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August 10, 2007

Evolution-21: Why evolution speeds up with time

(Please see here for previous posts in this series.)

One of interesting things about evolution is that it seems to be speeding up with time. Earth was formed about 4.7 billion years ago and it took about a billion years for the first single-celled life to appear about 3.5 billion years ago. It then took another 2.5 billion years for the first multi-cellular life form (like sponges) to appear. So everything else, all the insects, animals, and birds, came into being within the last one billion years or so.

One reason that things seem to be speeding up is that once complex organisms appeared, selection advantages increased due to more sophisticated competition among them. For example, when you have a predator-prey relationship, the prey species will have a huge selection advantage for those qualities that enable it to elude the predator (such as the ability to run faster or climb quicker or hide better or hear and smell better) while the predator will also have a huge selection advantage for those features that make it better able to capture prey (run faster, jump higher, and more acute vision, hearing and smell.) It is like an arms race. Two nations that are locked in a battle for supremacy are more likely to rapidly develop sophisticated weaponry than a nation without enemies.

Such factors, along with things like sexual selection, speed up the evolutionary process considerably, by increasing the selection advantage.

But new discoveries keep coming in and just this year, researchers have found that bacteria and viruses are also speeding up the process of evolution. Scientists at Rice University report that "the speed of evolution has increased over time because bacteria and viruses constantly exchange transposable chunks of DNA between species, thus making it possible for life forms to evolve faster than they would if they relied only on sexual selection or random genetic mutations." Theories like this support suggestions that there is a selection advantage for those organisms that are more adaptable to change. In other words, evolution favors those organisms that evolve more readily, leading to ever-increasing rates of change.

In fact, the problem with the evolution of species is not (as some religious people would have you believe) whether it occurs at all but that it is impossible to stop it from occurring. Almost invariably, when some members of a species get isolated from the rest for whatever reason, they begin to diverge. This is why the isolation of islands makes them excellent breeding grounds for new species. All the islands smaller than New Guinea account for one-thirtieth of land surface but contain about one-sixth of the total number of known species (Almost Like a Whale, Steve Jones, p. 345). In the Caribbean, for example, different lizards have different kinds of legs suitable for the kinds of vegetation that they climb on. In 1977, when lizards from one island were moved to another that had no lizards and only plants with thin twigs, within ten years their legs had evolved to meet the needs of the new vegetation by becoming stubby (Jones, p. 96).

But Darwin also proposed that one did not need actual physical separation like islands for speciation to occur. Diversity could arise within the same geographical area as organisms adapted to fit different niches in the same environment. Just yesterday it was reported that new evidence suggests that the two species homo habilis and homo erectus lived side by side at the same time, challenging the earlier idea that there was a linear progression from homo habilis to homo erectus to us, homo sapiens. The news report of the findings says that "The fact that the two hominid species lived together in the same lake basin for so long and remained separate species, Meave Leakey said in a statement from Nairobi, “suggests that they had their own ecological niche, thus avoiding direct competition.” "

Zoos face this problem with trying to preserve rare species. Although the zoos are trying to preserve the animals that are being lost in the wild, the very fact that zoo animals breed within a small group paradoxically causes them to actually accelerate their evolution into new forms. (Jones, p. 47)

As a result of all these factors favoring evolution, "Over the past five hundred million years, through all its ecological alarms and excursions, new kinds appeared at an almost constant rate. A survey of tens of thousands of marine animals over that time gives a rate of four hundred and fifty new species a year." (Jones, p. 231)

This is the last post in this series on evolution. To be frank, I had not expected it to be this long when I started but the breadth and scope of the subject just kept drawing me in deeper. While I will definitely return to this topic many times (because it is inexhaustible and new and interesting discoveries keep popping up), the planned and sequential nature of these posts will cease. My goal was to move the discussion of the theory of evolution away from a high level of generality and show that evolution is not just a good idea but that, like quantum mechanics and relativity, it is a theory that has been developed in great detail and its ramifications explored using a wide array of scientific tools.

The mathematics of evolution has played an important role in substantiating its claims and advancing our understanding of how it works. Charles Darwin would have found this highly amusing because he had great difficulty with mathematics as a student, struggling with even elementary algebra. Because of the complexity of biological systems, the probabilistic nature of the processes, and the interplay of organisms with other organisms and the environment in general, modern biological calculations use advanced mathematics, computer simulations, and game theoretical techniques in addition to the more conventional differential equations. There is even a new game by the creators of the Sims series that enables you to manipulate the conditions of evolution and see what happens. You can "determine the evolution of a species, from an amoeba to an inter-stellar race."

This is how science works and how we build up knowledge. People with different skills and expertise bring them to bear on complex problems, publish so that it can be checked by others, and over time we create reliable knowledge. This does not mean that scientific knowledge is infallible by any means. It is not uncommon for people to find that new data or a different set of assumptions lead to quite different results, and so scientists continually probe for weaknesses.

But such revisions and critiques are of a very different class from those of people who reject scientific ideas as absurd simply because it conflicts with their intuitions or because they seem unimaginable, without looking into the details. Such people are doing the same thing as those who reject quantum mechanics and special relativity because the results seem so weird to them.

POST SCRIPT: Pampered elites

Jason Jones of The Daily Show has a very funny piece on how the very rich in this country don't want to allow even the slightest thing to disturb their lives. People like the Kennedys, who vociferously support environmental causes everywhere else, turn against eco-friendly projects when those might have an infinitesimal impact on their own neighborhoods.

August 08, 2007

Evolution-20: How selection advantage arises in evolution

(Please see here for previous posts in this series.)

In the mathematics of evolutionary change, the selection advantage is a key mathematical quantity that determines the rate at which a favorable mutation spreads through the population. The selection advantage is a quantification of the net result of advantages that a variety of a species gains by virtue of its fertility and fecundity and longevity. As we saw before, even a small selection advantage can lead to rapid spread of the mutation.

One of the interesting things that occurs is that since the entire organism is subjected to the same environment, a selection advantage for one feature can act simultaneously on many different features and can lead to a group of changes that might seem on the surface to be unrelated. Thus one can have many simultaneous changes in an organism, a process known as coherence.

Jerry Coyne (a professor in the Department of Ecology and Evolution at the University of Chicago) describes how this works.

Coherence is precisely the product of natural selection working with mutation. Yes, mutations are random in the sense I have described, but to say that an evolutionary step taken by an organism is unconnected to its predecessor completely ignores the fact that during evolution organisms are adapting to something in their environment, and that this adaptation can involve a coherent, coordinated response of many features. Consider the evolution of whales from terrestrial animals, now documented by a superb fossil record. The fossils show a wolf-like creature gradually becoming aquatic, with the hind limbs being reduced and finally lost, the forelimbs transformed into flippers, and the nostrils gradually moving atop the head to form the blowhole. How can anyone say that these changes (which of course look planned at the end) are unconnected or incoherent? They represent a case of natural selection eventually turning a land animal into a well-adapted aquatic one.

In Almost Like a Whale (p. 36), Steve Jones says that when some wolves were domesticated to become companions to humans and became the dogs we now have, its other features also changed, although these were not deliberately sought for.

Its ears, once pricked, are floppy, and the sounds of the world dulled. Its sharp eyes are blurred by a fringe of hair and can no longer stare an opponent into submission. The lupine tail, an expression of rage or delight, is in many breeds so curled as to bear no message at all. Most pets cannot even raise their hackles in anger as their hair is too long. All this comes from an unconscious preference by man for an animal that knows its place.

What was once done without thought has been echoed by science. In the 1950 Russia, silver foxes were farmed for fur. They were savage, suspicious and liable to die from anxiety. On a certain collective, in an attempt to improve matters, only those willing to accept human company were chosen as parents. Within twenty years and a mere ten thousand foxes, the farmers saw a great shift in their charges. The ranch was filled with well-behaved animals that looked more like dogs, with lowered tails and drooping ears. Many had piebald coats, quite unlike their unrestrained kin, and the females reproduced – like dogs – twice rather than once each year. To breed for tameness was enough to make the change. The other characteristics followed.

There are other factors that increase the selection advantage and thus speed up evolution considerably. The powerful driver that is sexual selection in the wild (usually females selecting males for mating based on certain qualities) prevents random mating and can result in generating significant selection advantages, and is believed to be the source of the exotic and elaborate plumage and songs of some male birds and the gaudiness of flowers (Jones p. 102). Animals tend to prefer to mate with others that either look like themselves or with those animals that look like the ones that raised them, if they had foster mothers (Jones p. 49). Darwin himself first emphasized the importance of sexual selection (On the Origin of Species, 1859, p. 87).

All kinds of factors can come into play that result in one variety of a species separating from the rest, and evolving into a new species as a result. As Jones says (p. 231):

Species are divided from each other in many ways – by space, by time, by mating preference, by the inability to fertilize an egg or produce healthy young, or by the sterility of offspring. The hurdles at which the sexual athletes fail are as varied as life itself. Those involved may never meet, or may mate at their own special time or season. Males and females of different kinds may choose not to pair, or may – with more or less enthusiasm – mate but fail to make a fertile egg. The geographical checks can be as narrow as the few inches between different orchids upon which certain bees feed or as wide as the ocean that separates American and European species of gull. When it comes to time, some flies mate in the morning and some in the evening and some crickets in the spring and others in the autumn; but two kinds of cicadas in North America emerge and mate every thirteen or seventeen years. The difference ensures that they almost never get together (in spite of a certain confusion every couple of centuries).

Colour, song, scent and more all play a part in settling who is, and who is not acceptable.

As soon as one group within a species separates out from the rest and breeds within itself in a new environment, differences get accentuated leading to the eventual formation of new species with new characteristics. But some aspects of the environment (like gravity) are the same everywhere on the Earth and have remained unchanged for a long time. For example, the radiation from the Sun has not changed, and the visible spectrum of light that reaches the surface of the Earth is pretty much the same everywhere on the Earth and has been stable for a long time. Hence it should not surprise us that the ability to see has a huge selection advantage and has evolved independently over 40 times in evolutionary history, although the resulting eyes differ in detail.

Thus if we could run the evolutionary clock all over again, while some things will be quite different, certain features like the eye are likely to recur in some form simply because the environment that makes them advantageous is stable and unchanged by the life forms that happen to come into being. Such a process is called convergent evolution.

All these things constitute evidence that evolution, far from being purely random, is a strongly constrained and law-like process.

POST SCRIPT: Religion as divider

In the film Deconstructing Harry Woody Allen discusses the role that religion plays in creating us-them distinctions.

August 06, 2007

Evolution-19: The Boeing 747 in the junkyard

(Please see here for previous posts in this series.)

As I have emphasized repeatedly in this series, the hardest thing to appreciate about evolution is how a cumulative sequence of very tiny changes can lead to big changes. The problem is that our senses can only detect gross differences between organisms and our minds can only comprehend short time scales and to appreciate evolution requires us to overcome those limitations. This is why skeptics need to actually study the details and convince themselves that it works.

I have the same problems when it comes to teaching modern physics topics like quantum mechanics or special relativity. Our senses and intuition have evolved to enable us to deal with objects that are on a human (or 'classical') size scale and traveling at speeds that are not too great. But the effects of quantum mechanics only become manifest when describing the very small, subatomic level of particles that we cannot see, and there our intuition completely breaks down. Similarly, the effects of special relativity become manifest only for objects traveling close to the speed of light, which we do not encounter in everyday life and again our intuition is incapable of dealing with it. So when physicists talk about a single electron simultaneously traveling by many different paths from a single initial starting point to a final point, or twins aging at different rates depending on their speed of travel, these ideas initially seem preposterous.

When teaching these subjects, I warn my students that their intuition is quite likely to lead them astray, that what their gut feelings tell them is reasonable or unreasonable is undependable, and that they have to constantly check those intuitive reactions by doing calculations to convince themselves that these counter-intuitive results drop out naturally from a coherent theory

The same thing is true for evolution. Mutations are too small to be visible and time scales are too long to comprehend, so one should not depend upon what seems reasonable to make judgments. Steven Pinker (How the Mind Works 1997, p. 163) points out that: "A hypothetical mouse subjected to a selection pressure so weak that it cannot be measured could nonetheless evolve to the size of an elephant in only twelve thousand generations." This is quite an amazing result. It is not at all intuitive and is hard to convince oneself that this could be possible unless one does the calculations, or trusts those who do the calculations.

But people who want to throw doubt on evolution exploit this breakdown of intuition by making statements of broad generality. For example, one often hears that the evolution of life as described by natural selection is as likely as a tornado sweeping through a junkyard and spontaneously assembling a Boeing 747 airplane. This analogy was initially proposed by astrophysicist Fred Hoyle in his 1983 book The Intelligent Universe. Hoyle and his co-worker Chandra Wickremasinghe used this example to support their alternative theory of panspermia, that life originated elsewhere in the universe and arrived on Earth from outer space via meteors.

Neither Hoyle nor Wickremasinghe are creationists and have their own reasons to want to discredit natural selection, but intelligent design creationists seized on this vivid image of the 747 in the junkyard and exploit it heavily in their anti-Darwin crusade, and Wickremasinghe has even appeared as a witness for them at some court trials.

To counter this analogy, one needs to look at exactly what natural selection says and compare it with what its opponents portray it as. Jerry Coyne (a professor in the Department of Ecology and Evolution at the University of Chicago) in a devastating review of intelligent design creationist Michael Behe's new book gives a nice example using the familiar example of throwing dice.

Take for example, some adaptation of a gene that, starting from the original organism, requires twenty mutations at twenty different locations for the desirable new feature of the organism to appear, with the mutations occurring in a specific order so that each mutation confers a slight selection advantage to the organism. Suppose that the random mutations are represented by the throw of a die and the required mutation at a particular site occurs when you throw a six. This means that it will take an average of six throws for the first mutation to occur. Recall that evolution is a step-by-step process that builds on past successes and I have already described how even a slight selection advantage is sufficient for a single mutation to become universal in the population, so this mutation will be stable. It will then take another six throws for the second advantageous mutation to occur, and so on, so that it will take an average of 120 throws for all twenty mutations to occur. If the dice is thrown at the rate of one a second, that means it will take about two minutes for all twenty mutation to have gone into effect.

What the Boeing 747 analogy does is to assume that you have twenty dice and throw them all at once and that all twenty must come up six simultaneously for the new feature to appear. The odds against this are astronomically high. At the same rate of one toss per second, this would take more than one hundred million years. As Coyne says, "This sequential way of getting twenty sixes is infinitely faster than Behe's method. And this is the way natural selection and mutation really work, not by the ludicrous scenario presented by Behe."

Arguing by analogy and example is often necessary when trying to explain esoteric points, but is also tricky and has to be done with care. No analogy is a perfect replica of the actual process and you have to make sure that the analogy you select corresponds accurately to the phenomenon being analogized as far as the crucial elements are concerned. In the case of evolution, the key point to bear in mind is that a sequential series of changes, each of which is beneficial and stable, takes much less time (i.e. is far more likely) to occur than for them to occur simultaneously. This is why intelligent design creationists try to desperately find examples of systems that (they argue) could not have occurred by sequential changes. But they have failed.

POST SCRIPT: If FDR had been like George Bush. . .

Jacob Sager Weinstein says that he "got tired of right-wingers saying, "If the media had been as hard on FDR as they are on Bush, we'd have lost World War II." So I started wondering. . . What if FDR had run his war like GWB?"

Here is the video that resulted from his musings.

August 03, 2007

Evolution-18: Missing links

(Please see here for previous posts in this series.)

About ten years ago, a group of engineering students came into my office. They were taking part in a scavenger hunt during Engineers Week and the one item that was very hard for them to find was a 'slide rule'. They had little idea of what it was and no idea how it worked or what one even looked like but they knew it was old technology and they figured that I was old enough to possibly own one.

They were partly right. I had once owned a slide rule as a physics undergraduate in Sri Lanka but unfortunately did not have mine anymore.

For those not familiar with slide rules, the standard type looks like a ruler with another sliding ruler attached, and you use it to do complicated calculations. It was the precursor to the handheld calculator but with the arrival of cheap electronic versions of the latter, the slide rule went extinct. I actually owned a more unusual type of slide rule that was cylindrical rather than linear and was like a collapsible telescope. It had the advantage that it was small enough to carry around in your pocket, and being able to whip out a slide rule when the occasion demanded defined the nerds of that time.

The difficulty that the engineering students had in getting hold of a slide rule is due to the fact that when a new technology comes along, the old technology is superceded and devices built using it become extinct because no more units get produced and the old units get thrown away and end up in landfills. As another example of this phenomenon, at Case we have a state of the art Freedman Center where you can take information stored in any form (say phonograph records of any vintage, old 8mm home movies, etc.) and convert to digital formats. The one old format they cannot currently convert is videotapes made using the Betamax format and this is because they simply cannot get hold of any working Betamax players anywhere anymore. It has gone extinct. (If anyone has an unused but working Betamax player they would like to donate to the Freedman Center, they would be happy to take it off your hands.)

Like slide rules and Betamaxes, you would be hard pressed now to find many things that were mass-produced even just a decade or two ago. Apart from those in the collections of museums and idiosyncratic collectors, most other artifacts have disappeared forever.

Imagine an extraterrestrial archeologist visiting the Earth and seeing an electronic calculator. Even if he looks around fairly carefully, he would likely not find slide rules or indeed any earlier versions of such devices and conclude, erroneously, that Earthlings are brilliant designers who went straight from nothing to a fairly sophisticated calculator in one jump.

The analogy with missing links in evolution is obvious. This difficulty of finding well-preserved specimens of old things is even worse with the fossil record in evolution. As an organism evolves to a newer form, the old versions rapidly disappear and become extinct. As Steve Jones points out (Almost Like a Whale, 1999, p. 161), "When we see any structure highly perfected for any particular habit, as the wings and birds for flight, we should bear in mind that animals displaying early transitional grades of the structure will seldom continue to exist to the present day, for they will have been supplanted by the very process of natural selection."

Even when it comes to fossils, since fossilization occurs only under very special conditions of organism and soil and climate, most of these dead organisms disappear forever and thus it is hard to find a continuous record of evolution. Even if a fossil is formed, the Earth itself is a dynamic system, with its crusts moving over each other, erosion, sedimentation, glacier movement, and even the rise and fall of mountains and oceans, all of which can destroy or bury or hide any fossils unfortunate enough to be in the way. As a result, "We continually overrate the perfection of the geological record and falsely infer, because certain genera or families have not been found beneath a certain stage, that they did not exist before that stage." (Jones, p. 269) "The Cambrian Explosion [beginning about 545 million years ago], so called, is a failure of the geological record rather than of the Darwinian machine. Its radical new groups reflect not a set of exceptional events but something more banal: the first appearance of animals with parts capable of preservation. Before then, there were soft creatures that decayed as soon as they died. Why shells appeared all of a sudden is not certain." (Jones, p. 274)

The rarity of fossilization can be seen by the fate of the passenger pigeon. Estimates put the number of them at over nine billion alive during the time of the Mayflower, more than the total of all the birds in the US today. They were still flourishing in the US as late as the times of the Civil War but the species went extinct in 1914 and not a single fossilized specimen has ever been found. If not for the existence of written records about this bird, we would not have known it even existed. (Jones, p. 266)

What gets preserved as fossils tend to be big and hard things like dinosaurs and mammoths, just like it is easier to find earlier versions of cars and ships than of slide rules. But thanks to the new techniques of DNA mapping, we do not have to depend exclusively on fossils to learn about how our ancestors evolved and diverged. DNA can interpolate the gaps in the record much better than even fossils can.

POST SCRIPT: Family Guy's Stewie and Brian go to Iraq

August 01, 2007

Evolution-17: How species diverge

(Please see here for previous posts in this series.)

When my daughter was quite young, about five or so, the question of where people came from came up in a mealtime conversation. Naturally we told her that human beings had evolved from ancestors who were monkey-like and then became human-like. She sat there for a while silently digesting this interesting bit of new information and mulling it over in her mind. It seemed clear that she was not at all disgusted or even bothered by the thought that we were related to the monkey family. That kind of revulsion seems to be something that has to be acquired, often nurtured by religions.

But something was bothering her and she finally articulated it, asking "But when that happened, wouldn't the mother monkey notice that her child looked different?"

She had hit upon an issue that many skeptics of evolution raise. They argue that there is a contradiction if we assume that we had evolved from an ancestor species that was so different from us that we could not interbreed with that species. Surely, the argument goes, doesn't evolution imply that if species A slowly evolves into species B, then there must be a time when the parent is of species A while the child is of species B? Isn't it a ridiculous notion for parent and child to belong to different species?

The answer is that it is perfectly possible that as we go from generation to generation, for each child to be the same species as the parent, while of a different species from a distant ancestor. In fact, we have living examples of such a phenomena,

In The Ancestor's Take (p. 302), Richard Dawkins uses the example of the ring speciation of the herring gull and lesser black-backed gull to illustrate how this happens. In Britain, these two kinds of birds don't hybridize even though they meet and even breed alongside one another in mixed colonies. Thus they are considered different species. But he goes on to say:

If you follow the population of herring gulls westward to North America, then on around the world across Siberia and back to Europe again, you notice a curious fact. The 'herring gulls', as you move around the pole, gradually become less and less like herring gulls and more and more like lesser black-backed gulls, until it turns out that our Western European lesser black-backed gulls actually are the other end of a ring-shaped continuum which started with herring gulls. At every stage around the ring, the birds are sufficiently similar to their immediate neighbors in the ring to interbreed with them. Until, that is, the ends of the continuum are reached, and the ring bites itself in the tail. The herring gull and the lesser black-backed gull in Europe never interbreed, although they are linked by a continuous series of interbreeding colleagues all the way around the other side of the world.

Dawkins gives a similar example of this kind of ring speciation with salamanders in the Central Valley of California, which is ringed by mountains. If you start with salamanders at one end of the valley and proceed clockwise around the mountain range to the opposite side of the valley, the salamanders change slowly, at each stage being able to interbreed with the neighbors. The same thing is true when you go counterclockwise from the same starting point. But when you arrive at the opposite point of the valley where the two chains of evolution arrived at by going in different senses meet, you find they are now two different species.

The herring gulls and salamanders are the examples separated in space (which we can directly see now) of the same argument separated in time (which we can only infer) that says that as descendants are produced, they form a continuum. Each generation, while differing slightly, can interbreed with its previous generation, but over a long enough period of time, the two end points of the continuum need not be able to interbreed.

Thus it is possible for one species to evolve into another and for an organism to be intermediate between two species.

POST SCRIPT: Family Guy on why Congress voted for the Iraq war

July 30, 2007

Evolution-16: The evolution of the eye

(Please see here for previous posts in this series.)

The eye is one organ almost invariably brought out by creationists to argue against evolution. How could something so complex have possibly evolved incrementally, they ask?

Darwin himself suggested the way that the eye could come into being. Due to the fact that eyes don't fossilize and thus leave a permanent record, it is hard to trace back in time and see the various stages in the evolution of the eye as linear developments. So he looked instead at the eyes of currently existing different organisms at intermediate stages of development, and concluded (On the Origin of Species, 1859, p. 188):

With these facts, here, far too briefly and imperfectly given, which show that there is much graduated diversity in the eyes of living crustaceans, and bearing in mind how small the number of living animals is in proportion to those which have become instinct, I can see no very great difficulty (not more than that in the case of many other creatures) in believing that natural selection has converted the simple apparatus of an optic nerve merely coated with pigment and invested with transparent membrane, into an optical instrument as perfect as is possessed by any member of the great Articulate class.

Steven Pinker (How The Mind Works, 1997, p. 159) describes how Darwin established how the eye could have evolved, according to the step-by-step process that I have described earlier, each step having a low probability for an individual but becoming likely when large numbers of organisms are involved over long times.

By looking at organisms with simpler eyes, Darwin reconstructed how that could have happened. A few mutations made a patch of skin cells light sensitive, a few more made the underlying tissue opaque, others deepened it into a cup and then spherical hollow. Subsequent mutations added a thin translucent cover, which subsequently was thickened into a lens, and so on. Each step offered a small improvement in vision. Each mutation was improbable, but not astronomically so. The entire sequence was not astronomically impossible because the mutations were not dealt all at once like a big gin rummy hand; each beneficial mutation was added to a set of prior ones that had been selected over the eons.

Still think it is implausible? Once again, using mathematics and computer simulations based on strict natural selection principles and starting, as Darwin himself suggested, with a light-sensitive nerve, it is possible to estimate how long the process of eye evolution took (Pinker, p.164):

The computer scientists Dan Nilsson and Susanne Pelger simulated a three-layer slab of virtual skin resembling a light-sensitive spot on a primitive organism. It was a simple sandwich made up of a layer of pigmented cells on the bottom, a layer of light sensitive cells above it, and a layer of translucent cells forming a protective cover. The translucent cells could undergo random mutations of their refractive index: their ability to bend light, which is real life often corresponds to density. All the cells could undergo small mutations affecting their size and thickness. In the simulation, the cells in the slab were allowed to mutate randomly, and after each round of mutation the program calculated the spatial resolution of an image projected onto the slab by a nearby object. If a bout of mutations improved the resolution, the mutations were retained as the starting point for the next bout, as if the slab belonged to a lineage of organisms whose survival depended on reacting to looming predators. As in real evolution, there was no master plan or project scheduling. The organism could not put up with a less effective detector in the short run even if its patience would have been rewarded by the best conceivable detector in the long run. Every change had to be an improvement.

Satisfyingly, the model evolved into a complex eye right on the computer screen. The slab indented and then deepened into a cup; the transparent layer thickened to fill the cup and bulged out to form a cornea. Inside the clear filling, a spherical lens with a higher refractive index emerged in just the right place, resembling in many subtle details the excellent optical design of a fish's eye. To estimate how long it would take in real time, rather than compute time, for an eye to unfold, Nilsson and Pelger built in pessimistic assumptions about heritability, variation in the population, and the size of the selective advantage, and even forced the mutations to take place in only one part of the "eye" each generation. Nonetheless, the entire sequence in which flat skin became a complex eye took only four hundred thousand generations, a geological instant.

In his book The Ancestor's Tale, Richard Dawkins points out (p. 388) that after the evolution of light-sensitive cells in worms about 600 million years ago, the kinds of image-forming optics that we now call the eye is estimated to have independently evolved more than 40 different times in various parts of the animal kingdom. Vastly different eye forms like the human eye and the compound eye of the crustaceans evolved differently and independently from a primitive common light sensitive cell that formed a proto-eye.

So far from being an event of unimaginably breathtaking improbability, the evolution of the eye is relatively mundane, although the organ itself is quite remarakable.

That is exactly the point that those opposed to natural selection refuse to acknowledge when they act as if all the parts of the eye must have come together almost at once. What is highly improbable to happen in one fell swoop becomes possible when it happens gradually.

Richard Dawkins in his book Climbing Mount Improbable looks at case after case of things that seem to be very complex and how they could have come about by natural selection. But Darwin did not need Dawkins to be convinced. In his own day, he had enough evidence to satisfy him. "If it could be demonstrated that any complex organ existed, which could not possibly have formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find no such case." (Darwin, p. 189)

He further added (Darwin, p. 109): "Slow though the process of selection may be, if feeble man can do so much by his powers of artificial selection, I can see no limit to the amount of change, to the beauty and infinite complexity of the coadaptations between all organic beings, one with another and with their physical conditions of life, which may be effected in the long course of time by nature's power of selection."

POST SCRIPT: Great moments in the evolution of technology

Have you seen the the sideways bike?

July 27, 2007

Evolution-15: How species evolve

(Please see here for previous posts in this series.)

The final feature that needs to be addressed is the probability of mutations cumulating to produce new organs and species.

This question lies at the heart of many people's objections to evolutionary ideas. They cannot envisage how infinitesimal changes, each invisible to the eye, can add up to major changes. That is because they tend to think that the two foundations for this to occur (the occurrence of successful mutations and the mutations then spreading throughout the population) are both highly unlikely, and so that the chance of a whole sequence of such processes occurring must be infinitesimally small.

What this series of posts has shown is that given large population sizes and the long geological times available, not only are those two things not unlikely, they are almost inevitable. The mathematical results discussed in the previous posts have shown two very important results. The first is that when the large sizes of populations and the long times involved are taken into account, the probability of favorable mutations occurring is quite high. The second is that the probability of a single favorable mutation spreading to every organism in the population is also high. These two results undercut the arguments of those who simply throw their hands up in the air and declare that evolution is extremely unlikely to have occurred.

Once that is understood, it is not hard to see how successive mutations that each have a selection advantage can pile one on top of another to produce new species leading to the diverse and complex biological system that we see today. The history of twentieth century biology is the discovery of case after case of the evolutionary history of organisms. Richard Dawkins's book Climbing Mount Improbable describes many such cases.

In order to understand how speciation comes about, we need to understand better what constitutes different species. As pointed out by biologist Steve Jones, "Species are divided from each other in many different ways – by space, by time, by mating preference, by the inability to fertilize an egg or produce healthy young, or by the sterility of the offspring." (Almost Like a Whale, p. 231)

The most famous historical example is that of the finches of the Galapagos Islands. During his five year trip on the Beagle Darwin had periodically shipped various specimens back to England to specialists to study them, and a respected ornithologist John Gould had agreed to study the birds. Soon after his return to England in 1836, Darwin met with Gould who gave him the surprising news that birds that Darwin had thought were different species like wrens and finches and orioles were actually all different kinds of finches. Furthermore, Gould had also found among Darwin's specimens three mockingbird species, each set of which came from a different island in the Galapagos. (The Reluctant Mr. Darwin, David Quammen, (2006), p. 24)

This fueled Darwin's suspicions that these birds had evolved from a single species that had somehow made the difficult journey to the Galapagos from the South American mainland, and after spreading out to each island had then become isolated from the others and evolved into separate species under the different selection pressures they experienced on the different islands.

Darwin decided to devote himself to the study of speciation and in order to do so, started with the breeding of animals in captivity. He extensively studied another bird (the pigeon) that was highly popular among breeders in England at that time and for which there existed a huge number of breeds. By studying pigeons (the first chapter of On the Origin of Species deals exhaustively with them), Darwin satisfied himself that all the species of pigeons were descended from a single type, the rock pigeon. "Great as the differences are between the breeds of pigeons, I am fully convinced that the common opinion of naturalists is correct, namely, that all have descended from the rock-pigeon (Columba livia)." (On the Origin of Species, Charles Darwin, (1859), p. 23)

In an interesting follow up to the Darwin finch story, Rosemary and Peter Grant spent twenty years in the Galapagos studying the finches and they actually observed the evolution that Darwin could only speculate about. For example, Darwin had noticed that the finches' beaks "resembled different kinds of pliers: heavy duty lineman's pliers, high-leverage diagonal pliers, straight needle-nose pliers, curved needle-nose pliers, and so on. Darwin eventually reasoned that one kind of bird was blown to the islands and then differentiated into thirteen species because of the demands of different ways of life on different parts of the island, such as stripping bark from trees to get at insects, probing cactus flowers, or cracking tough seeds." (How the Mind Works, Steven Pinker (1997), p. 163)

Darwin felt that such changes would occur too slowly to be observed. But what the Grants did 150 years later was to show that such changes could in fact be observed in real time. They "painstakingly measured the size and toughness of the seeds in different parts of the Galapagos at different times of the year, the length of the finches' beaks, the time they took to crack the seeds, the numbers and ages of the finches in different parts of the islands, and so on – every variable relevant to natural selection. Their measurements showed the beaks evolving to track changes in the availability of different kinds of seeds, a frame-by-frame analysis of a movie that Darwin could only imagine." (Pinker, p. 163)

Evolution is a fact. Natural selection is far and away the only theory that comes even close to explaining in detail how it happened, although will always be many things as yet unexplained. As biologist Steve Jones writes, "Although biologists still argue about how the process works, fossils make it impossible for anyone, biologist or not, to deny that it happened." (Almost like a Whale, 1999, p. 306)

Next in the series: The evolution of the eye

POST SCRIPT: The Darwin Year 2008-2009

This series of posts was inspired by the fact that 2009 will be the 200th birth anniversary of Charles Darwin and the 150th anniversary of the publication of On the Origin of Species. Case is planning a year long celebration of this event for the 2008-2009 academic year.

As part of this, the Common Book Reading committee has selected David Quammen's The Reluctant Mr. Darwin as the book that all incoming first-year students in fall 2008 read, and will also try to expand the program to make it a campus-wide reading experience.

Quammen has agreed to be the fall convocation speaker in September 2008. There are also plans to have E. O. Wilson (one of the most eminent evolutionary biologists and author of Sociobiology), Sean B. Carroll (The Making of the Fittest), and Rosemary and Peter Grant also give talks during that year.

July 25, 2007

Evolution-14: How a single mutation spreads everywhere

In the previous post, we saw that if we start with a trait that is present in just 0.1% of the population (i.e., f=0.001), and if this has a small selection advantage of size s=0.01, this will grow to 99.9% (F=0.999) in just under 1,400 generations, which is a very short time on the geological scale.

But in a population of one million, an initial fraction of f=0.001 means that we are starting with about 1000 organisms having the favorable mutation. But it could be argued that new mutations usually start with just a single new kind of organism being produced in one single organism. How does that affect the calculation?

Suppose that you have a population of organisms of size N and they all start out having the same gene at a particular position (called the 'locus') on one of the chromosomes that make up the DNA. Now suppose a random mutation occurs in just one organism, the way that it was described in an earlier post in this series describing the shift from violet to UV sensitive sight in some birds. Most of the time, even a favorable mutation will disappear because of random chance because (say) that mutated organism died before it produced any offspring or it did produce a few and that particular gene was not inherited. But on occasion that mutation will spread. How likely is it that such a single mutation will spread to every single organism (i.e., become 'fixed' in the population)?

When one is not dealing with deterministic systems involving smoothly varying numbers (as was done in the previous case), a different kind of calculation (based on probabilities and known as 'stochastic') has to be done, and in this case the expectation value for the number of generations T taken for the single new mutation to spread all over and become fixed in the population (i.e. to spread to 100% of the organisms) is given by T=(2/s)ln(2N) generations, where 'ln' stands for natural logarithms. (Molecular Evolution, Wen-Hsiung Li, 1997, p. 49)

Even if s is taken as a very small advantage of size 0.01, for a population of N=one million, the average time taken for just a single mutation to become fixed is just 2,900 generations. So we see that mutations occurring in a single organism can become universal in a very short period on the geological time scale.

There are two important points that need to be emphasized.

There first is that even a very small selection advantage is sufficient to have that mutation dominate the species. This means that the advantage may not be even visible in the organism itself, which may look like every other organism in the species. For example, an eye mutation that works better by just a tiny bit may look like every other eye. Thus we should not think in terms of big changes for natural selection to work.

The second point is that even starting from a single mutation, as long as it takes hold (which has a probability of 2s of happening) and does not disappear and has an selection advantage however small, the mutation can spread surprisingly rapidly in the population and become universal and form the basis for future mutations.

It is interesting that even if there is no survival advantage to the new gene (i.e., s=0 and the mutation is said to be 'neutral'), the mutation can on occasion still spread and become fixed, except that now the average time taken is much longer and given by T=4N generations. So that for a population of one million it would take on average about 4 million generations for a neutral mutation to spread everywhere, as compared to just 2,900 generations for a selection advantage of 0.01.

Darwin did not have access to this kind of mathematical analysis, which came long after his death. It is a tribute to his genius that he intuitively sensed the power of cumulative change over long time scales.

So far, I have shown how the first two items in the three components of natural selection, although seeming to have small probabilities of occurring, actually are quite likely. The third aspect of natural selection that has to be looked at is how the cumulative effects of small changes lead to big changes.

POST SCRIPT: Some real fact-checking

In yesterday's post, I spoke about how the media does almost no fact-checking on Bush. Well, except for Jon Stewart who catches Bushies making up stuff about Iraq.

July 23, 2007

Evolution-13: Differential rates of survival

(Please see here for previous posts in this series.)

Of the three stages of natural selection outlined before, the only one that occurs purely by chance is the first one, that of the occurrence of mutations. I discussed how although the chances of producing a favorable mutation by changes in any individual site in the DNA (called 'point mutations') on an individual member of the species is very small, when the number of individuals in a species and the long times available for the changes to occur are factored into the calculation, the result is that such mutations are not only likely, they are almost inevitable to occur and furthermore are likely to occur many times.

The Hardy-Weinberg law showed that if natural selection was not at work (along with some other conditions), populations settled into stable equilibrium values after just one generation of random mating. The next question to be addressed is to see how the populations change when natural selection is allowed to act. How likely is it that favorable mutations produced in the set of genes (the genotype) that characterize the organism (the phenotype) will end up with that actual organism predominating in the species? (Recall that natural selection acts on the phenotype and not the genes directly, while mutations act only on the genes and inheritance is passed on purely via the genes. A genetic change that has no effect on the phenotype will not influence the fitness of the organism.)

It is not the case that this happens every time. Most mutations are deleterious and do not spread and even favorable changes usually disappear by chance before they can spread to become a significant number in the population. But when the favorable mutations do take hold, that particular variety becomes widespread and dominates the population.

There are many such cases that have occurred in nature. The most famous and widely quoted example of this kind of growth of a favored phenotype is the case of the peppered moths in industrial areas of England and America. As a result of the pollution that created dark backgrounds on the lichen covering the trees where the moths rested, the darker varieties of the moths were camouflaged better from predators than the lighter ones and thus had a significant survival advantage. From 1848 to 1896, the darker forms grew to as much as 98% of the population. Subsequently, with the advent of pollution control measures that cleaned up the environment and reduced the soot pollution, the dark moth population decreased to as low as 10%. In The Making of the Fittest (2006, p. 52-53), Sean B. Carroll points out that peppered moths are not the only such examples, that many similar changes in coloration due to selection pressures have occurred in land snails, ladybird beetles, desert mice, and other species.

The way that even a very small natural selection advantage can result in that variety dominating a species can be appreciated using the more familiar example of compound interest. Suppose a parent gives each of two children $1,000 at the same time. One of the children invests in a bank that offers an interest rate of 5.0% while the other, being slightly more thrifty, shops around and invests in a different bank at 5.1%. Although they start out with the total money being split 50-50, in 7,000 years the second child (or rather that child's descendents) will have 99.9% of the total money, thanks to that very small advantage in the annual rate of return.

It is exactly this kind of differential survival rate that plays such an important role in natural selection. Even minute differences in fitness can result, over the long term, in the runaway domination of a preferred variety. To see how fast this can happen, population geneticists have carried out calculations.

Suppose one variety has a mutated gene that has a very slight fitness advantage over the existing gene. 'Fitness advantage' can be quantified by defining the fitness w as the measure of the individual's ability to survive and reproduce. (The concept of fitness is a combination of the organism's ability to survive for any length of time (at least until its reproducing age is over) and its fecundity in terms of the number of offspring it produces.) Suppose the original gene has fitness w=1 and the new mutation has fitness w=1+s, where s is the selection advantage.

The selection advantage is a measure of how much more likely it is that that particular variety will propagate itself in future generations when compared with the standard type. So if, on average, the new mutated variety produces 101 fertile adult descendents while the same number of the standard organism produces 100, then s=0.01.

When this selection advantage is included in the calculation, the number of generations T it will take for a mutation to increase its frequency in the population from an initial value of f to a final value of F is given by the formula T=(1/s)ln[F(1-f)/f(1-F)], where 'ln' stands for the natural logarithm. (Molecular Evolution, Wen-Hsiung Li, 1997, p. 39)

So if we start with a trait that is present in just 0.1% of the population (i.e., f=0.001), and if this has a small selection advantage of size s=0.01, this variety will grow to 99.9% (F=0.999) of the population in just under 1,400 generations, which is a very short time on the geological scale.

But in a population of one million, an initial fraction of f=0.001 means that we are starting with about 1000 organisms having the favorable mutation. In reality, we are likely to begin with just one mutation in one organism. How does that affect the calculation?

That will be discussed in the next post in the series.

POST SCRIPT: Lil George and evolution

This clip from a cartoon show I had never heard of (probably because it is on cable) is pretty funny.

July 20, 2007

Evolution-12: Population genetics and the Hardy-Weinberg law

(Please see here for previous posts in this series.)

In the previous post, I discussed the puzzle posed by a naïve understanding of Mendelian genetics, which was that one might expect that organisms that displayed recessive gene traits would slowly disappear in a population while those with dominant gene traits would grow in number. But if that were true that would prevent new mutations from gaining a foothold in the population and growing in number, if it happened to be a recessive trait.

The crucial work that formed the breakthrough that revived the theory of natural selection was done in 1908 by G. H. Hardy (a Cambridge University mathematician and author of a fascinating book A Mathematician's Apology) and Wilhelm Weinberg (a German physician), working independently. What is nice is that the result is quite simple to derive, and surprising.

The main result is that whatever the distribution of gene pairs AA, Aa, and aa you start with in a population, after just one generation the number of people with those distributions will reach an equilibrium value that will never subsequently change. In other words, the numbers of the different types of genes in a population are stable. So traits, once they appear, do not disappear simply because of the accidents of random mating. This counters the 'blending inheritance' objections to Darwin's theory.

The proof of this result assumes that certain conditions apply so that only mating effects are at play: that the total population is large enough (effectively infinite for statistical purposes) to avoid the phenomenon of genetic drift, whereby the ratio of a particular gene varies purely due to statistical fluctuations (i.e., say the population with a particular gene happens to breed disproportionately, thus causing that gene's frequency to change), is diploid, that the population reproduces sexually and that mating within the population is totally random, that natural selection is not working to change the distributions of the genotypes, and that other factors like genetic mutations and migrations in or out of the population are not occurring (i.e., no gene flow).

Here's the result. Suppose that you start with a population in which AA types occur with probability p, Aa types occur with probability 2q (where the 2 is inserted just to make the arithmetic a little simpler), and aa types account occur with probability r. Since the total population must add to 100%, this means that the total probabilities p+2q+r=1.

Under the conditions given above, the Hardy-Weinberg result says that: (1) after just one generation, the AA types occur with probability P where P=(p+q)2, Aa with probability 2Q where Q=(p+q)(q+r), and aa with probability R where R=(q+r)2; and (2) these new probabilities will remain unchanged with each succeeding generation.

As an example, if we started with the population of AA being 50% (p=0.5), Aa being 40% (2q=0.4), and aa being 10% (r=0.1), then after just one generation, the Hardy-Weinberg result predicts that the proportions will be P=0.49 or 49% for AA, 2Q=0.42 or 42% for Aa, and R=0.09 or 9% for aa, and remain fixed at these values forever afterwards.

The proof of this result is quite simple and elegant and here it is:

If there is random mating, then the probability of any particular mating combination is just the product of their individual probabilities.

The probability of an AA mating with another AA is p2. The offspring will get just one gene from each parent, and in this case the result will always be AA.

The probability of an AA mating with an Aa is 4pq (the extra factor of 2 comes from the fact that this mating combination can occur two ways, that either the father could be AA and the mother Aa, or the father could be Aa and the mother AA) and there is a 50% chance that the offspring will be an AA and 50% chance of being an Aa.

Similarly, the probability of an AA mating with an aa is 2pr. The offspring will get just one gene from each parent, and in this case the result will always be Aa.

The probability of an Aa mating with an Aa is 4q2 and there is a 25% chance that the offspring will be AA, 50% chance of being an Aa, and 25% of being an aa.

The probability of an Aa mating with an aa is 4qr and there is a 50% chance that the offspring will be Aa and 50% chance of being an aa.

The probability of an aa mating with another aa is r2. The offspring will get just one gene from each parent, and in this case the result will always be aa.

When you add all the probabilities for each type of offspring together, the probabilities of getting AA and Aa and aa are just the expressions for P, 2Q, and R given above.

What Hardy and Weinberg noticed was that if, by some chance, the starting values p, q, and r were such that they satisfied the equation q2=pr, then after one generation, P=p, Q=q, and R=r. In other words, if the starting values satisfied that particular relationship, the probabilities are unchanged from one generation to the next.

Of course, the values of p, q, and r we actually start with for a random population can have any value, as long as p+2q+r=1. But after the first generation of mixing, the values P, Q, and R actually do satisfy the relationship Q2=PR, irrespective of the starting values of p, q, and r.

Since the values of P, Q, R that are obtained after one generation become the starting values to calculate the distributions for the subsequent generation, and since P, Q, R satisfy the required relationship Q2=PR, these values will remain the same for every succeeding generation after the first.

What I found particularly surprising is that usually equilibrium conditions tend to be approached gradually and even asymptotically. Here, whatever the starting point, you get equilibrium after just one iteration.

The stability of population distributions under conditions of random mating is an important result. It implies that gene distributions do not change due to mating but only under some kind of pressure to do so..

From the year 1908 onwards, mathematical biologists proceeded to make rapid advances in the embryonic field now known as population genetics. The names of R. A. Fisher, Sewall Wright, and J. B. S. Haldane are the ones associated with the birth of this field and by the 1930s or so, their work had put Darwinian natural selection and Mendelian genetics on a firm scientific and mathematical footing (William B. Provine, The Origins of Theoretical Population Genetics, 2001).

In the next post in the series, I will look at how natural selection causes the population distributions to shift.

POST SCRIPT: Iraq war lies

Watch this video to see the brazenness with which the country was lied into war.

July 18, 2007

Evolution-11: The rise of population genetics and the neo-Darwinian synthesis

(Please see here for previous posts in this series.)

The joining of Darwin's theory of natural selection with the Mendelian theory of genetics is one of the great triumphs of biology, now called somewhat grandly the 'neo-Darwinian synthesis'. It forms the basis of all modern biology, and was strengthened by the discovery of DNA as the structure of genetic information and which explained how Mendelian genetics worked on a microscopic scale. The modern ability to map out the entire genome of humans and other species has produced overwhelming evidence in support of Darwin's theory of how organisms evolve and branch out into different forms. The rough tree of life that Darwin sketched out in his book based on the anatomy of biological species has now been made more precise and detailed by the mapping of the DNA of species, showing ever more clearly how species are related to one another and when they separated from a common ancestor.

Mendel showed that genes were discrete objects that retained their identity as they were handed down from generation to generation and that thus any changes in genes, however small, did not get blended away in a regression towards the mean. So you would have thought that the rediscovery and rapid popularization of Mendel's ideas in 1900 would have signaled a resurgence of Darwin's idea that natural selection worked on very small, almost continuous changes, and the defeat of those who argued that one needed discontinuous changes for evolution to occur.

Ironically, the exact opposite happened. Because Mendelian genetics was a discrete mechanism with the genetic information seeming to occur in small lumps that remained intact, it superficially seemed to support the discontinuous model of natural selection, and the proponents of discontinuous changes were able to co-opt Mendel's theory to their cause. By around 1908 or so, it seemed like Darwin's own favored model of small continuous changes leading to large changes was in almost total retreat, actually doomed by the arrival of Mendel. While there was a sprinkling of mathematicians like Udny Yule (what a wonderful name!) who argued that Mendel's theory was compatible with Darwin's model of continuous evolution, their voices were lost in the volume of controversy generated by the competing biological schools. (The Origins of Theoretical Population Genetics, William B. Provine, 2001, p. 85)

Part of the problem was that scientists were still struggling to understand the workings of both Darwin's theory and Mendelian genetics and many misunderstanding of each were then prevalent. For example, one thing that was puzzling about genetics (and puzzled me for a long time too) was this whole business of dominant and recessive genes and how it affected population distributions.

It was Mendel's work that argued for the existence of these two types of characteristics, the actual mechanism of which became better understood with the discovery on DNA and increased understanding of the way that chromosomal information was handed down from parent to child.

Simply put, each person has pairs of genes, one from each parent on the respective inherited chromosome. To be concrete, we can look at the gene for eye color. Each gene may be of a dominant type (denoted by A, for say brown eyes) or a recessive type (denoted by a, for say blue eyes). So a person would have one of the pairs AA, Aa, or aa on the pair of chromosomes that contain the genes for eye color. Since A is the dominant one, it always wins, and so those people with either AA or Aa will have the characteristic A (brown eyes) manifest itself in their features, and only the person who has aa will display the characteristic a (blue eyes). Each parent will also have AA, Aa, or aa, and will randomly pass on just one of the pair of genes it possesses to the child.

It seems intuitive that if a population starts out with some distribution of AA, Aa, and aa types, and there is random mating in the population, then the number of people displaying the dominant characteristic A will steadily increase in the population, while the manifestation of the recessive characteristic a will decrease and perhaps eventually even disappear altogether, since only someone possessing the relatively unlikely combination aa will manifest it. Since regressive characteristics did not seem to be disappearing in real life populations, and in fact seem quite stable in their numbers, early geneticists had some doubts about whether they were interpreting Mendel's model correctly.

But starting around 1908, things started to change as better experiments were done and more mathematical versions of the two theories started being used. Mendelian and Darwinian theories started to get quantified and people began to realize that Darwin's version of natural selection with continuous changes was in fact compatible with Mendel's theory. By 1918, the reversal was complete and Darwin was ascendant and has remained so ever since. This was largely due to the rise of the field now known as population genetics, whose practitioners developed mathematical models that looked at the consequences of Mendelian genetics in natural selection.

What started the shift was the result now known as the Hardy-Weinberg law, which will be discussed in the next posting in this series.

POST SCRIPT: American beliefs about evolution

Gallup has done one of its periodic surveys about Americans views on evolution

These results show that:

  • 24% of Americans believe that both the theory of evolution and the theory of creationism are probably or definitely true.
  • 41% believe that creationism is true, and that evolution is false.
  • 28% believe that evolution is true, but that creationism is false.
  • 3% either believe that both are false or have no opinion about at least one of the theories.

That first group of 24% is definitely confused, since there is no way that evolution could have occurred in the 10,000 years or less allowed by creationism. The survey creators speculate that these were people who believed that god influenced evolution and somehow wanted to incorporate that view and responded in contradictory ways depending on which question was asked.

Also:

  • The reasons for rejecting evolution were mostly religious.
  • The more regularly you attended church, the less likely you were to believe in evolution.
  • Republicans were less likely to believe evolution (30%) than Democrats (57%).

Summary:

It is apparent that many Americans simply do not like the idea that humans evolved from lower forms of life. This appears to be substantially based on a belief in the story of creation as outlined in the Bible -- that God created humans in a process that, taking the Bible literally, occurred about 10,000 years ago.

July 16, 2007

Evolution-10: The debate over natural selection in Darwin's own time

(Please see here for previous posts in this series.)

In Darwin's own time, there was a three-way dispute concerning the theory of evolution. Strange as it may sound these days in the US where so many question whether evolution even occurs at all, the idea that evolution had occurred and new species were being created and old ones dying out was not such a major problem in the mid-to-late 19th century. Elite opinion of that time had been exposed to that idea and had accepted it even before Darwin because of all the fossil records that were being discovered all the time. Even Darwin's own grandfather Erasmus Darwin, a freethinker, had around 1795 published a book Zoonomia that had floated the idea that species had evolved, but he used a Lamarckian model. What religious people mostly shied away from was the idea that human beings were also part of the evolutionary process and shared common ancestors with other species, a reluctance that still persists.

In Darwin's time what the dispute mainly centered on was the mechanism of evolution and how it operated.

Apart from Biblical literalists and believers in special creation, there were those of a religious bent who argued that god had to intervene somehow at least occasionally to create new species (especially humans) and this view persists down to this day among people who seek a tangible role for religion. At the very least, believers in an immortal soul needed a god to insert it into humans at some point in that person's development.

But the more interesting dispute was among those scientists who were not invoking religious ideas. Their dispute centered on the scale of the mutations necessary for natural selection to work.

Due to all the buffeting that Darwin's theory had received from those who argued that the age of the Earth was too short for evolution to have occurred and that mutations would get blended away, in the later editions of his book, Darwin himself started qualifying some of the more ambitious claims that he had forthrightly stated in the 1859 edition. As a result, his later editions lost some of the directness and clarity of his first edition, and scholars now recommend reading the first edition as being the best. I personally found it a fascinating book, remarkably accessible to the layperson.

For example, his first edition contained a rough estimate by him, based on geological phenomena he observed in England, that the Earth was about 300 million years old, which was in his view sufficient time for evolution to have occurred. He arrived at this by assuming that the Weald, a valley in the south of England, had been created by erosion that had always occurred at the same rate it was occurring now. He removed this claim in later editions, presumably due to unease over physicist William Thomson's calculations that the Earth was only 30 million years old. As it turns out, Darwin had no need to be worried since the current age of the Earth is calculated to be more than ten times his own estimate.

But while willing to give ground on some peripheral issues, Darwin steadfastly stuck until his death (in 1882) to one central idea, and that was that natural selection was able to act on even extremely small advantages in the fitness of some organisms, causing them to grow in the population, and that it was the cumulative effect of these minute changes that led to new species.

Contrasted with Darwin's continuous model of change were those scientists (including even Darwin's staunch defender and ally Thomas Huxley) who argued that natural selection could not really work with very tiny changes because they would get washed away because of blending inheritance. These people argued in favor of a discontinuous model which only valued those mutations that produced significant changes in the organism that represented a new and stable phenotype whose qualities were robust enough that they would not get blended away by breeding.

To better understand the difference, compare a sphere and (say) a twenty-sided die, which is almost a sphere, both resting on a table. The sphere can be shifted by any small amount and would stay in that new position. The die on the other hand, if tilted slightly and released, would revert to its original position unless the tilt were sufficient to topple it to rest on the adjacent flat face. Then it would be stable in the new position and would resist any further shift, even back to its original state. One faction led by Darwin was arguing that natural selection could act on the continuous changes represented by the sphere while others said that only the changes beyond a certain critical amount and represented by the die were stable enough for selection to work on.

It must be emphasized that both sides supported the mechanism of natural selection for driving evolution. They simply disagreed on its ability to act on very small changes. While we may think that this was a small issue to disagree on, in actual fact the debate was fierce and very acrimonious, with both sides trying to marshal evidence for their side and picking holes in the evidence of their opponents. William B. Provine in his book The Origins of Theoretical Population Genetics (2001) gives a fascinating account of this controversy, the personalities involved, and the heated nature of the exchanges, which grew increasingly bitter by the time 1900 rolled around.

The rediscovery of Mendel's work on genetics (he was a monk who lived from 1822-1884 and published his major work in 1865, but it remained obscure until it was rediscovered in 1900) provided new fuel to the controversy. Scientists quickly recognized the significance and importance of Mendel's work. While Mendel's model was accepted as having finally produced the correct theory of how inheritance works, this did not immediately resolve the dispute because there was still disagreement about what Mendel's theory actually implied and how it fitted into Darwin's theory.

Next in this series: The synthesis of Mendelian genetics and natural selection.

POST SCRIPT: Why a secular public sphere works best

As I understand it, both US houses of Congress open with a ceremonial prayer which hardly any members bother to attend. Although each house has an official chaplain, it has become the practice to make this event more inclusive and ecumenical by having people of diverse faiths give the prayer.

For the first time last week, a Hindu was invited but his prayers were disrupted by hecklers from a Christian group, who saw this as an affront to their own god. See the video here.

Steve Benen provides some background on what happened.

Interestingly, some Christians see the saying of Hindu prayers in Congress as a sign that the end of the world is almost upon us, and their anger about this act of sacrilege is mixed with eager anticipation at seeing Jesus any day now.

One doesn't know whether to laugh or cry. I think I'll laugh.

July 13, 2007

Evolution-9: Early challenges to Darwin's theory

(Please see here for previous posts in this series.)

In an earlier post in this series, I listed the three stages involved in natural selection, each of which seemed to have seemingly small probabilities. In the previous post, I showed how because of the large numbers of organisms and long time scales involved, the first item got converted into a very high probability event.

The next item in the list, the issue of how a mutation with a small advantage in the properties of an organism can end up with that property dominating the species, was both Darwin's greatest challenge and his greatest triumph.

The triumph came from a crucial insight that Darwin had concerning the importance of varieties within species. Recall that Platonic ideas were dominant at that time, and that laid the emphasis on the idealized forms of things. So for example while a real triangle drawn on paper would contain imperfections, these were considered incidental, the drawing being a mere approximation to the idealized triangle that one could envision in some abstract space.

In Darwin's time, the biological equivalent of this thinking was that while it was plain to see that (say) chickens were different from one another in small ways, these differences were not considered important. They were considered mere approximations to an idealized chicken that represented the essence of chickenhood (so to speak), and it was the latter that was important.

But Darwin realized that the variety that he saw in species, rather than distracting from an understanding of the ideal, was important in its own right. In fact, he recognized that the diversity within a species was so vast that it was often hard to say what was a variety within a species and what was a different species altogether. As he wrote, "[I]t will be seen that I look at the term species, as one arbitrarily given for the sake of convenience to a set of individuals closely resembling each other, and that it does not essentially differ from the term variety, which is given to less distinct and more fluctuating forms" (Charles Darwin, On the Origin of Species (1859) p. 52). It was this wide variety that allowed some animals to survive better than others and was the driver of natural selection. The existence of variety lay at the heart of his theory.

(The problem with all classification schemes is that it is often impossible to specify both necessary and sufficient conditions to make unerring judgments as to which category some organism belongs. The fact that there is often no sharp line that can be drawn between varieties within species and differences between species should put to rest the artificial distinction made by intelligent design creationists who say they have no trouble with what they call 'microevolution' (what they define as change within a species) but cannot accept 'macroevolution' (the creation of new species). This is a distinction without much merit.)

But Darwin faced a serious problem. Even though people might accept his idea that one variety of an species might be more suited to survive than another, the lack of a real understanding at that time of the mechanism of inheritance worked against him. It was believed that sexual reproduction resulted in features being mixed (called 'blending inheritance'), with the child of parents being intermediate in terms of properties such as height, skin color, etc. Hence even if an occasional particular mutation had better chances for survival, it was believed that its advantageous properties would soon get diluted and disappear by mating with those animals that did not have this same property. This is the well-known phenomenon of 'regression towards the mean,' first articulated by the polymath Francis Galton, a cousin of Darwin.

In artificial breeding one could avoid this blending outcome by simply restricting the breeding of animals to those organisms with the desired properties and thus preserve and enhance desired changes. But in the wild, organisms would mate more indiscriminately and this raised the question of how advantageous mutations could be preserved.

Around the same time that Darwin's theory was already reeling from estimates of a short age of the Earth from William Thomson (aka Lord Kelvin), Fleeming Jenkins wrote a long article in 1867 criticizing Darwin's theory on precisely the blending inheritance issue. In addition, the co-discoverer of natural selection Alfred Wallace (who had initially been seen as an even more zealous advocate of natural selection than Darwin) had become interested in spiritualism and in 1869 unexpectedly published a paper in which he asserted that natural selection, although it could explain everything else, couldn't account for the human brain, and he even went so far as to espouse an early version of intelligent design creationism saying that while the living world is governed by laws, "an Overruling Intelligence has watched over the action of those laws, so directing variations and so determining their accumulation" in order to produce the wonderful thing that is the human brain (David Quammen, The Reluctant Mr. Darwin (2006), p. 215). (The idea that the workings of the human brain, and that the mind and consciousness lie outside the realm of natural selection and the laws of biology, is something that persists down to this day, a topic I will examine in the future when I look at what we are now learning about the nature of consciousness.)

There was nothing much that Darwin could do about Thomson's criticism but hope that someone else would prove the physicist wrong, which did happen with the discovery of radioactivity in the first decade of the 1900s. There was also nothing that Darwin could do about Wallace going against one of the fundamental precepts of natural selection, although Darwin felt that the whole idea of natural selection was meaningless if an outside 'intelligence' could drive organisms towards a pre-ordained result. Darwin simply wrote "No!!!" in the margins of Wallace's paper.

As for Jenkins's criticisms, Darwin had not been unaware that this would be a problem for his theory and had tried to anticipate it by suggesting that successful mutations would take hold in only those cases where the mutations appeared concurrently in numerous individuals and that these would then breed with each other, allowing that variety to grow and take root in the population. (Quammen p. 212)

Darwin's defense was not very persuasive but it was all he had. Although the real defense against Jenkins's critique was already at hand in the form of Mendel's theory of genetics (which showed that genes are discrete entities that remain intact on breeding and do not get blended away), Mendel's work was not widely known at that time and Darwin's theory had to wait until its rediscovery in 1900 to fully overcome objections of the type put forward by Jenkins.

Darwin the man and the scientist are fascinating character studies. He was painstakingly thorough in his work and conscientious about the need to amass evidence to buttress the main argument he was making. But once he felt convinced by the evidence that the theory of natural selection was sound, he was determined. While he was willing to give ground on the periphery of his theory, he was firm in his commitment to its core ideas, and one of these was that his theory would make no sense if you allowed an outside agency (an 'intelligence' or whatever name you gave to a god-like power) to intervene in the process at any time in any way. He was a methodological naturalist, a necessary condition for any good scientist.

But it is a very thin line that separates methodological naturalism from philosophical naturalism (or atheism) and this, at heart, which is why Darwin's theory is so subversive to beliefs about god.

Next in this series: The debate over natural selection in Darwin's own time

POST SCRIPT: Science? Evidence? Who cares?

In congressional testimony this week, outgoing US Surgeon-General Richard Carmona spoke of how in the Bush administration, ideology trumped science every time, with constant political interference muzzling him on scientific issues like embryonic stem cell research. He said, "Anything that doesn't fit into the political appointees' ideological, theological or political agenda is ignored, marginalized or simply buried."

His testimony reminded me of this Tom Tomorrow cartoon from February 27, 2007.

Meanwhile, Secretary of Homeland Security Michael Chertoff's extraordinary statement, also this week, that he felt 'in his gut' that a terrorist attack might occur in the US this summer reminded me of astronomer Carl Sagan's reply when an interviewer pressed him for his 'gut feeling' as to whether there was life elsewhere in the universe. Sagan replied, "But I try not to think with my gut. Really, it's okay to reserve judgment until the evidence is in." (Richard Dawkins, The God Delusion, p. 47.)

Chertoff would be well-advised to follow Sagan's advice.

July 11, 2007

Evolution-8: The sufficiency of the mutation rate

(Please see here for previous posts in this series.)

One of the challenges faced by Darwin was whether the rate at which mutations creating new favorable varieties would occur was sufficiently rapid for his purposes. Since during his time the laws of inheritance were not known and neither was the mathematics involved, advocates of natural selection had to assume that things would work out eventually.

In his excellent book The Making of the Fittest (2006), Sean B. Carroll demystifies the various numbers and calculations involved in natural selection using our current knowledge.

Recall from the previous post in this series that DNA is made up of a string of bases A, C, T, and G. New genetic information is created when there is a change in the DNA and the most basic (but not the only) way that this can occur is by mutations acting at the level of a single base site in the DNA, changing one of the bases A, C, T, and G to a different one.

This long string of bases that constitute DNA is split into chromosomes. As one travels down the length of a chromosome, one encounters strings of bases that are called genes and these contain the code for manufacturing the vital proteins. Proteins are made up of strings of amino acids and the genes specify the arrangement of amino acids that are to be lined up, one after another, in each protein. The code for specifying which amino acid is to be added on is made up of three consecutive base sites, each triplet being either a code for one of the twenty amino acids or a code to stop the manufacturing process and release what has been created so far. Think of the whole process as a tape recorder with the DNA string being the tape being read and the tape recorder as a machine that produces the amino acids depending on what it reads in sequence on the tape.

There are 64 possible combinations of three sites made up of four distinct bases (64=4x4x4). But since there are only twenty amino acids, this allows for some redundancy to be built into the system. For example, the amino acid serine is coded for by any of the six triplets TCT, TCC, TCA, TCG, AGT, and AGC, while the amino acid cysteine is coded for by just two triplets TGT and TGC. The three triplets TAA, TAG, and TAA represent the 'stop' code that says that the process of adding on amino acids is to be halted and the completed molecule released into the body.

Because of this redundancy, some random single site mutations (say from TCT to TCG) will have no effect on the coding of the amino acid or the resulting protein. This is a good thing since it reduces the chances of the production of 'good' proteins being destroyed by a random mutation. Alternatively, a single base switch from TGT (cysteine) to TGA (stop) will result in the protein manufacture being prematurely halted and could be calamitous for the organism.

But if there is a random mutation at a single site that changes AGT to TGT, then we see that a cysteine amino acid will be added on instead of a serine in the creation of the protein. It turns out that which of these two codes for amino acids occupies the sites numbers 268-270 of the gene to produce an opsin protein determines whether the organism's eye is sensitive to violet light or to ultraviolet (UV) light. Certain birds (ducks and ostriches) are sensitive to violet while others (zebra finch, herring gull, budgerigar) are sensitive to UV light. There are four different orders of birds that contain both violet or UV sensitive species, suggesting that this switch between base A and base T in location 268 of this opsin gene has occurred on at least four different occasions in evolutionary history. Given that there are over one billion base sites in the genome of birds, is this switch in one particular site likely to occur even once, let alone on four different occasions?

The instinctive conclusion is of course 'very unlikely', but Carroll (p. 156-158) says we need to get beyond that initial guess and actually crunch the numbers to see what is involved, taking into account the size of populations and the long time scales involved.

The per site rate of mutation averages between 1 per 500,000,000 bases in DNA in most animals – from fish to humans. This means that the exact A in position in position 268 in one copy of the bird SWS [short wavelength sensitive] opsin gene will be mutated, on average, about once every 500 million offspring. It has two copies of the gene, so this cuts the average to 1 in 250,000,000 chicks. However, there are three possible kinds of mutations at this site: A to T, A to C, and A to G. Based on the genetic code, only the A to T mutation will create a UV-shifting cysteine. If the probability of each mutation is similar (they aren't but we can ignore the small difference), then one out of three mutations at this position will cause the switch. One A to T mutation will occur in roughly 750,000,000 birds (that's 750 million).

Seems like a long shot?

Not really. It is important to factor in the number of offspring produced per year. According to long-term population surveys, many species consist of 1 million to more than 20 million individuals. With annual reproduction, a plentiful species like herring gull will produce at least 1 million offspring in a year (probably a very conservative number). Divide this into the rate of one mutation per 750 million birds; the result is that the serine-to-cysteine switch will arise once every 750 years. This may seem like a long time in human terms but we need to think on a much longer timescale. In 15,000 years, a short span, the mutation will have occurred 20 separate times in this species alone.

The four orders that these birds belong to are ancient – their ancestors have had tens of millions of years to evolve UV or violet vision. At the rate calculated in gulls, the A to T mutation will occur more than 1200 times in 1 million years in just this one species. Getting the idea?

Steve Jones (Almost Like a Whale, p. 149) estimates that among domestic cats there occur around 200,000 genetic changes each year in London alone. He adds, "Worldwide, any mutation is almost a certainty. If it is useful it will at once be picked up by natural selection." He also discusses (p. 176) how a mutation in a single base site (similar to the serine to cysteine switch) enables the bar-headed goose better able to bind oxygen to haemoglobin and thus enables it to migrate at an altitude of over five miles (i.e., the height of Mount Everest), a height where humans would collapse and die within a few hours.

So small probability events cannot be considered in isolation. When factored in with large populations and long time scales, they not only become likely, they become almost inevitable.

But changes in single sites are not the only way that changes in DNA occur. They can also occur when entire chunks of the DNA molecule are changed during reproduction in the formation of the sex cells (meiosis) because of copying errors, duplication, recombination, insertional mutations, transposition, and translocation. (See here for fuller descriptions for some of these mutations.)

For example, humans have three kinds of opsin genes that code for three different proteins that are important for color vision. LWS [long wavelength sensitive] opsin enables us to see in the long-wave or red portion of the spectrum of light, MWS [medium wavelength sensitive] enables us to see in the medium-wave or green portion of the spectrum, and the already mentioned SWS type works for the short wave or blue region. It is the presence of all these three opsin proteins that gives us the full color spectrum vision humans enjoy. We share this ability with colobus monkeys, chimpanzees, and other primates such as all apes and all African and Asian monkeys.

But most other mammals have only dichromatic vision, having only two (SWS and MWS) opsin genes and consequently seeing only blue and yellow. They cannot distinguish between red and green. How humans and other primates achieved tricolor vision is by one of the dichromatic genes (the entire gene, which can consist of hundreds of thousands of bases) being erroneously duplicated during the copying process, resulting in three genes being created, and then one of the duplicate genes later undergoing changes in its bases similar to the way the violet-to-UV switching occurred, resulting in the creation of red-sensitivity in our eyes. (Carroll, p. 97)

But although this calculation shows that favorable mutations are by no means as rare as one might naively think, and are in fact quite likely when the large size of populations and long times are taken into account, how likely is it that a mutation that occurs in a single organism will succeed in ending up dominating the species? After all, even a few hundred mutations in a population of millions may not seem like a significant amount.

That question will be examined in the next posting in this series.

POST SCRIPT: Michael Moore blasts CNN and Wolf Blitzer

Michael Moore goes on CNN and blasts Wolf Blitzer and their resident medical apologist for the health industry Dr. Sanjay Gupta for effectively acting as shills for the medical industry, not to mention their abandonment of any real journalism prior to the invasion of Iraq. This is a must-see video.

Moore followed up with a detailed analysis of Gupta's shallow reporting.

July 09, 2007

Evolution-7: Genes, chromosomes, and DNA

(Please see here for previous posts in this series.)

In order to understand how inheritance works and the mathematics involved, it may be helpful to have a quick summary of some basic facts about genetics (a little simplified), using the human genome for concreteness.

All the genetic information in our bodies is found in the DNA, whose famous double helix structure was discovered in 1953. Thanks to the Human Genome Project, we now have a complete map of the DNA of humans, called the human genome, and know that it consists of a sequence of 3.1647 billion sites arranged in a row, each site containing one of four complex molecules (called bases) labeled A, C, T and G. It is this long arrangement of the four bases that define each of us genetically. Almost 99.9% of the arrangement of these bases is identical in all humans, and about 98% is identical between chimpanzees and us.

Human DNA is not a single long strand of bases however, but is broken up into 23 pairs of chromosomes, one of each from each parent, making 46 chromosomes in all. A gene is a contiguous string of sites on a chromosome that on average contains 3,000 sites, although the sizes vary greatly, with the largest gene being 2.4 million sites long. Each gene contains the code for manufacturing a specific protein in the body and it is these proteins that determine how the various systems and organs in the body function.

The first 22 chromosome pairs referred to above have the same sequence of gene arrangements along their length, but the two specific genes (called 'alleles') that they contain at any given gene location could be different. So while both chromosomes would have genes for eye color at identical locations along the chromosome, one might code for blue eyes while the other might be slightly different and code for brown eyes. One of the genes might be dominant and the other recessive, resulting in just the dominant quality being the one that is seen in the actual organism.

Hence in 22 pairs of the chromosomes, each member of the pair contains the same kind of genetic information, which differ only in detail. Only the two in pair #23, which consists of the X and Y chromosomes that distinguish the sexes, differ considerably in basic structure. So it is sufficient for the purpose of cataloging the human genome to identify the arrangement of just 24 chromosomes, one from each of the first 22 pairs, plus the X and Y from pair #23. These 24 chromosomes vary in length from 50 million to 250 million bases,

The genes specify the code for manufacturing proteins and each protein is made up of a string of amino acids. How the genes specify the order of amino acids to be put together to make up the proteins to be produced is that three consecutive base sites in the gene either specify the identity of a single amino acid to be made or alternatively signals an end to the process if the protein has been completed. There are twenty distinct amino acids in all and as you read along the string of gene bases, every three consecutive sites specify which amino acid is to be added on to what has already been produced. The process continues until a sequence of three bases signals that the process should stop since the required protein has been completed. That protein is then released into the body.

The total number of human genes in the DNA is now estimated to be about 20,000-25,000, about the same as possessed by mice and fish. Even the lowly nematode worm has over 20,000 genes, while the fruit fly has over 13,000 and yeast has over 6,000. Bacteria such as E. coli, and those that cause salmonella and staph infections have genes that number in the range 1,500 to 4,500. (The Making of the Fittest, Sean B. Carroll, 2006, p. 77) About a thousand genes are found in every single organism, evidence of how we are all linked together, descended from a common ancestor who lived over a billion years ago. (Almost Like a Whale Steve Jones, 1999, p. 376)

For humans, all the genes are distributed in the chromosomes, with chromosome #1 containing the most genes (2,968) and chromosome Y containing the fewest (231). Although the portions of the DNA that contain genes are the most useful functionally (since they are the ones that cause proteins to be produced), they constitute less than 2% of the DNA, and of these genes, the functions are still unknown for over 50% of them. Repeated sequences of bases in the DNA that do not cause proteins to be made are called "junk DNA" and while they seem to have no known function (although very recent research throws this assumption into doubt), they can shed a lot of light on how life evolved.

The double helix structure of DNA explains how it is that cells can multiply by copying themselves with such accuracy during normal cell growth (called mitosis). If the copying mechanism were perfect, then no new genetic information would be created and species would never change. But fortunately for evolution, the copying mechanism is subject to small errors and when this happens during the creation of germ (or sex) cells that are the cells that are involved in reproduction (i.e., the sperm and ovum), the resulting changes are then passed on down to the next generation. (The creation of these germ cells by the body is called meiosis.) This is how random changes in genetic information leads to the next generation of organisms having new properties.

We now have, with the discovery of the double helix of DNA, far more detailed knowledge than Darwin ever had about how these mutations occur. The next question to be examined is whether these mutations occur at a sufficiently rapid rate to explain the facts of complexity we see around us.

Next in this series: The sufficiency of the mutation rate

POST SCRIPT: Impeachment

There is an increasing sentiment in the country to impeach Bush and Cheney.

Independent documentary filmmaker Robert Greenwald has made a short film making the case for impeaching Cheney, and there is also a petition that you can sign.

July 05, 2007

Evolution-6: The probabilities of natural selection

(Please go to 'Categories' and choose 'Science' to see the previous posts in this series.)

There are three mathematical ideas that one needs to come to terms with in order to get the full flavor of how natural selection works.

  1. One is the rate at which favorable mutations occur in organisms. These do occur by chance and the question is whether the frequency of such occurrences is sufficient to explain evolution.
  2. The second is the rate at which favorable mutations become more numerous in the population. It is not enough to produce a single favorable organism. The population of varieties with advantageous properties has to eventually grow to sufficiently high numbers that it dominates the population and can form the basis for yet further mutations.
  3. The third is whether the rate at which repeated small and favorable mutations build on each other is sufficient to produce major changes in complex systems (the eye, ear, and other organs for example) and even entirely new species.

It is only the very first item that works by pure chance. The other two are highly directed processes, not because there is an external intelligence at work but because they are subject to the pressures of natural selection, which considerably reduces the contributions of chance to the outcome.

Now it is undoubtedly true that the chance of producing a favorable mutation is small. Most mutations are deleterious to the organism. The chance of a favorable mutation, once produced, taking hold and becoming widespread in a species population is also small. And the chance of favorable mutations building on each other to produce complex organisms is also small. So if we leave things at this high level of generality, skeptics of natural selection can (and do) argue that the complexity of life as we know it is too unlikely to have occurred and that therefore some intelligence must be behind it. To get beyond that superficial argument and appreciate the power of the theory, one has to actually do the calculations.

Darwin himself was well aware of these difficulties but also had the intuitive sense that even events with very small individual probabilities have a good chance of occurring if you wait long enough and have large enough populations. Although he could not quantify it, Darwin knew that he needed a very long time for his theory to work, which is why he viewed with such interest research on the age of the Earth. All three processes listed above must be able to fit within the timeline allowed by the age of the Earth, which is why research in geology and physics have had important implications for the theory of evolution. But since the time scales involved are well beyond our own lifetimes, people have a hard time comprehending the workings of evolution.

As an example of this, take the lottery. The chance of buying one ticket and selecting six numbers from 1 to 49 that match the winning numbers is incredibly small (to be precise 1 in 13,983,816). But you can greatly improve your chances if you buy many tickets and plan to play week after week. The greater the number of tickets you buy, the shorter the time in which you can expect to hit the jackpot. Of course, even if you live long enough and invest enough, the total amount you spend on your tickets will almost always be much more than the amount you win but that is because the organizers of the lottery have pegged the prize money that way so that they can make a profit.

Only the first of the three items listed above for natural selection (the occurrence of favorable mutations) works the same way as the lottery, except that nature hasn't rigged the system against you. Nature just doesn't care. And this means that if there are large enough populations and long enough times available, natural selection will repeatedly hit the jackpot and produce the wonderful complexity we see.

One of the fundamental features of the theory is that mutations, or changes in organisms, occur at random. Most of these mutations are either fatal or sufficiently harmful to the organism so that the mutated variety dies away. After all, if you make random changes in anything (say the wiring of your computer or even your toaster) there is a much greater chance of making it worse than making it better. But on rare occasions, a beneficial mutation will occur that results in that new variety flourishing because it is better adapted to succeed in its current environment.

We now know something that Darwin did not, that these mutations occur at the level of the genes. Although the work that led to the discovery of the genetic laws of inheritance was done by Gregor Mendel at roughly the same time as Darwin and provided the material basis for understanding inheritance, Darwin was not aware of that cloistered monk's research, although Mendel was aware of Darwin's work. Mendel published his seminal paper in 1865 (Darwin's On the Origins of Species appeared in 1859) but it went largely unnoticed until 1900 when several biologists who had been working on the problem of inheritance, independently came across Mendel's work.

The synthesis of Mendel’s work on genetics with Darwin’s theory of natural selection is one of the great advances in modern science and the next post in this series will discuss that relationship.

Next in the series: The effect of Mendel’s work on Darwin’s theory

POST SCRIPT: Onion parody on evolution

The nice thing about this parody is that it captures very well the central problem with the arguments of intelligent design creationists and other religious believers who want to preserve a role for god by carving out a little niche for god to intervene in evolution.

June 29, 2007

Evolution-5: How probability intuition can lead us astray

(See part 1, part 2, part 3, and part 4.)

One of life's ironies is that the difficulty in understanding the mathematics of Darwin's theory of natural selection may actually be caused by natural selection itself.

As we saw earlier, natural selection does not try for maximum benefit but instead works on a 'just good enough for now' principle. Steven Pinker in his book How the Mind Works (1997) is a cognitive scientist who believes that natural selection has been the driver for most aspects of our bodies and our behavior, and that the brain, being just another organ, has evolved to do what it does to effectively meet the challenges it faced at various times in our somewhat distant past. Pinker points out that humans, when compared with other animals, have unusually large brains compared to body size but that this rapid expansion in brain size occurred more than 100,000 years (or about 5,000 generations) ago (Pinker, p. 198) and then leveled off after that. This means that the structure of our present brains has been largely determined by a time when humans were hunter-gatherers and foragers.

This means that although modern life is undoubtedly very complex and require us to meet a vast array of challenges, our brains are best suited to meet the challenges of our ancient forebears, not those of driving on a highway or learning to operate a computer or solving sudoku puzzles. Thus we are very good at identifying faces and shapes, seeing things in depth, reacting to predatory dangers, and acting on instincts such as ducking when an object is thrown at our heads, etc, because our brains have probably evolved modules that handle such things efficiently. But we are not so good at solving quadratic equations. The kind of mathematics that helped our hunter-gatherer ancestors survive did not require much beyond an elementary sense of number. As for probability, simple concepts largely based on induction and extrapolating from past experiences, are sufficient.

But as culture developed in the last 10,000 years with the advent of more settled agrarian societies and written language, we now find ourselves having to struggle a bit to master the concepts needed to face today's challenges. They do not come 'naturally' to us, by which I mean that there are no brain modules that have evolved to enable us to quickly grasp and understand and respond to them.

This is especially true of probability and statistics. There was no need for our ancestors to develop modules to make Bayes' Theorem or the Central Limit Theorem easily understandable, which explains why our intuitions are so often led astray. For example, many people fall prey and lose money because of the 'gambler's fallacy' because they put their faith in a spurious 'law of averages', believing that the more repeated occurrences you have of the same thing (say getting heads on a coin toss or coming up black in a roulette wheel), the more likely a different outcome becomes on the next play. Similarly people who play the lottery numbers tend to avoid numbers that have won recently.

While mathematical sophisticates may look down on such naïvete , Pinker points out that such expectations are perfectly consistent with the kinds of probability experiences our hunter-gatherer ancestors experienced and which we still experience in most everyday life. After several days of rain, a dry day is more likely. After seeing several elephants appear in a line, it was more likely not to see one. In fact, event repetitions that are finite and terminate and change are the norm in nature, not the exception. Hence believing such things and acting upon such beliefs has some survival value that makes it plausible that our brains evolved modules that encoded those expectations, making us instinctively sympathetic towards believing things like the gambler's fallacy.

The reason that so many are fooled by the gambler's fallacy is that the creators of the gambling devices go to great lengths to make each event independent of the previous ones, thus violating our natural expectations. We thus have to consciously learn to sometimes go against our 'natural' instincts and this takes effort and is not easy.

Even though I consider myself fairly adept at mathematical manipulations, I am often humbled by how easily my intuition is led astray when confronted with a novel statistics problem. Take for example this case, which may be familiar to people who have taken an elementary statistics course, but fooled me when I first encountered it.

Suppose the incidence of some disease is fairly rare in a population, say about one in a thousand. You are told that there is a test for this disease that is pretty good in that it that has a 'false positive' rate of only 5%, meaning that if a randomly selected group is tested, only 5% of the people who do not have the disease will have test results that come out positive. Also you are told that the false negative rate is zero, meaning that if someone does have the disease, the test will definitely come out positive.

Suppose you are among those who are part of this random testing. To your dismay, the result is positive. What do you think are your chances of actually having the disease?

Most people would think that it is very high. They may put it as high as 95%, thinking that if there is a 5% false positive rate and 0% false negative rate, that means that the likelihood of someone testing positive having the disease is 95%. This sounds eminently reasonable.

But the actual chance of you having the disease despite testing positive is just 1 in 51 or less than 2%! How come? This becomes easier to understand if we shift from talking in terms of probabilities (which I have pointed out are not so intuitive) to talking about numbers. Suppose you are one of 1000 people being randomly tested. (Any size will do. I have chosen 1000 because it is a nice round number.) Then an incidence of 1 in 1000 means that we expect only one person to actually have the disease (and who will test positive), and 999 to be free of the disease. But a 5% false positive rate will result in about 50 of the 999 people who do not have the disease also testing positive. So your chance of actually having the disease is the chance that you happen to be that one person with the disease out of the 51 testing positive.

What the positive test result has done is provide a twenty-fold increase in the odds of your having the disease from 1 in 1000 (or 0.1%) to 1 in 51 (or slightly less than 2%), but your chances are still extremely good (over 98%) of not having the disease. I suspect a lot of people get unduly terrified by test results of this kind because doctors may not know how to present the data in ways that give them a better sense of estimating the probability. (Of course, I am assuming that you were selected randomly for this test. If the doctor recommended that you get the test because you had other symptoms that caused her to suspect you had the disease, then that would further increase the odds of you having the disease.)

The lesson here is to be wary of our 'gut' feelings when dealing with certain mathematics concepts, especially involving probability and statistics. This may partially explain why Darwin's theory of natural selection, dealing as it does with small probabilities and long time scales, is so hard for many to digest because they are outside the range of things we experience on a daily basis. In future postings, I will look at some of the issues that come up.

POST SCRIPT: Sicko opening nationwide on Friday

Michael Moore's new documentary on the health care system Sicko will be at the Cedar-Lee (2163 Lee Rd) in Cleveland Heights starting on Friday, June 29, 2007. The show times are noon, 2:30, 5:00, 7:30, and 10:00 but you should check before you go.

Moore also appeared on The Daily Show to point out once again what a scandal the health care system in the US is, where it is actually in the interests of the profit-driven health insurance companies to deny health care to patients.

June 27, 2007

Evolution-4: Darwin gets an idea from Malthus

(See part 1, part 2, and part 3.)

In Darwin's travels to distant lands from 1831 to 1836 on the Beagle, the different climates and environmental conditions he encountered made him aware of the weakness of the existing theory of 'special creation', where god was assumed to have created creatures best suited for their environment. Darwin saw for himself that very similar climates could produce hugely different kinds of species, and that the nature of these species seemed to be more influenced by the species in nearby areas than by anything else. This seemed to him to suggest that new species arose from the modifications of the old.

The discovery that the Earth was much older than had been previously thought, and the evidence for which was in the geology book by Charles Lyell that he had read on the boat, told him that it may be possible for these changes to occur gradually by very small steps provided that there was enough time for the changes to accumulate.

But why should species change at all? Why shouldn’t they stay the same forever? Or if they changed, why wouldn't they change randomly instead of seeming to have a direction towards increasing complexity?

What Darwin still lacked was a mechanism that drove the change in organisms. The idea for this came in September 1838 when, after his return from his voyage and he was thinking about all the evidence he had gathered, he read Thomas Malthus's Essay on the Principle of Population in which that political economist argued that the only thing that kept the population of anything (humans, other animals, plants) from experiencing runaway exponential growth was the limitation of essential resources (such as food and suitable habitats), and deprivations such as cruel climates, predators, and the like. (David Quammen, The Reluctant Mr. Darwin (2006), p. 42.)

Darwin knew that the size of plant and bird and animal populations in nature were fairly stable and he reasoned that the factors identified by Malthus might act differentially on members of the population, being more likely to remove the ones less suited and thus increasing the proportions of those more suited to the conditions. This kind of selection pressure, he felt, must be the driver of evolutionary change. Here at last was the mechanism that he had been seeking.

For the next twenty years, he carefully studied this process, starting with the breeding practices of pigeon owners and moving on to many others species. He even spent eight years studying barnacles. While breeders had the ability to artificially control the selection process, Darwin had the insight that the forces at work in nature might produce the same effect in the wild, hence his term 'natural selection'.

Darwin eventually arrived at the basic tenets of evolution by natural selection. (The Advancement of Science, Philip Kitcher, 1993, p. 19. I have mentioned these before but reproduce them here for completeness.)

1. The Principle of Variation: At any stage in the history of a species, there will be variation among the members of the species: different organisms belonging to the species will have different properties.

In other words, children are never identical with their parents. Within each species there is considerable diversity in properties (the larger the population, the greater the diversity) and in support of this position, Darwin took great pains to point out how hard it was to distinguish between different varieties within the same species, and between species.

2. The Principle of the Struggle for Existence: At any stage in the history of a species, more organisms are born than can survive to reproduce.

If there is an abundance of food and other resources, the population of any species would multiply exponentially, as suggested by Malthus. The fact that it doesn't is due to limitations in these necessary elements and this is what results in only some surviving and populations reaching more or less stable values.

3. The Principle of Variation in Fitness: At any stage in the history of a species, some of the variation among members of the species is variation with respect to properties that affect the ability to survive and reproduce; some organisms have characteristics that better dispose them to survive and reproduce.

The members of a species that are more likely to survive and pass on their properties to the next generation are those that have properties that give them some survival advantage in the environment in which they find themselves. It is important to note that only some of the properties need to be advantageous for the organism to have preferential survival. Other properties may also flourish not because they have an advantage but because they are somehow linked to advantageous properties and are thus carried along. Thus some properties may simply be byproducts of selection for other properties.

4. The Strong Principle of Inheritance: Heritability is the norm; most properties of an organism are inherited by its descendents.

Most properties that we have (five fingers, four limbs, one heart, etc.) are inherited from our ancestors.

All these four things were not controversial and were not hard to accept even for religious people. What gave Darwin's theory its uniqueness and created controversy was that from these four principles, he inferred the crucial fifth. It was this extrapolation that is the key to Darwin's theory of natural selection.

5. The Principle of Natural Selection: Typically, the history of a species will show the modification of that species in the direction of those characteristics which better dispose their bearers to survive and reproduce; properties which dispose their bearers to survive and reproduce are likely to become more prevalent in successive generations of the species.

So natural selection will favor those organisms that, by chance mutation, have properties that give them better chances for survival, and thus these characteristics will appear in the next generation in greater abundance. And from this he inferred that as these changes accumulate, eventually new species emerge.

But it was one thing to have a theory that satisfied him. It was quite another to convince others that it was the explanation for the diversity of life. There were many obstacles he had to overcome, not the least of which was the scale of time he was asking people to envisage was much longer than they were used to, the size of the mutations that underlay the process were so small as to be mostly invisible, and there was no agreement at that time on the whole question of how characteristics were inherited and how variations occurred in species.

It was to try and meet these objections that Darwin spent the rest of his life accumulating vast amounts of evidence from all over the world. Darwin, great scientist that he was, knew that just having a good idea wasn’t enough in science, however beautiful the idea was. You had to have evidence to support it.

Next in the series: How probability ideas can lead us astray

POST SCRIPT: How can we miss you if you won’t go away?

I was looking forward to British Prime Minister Tony Blair leaving office today. I found his preening pieties, his obsequious behavior toward Bush, and his self-righteous attitude irritating in the extreme and was looking forward to not having to see that on public display. But now comes the alarming news that Bush is thinking of making him some kind of special envoy to the Middle East, so we will be forced to endure even more of his grating presence.

Maybe Bush likes having his 'pet poodle' (which is actually an insult to a fine and dignified breed of dogs) around but as long-time Middle East correspondent Robert Fisk points out in the British newspaper The Independent, those who think that Blair, whom he describes as "this vain, deceitful man, this proven liar, a trumped-up lawyer who has the blood of thousands of Arab men, women and children on his hands," has any credibility at all in the Middle East are woefully mistaken.

June 25, 2007

Evolution-3: Natural selection and the age of the Earth

(See part 1 and part 2.)

It is clear that many people find it hard to accept Darwin's theory of evolution by natural selection. One reason is of course because it completely undermines the need to believe in a creator, making god superfluous when it comes to explaining the nature and diversity of life, and thus people may have a negative emotional reaction that prevents them from seeing the power of the theory. As I have discussed earlier, people are quite able to develop quite sophisticated reasons to believe what they want and reject what they dislike.

Another reason that Darwin's ideas were so hard to accept is because, as Daniel Dennett says in his book Darwin's Dangerous Idea (1995), he turned the whole model of how things come to be on its head. Up until then, people had thought that to make anything always required a more complex thing. Simpler things never made more complex things. You did not find a horseshoe making a blacksmith, for example. But what Darwin was suggesting was that a very simple mechanism, natural selection, could result in simpler things becoming more complex without an external agent, but just from the ground up, as it were. What is worse was that, according to Darwin's theory, intelligence, which had been thought as a precursor to creation and often used synonymously with god, turned out to be something that occurred much later in life's evolution. In other words, intelligence itself came into being by a non-intelligent mechanism. These ideas made people who thought of human beings as possessing some special divine qualities uncomfortable, to put it mildly.

People find it hard to accept the fundamental idea of evolution that very small changes, if cumulative over very long times, can result in big changes. This should not be an entirely foreign concept, especially to those with savings accounts who are familiar with the way that interest grows when compounded. If you keep some money in a savings account at a rate even as low as 1%, it will double in 70 years, quadruple in 140 years, become eight times as much 210 years, and so on, becoming over a thousand times as large in 700 years, and over a million times as large in 7,000 years. But therein lies the difficulty. People do not fully appreciate the power of compounding because they tend not to be able to grasp time scales much longer than their own life spans.

The mathematics and statistics that are relevant to understanding how natural selection works does not come easily to people, partly because we do not have a firm intuitive grasp of geological time scales which are so large as to be almost impossible to comprehend. I once had a college first year student say that she did not think evolution could have happened. I asked her why and she said that when you saw the images drawn on 'ancient' Egyptian inscriptions, those people looked just like us today. So in her view, since there had been no visible evolutionary change over what to her was an enormous length of time, this disproved evolution!

It is not easy to grasp that even written language only goes back 5,000 years or so. When we factor in that the more appropriate unit of time for evolutionary change is the generation (which for humans is about 20 years), we see that written language emerged only 250 generations ago. It is hard for us to even imagine what life was like back then. Even the Vietnam war, which was just one generation ago, seems like ancient history to college students today, almost obscured by the murky mists of time.

So it is almost impossible to wrap our minds even around the fact that the common ancestor of humans and chimpanzees lived 300,000 generations or 6 million years ago, even though that itself is a blip compared to the origin of life itself (over 3 billion years ago) or age of the Earth (4.5 billion years ago). When we realize that the lifetime of a generation for many species is usually much less that 20 years, and is often measured in months and even days, the number of generations that have been available for evolutionary change to take place is staggeringly huge.

Although he could not quantify it at that time, Darwin knew that his theory of natural selection required very long time scales in order to be feasible. But he was born at a time when Biblical cosmology was dominant and the idea of an Earth that was less than 10,000 years old was widespread. This would not have been long enough for his ideas to work and it is unlikely that he would have hit upon his great discovery if not for having been born at a fortuitous time. In another example of how science is deeply interconnected in its theories, Darwin's theory was made possible because of the work of his contemporary and later friend, geologist Charles Lyell and his theory of uniformitarianism.

Prior to Lyell, ideas in geology were strongly influenced by the book of Genesis and it was believed that the Earth had had a series of catastrophes (floods, volcanic eruptions, earthquakes, etc.) that had produced its major geologic features. The advantage of this theory of catastrophism was that it enabled people to believe that the Earth was quite young, since it made it plausible that major geological fractures like the Grand Canyon and Niagara Falls could come into being suddenly.

Lyell in his three volumes The Principles of Geology: Being an Attempt to Explain the Former Changes of the Earth's Surface, by Reference to Causes now in Operation (published over the years 1830-33) advanced evidence that the Earth had been around for a very long time and in particular, from his study of fossils, that human beings were much older than had been thought. Darwin read the first volume of this work on his life-changing trip on the Beagle (which lasted from 1831 to 1836) and it opened his eyes to a new way of seeing the diverse life forms in the exotic faraway places he visited. Lyell's work not only gave Darwin the large window of time necessary to fit his own theory, it also was a precursor of Darwin's central idea that very small changes, accumulated over very long times, could produce dramatic effects.

Although Lyell's estimate of the age of the Earth was only about 250 million years, smaller in comparison to current estimates by a factor of almost twenty, this was still a huge increase from earlier ideas, and Darwin saw in it an opening that the Earth was possibly very old, old enough that made it possible for the evolution of life as he saw it to occur and it encouraged him in his work. But after Darwin published his landmark On the Origin of Species in 1859, the old Earth theory of Lyell received a major setback when in1864, one of the most eminent physicists of that time, William Thomson (later Lord Kelvin), said that his calculations of the rate of cooling of the Earth's magma suggested that the Earth became a solid body between 20 and 400 million years, a disturbingly low lower limit. But it got worse, with later calculations reducing even the upper limit to much less than what Lyell had proposed, coming down to about just 10 million years. This was much less than what Darwin needed for his theory to work, and Thomson in 1868 explicitly challenged the validity of natural selection on these grounds. (David Quammen, The Reluctant Mr. Darwin (2006), p. 211.)

While this was undoubtedly a setback, Darwin doggedly persevered, accumulating more biological evidence for his theory, confident that future work in physics would vindicate him that the Earth was much older. But conclusive support on this question would only come after his death in 1882. Following the discovery of radioactivity, Rutherford and others in 1907 found evidence of rocks that were 1.6 billion years old. Further studies since then have increased the age to the current estimates of 4.5 billion years, more than enough for the theory of evolution to work.

Once again, we see how the interconnectedness of science can provide powerful constraints when it comes to constructing new theories, because theories in one area (such as biology) have to be consistent with theories in seemingly disparate areas (like physics and chemistry and geology). When creationists attack the theory of evolution and try to replace it with ad hoc theories of great floods, they are also severing ties with an entire network of scientific theories, and adding on yet more ad hoc hypotheses to fill in the obvious gaps does not help. When they reject a comprehensive theory like the theory of evolution by natural selection without replacing it with another one that is consistent with the findings of other scientific theories, they are pretty much rejecting the foundations of modern science.

As the philosopher of science Pierre Duhem wrote long ago in his book The Aim and Structure of Physical Theory (1906): "The only experimental check on a physical theory which is not illogical consists in comparing the entire system of the physical theory with the whole group of experimental laws, and in judging whether the latter is represented by the former in a satisfactory manner." (emphasis in original)


POST SCRIPT: The Lion Sleeps Tonight

Hank Medress, vocalist of the group the Tokens, died last week at the age of 68. Here he is singing their big hit The Lion Sleeps Tonight.

June 21, 2007

Evolution-2: The lack of evidence for perfect design

In the first post in this series, I showed with the example of a soap spray nozzle how natural design could come up with systems whose intricacy and complexity is such that it was superior to the efforts of intelligent human designers. But what about the argument that a god-like designer would be able to come up with an even better nozzle design? It is true that if we allow for the existence of such a designer, we could get the best possible design for a nozzle. The catch is that assuming that god is a perfect designer opens up a whole set of new problems, not the least of which is why if god is so powerful he would need any kind of nozzle at all and not simply create any kind of spray he/she needed.

Let me start with a limitation of natural selection. There is a well known result about any method of solving a problem that starts (like natural selection does) with some state, tries out small variations, selects the one that shows the greatest improvement over the starting point, tries out variations based on that new state, selects the best one again, and so on, which is exactly the way that natural selection works. The problem is that while you will end up with a better result than the one with which you started, it may not be the very best solution that is conceivable. Such algorithms result in finding a locally optimal solution but not a globally optimal one.

As an example, suppose you are in open ground and totally in the dark. For some reason, you need to get to the highest point in the ground, say because flooding is occurring and you know the water is rising very slowly. (The specific reasons are not important. The point is to have some kind of external pressure that drives the selection process in one direction.) You could gingerly take small steps in every direction, see which way went up the most, and move one step in that direction. Then you again take tiny steps in all directions and select the one direction that moved up most, and move to that position. And so on. By repeatedly doing this, you are guaranteed to arrive at a peak.

(This is how natural selection works, though to be a more accurate analogy, we need to start with many people at the starting point, have couples move in each direction, have only the couples that get to higher ground survive while the others drown, have those successful couples produce lots of children at that location, who then move as couples in different directions, and so on.)

The catch is that the peak you arrive at may not be the highest peak in the vicinity. If a yet higher peak were to be separated from your initial starting point by even a small dip in the ground, you would miss it using this algorithm, since it does not allow you to make a short-term disadvantageous change in anticipation of future benefits. Natural selection is not guaranteed to produce the very best or the most perfect solution or design. It instead works on a 'just good enough for now' basis. This means that biological systems do not necessarily make progress towards perfection even though they do become more complex over time.

Now a god-like designer would presumably be able to see all the possible solutions (even in the dark) and pick the one that is best overall and guide you to that point. But the interesting thing is that the results of nature are more consistent with the 'just good enough for now' strategy of natural selection than that of a perfect designer. After all, we know that while nature's designs (by which I mean designs arrived at by natural selection) are marvelously adapted and successful for many things, they are by no means perfect.

As Sean B. Carroll says in his book The Making of the Fittest (2006) which examines the DNA evidence for natural selection:

Modern species are not better equipped than their ancestors, they are mostly just different. They have often gained some coding information in their DNA and, as I have shown throughout this chapter, they have often lost some, or even many, genes and capabilities along the way.

The fossilization and loss of genes are powerful arguments against notions of "design" or intent in the making of species. In the evolution of the leprosy bacterium, for example, we don't see evidence that this pathogen was designed. Rather, we see that the organism is a stripped-down version of a mycobacterium, which still carries around over a thousand useless, broken genes that are vestiges of its ancestry. Similarly, we carry around the genetic vestiges of an olfactory system that was once much more acute than what we have today.

The patterns of gain and loss seen species' DNA are exactly what we should expect if natural selection acts only in the present, and not as an engineer or designer would. Natural selection cannot preserve what is not being used and it cannot plan for the future. (p. 136)

The very fact that it is estimated that over 99% of all the species that ever existed are now extinct is powerful evidence against perfect creation. The only way out of this for the religious believer is to think that god, although perfect, is somehow holding back and deliberately creating imperfections and thus making it merely look like something like natural selection is at work. Or god does not interfere at all, ever in the natural selection process once it began way back at the beginning of life. Or is simply careless and produces sloppy designs.

Darwin himself, based on his careful study of plants and animals, found it hard to believe in the idea of an intelligent designer. His biographer David Quammen in the book The Reluctant Mr. Darwin (2006, p. 120) highlights the kinds of questions that troubled Darwin, and which he expressed in letters to the Harvard botanist Asa Gray, who believed in the idea of special creation of humans.

I cannot see, as plainly as others do, evidence of design & beneficence on all sides of us. There seems to me too much misery in the world.
. . .
Why would a benevolent God design ichneumon wasps, for instance, with the habit of laying eggs inside living caterpillars, so that the wasp larvae hatch and devour their hosts from inside out? Why would such a God design cats that torture mice for amusement? Why would a child be born with brain damage, facing a life of idiocy?
. . .
An innocent & good man stands under [a] tree & is killed by [a] flash of lightning. Do you believe (& I really shd like to hear) that God designedly killed this man? Many or most persons do believe this; I can't and don't.

The question of pointless suffering and loss were not hypothetical issues for Darwin. He had been devastated when his own beloved daughter Annie had, at the age of ten, died after a long and mysterious and undiagnosed wasting illness. Darwin seemed to feel that such things were incompatible with a benevolent deity. As Quammen writes, "Any god who controlled events on Earth closely enough to preordain such an occurrence – or to permit it, if permission was necessary – wasn't one that Darwin could take seriously."

Darwin's theory of evolution by natural selection, although not aimed at doing so, ultimately provided the basis on which belief in a designer god, and thus god itself, could be abandoned.

June 19, 2007

Evolution-1: The power of natural selection

We are rapidly approaching 2009, a year that marks a major scientific milestone that is going to be commemorated worldwide. It is both the 150th anniversary of the publication of the landmark book On the Origin of Species that outlined the theory of evolution by natural selection, and the 200th anniversary of the birth of its author Charles Darwin.

Darwin's theory represents arguably one of the most, if not the most, profound scientific advances of all time, ranking well up with those scientific revolutions associated with the names of Copernicus, Newton, and Einstein. And yet it is widely misunderstood, or more appropriately, under-understood because most discussions of it remain on too high a level of generality, enabling critics to make statements about the theory that are not valid but yet seem plausible.

In order to create a better awareness of what the theory involves, today I will begin an occasional series of posts that looks at the details of the theory, including the mathematics that underlies it and which was developed later by people like J. B. S. Haldane, Sewall Wright, and R. A. Fisher.

One of the most common misconceptions about evolution by natural selection is that it works purely by chance. After erroneously assuming that notion, people then look around them, see the wonderful complexity of nature, and conclude that this simply could not have occurred by chance and that therefore this points to the existence of a designer who must be god. This is exactly the explicit argument of intelligent design creationists, but also the implicit argument of some people who want to somehow find evidence for the necessity of god's existence.

It seems as if no amount of reiteration (by those who have studied the theory of evolution) that this basic assumption of chance is not true, seems to have any effect. I recently had a correspondence with someone who, despite my repeatedly pointing out that chance was not the sole driver of natural selection, kept saying things like "How can you think all this came about by chance?"

Now chance does play a role in the way that genetic changes occur, externally from the occurrence of mutations due to things like ultraviolet radiation, and internally in the way that genetic shuffling occurs in the copying of the genetic information during reproduction. You cannot be sure, for example, what genetic features you will inherit from your mother and what from your father. But these chance variations are then acted upon by selection forces that are the very opposite of chance in that they pick out only those varieties that are beneficial for future propagation. This is a highly directed process that acts without an intelligent director and it is these selection forces that are behind the complexity of the systems that have evolved.

In response to the "evolution is just chance and is very unlikely to produce complexity" argument, those who understand the theory of evolution sometimes argue in its defense that the theory is just as good at producing complex things as any conscious designer. But such people are really selling the theory short. In actual fact, the theory of evolution by natural selection produces results that are often much better than those produced by conscious design.

A wonderful example that illustrates this point is given by biologist Steve Jones, as recounted in his book Almost Like a Whale: The Origin of Species Updated (1999) (Chapter IV, Natural Selection). (Thanks to Heidi Cool for alerting me to the podcast of a talk by Jones which is where I first heard this story.)

I once worked for a year or so, for what seemed good reasons at the time, as a fitter's mate in a soap factory on the Wirral Peninsula, Liverpool's Left Bank. It was a formative episode, and was also, by chance, my first exposure to the theory of evolution.

To make soap powder, a liquid is blown through a nozzle. As it streams out, the pressure drops and a cloud of particles forms. These fall into a tank and after some clandestine coloration and perfumery are packaged and sold. In my day, thirty years ago, the spray came through a simple pipe that narrowed from one end to the other. It did its job quite well, but had problems with changes in the size of the grains, liquid spilling through or − worst of all − blockages in the tube.

Those problems have been solved. The success is in the nozzle. What used to be a simple pipe has become an intricate duct, longer than before, with many constrictions and chambers. The liquid follows a complex path before it sprays from the hole. Each type of powder has its own nozzle design, which does the job with great efficiency.

What caused such progress? Soap companies hire plenty of scientists, who have long studied what happens when a liquid sprays out to become a powder. The problem is too hard to allow even the finest engineers to do what enjoy the most, to explore the question with mathematics and design the best solution. Because that failed, they tried another approach. It was the key to evolution, design without a designer: the preservation of favourable variations and the rejection of those injurious. It was, in other words, natural selection.

The engineers used the idea that moulds life itself: descent with modification. Take a nozzle that works quite well and make copies, each changed at random. Test them for how well they make powder. Then, impose a struggle for existence by insisting that not all can survive. Many of the altered devices are no better (or worse) than the parental form. They are discarded, but the few able to do a superior job are allowed to reproduce and are copied − but again not perfectly. As generations pass there emerges, as if by magic, a new and efficient pipe of complex and unexpected shape.

Natural selection is a machine that makes almost impossible things.

In other words, by mindlessly applying an algorithm based on the principle of natural selection, they were able to come up with a complex design for a superior spray nozzle that was inconceivable to the scientists trying to design one using engineering and science principles.

Believers in a god-like designer might argue that what natural selection did here was outperform mere mortal designers and that god, being a perfect designer, would be able to come up with a better design. But that argument doesn't work that well, either, as I will discuss in the next posting in this series.