is considered to be effectively dead.

In this debate, both sides usually ignore the need for consistency across species. Why should only human life be so valued? What makes us superior and worthy of special consideration? If life is precious and life begins with a fertilized egg or with higher brain function, then what about the lives of other species? After all, we kill animals, even though they are fully functioning living things with a level of brain function that we would undoubtedly value if a human had it. We even think nothing of eating them after killing them. Why should we have one standard for humans and another for nonhuman animals?

One can take a speciesist position and simply assert as a given that human beings are superior to others and so we have a right to do what we like to other animal forms while treating human life as sacrosanct. But that is hard to justify on general moral or ethical grounds. There is no clear marker that justifies treating humans as special, unless you throw in ideas such as that humans have a soul and other animals do not. This is an argument based on a particular religious viewpoint and should have no place in determining public policy, which should always be based on secular arguments.

In my opinion, the position taken by ethicists such as Peter Singer is the most consistent moral and ethical one, that does not give humans special privileges. They take a utilitarian position, that what one should seek is the minimization of suffering. Since suffering involves sentience, this requires that an organism must have at least some primitive brain function and the development of a nervous system before it can be said to have the possibility of suffering. So it would be acceptable to destroy any system of cells (whether from a human or non-human animal) as long as it has not yet reached the stage where it has the ability to suffer, or it has passed that stage at the end of life.

Even if we do not achieve the high level of consistency that it requires of us, the utilitarian argument that says that what we should aim for is a net reduction of global suffering seems to me to be a workable ethical principle on which to base decisions like these. Hence it is ethically allowable to use embryonic stem cells from a blastocyst (before the cells themselves have reached the capacity to suffer) in order to do research to reduce the suffering of actual living organisms.

Of course, this raises other potential problems that are sure to come down the road. Is it ethical, for example, to deliberately produce blastocysts purely for the purpose of research, as opposed to using those that are the by-products of infertility treatments? If, for example, one wanted to study the early development of a disease that had a genetic basis, would it be ethical to take an egg and sperm from people who have that disease and create a fertilized egg purely in order to study the early onset of that disease or to develop treatments for it?

These are very tough questions but ones that are going to come at us thick and fast in the near future as science and technology inexorably advance.

POST SCRIPT: God will decide if and when and how the world will end

Two days ago, I suggested that religious people make unreliable allies in the battle to save the environment because of their belief in god's plan. Right on cue, we have a member of the US Congress during hearings last week on cap-and-trade policies to reduce carbon emissions, quoting the Bible (Genesis 8:21,22 and Matthew 24:31) to support his belief that the future of the Earth is part of god's plan. Yes, god has our back, based on what he supposedly told Noah after the flood. So don't worry, burn those fossil fuels because Jesus has it covered!

April 02, 2009

The stem cell issue-1: The science

The decision by the Obama administration to reverse the Bush-era policy of banning the use of federal funds for stem cell research has created some controversy. The earlier policy had led to some frustration in the scientific community.

Bush's policy was intended to be a compromise: it banned the use of federal funds for the creation of new embryonic stem-cell lines while allowing scientists to study 21 lines that had already been created. But researchers say those lines aren't diverse enough and they have been eager to study hundreds of other lines, some of which contain specific genetic mutations for diseases like Parkinson's. There have been practical challenges as well. The restrictions forced scientists to use different lab equipment for privately funded and government-funded research; some even built entirely separate lab space. One of the most disconcerting aspects, researchers say, has been the negative effect on collaboration, a hallmark of the scientific process. Researchers supported by private money haven't been able to team up with scientists funded by the government, potentially holding back new insights and advances.

Stem cells are those that have three properties. Unlike most cells like muscle or blood or nerve cells, 91) they are capable of replicating themselves for a long period (making them a valuable source to regenerate the body by replacing cells that die), (2) they are unspecialized, and (3) when they reproduce they can produce either more stem cells or become specialized cells like muscle or nerve or bone (a process known as differentiation). The National Institutes of health has an informative FAQ page on this topic.

The two main kinds of stem cells are the embryonic ones and the non-embryonic ones. The embryonic ones can proliferate for a year or more in the laboratory without differentiating while the non-embryonic ones cannot do so for very long, but the reasons for this difference are not known as yet. The embryonic stem cells are capable of eventually differentiating into any type of specialized cell, and are called pluripotent. Such pluripotent cells are valuable because they can be used to repair tissue in any part of the body as needed. But eventually they need to differentiate into specialized cells in order to perform the functions that those specialized cells carry out in the body. The process by which stem cells differentiate is still not fully understood, but part of it involves interaction with the external environment in which the stem cell finds itself.

Adult stem cells are one form of non-embryonic cells and are found amongst the differentiated cells that make up the tissues of the body, such as the brain and heart and bone marrow, and they are the cells that are used to maintain and repair those tissues by differentiating when needed to produce new tissues. Some adult stem cells seem to have the capacity to differentiate into more than one type of specialized cell though the range is limited, unlike in the case of embryonic stem cells. Such cells are called multipotent.

For example, some multipotent stem cells found in the bone marrow can generate bone, cartilage, fat, and connective tissue. Stem cells taken from umbilical cord blood and the placenta seem to also have multipotent properties and thus in the future it may become routine that a stock of umbilical or placental cells will be taken after every birth and preserved for possible future use. Adult stem cells have some uses but working with them is much more difficult since they are harder to obtain and are less flexible.

To understand the ethical issues involved in using embryonic stem cells, one should be aware that creating embryonic stem cell lines for research requires extraction of cells from the blastocyst. This is the stage reached by a fertilized egg after about three to five days when, after repeated cell division and duplication, there are about 70-100 identical cells in the shape of a hollow ball containing an inner clump of cells. The inner clump becomes the embryo and the outer hollow ball becomes the placenta. When this occurs in the uterus, this stage is reached before this collection of cells gets implanted in the uterus wall. Sometimes implantation does not occur, in which case the pregnancy is spontaneously terminated.

This video explains what stem cells are and how they work.

The embryos from which embryonic stem cells are taken are produced during treatment for infertility when a woman's egg is taken from her body and fertilized and grown to blastocyst stage in a culture outside the woman's body. In the very early days after the egg is fertilized and the cell starts splitting and reproducing itself, all the cells are identical. Embryonic stem cells are obtained from that inner clump of cells and thus the blastocyst has to be destroyed in the process. The cells from a single blastocyst can be used to generate millions of embryonic stem cells that can be divided among researchers, and these are the stem cell 'lines' that are referred to. The cells in a single line are all genetically identical.

While there are promising new ways of creating embryonic stem cells using adult skin cells (called induced pluripotent stem cells), they have their own ethical issues.

Since tissues created from a person's stem cells have the same genetic information as the host, the host body will not reject the implanted tissues as a foreign body, thus overcoming one of the biggest hurdles in organ transplants. While the possibility of growing tissues and entire organs for transplant purposes is often publicized as the biggest potential benefit of using stem cells, there are other more immediately realizable potential uses for embryonic stem cells.

One is that it enables the process by which cells differentiate into their specialized forms to be studied. Another is that by creating cells that have a particular disease, say Parkinson's or Lou Gehrig's, one can observe under a microscope even the earliest stages of the progression of the disease and thus hope to develop better treatments. Another use is to test the effects of drugs on cells before testing them on a real person. That would enable you to see if they are toxic to a particular individual, creating a level of personalized medicine that we do not currently have.

The potential benefits of embryonic stem cells in research are clear, even though it is very early days yet and there is still a long way to go before we can hope to even begin realizing those benefits. The key question is how to balance the ethical concerns involved in using such cells with the benefits.

This question will be examined in the next post.

POST SCRIPT: The Daily Show on stem cells

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August 25, 2008

Why Darwin scares people

(The text of a talk given at CWRU's Share the Vision program on Friday, August 22, 2008 at 1:00 pm in Severance Hall. This annual program is to welcome all incoming first year students. My comments centered on this year's common reading book selection The Reluctant Mr. Darwin by David Quammen.)

Welcome to Case Western Reserve University!

You are fortunate that in your first year here you are going to part of a big year-long celebration, organized by this university, to mark the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of his groundbreaking book On the Origin of Species.

In my opinion, Darwin is the greatest scientist of all time. You have no idea how hard it is for me to say that because I am a physicist and had long thought that the only competitors for that exalted title were Isaac Newton and Albert Einstein. But the more that I have learned about the theory of evolution over the last decade, the more I have to concede that Darwin has had the most impact on our thinking.

As you have heard today, the Share the Vision program at Case is part of the university's commitment to create a welcoming and unifying environment for people from all backgrounds. Darwin's ideas should be warmly welcomed by those who share those goals because one important implication of his work is that all of us are biologically linked because we all share common ancestors.

If any two of you in this auditorium could trace your ancestors back in time, it will not be long before you find that you share a common ancestor. In fact, we would find that everyone who lives in the world now shares at least one common ancestor who lived only as far back as around 1500 AD. So around the time of Copernicus and the Renaissance, some one was walking around who is the common ancestor of each and every one of us.

If that doesn't boggle your mind, then listen to this. If you go back to just around 3,000 BC, of all the people who lived then, about 20% have no living descendents. Their lines died out. But the remaining 80% are the shared, common ancestors of all of us. Think about that for a minute. This is quite amazing. We are all, literally, part of one big family. We are all cousins under the skin.

It gets even better. If we go back even further, we find that we are cousins with all the nonhuman animals as well, and going back further still, with all the plants and even bacteria, all of us tracing our ancestors back to possibly a single ancestral organism. All of life that presently exists and ever existed is connected by this tree of life.

No wonder that Darwin was moved by this stupendous insight to end his book On the Origin of Species, by saying, "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved."

But, sadly, not everyone is as delighted as I am with the idea that worms are our cousins, and that we are both part of one big family with every organism that ever lived. Those who want to believe that humans possess some unique and special quality not possessed by other animals have found Darwin's idea deeply disturbing, and this is the source of much of the antagonism to him. Even the cautious Darwin himself, aware of this problem and the hostility it would arouse, only obliquely hinted at the linkage of humans to all other species in On the Origin of Species, leaving a full treatment to a subsequent book The Descent of Man published twelve years later.

Darwin's theory of natural selection and the tree of life is not only eminently plausible, but has been put on a rigorous mathematical footing and has abundant evidence in support of it. So why does the theory still arouse such strong opposition?

The superficial answer is that Darwin's theory goes against the religious belief that each species, and especially humans, were the result of a special act of creation by god. That idea seemed plausible at a time when it seemed obvious that every complex thing needed an even more complex designer to create it. But with Darwin, for the first time we had a scientific theory that showed how complex things could emerge from simpler things, without any outside intervention or agent or intelligence or design. Once the first primitive replicator, an early ancestor of DNA, had been created in the primeval soup, it multiplied and diverged, under the action of purely physical and algorithmic laws acting mindlessly, to eventually become the wide array of life we have now.

What is even more unnerving to some is that Darwin's theory reaches into every aspect of existence. As philosopher Daniel Dennett says, it is like an immensely powerful acid that once created cannot be contained by any boundaries because it can eat through any wall. People first tried to restrict it to nonhuman life but it broke through that barrier. They then tried to restrict it only to the human body but it broke through that too. Darwin's theory is now being applied to explain the origins of language and altruism and morality and other aspects of behavior, and to the workings of the brain and mind and consciousness.

Even intelligence, the feature that humanity prizes itself upon and which had been thought to be a precursor to creation, we now know occurred much later in life's evolution and came into being as a result of the same non-intelligent, undirected, natural selection mechanism that produced our arms and legs.

There seems to be no quality that we humans possess that could not have come into existence by the evolutionary processes described by Darwin and his successors.

Darwin's theory has extended even to what used to be considered purely philosophical questions. Paleontologist George Gaylord Simpson said that all attempts before the publication of On the Origin of Species to answer the question of what does it mean to be human were worthless and that we would be better off if we ignored them completely. Such is the significance of Darwin's work.

People who are wedded to the idea that human beings must possess some unique, non-material, and possibly divine quality, and that there must be some externally imposed purpose to their lives and the universe are highly uncomfortable by these developments. As cognitive scientist Steven Pinker says, "People desperately want Darwin to be wrong . . . because natural selection implies there is no plan to the universe, including human nature."

But the fact that the theory of evolution causes unease for some is hardly grounds for its rejection. The test of validity of a scientific theory is not whether it is perfect or whether it explains everything or whether it makes us feel happy or satisfies some deep emotional need, but whether it works better than any of its competitors. And there is nothing that comes even close to replacing the neo-Darwinian synthesis as the explanation of life's diversity.

As you will have read in the book, Darwin was nervous about where his ideas were taking him, even though he was increasingly convinced that he was right. He knew that in science just having a good idea isn’t enough, however beautiful the idea is. You had to have evidence to support it and to that end he doggedly spent most of his life, observing, experimenting, and collecting data from all over the world, despite ill health and recurring headaches and vomiting attacks and personal tragedy.

Since his death, the evidence in favor of his theory has increased with other revolutionary discoveries like genes and DNA and continental drift and fossils. The evidence in support of Darwin's theory of natural selection and the resulting interconnectedness of all life now exists in abundance.

This has not stopped the critics though. But they have been reduced to merely trying to find problems as yet unsolved by the theory of evolution because no alternative theory has been able to produce the kinds of evidence necessary to be taken seriously as a competitor. But as Herbert Spencer pointed out as long ago as 1891, "Those who cavalierly reject the Theory of Evolution as not being adequately supported by facts, seem to forget that their own theory is supported by no facts at all."

This year, you will all be able to be part of the Darwin celebration as eminent scientists, philosophers, and legal scholars from all over the world come to Case to discuss all the ramifications of his work. You have a unique opportunity to be part of that exciting year and I hope you take full advantage of it.

POST SCRIPT: Teaching evolution in high schools

Florida has just introduced evolution explicitly into its science standards. This story illustrates one teacher's efforts to teach it to his high school students.

July 22, 2008

Scientific consistency and Conservapedia loopiness

One of the drivers of scientific research is the desire to seeking a greater and greater synthesis, to seek to unify the knowledge and theories of many different areas. One of the most severe constraints that scientists face when developing a new theory is the need for consistency with other theories. It is very easy to construct a theory that explains any single phenomenon. It is much, much harder to construct a theory that does not also lead to problems with other well-established results. If a new theory conflicts with existing theories, something has to give in order to eliminate the contradiction.

For example, Darwin's theory of evolution is a slow process, incompatible with the young Earth creationist theory of a 6,000-year old Earth. The acceptance of Darwin's theory was only made possible with the almost concurrent emergence of geological theories that argued that the Earth was far older than that. Creationists, on the other hand, want to go in the opposite direction and seek to discredit evolution so that they can hold on to a young Earth.

But while the scientific search for overall consistency results in more logical and satisfying theories and new breakthroughs, the parallel religious attempt to build consistency around a 6,000 year Earth leads to greater and greater loopiness, to the construction of an alternative reality that one can only marvel at.

Take for example, the fascinating response of some religious people to reports of Richard Lenski's interesting evolution experiment I wrote about yesterday. Andrew Schlafly (son of Phyllis Schlafly, a conservative icon) is the founder of Conservapedia, a religious alternative started to counter what they perceive as the anti-Christian, liberal agenda of Wikipedia. Conservapedia views everything through a Christian, right-wing, America-centered lens. It gives a lot prominence to arguments in favor of a 6,000-year old Earth.

The anti-evolution crowd contains many people who combine ignorance of science with arrogance and Schlafly exemplifies this. Even though he is not a microbiologist, he challenged Lenski's work with extraordinarily rude letters implying that there was shady work afoot and demanding to see the raw data, leading to a back-and-forth correspondence. You can read all the gory details here. Lenski's second reply to Schlafly is a masterpiece, combining a lesson in how to get slapped around politely with a good scientific explanation of his experiment.

One benefit of Schlafly's crusade is that Lenski's experimental results became elevated from something that just his biology subcommunity knew about to an internet phenomenon, widely discussed in the wider science and religion world. I myself heard about Lenski's work only because of the fuss that Andrew Schlafly created, so thanks Andy!

If you have not yet experienced the goofiness of Conservapedia, you are missing a treat. Take this gem from its article on the theory of relativity.

A prevailing theory among creation scientists such as physicist Dr. John Hartnett believe that the Earth was once contained in a time dilation field, which explains why the earth is only 6,000 years old even though cosmological data (background radiation, supernovae, etc.) set a much older age for the universe. It is believed that this field has since been removed by God, which explains why no such time dilation has been experienced in modern times. (my italics)

That is a typical religious explanation for phenomena – god did it and then hid the evidence that he did it. It always amazes me that these people claim to know exactly what god does and what god wants but plead ignorance as to why.

Take, as another example, Conservapedia's article on kangaroos. These marsupials are found only in Australia and the scientific understanding of how this happened involves theories of changes in ocean levels, the splitting apart of continents, and the speciation that results when animal populations get separated geographically and evolve independently from their ancestral forms, and thus diverge from their cousins on other continents.

After devoting just one line to the evolutionary explanation for the origin of kangaroos in Australia, Conservapedia expansively discusses the creationist explanation:

According to the origins theory model used by young earth creation scientists, modern kangaroos are the descendants of the two founding members of the modern kangaroo baramin that were taken aboard Noah's Ark prior to the Great Flood. It has not yet been determined by baraminologists whether kangaroos form a holobaramin with the wallaby, tree-kangaroo, wallaroo, pademelon and quokka, or if all these species are in fact apobaraminic or polybaraminic.

After the Flood, these kangaroos bred from the Ark passengers migrated to Australia. There is debate whether this migration happened over land with lower sea levels during the post-flood ice age, or before the super-continent of Pangea broke apart.

The idea that God simply generated kangaroos into existence there is considered by most creation researchers to be contra-Biblical.

Notice that this article disparages the notion that god created kangaroos out of nothing in Australia, but finds perfectly plausible the idea that god created the kangaroos out of nothing earlier, saved just a pair of them in Noah's Ark, and then after the flood had them hopping over to Australia to raise a family start a new life, like homesteaders in old Western films.

One would think that once one allowed that kangaroos could be created out of nothing, Ockham's razor would prefer the former theory. The only reason not to do so is to conform to Biblical myths. The Noah's Ark bottleneck has to be preserved at all costs.

It is a long journey from Mount Ararat in Turkey (where the Ark supposedly finally ended up) to Australia and this theory requires that the pair of kangaroos from the Ark either live long enough to get to Australia before they started breeding or that all their offspring produced along the way stuck with the family for the entire journey (can you imagine how maddening their cries of "Are we there yet?" would become) or that the successor lines of all the ones that were left behind along the way became extinct, leaving no fossil record anywhere else in the world. Or maybe they were raptured early.

Another possibility (which I just thought up or maybe it was god revealing the truth to me, undeserving heathen though I am) is that Noah's Ark was less like an emergency lifeboat and more like a round-the-world cruise ship, and that different animals left the liner at different ports of call: kangaroos at Sydney, koalas at Auckland, penguins in the Antarctic etc. This theory actually explains a lot about the geographic diversity of species and I offer it free to the creators of Conservapedia to add to their site.

Since Conservapedia, like Wikipedia, is a fairly open system that allows almost anyone to edit its entries, some suspect that much of the site's content consists of subtle parodies by people pulling the legs of Schlafly and his co-religionists, and that they have not cottoned on to it yet. For example, I found the above passage about relativity just last week but today noticed that the passage has been changed, to be replaced by the briefer "Prevailing theories among creation scientists such as physicists Dr. Russell Humphreys and Dr. John Hartnett are time dilation explains why the earth is only 6,000 years old even though cosmological data (background radiation, supernovae, etc.) set a much older age for the universe." Was the original a parody that the site editors discovered and scrubbed? Is the kangaroo explanation a parody? It is hard to tell.

It is a sad reflection on your credibility when readers cannot tell when the material has been created in good faith and when it is a hoax.

POST SCRIPT: Platypus

Steve Benen points out that new research mapping the genome of the platypus causes yet more headaches for creationists.

July 21, 2008

Seeing evolution in real time

Evolution opponents tend to try and dismiss the evidence in its favor, as a last resort often resorting to the argument that no one has actually seen evolution occurring and a new species emerging, with all the intermediate stages clearly identified. One reason for this is, of course, that evolutionary change occurs very slowly, not visible in the transition from one generation to another. The emergence of a new species is almost always a retrospective judgment, made long after the fact, of a process that often takes thousands, or tens of thousands, of generations. By that time, most of the intermediate forms have become extinct and left no trace, since fossilization is such a rare event.

This is why researchers are finding that bacteria and other microbes, organisms that can go through multiple generations in a single day, to be valuable targets for study, allowing them to see evolutionary change and speciation within the span of a human lifetime.

In a truly remarkable piece of work, Richard Lenski of Michigan State University, starting from a single E. coli bacterium in 1989, kept breeding them in environments with a limited supply of food to see how they would adapt to their situation.

The experiment ran as follows:

He created 12 identical lines of E. coli and then fed them a meager diet of glucose. The bacteria would run out of sugar by the afternoon, and the following morning Dr. Lenski would transfer a few of the survivors to a freshly supplied flask.

From time to time Dr. Lenski also froze some of the bacteria from each of the 12 lines. It became what he likes to call a “frozen fossil record.” By thawing them out later, Dr. Lenski could directly compare them with younger bacteria.

Within a few hundred generations, Dr. Lenski was seeing changes, and the bacteria have been changing ever since. The microbes have adapted to their environment, reproducing faster and faster over the years. One striking lesson of the experiment is that evolution often follows the same path. “We’ve found a lot of parallel changes,” Dr. Lenski said.

The clever part of this experiment was that by freezing samples every 500 generations or so along the way, Lenski could go back in time if necessary and identify when specific changes occurred. He now has over 40,000 generations of bacteria and has thus been able to track closely the way that random mutations and natural selection, the fundamental basis of evolution, works. What these and other similar experiments do is show evolution occurring in real time.

One result of his experiments is that the bacteria are now twice as big as their common ancestor and reproduce 75 percent faster.

But the more dramatic result that Lenski observed was that after 33,127 generations, suddenly one of the colonies of the E. coli bacteria evolved the ability to absorb citrate, a nutrient found in abundance in the broth in which the bacteria are cultured. One of the signature marks of standard or 'wild' E. coli is their inability, unlike many other microbes, to absorb citrate.

Science reporter Carl Zimmer, who has been following these experiments, reports on the analysis they did of what happened.

[Lenski's graduate student Zachary] Blount took on the job of figuring out what happened. He first tried to figure out when it happened. He went back through the ancestral stocks to see if they included any citrate-eaters. For the first 31,000 generations, he could find none. Then, in generation 31,500, they made up 0.5% of the population. Their population rose to 19% in the next 1000 generations, but then they nearly vanished at generation 33,000. But in the next 120 generations or so, the citrate-eaters went berserk, coming to dominate the population.

This rise and fall and rise suggests that the evolution of citrate-eating was not a one-mutation affair. The first mutation (or mutations) allowed the bacteria to eat citrate, but they were outcompeted by some glucose-eating mutants that still had the upper hand. Only after they mutated further did their citrate-eating become a recipe for success.

So we see the clear emergence of a new form of E. coli, able to live on citrate in a way that 'wild' E. coli are not found to be able to do. The fact that these bacteria developed the ability to switch their diet from the meager glucose to the abundantly available citrate is a significant evolutionary step, showing how an organism can adapt to its environment in ways that make it better able to survive.

This really is a beautiful experiment, illustrating once again how much of science depends on painstaking, long-term, careful study.

Next: Religious anti-evolutionists attack Lenski's work.

POST SCRIPT: Comedian Dave Allen on the story of Genesis

June 27, 2008

The difference between human and other animal communication

In his book The Language Instinct (1994) Steven Pinker pointed out two fundamental facts about human language that were used by linguist Noam Chomsky to develop his theory about how we learn language. The first is that each one of us is capable of producing brand new sentences never before uttered in the history of the universe. This means that:

[A] language cannot be a repertoire of responses; the brain must contain a recipe or program that can build an unlimited set of sentences out of a finite list of words. That program may be called a mental grammar (not to be confused with pedagogical or stylistic "grammars," which are just guides to the etiquette of written prose.)

The second fundamental fact is that children develop these complex grammars rapidly and without formal instruction and grow up to give consistent interpretations to novel sentence constructions that they have never before encountered. Therefore, [Chomsky] argued, children must be innately equipped with a plan common to the grammars of all languages, a Universal Grammar, that tells them how to distill the syntactic patters out of speech of their parents. (Pinker, p. 9)

Children have the ability to produce much greater language output than they receive as input but it is not done idiosyncratically. The language they produce follows the same generalized grammatical rules as others. This leads Chomsky to conclude that (quoted in Pinker, p. 10):

The language each person acquires is a rich and complex construction hopelessly underdetermined by the fragmentary evidence available [to the child]. Nevertheless individuals in a speech community have developed essentially the same language. This fact can be explained only on the assumption that these individuals employ highly restrictive principles that guide the construction of grammar.

The more we understand how human language works, the more we begin to realize how different human speech is from the communication systems of other animals.

Language is obviously as different from other animals' communication systems as the elephant's truck is different from other animals' nostrils. Nonhuman communication systems are based on one of three designs: a finite repertory of calls (one for warnings of predators, one for claims of territory, and so on), a continuous analog signal that registers the magnitude of some state (the livelier the dance of the bee, the richer the food source that it is telling its hivemates about), or a series of random variations on a theme (a birdsong repeated with a new twist each time: Charlie Parker with feathers). As we have seen, human language has a very different design. The discrete combinatorial system called "grammar" makes human language infinite (there is no limit to the number of complex words or sentence in a language), digital (this infinity is achieved by rearranging discrete elements in particular orders and combinations, not by varying some signal along a continuum like the mercury in a thermometer), and compositional (each of the finite combinations has a different meaning predictable from the meanings of its parts and the rules and principles arranging them). (Pinker, p. 342)

This difference between human and nonhuman communication is also reflected in the role that different parts of the brain plays in language as opposed to other forms of vocalization.

Even the seat of human language in the brain is special. The vocal calls of primates are controlled not by their cerebral cortex but by phylogenetically older neural structures in the brain stem and limbic systems, structures that are heavily involved in emotion. Human vocalizations other than language, like sobbing, laughing, moaning, and shouting in pain, are also controlled subcortically. Subcortical structures even control the swearing that follows the arrival of a hammer on a thumb, that emerges as an involuntary tic in Tourette's syndrome, and that can survive as Broca's aphasic's only speech. Genuine language . . . is seated in the cerebral cortex, primarily in the left perisylvian region. (Pinker, p. 342)

Rather than view the different forms of communication found in animals as a hierarchy, it is better to view them as adaptations that arose from the necessity to occupy certain evolutionary niches. Chimpanzees did not develop the language ability because they did not need to. Their lifestyles did not require the ability. Humans, on the other hand, even in the hunter-gatherer stage, would have benefited enormously from being able to share kind of detailed information about plants and animals and the like, and thus there could have been an evolutionary pressure that drove the development of language.

Human language was related to the evolution of the physical apparatus that enabled complex sound production along with the associated brain adaptations, though the causal links between them is not fully understood. Did the brain increase in size to cope with rising language ability or did the increasing use of language drive brain development? We really don't know yet.

The argument against a linguistic hierarchy in animals can be seen in the fact that different aspects of language can be found to be best developed in different animals.

The most receptive trainee for an artificial language with a syntax and semantics has been a parrot; the species with the best claim to recursive structure in its signaling has been the starling; the best vocal imitators are birds and dolphins; and when it comes to reading human intentions, chimps are bested by man's best friend, Canis familiaris. (Pinker, PS20)

It seems clear that we are unlikely to ever fully communicate with other species the way we do with each other. But the inability of other animals to speak the way we do is no more a sign of their evolutionary backwardness than our nose's lack of versatility compared to the elephant's trunk, or our inability to use our hands to fly the way bats can, are signs that we are evolutionarily inferior compared to them

We just occupy different end points on the evolutionary bush.

POST SCRIPT: But isn't everyone deeply interested in golf?

If you want yet more reasons why TV news is not worth watching . . .

June 26, 2008

Can animals talk?

One of the most interesting questions in language is whether animals can talk or at least be taught to talk. Clearly animals can communicate in some rudimentary ways, some more so than others. Some researchers are convinced that animals can talk and have spent considerable efforts to try and do so but with very limited results. In the comments to an earlier post, Greg referred to the efforts by Sue Savage-Rumbaugh (and Duane Rumbaugh) to train the bonobo chimpanzee Kanzi to speak, and Lenen referred to the development of spontaneous language in children who had been kept in a dungeon. There have been other attempts with chimps and gorillas named Washoe, Koko, Lana, and Sarah.

One thing that is clear is that humans seem to have an instinctive ability to create and use language. By instinctive, I mean that evolution has produced in us the kinds of bodies and brains that make learning language easy, especially at a young age. It is argued that all humans are born possessing the neural wiring that contains the rules for a universal grammar. The five thousand different languages that exist today, although seeming to differ widely, all have an underlying grammatical similarity that is suggestive of this fact. For example, this grammar affects things like the subject-verb-object ordering in sentences. In English, we would say "I went home" (subject-verb-object) while in Tamil it would be "I home went" (subject-object-verb).

What is interesting is that of all the grammars that are theoretically possible, only a very limited set is actually found in existence. We do not find, for example, languages where people say "Home went I" (object-verb-subject). What early exposure to language does is turn certain switches on and off in the universal grammar wiring in our brains, so that we end up using the particular form of grammar of the community we grow up in. This suggests that language structures are restricted and not infinitely flexible, indicating a biological limitation.

The instinctive nature of language can be seen in a natural experiment that occurred in Nicaragua. There used to be no sign language at all in that country because the children were isolated from one another. When the Sandinistas took over in 1979, they created schools for the deaf. Their efforts to formally teach the children lip reading and speech failed dismally. But because the deaf children were now thrown together in the school buses and playgrounds, the children spontaneously developed their own sign language that developed and grew more sophisticated and is now officially a language that follows the same underlying grammatical rules as other spoken and sign languages. (Steven Pinker, The Language Instinct, 1994, p. 24)

What about animals? Many of us, especially those of us who have pets, would love to think that animals can communicate. As a result, we are far more credulous than we should be of claims (reported in the media) by researchers that they have taught animals to speak. But others, like linguist Steven Pinker, are highly skeptical. When looked at closely, the more spectacular elements of the claims disappear, leaving just rudimentary communication using symbols. The idea that some chimps can be taught to identify and use some symbols or follow some simple spoken commands does not imply that they possess underlying language abilities comparable to humans. The suggestion that animals use sign 'language' mistakenly conflates the sophisticated and complex grammatical structures of American Sign Language and other sign languages with that of a few suggestive gestures.

The belief that animals can, or should be able to, communicate using language seems to stem from two sources. One lies in a mistaken image of evolution as a linear process in which existing life forms can be arranged from lower to higher and more evolved forms. One sees this in posters in which evolution is shown as a sequence: amoebas→ sponges→ jellyfish→ flatworms→ trout→ frogs→ lizards→ dinosaurs→ anteaters→ monkeys→ chimpanzees→ Homo sapiens. (Pinker, p. 352) In this model, humans are the most evolved and it makes sense to think that perhaps chimpanzees have a slightly less evolved linguistic ability than we do but that it can be nudged along with some human help. Some people are also convinced that to think that animals cannot speak is a sign of a deplorable species superiority on our part.

But that linear model of evolution is wrong. Evolution is a branching theory, more like a spreading bush. Starting from some primitive form, it branched out into other forms, and these in turn branched out into yet more forms and so on, until we had a vast number of branches at the periphery. All the species I listed in the previous paragraph are like the tips of the twigs on the canopy of the bush, except that some (like the dinosaurs) are now extinct. Although all existing species have evolved from some earlier and more primitive forms, none of the existing species is more evolved than any other. All existing species have the same evolutionary status. They are merely different.

In the bush image, it is perfectly reasonable to suppose that one branch (species) may possess a unique feature (speech) that is not possessed by the others, just like the elephant possesses a highly useful organ (the trunk) possessed by no other species. All that this signifies is that that feature evolved after that branch separated from the rest of the bush and hence is not shared by others. The fact that nonhuman animals cannot speak despite extensive efforts at tutoring them is not a sign that they are somehow inferior or less evolved than us.

Some efforts to teach animals language skills seem to stem from a sense of misguided solidarity. It is as if the more features we share with animals, the closer we feel we are to them and the better we are likely to treat them. It is undoubtedly true that the closer we identify with some other living thing, the more empathy we have for it. But the solution to that is to have empathy for all living creatures, and not try to convince ourselves that we are alike in some specific ways.

As Pinker says:

What an irony it is that the supposed attempt to bring Homo sapiens down a few notches in the natural order has taken the form of us humans hectoring another species into emulating our instinctive form of communication, or some artificial form we have invented, as if that were a measure of biological worth. The chimpanzees' resistance is no shame to them; a human would surely do no better if trained to hoot and shriek like a chimp, a symmetrical project that makes about as much scientific sense. In fact, the idea that some species needs our intervention before its members can display a useful skill, like some bird that could not fly until given a human education, is far from humble! (p. 351)

While any animal lover would dearly love to think that they can talk with animals, we may have to reconcile ourselves to the fact that it just cannot happen, because they lack the physical and perhaps cognitive apparatus to do so.

Next: The differences between animal and human communication.

POST SCRIPT: Superstitions

One of the negative consequences of religious beliefs is that it leads to more general magical thinking, one form of which is superstitions. Steve Benen lists all the superstitions that John McCain believes in.

It bothers me when political leaders are superstitious. Decision-makers should not be influenced by factors that have no bearing whatsoever on events.

June 25, 2008

When did language originate?

Trying to discover the origins of language is a fascinating scientific problem but the evidence is necessarily indirect. Clearly our bodies' physical capacity to articulate sounds is a biological development. Language had to be preceded by the evolution of the physical organs responsible for vocalization. Those organs must have co-evolved with those parts of the brain that can process language. But this evolutionary history is hard to reconstruct since the voice organs and brains are made of soft tissue and are thus unlikely to fossilize. Even if we could get an accurate fix on when the actual physical ability to speak came into being, this the could only be used to set a limit on the earliest time at which language could have occurred, but tells us nothing of when it actually did.

Since humans have these language organs and our closest existing cousins the chimpanzees do not, and since our branch of mammals split off from chimpanzees about 5-7 million years (or about 350,000 generations) ago, it is theoretically possible for language to be that old and still be consistent with only humans being able to speak.

At the other end, the discovery of cave art in Europe consisting of depictions of animals and humans in carved and painted and sculpted forms by Cro-Magnon humans in the Upper Paleolithic era about 35,000 years ago indicate complex social thinking indicative of the presence of language, suggesting that this sets a limit on the latest time for the origin of language.

But 35,000 to 5-7 million years is a huge time interval and attempts have been made to get a more precise fix on the origin of language. Various approaches have been attempted. One avenue of exploration comes from linguistics: the study of languages themselves and how they evolved. Another is to look at the physiological development of the human body. A third method is to look at the development of lifestyles to discern levels of complexity that suggest the kinds of social organization that would require language. A fourth is to look at the use of tools, to see if there is sophistication and uniformity over a wide area suggesting that knowledge was being shared and transmitted to distant locales.

While these are all promising avenues of research, unfortunately the lines of evidence from these different approaches currently do not converge on a single time, suggesting that we still have a long way to go in determining when language might have arisen.

Starting with linguistics, it is known that the structure of languages is very analogous to the biological tree of living organisms. Just as the fossil and DNA evidence all point to all living things being descended from a common ancestor, the approximately five thousand languages that currently exist exhibit grammar and vocabulary relationships strongly suggestive of the fact that they are all derived from a single common proto-language that existed long ago that evolved and split into branches the way that living organisms did. By tracing that linguistic tree back in time, we may be able to fix narrower bounds on the date of origin of that proto-language.

Steven Pinker argues that since modern humans Homo sapiens first appeared about 200,000 years ago and spread out of Africa about 100,000 years ago, and since all modern humans have identical language abilities along with a universal grammar, it seems likely that language appeared concurrently with the first appearance of modern humans. (Steven Pinker, The Language Instinct, 1994, p. 363, 364) Furthermore, there was a more than a tripling of brain size (from 400cc to 1350cc) during the period between the first appearance the genus Homo (in the form of Homo habilis) about two million years ago until Homo sapiens appeared, suggesting that the brain developed in that period partly in order to accommodate the new language centers. Pinker suggests that since Homo sapiens are us, it seems reasonable that language came into being as long ago as 200,000 years ago.

As for biological development. Richard Leakey explains what it is about the human body that enables speech. (The Origin of Humankind, 1994)

Humans are able to make a wide range of sounds because the larynx is situated low in the throat, thus creating a large sound-chamber, the pharynx, above the vocal chords . . . the expanded pharynx is the key to producing fully articulate speech . . . In all mammals except humans the larynx is high in the throat, which allows the animal to breathe and drink at the same time. As a corollary, the small pharyngeal cavity limits the range of sounds that can be produced. . . Although the low position of the larynx allows human to produce a greater range of sounds, it also means that we cannot drink and breathe simultaneously. We exhibit the dubious liability for choking.

Human babies are born with the larynx high in the throat, like typical mammals, and can simultaneously breathe and drink, as they must during nursing. After about eighteen month, the larynx begins to migrate down the throat, reaching the adult position when the child is about fourteen months old. (p. 130)

The unique position of the larynx in human speech suggests that if were able to identify when it got lowered to its present position, we might be able to determine when we first had the ability to speak. But the problem is that those parts of the body are made of soft tissues and do not fossilize easily. However, the shape of the bottom of the skull called the basicranium is arched for humans and essentially flat for other mammals and this part of the skull is an indicator of how well it can articulate sounds. "The earliest time in the fossil record that you find a fully flexed basicranium is about 300,000 to 400,000 years ago, in what people call archaic Homo sapiens." (Leakey, p. 132)

But of course that does not mean that language developed simultaneously with the basicranium. Leakey says that it is unlikely that language was fully developed among archaic Homo sapiens.

The brain is another indicator of possible language origins. The part of the brain known as Broca's area is a raised lump near the left temple associated with language and the use of tools. Furthermore, the left hemisphere of the brain (which is associated with language) is larger than the right. So if we can find fossilized skulls that indicate the presence of either of these features, that would also indicate the onset of possible linguistic ability. A fossil found nearly two million years ago seems to have just such features. Combined with the discovery of tool-making around this time Leakey thinks it is possible that it was with the advent of Homo habilis (the handyman) about two million years ago that language first started to appear, at least in a very crude form. (Leakey, p.129)

Another strategy is to look at the various tools and other artifacts that humans created and see if there is an increase in sophistication and increased spread of similar designs, which would suggest the sharing of knowledge and ideas and thus speech. The more complex the social structures in which people lived, the greater the need for language. As for tools, although they started being made about two million years ago, the earliest kinds were opportunistic in nature. More conscious tool making began about 250,000 years ago but then stayed static for about 200,000 years. The kinds of ordering of tools that are really suggestive of language does not seem to occur until suddenly about 35,000 years ago, coinciding with the sudden spurt in cave art in the Upper Paleolithic period. (Leakey, p. 134)

So basically the situation is confused. While it is possible that language began to appear in some primitive form as early as two million years ago, it seems more likely that real language skills began about 200,000 years ago. Also it is not clear whether language evolved gradually since that time or whether it remained in a low and more-or-less static state before suddenly exploding about 35,000 years ago into the complex language structures that we now have.

Next: Can animals talk?

POST SCRIPT: Fred and Wilma? Who knew?

The most unforgettable act of the 1969 Woodstock festival was Joe Cocker's rendering of the Beatles' A little help from my friends, a gentle song sung by Ringo Starr, which Cocker turned into an over-the top, weird, air-guitar-playing, frenzied, incoherent performance that looked like he was having some kind of seizure. Throughout it, you kept wondering what the hell he was singing since the lyrics seemed to have only a passing resemblance to the original.

Some helpful soul has now provided captions for Cocker's words. It all makes sense now. Or maybe not.

(Thanks to Jesus's General.)

June 24, 2008

The power of language

One of the things that makes some people uneasy about the theory of evolution is its implication that humans are just one branch in the tree of life, connected to every other living thing through common ancestors, and thus not special in any mysterious way. It is surely tempting to think that we must be somehow unique. Look at the art and culture and science and technology we have produced and for which nothing comparable exists by any other species. How can we explain that if we are not possessed of some quality not present in other species?

One doesn't have to look far to find one feature that distinguishes the human species from all its cousins in the evolutionary tree of life. It is language. Somehow, at some point, we developed the capacity to speak and communicate with each other through well-articulated sounds and that has had a profound impact on our subsequent development. Although the number of phonemes (units of sound) that humans can make (about fifty) is not vastly greater than the number available to apes (about a dozen), we can use them to generate an average vocabulary of about 100,000 words. "As a consequence, the capacity of Homo sapiens for rapid, detailed communication and richness of thought is unmatched in the world of nature." (Richard Leakey, The Origin of Humankind, 1994, p. 122)

Without language, the knowledge of animals is restricted to what they are born with as a result of their evolutionary development (i.e., their instincts) and what they acquire during their own lifetimes. That is necessarily restricted and each generation essentially starts life at the same point in knowledge space as the previous one.

But with language, all that changes. Now knowledge can be passed on from generation to generation and we can learn from our ancestors. Knowledge becomes cumulative and the process accelerated with the discovery of writing about 6,000 years ago, resulting in the ability to store and retrieve knowledge over long times and long distances.

I have sometimes wondered why religious people, always on the lookout for a sign that humans are special in god's eyes and possessed of some quality that could not be accounted for evolutionarily, have not seized on language as that which makes us uniquely human. Why don't intelligent design advocates suggest that it was god's intervention that enabled us to develop the ability to speak?

One advantage to religious people of using the introduction of language as a mysterious sign of god's actions is that it is hard to pin down exactly when and how language started, and thus might make it hard to explain scientifically, making it an even better choice for a religious explanation than the bacterial flagellum or even the origin of life. Language was a significant development in our evolutionary history but how it came about is murky because spoken language leaves no trace.

Of course, the fact that we humans possess a unique feature does not necessarily imply that we are special. After all, elephants can also boast of a uniquely useful organ, the trunk, that can do truly amazing things. It is strong enough to uproot trees and stack them carefully in place. It is delicate enough that it can pick a thorn, draw characters on paper with a pencil, or pick up a pin. It is dexterous enough that it can uncork a bottle and unbolt a latch. It is sensitive enough to smell a python or food up to a mile away. It can be used as a siphon and a snorkel. And it can do many more things, both strong and delicate. (Steven Pinker, The Language Instinct, 1994, p. 340)

Why did only elephants evolve this extremely useful organ compared to which the human nose seems so inadequate? It presumably developed according to the laws of natural selection, just like everything else. But if elephants were religious, they might well be tempted to argue that having a trunk was a sign from god that they were special and made in god's image, and thus that god must have a trunk too.

So uniqueness alone doesn't imply that we are possessed of some spiritual essence. But even if the ability to speak does not confer on us a mystical power, the question of when and how humans developed this profound and incredibly useful ability is well worth studying.

Next: When did language originate?

POST SCRIPT: George Carlin on language

I had written this post on language last week but then learned that comedian George Carlin died yesterday at the age of 71. He pushed the boundaries of comedy and many of his riffs dealt with the hypocritical use of language. His famous routine "Seven words you can't say on TV" ended up in 1973 as a case in the Supreme Court, which ruled that the government did have a right to limit the words used on broadcasts.

That routine is below. As to be expected, there is extensive and repeated use of the seven naughty words so don't watch if such language offends you.

Bonus video: George Carlin was also an atheist who poked fun at the lack of logic underlying religious beliefs.

June 23, 2008

Cloning and stem cell research

(This series of posts reviews in detail Francis Collins's book The Language of God: A Scientist Presents Evidence for Belief, originally published in 2006. The page numbers cited are from the large print edition published in 2007. The complete set of these posts will be archived here.)

In the Appendix of his book The Language of God: A Scientist Presents Evidence for Belief (2006), Francis Collins gives a very clear and brief exposition of the issues involved in stem cell research and cloning, which are not the same thing despite popular impressions.

A human being starts out as a single cell formed by the union of an egg and a sperm. The nucleus of this cell contains the contributions of DNA from each of the two parents and thus all the genetic instructions, while the region outside the nucleus, called the cytoplasm, contains the nutrients and signaling mechanisms that enable the cell to do whatever it is meant to do.

The single cell starts multiplying by copying itself, a process known as mitosis. In the very early stages, all the cells are identical and capable of eventually becoming any specialized cell like a liver cell, blood cell, etc. Such cells are called 'pluripotent' because of their ability to become any of the tissues that make up the body and it is these cells that are called embryonic stem cells and the center of the ethical debate.

Soon these embryonic cells begin to specialize and differentiate into cells that begin to form different organ tissues. They do this by having the DNA start turning switches on and off in its genes. Some of these specialized cells, such as those found in limited amounts in bone marrow, become what are known as adult stem cells in that while they still have the ability to differentiate further, they can do so only into a much more limited variety of adult tissues. Such stem cells are called 'multipotent'.

The promise of stem cell research is that one can use a person's own stem cells to regenerate tissues lost or damaged by all kinds of diseases. Since these cells are not perceived as foreign matter, this would not trigger the body's immune mechanism that rejects foreign tissues, as occurs currently with transplants. At present, this immune response has to be suppressed with powerful drugs, leaving the patient vulnerable to other infections.

The ethical problem is that although adult stem cells can be obtained and used from an adult without harming that person, they have only a very limited flexibility. Pluripotent cells are preferred but at present using such cells results in the loss of the embryos from which they are taken, and this immediately raises the ethical issue of whether by destroying an embryo, we are destroying life.

Currently pluripotent stem cell lines are created during the process of in-vitro fertilization, by taking an egg from a woman, fertilizing it in a petri dish with sperm from a man, and growing the resulting cell in solution containing the necessary nutrients for its growth. After about five days, what is called a 'blastocyst' is formed which consists of about 70-100 cells. This consists of an outer wall of cells encompassing a hollow cavity, and an inner clump of about 30 cells (called the inner cell mass) at one end of the cavity. It is the inner cell mass that eventually turns into the tissues that make up the growing fetus, while the outer wall becomes the placenta.

In-vitro fertilization is done to assist childless couples. The selected blastocyst is implanted in the uterus of either the person who donated the egg (the biological mother) or a surrogate, and once it adheres to the wall of the uterus, it receives oxygen and other nutrients from the mother and develops as any other fetus.

The ethical dilemma arises because the process is not 100% certain, and thus many more fertilized eggs and blastocysts are created this way than are currently used to generate actual pregnancies, and this has resulted in hundreds of thousands of unused fertilized eggs. They are currently kept frozen.

Researchers suggest that these fertilized eggs be used (with the donors' permission) to generate embryonic stem cell lines that can be used for research purposes. To do this, the inner cell mass is extracted from the blastocyst and transferred into a dish containing a culture that enables it to grow. When this is done, the blastocyst is effectively destroyed and cannot be used to create a human.

Opponents of embryonic stem cell research say that even a single fertilized egg cell is a human life and thus the blastocyst created this way should never be destroyed. Others argue that a blastocyst has none of the qualities that we associate with being human and thus destroying it not taking a life.

This dilemma created by scientific advances may be resolved by further scientific advances.

One possible compromise arises from the discovery of the process by which animals have been cloned, starting with the famous cloned sheep Dolly. This process is known as somatic cell nuclear transfer (SCNT). What happened with Dolly is that a single cell was taken from the udder of an adult sheep and its nucleus (containing all the genetic information) was extracted. Then an egg cell was taken and its nucleus removed and replaced with the nucleus that had been extracted from the udder cell.

What one might have expected to have created was a cell that was specialized for udders since one had taken a cell from the udder of an adult and by that time the cell should have become specialized for just that purpose. It was once thought that this process of specilization was irreversible. i.e., once a pluripotent embryonic stem cell becomes an adult stem cell or an adult specialized cell, there was no going back to its unspecialized state.

What researchers found to their amazement was that when the udder cell nucleus was inserted into the egg cell that had had its nucleus removed, the nucleus seemed to effectively go back in time and become like the original embryonic cell that had eventually resulted in the sheep from which the udder cell was obtained. When this was then implanted in a sheep, it grew as if from a single fertilized egg and gave rise to a new sheep (Dolly) that had genes identical to those of the sheep from which the original udder cell was taken.

This process has now been repeated with other mammals like horses, cows, dogs, and cats. Although the Raelians made the spectacular claim that they had used this technique to clone a human being, that seems like a hoax.

As a result of this research, it looks like it should be possible to take a nucleus from (say) the skin cell of an adult human and insert it into an egg cell that has had its nucleus removed and thus create cells that have all the properties of embryonic stem cells. Thus it should be possible to create blastocysts in the laboratory without having them originate in the fusion of sperm and egg, the traditional way in which children are conceived. These stem cells would have DNA identical to those of the adult whose skin cell the nucleus was taken from, and not a fusion of mother and father DNA information, the way an embryo is normally formed.

Of course, if this cell is implanted in a uterus, one could potentially create a cloned human being but no one is suggesting that that be done. In fact, there is strong worldwide opposition to such an act. But if the cell is grown in a petri dish, then it could generate the equivalent of embryonic stem cells for both research and therapeutic purposes.

Would the process of SCNT be considered sufficiently different from the usual process of creating a fertilized egg to be considered not a potential human and thus overcome the ethical problems of stem cell research? That remains to be seen.

POST SCRIPT: Tough times

We know that the troubled economy is hurting many people. The Daily Show looks at how it is affecting the people of Beverly Hills.

June 20, 2008

Bioethical dilemmas

(This series of posts reviews in detail Francis Collins's book The Language of God: A Scientist Presents Evidence for Belief, originally published in 2006. The page numbers cited are from the large print edition published in 2007. The complete set of these posts will be archived here.)

In the Appendix of Francis Collins's book The Language of God: A Scientist Presents Evidence for Belief (2006), he tackles the difficult ethical issues raised by advances in science and medicine, especially in the field of molecular biology. His own major contributions to the human genome have undoubtedly made him acutely conscious of these issues. Collins's describes the science and the issues arising from them very clearly and this Appendix is well worth reading.

Having mapped out the entire human genome, scientists are now in the position of being potentially able to identify the presence of genes that may predispose people to certain diseases or behaviors long before those things have manifested themselves in observable ways. This ability has, of course, some obvious advantages in the prevention and treatment of diseases.

For example, breast cancer has a hereditary component that can be identified by the presence of a dangerous mutation in the gene BRCA1 on chromosome 17. This mutation, which also creates a greater risk for ovarian cancer, can be carried by fathers as well, even though they themselves may not have the disease. In those families in which breast cancer is prevalent, knowing who has the mutated gene and who hasn't may influence how closely they are monitored and what treatments they might be given.

As time goes by, our genetic predisposition to more and more hereditary diseases will be revealed. But is this an unqualified good thing?

On the plus side, having this knowledge may enable those people at risk to take steps (diet, exercise, preventative treatment) that can reduce their risk of actually contracting the disease. After all, genes are usually not the only (or even the main) factor in causing disease and we often have some degree of control over the other risk factors for diseases such as diabetes or blood clotting.

We may also be able to treat more genetic diseases by actually changing an individual's genes, although currently the only changes being made are to the genes in the somatic cells (the ones that make up our bodies) and not the ones in the 'germ' line cells (the ones that are passed on to children via the egg and sperm). At present, there is a scientific and medical consensus that influencing the genes of future generations by changing the germ line is not something we should do.

Furthermore, our bodies' reaction to drugs is also often affected by our genes. That knowledge can be used to individualize treatment, to determine which drug should be given to which patient, and even to design drugs that take maximum advantage of an individual's genetic makeup. This kind of personalized medicine lies in our future.

But there are negatives to this brave new world of treatment. Should everyone have their DNA mapped to identify potential risk factors? And who should have access to a person's genetic information?

Some people may prefer not to know the likelihood of what diseases they are predisposed to, especially in those cases where nothing much can be done to avert the disease or what needs to be done would diminish by too much the quality of life of the individual. Furthermore, they may fear that this information could be used against them. If they have a predisposition for a major disease and this knowledge reaches the health insurance companies, the latter may charge them higher premiums or even decline to cover them at all. After all, the profit-making basis on which these companies run makes them want to only insure the pool of healthy people and deny as much coverage as possible to those who actually need it.

It works the other way too. If someone knows they have a potential health problem but the insurance companies don't, they may choose health (and life) insurance policies that work to their advantage.

So genetic information can become a pawn in the chess game played between the individual and the health (and life) insurance agencies.

This is, by the way, another major flaw of the current employer-based private health insurance schemes in the US. If we had a single-payer, universal health care system as is the case in every other developed country, and even in many developing countries, this problem regarding genetic knowledge would not even arise. Everyone would be covered automatically irrespective of their history, the risk would be spread over the entire population, and the only question would be the extent to which the taxpayers wanted to fund the system in order to cover treatment. That would be a matter determined by public policy rather than private profit. There would still be ethical issues to be debated (such as on what basis to prioritize and allocate treatment) but the drive to minimize treatment to maximize private profit would be absent, and that is a huge plus.

There are other issues to consider. What if we find a gene that has a propensity for its bearer to commit crimes or other forms of antisocial behavior? Would it be wrong to use this knowledge to preventively profile and incarcerate people? It has to be emphasized that our genes almost always are not determinants of behavior but at best provide small probabilistic estimates. But as I have written before, probability and statistics is not easy to understand, and the knowledge that someone has a slightly greater chance of committing a crime can, if publicly known, be a stigma that person can never shake, however upstanding and moral a person he or she tries to be.

There is also the question of what to do with people who want to use treatments that have been developed for therapeutic purposes in order to make themselves (or their children) bigger, taller, stronger, faster, better-looking, and even smarter (or so they think) so that they will have an advantage over others. That thought-provoking film Gattaca (1997) envisions a future where parents create many fertilized eggs, examine the DNA of each, and select only those which contain the most advantageous genetic combinations to implant in the uterus. Collins points out that while this is theoretically possible, in practice it cannot be used to select for more than two or three genes. Even then, there are no guarantees that environmental effects as the child is growing up may not swamp the effects of the carefully selected genes. (p. 354)

Collins argues, and I agree with him, that these are important ethical decisions that should not be left only to scientists but should involve the entire spectrum of society. He appeals to the Moral Law as general guidance for dealing with these issues (p. 320). In particular he advocates four ethical principles (formulated by T. L. Beauchamp and J. F. Childress in their book Principles of Biomedical Ethics, 1994) that we might all be able to agree on in making such decisions. They are:

1. Respect for autonomy – the principle that a rational individual should be given freedom in personal decision making, without undue outside coercion.
2. Justice – the requirement for fair, moral, and impartial treatment of all persons
3. Beneficence – the mandate to treat others in their best interest
4. Nonmaleficence – "First do no harm" (as in the Hippocratic Oath)

These are good guidelines, though many problems will undoubtedly arise when such general secular ethical principles collide with the demands of specific religious beliefs and cultural practices. When supposedly infallible religious texts become part of the discussion, it makes it almost impossible to seek underlying unifying moral and ethical principles on which to base judgments.

POST SCRIPT: Brace yourself

Matt Taibbi warns that this presidential election is going to be very rough.

April 18, 2008

The changing problems of science and religion

(I will be away on travel this week so will be reposting an old series, edited and updated, that discusses the nature of science and the difference between science and religion. New posts start again on Monday, April 21, 2008.)

In the previous posting, I discussed some of the problems that arise is reconciling science and religion. These problems change with time as our understanding of science changes and the explanatory powers of science encompass more and more phenomena.

For example, in the pre-Copernican era, one could have had a plausible model of god that became much harder to sustain in the light of post-Copernican scientific developments. This was because the universe then was seen as consisting of a spherical Earth located at the center of a finite universe and surrounded by a concentric rotating sphere in which the stars were embedded. (See Thomas Kuhn's The Copernican Revolution for a detailed history.) People thought that the stars were very small objects, and thus the outer sphere containing them could be quite nearby.

In that model, it was possible to think of the heavens as lying beyond this outer sphere and this provided a home for god and angels and so on. There are no major conceptual problems in believing this model. This model enabled people to envision without much difficulty how god could intervene in the events on Earth. All that was required was to imagine god as having pretty much the same powers as human beings did, but just more powerful and extensive. Thus god has more refined senses, sees better, hears better, is more powerful, travels faster, etc. It was not hard to think of god in heaven actually seeing and hearing what was going on Earth, being able to send thunderbolts or other forms of signals from heaven to Earth, or even making a quick trip (either personally or by sending angels) to Earth. Believing that god intervened in everyday events was not that hard to conceive within the framework of a pre-Copernican cosmology.

But Copernicus' introduction of a heliocentric universe, and the more precise astronomical observations made possible by the invention of the telescope caused some serious problems for such early models, although the theological implications seemed to have taken some time to sink in.

As Kuhn points out (on page 193):

When it was taken seriously, Copernicus' proposal raised many gigantic problems for the believing Christian. If, for example, the earth were merely one of six planets, how were the stories of the Fall and of the Salvation, with their immense bearing on Christian life, to be preserved? If there were other bodies essentially like the earth, God's goodness would surely necessitate that they, too, be inhabited. But if there were men on other planets, how could they be descendents of Adam and Eve, and how could they have inherited the original sin, which explains man's otherwise incomprehensible travail on an earth made for him by a good and omnipotent deity? Again, how could men on other planets know of the Savior who opened to them the possibility of eternal life? Or, if the earth is a planet and therefore a celestial body located away from the center of the universe, what becomes of man's intermediate but focal position between the devils and the angels? If the earth, as a planet, participates in the nature of celestial bodies, it cannot be a sink of iniquity from which man will long to escape to the divine purity of the heavens. Nor can the heavens be a suitable abode for God if they participate in the evils and imperfections so clearly visible on a planetary earth. Worst of all, if the universe is infinite, as many of the later Copernicans thought, where can God's Throne be located? In an infinite universe, how is man to find God or God man?

Most of those new problems are metaphysical. The last point mentioned by Kuhn is the one I want to focus on because it represents a physical problem and the one that is of most interest to me as a physicist. If the universe if infinite, then where does god exist? Since telescopes can now observe vast sections of the universe, it strains the imagination to think of god occupying some part of the physical universe because if god is made of the same kinds of stuff as other things in the universe, then how is it that our telescopes and other devices don't detect anything?

I am not sure (not being an expert of the history of theology) but it may be that it was to solve this problem that popular ideas about god being a non-material entity (and hence undetectable by telescopes) who is everywhere began to gain ground. That way, it was possible to overcome the time and space problems associated with having a material god who necessarily has to occupy the same physical space as us.

But this raises yet other problems. If god is non-material and occupying a non-material space that co-exists with our more familiar material world, then how can he/she interact with the material world to influence it? After all, if (say) god intervenes to change the course of natural events, then it must involve changing the behavior of tangible physical objects and this requires the application of forces to those tangible objects, and such forces fall within the realm of the physical world.

One solution is to forego all interventions by god except in the form of changing people's minds, and postulate that human beings possess a mind that is independent of the body, and thus occupies a space similar to or identical with that occupied by god. Thus communication within this 'spirit world' can take place between god and people. Such models allow for the concept of an after-life.

But this just shifts the problem one step away, and does not solve it. Because then we have the problem of understanding the mind-body relationship of each person and this has all the problems associated with the god-people relationship. If the mind exists independently of the body, then where does it exist? If the mind is a non-material entity, then how does it influence the body (which is material)? And so on. Such concerns were articulated by the mathematician-scientist-philosopher Rene Descartes (1596-1650). Note that Descartes posed these concerns after Copernican ideas had taken hold and the potentially vast size of the universe became better appreciated, giving such problems a sense of urgency,

The way that I have formulated these questions obviously reveals my physics background. I treat space and time as meaningful physical entities and so cannot easily absorb platitudinous statements like "god is everywhere" without further exploration as to what that statement actually means. I am guessing that most people do not consciously consider these questions either because they do not occur to them or shy away from them because of the discomfort they can cause.

So how does one resolve all these problems created by the assumption of god's existence in the light of modern scientific knowledge about a vast universe? I think once again people have to resort to Ockham's razor and each person will choose a position that satisfies him or her. I found that using Ockham's razor resulted in my dispensing with the idea of god altogether.

Assuming the existence of god creates a vast number of contradictions and complications that can only be dealt with by pleading ignorance and invoking an inscrutable deity, neither of which is very satisfying.

April 17, 2008

Science, religion, and Ockham's razor

(I will be away on travel this week so will be reposting an old series, edited and updated, that discusses the nature of science and the difference between science and religion. New posts start again on Monday, April 21, 2008.)

A few days ago I was working in my backyard when I noticed that the outdoor thermometer that I had fixed to a fence had disappeared. The mountings were still there but had been pulled away slightly. I thought that maybe the wind had blown it off and so I looked at the ground underneath but the thermometer was not there. There is a bed of pachysandra nearby and I looked nearby in it but no luck. I was baffled.

I pondered the various options for explaining the missing thermometer. One was that the wind had been strong enough to rip the thermometer from its mounting and blow it farther away into the pachysandra. The other was that it had fallen to the ground below and had then been taken away by squirrels or the neighbor's cat. The third was that neighborhood children had borrowed it without permission for some experiment. The fourth was that the International Outdoor Thermometer Cartel (IOTC) had raised the price of these thermometers to such a high value that organized crime gangs were stealing them and selling them on the black market. The fifth option was that aliens had taken it away as a souvenir of their clandestine visit to Earth.

Given these options, I decided that #1 was the most likely one and looked in the pachysandra over a larger area and, sure enough, I found it.

The reason for this anecdote is that it illustrates that I used something that we all use all the time (whether we are consciously aware of it or not), and that is Ockham's razor to make choices among competing theories.

According to the Encyclopedia Brittanica, the principle behind Ockham's razor (also called the law of economy or the law of parsimony) was stated by the scholastic William of Ockham (1285–1347), as "Plurality should not be posited without necessity." The principle is also expressed as "Entities are not to be multiplied beyond necessity." Ockham did not himself use the word 'razor', that was added to his name later by others.

The principle gives precedence to simplicity, but there are two ways it can be used. In the first case (which is more closely aligned with Ockham's intent), it says that you should not postulate more elements for anything other than the minimum required. For example, in the case of my missing thermometer, if I postulated one theory that a cat had taken it and a competing theory was that a cat that had a striped tail and a scar on its forehead had taken it, then in the absence of any extra information, the former theory is to be preferred. The latter theory just adds elements that do not add any necessary information to the explanation. The application of this version of the principle is fairly straightforward. One seeks the smallest subset of elements of a theory that provides an adequate explanation of whatever you are trying to explain.

The more problematic (but common) use of Ockham's razor is when you try and apply it to a situation where there are two competing theories that share either no common elements or there exist at least some necessary elements of one theory that the other does not possess. We commonly interpret Ockham's razor in those situations as requiring us to choose the simpler of the two theories. But simplicity may well lie in the eye of the beholder and it may not be easy to get agreement.

So, for example, in the case of the thermometer that was found some distance away from its mountings, the simpler explanation (for me at least) was that of the wind. If called upon, I could cite Bernoulli's Principle and the laws of motion to support my preference. That explanation is enough to satisfy me.

But this may not be true for someone else. For someone who is a believer in the existence UFOs and space aliens, a theory that alien vandals landed in my garden, tore the thermometer from its moorings, threw it away in the pachysandra and left in their spaceship, might be the "simpler" explanation. After all, it does not involve the use of calculus.

That is exactly the problem in many of the science and religion discussions. Apart from those people who reject science altogether, the integration of science and religion into one coherent philosophical framework becomes one of the most difficult challenges and there is no simple solution to it. And all of us use Ockham's razor to resolve it, even though the results are not the same for everyone.

A belief in the existence of god implies that there must be at least some phenomena caused by the intervention of god that lie outside the purview of science. (I am not considering the point of view that god created the world and its laws in one instant of time long ago and then has had a completely hands-off policy since then.)

For example, Biblical literalists will start with the assumption that the Bible is a historical document and that the events described in it (the world was created in six days and is only 6,000 years old, Joshua caused the Sun to stand still, Noah's flood did occur, etc.) all actually occurred. They will then painstakingly and tortuously try and reinterpret all evidence to be consistent with these axioms. The website Answers in Genesis goes to extraordinary lengths to try and answer questions such as "Where did Cain find his wife?" and "Did dinosaurs live alongside humans?" These are questions that do not trouble anyone who does not treat the Bible as an authoritative source for science and history.

But even those who take the Bible less literally have to confront difficult questions because at some point, the question is going to arise about where you draw the line and ascribe something to the actions of god. Each person will draw the line between god's actions and the actions of natural laws differently, depending on their personal level of comfort with the explanation.

This is something that believers in any theistic religion have to confront. Some will believe that any event that does not have a ready explanation to hand (a death in the family, an escape from injury, an unexpected recovery from a serious illness) are directly due to god's intervention to change the course of events. In order to deal with the existence of evil in the presence of an omnipotent and loving god, believers usually end up having to postulate that god's actions are inscrutable and that we cannot know the answers to at least some of the events that occur in the world.

At the other end, others might believe that god does not actually cause a change in the natural sequence of events but instead exerts his/her influence by working through people. In other words, people are the agents of god's actions and the sole mechanism by which he/she influences events. So people are cured of illnesses because god inspires researchers and physicians, and so on.

There are also an infinite number of intermediate states between those two extremes. For example, people like the biochemist Michael Behe, who is an intelligent design advocate and author of the book Darwin's Black Box, accept natural explanations for everything except for a few selected phenomena at the biochemical level (such as the blood clotting mechanism or the creation of the bacterial flagellum) that he feels are unlikely to have been created by natural processes. (See the New Yorker article by H. Allen Orr for a clear description of what Behe's argument is. Cory also sent me a link to a nice article written by John Rennie, editor of Scientific American, that addresses some of the key points raised by ID advocates.)

Or one can use decide that there is no god (or supernatural entity of any kind), and all that exists is the material world. This is the position of philosophical naturalism or atheism. (I am treating the two terms as effectively synonymous, although professional philosophers might disagree).

So we are left with only Ockham's razor with which to make a decision but in this case, it is a very personal razor whose use will satisfy only us. I personally find that assuming no god exists makes everything simpler and much more meaningful.

But those who are committed to believing in the existence of god despite the lack of evidence for his/her existence will not agree with me that this is the simplest explanation. They will likely say that having an inscrutable god who for some reason allows unspeakable cruelties is a 'simpler' way of understanding the world.

Which position one ends up taking is thus largely determined by deciding which is 'simpler' to believe in, which usually means deciding which belief structure you want to believe in and find personally enriching and meaningful, since there is no unambiguous measure of simplicity for incommensurable theories.