April 26, 2010
The Last Day of Classes Part III
When I got the peer review of my proposal back I was a little nervous to look at it. But when I did read it and then went back over my proposal what they said made sense. I had never said anywhere just how large the colletion of placoderms in the CMNH was. They also pointed out that some of the information in my introduction would be better suited in the description of research since I have already taken a few preliminary measurements.
It was good to get some outsiders views on the paper and see what kind of questions they would come up with. A lot of their questions were on the list of things I wanted answered to research the specimen that I created at the very beginning of the semester. Somewhere along the line I'd either forgotten about some of the questions or had thought they weren't really relevant.
Once I got down to it the changes to the final proposal were nothing drastic. It mostly consisted of moving sections around and rewording or weaving them back together. Combing through the entire document for gramattical errors and awkward sentences was important too and making sure that the writing style and puncuation were consistent in the proposal.
Once that was done the final thing to do was get signatures. I would suggest to everybody doing this that you get it done as soon as possible, printing out a seperate page just for signatures works just fine. I unfortunately put it off and then on Friday when I was going to get some I realized that I wanted to add another person and myself as well. My advisor Dr. Ryan of the CMNH has been out of town for the past few weeks though he was supposed to return two weeks ago. So I sent him an email instead to ask for an e-signature. I still went to the museum earlier today though to get the signatures of the technicians who cleaned the specimen and made the research possible; Gary Jackson and Dale Zelinski. The last person I wanted to have sign the prosal was Professor McCall who could help me out with understanding the invertebrate ecology of the Devonian seas and maybe help pin down what the specimen might have eaten. I managed to catch him just before I had to hand in the paper and only because I had talked to him on Friday so I knew where he was.
Now that the proposal is done the real research can begin. I'm really looking forward to my project because the more I learn about the placoderms the more fascinating they become and I still feel that I have only scratched the surface. I plan on contacting the authors of the bite force paper on Dunkleosteus that was done a few years ago as well as Professor Robert Carr in Chicago who has done the most recent work on the Placoderms of the Cleveland Shale. I will also be taking vertebrate biology next semester with Dr. Oldfield who specializes in fish so there are many oppurtunities for outside knowledge and help that have been left untapped.
The Last Day of Classes Part II
The final draft of the proposal was due on the 14th of April. Once they were all turned in we were assigned into groups of three that would each be reviewing two other people's papers. I was a in a group with the graduate students Ruth Adler and Jian Han and we would be reading the papers by Katie(Undergraduate) on Twilight Sleep and a new method of detecting pollutants in sediements by Eliza Kaltenberg(Graduate). The peer panel review was held on the 19th and reading the papers before hand they were sharply contrasted.
I read Eliza's paper first. She is proposing to research a new method called optodes which use flouresence to monitor the concentration of the pollutant PCBs in sediments without having to interfere with the sediment. The material was interesting but the writing was often difficult to get through. For Katie's paper it was very different, I thought it flowed well but because it was a history thesis instead of a strictly scientific paper she was defending a position.
The peer review process was interesting and I think our group was very productive. Each paper took about 45 minutes and a good portion of that time was deciding how to phrase our critique of the paper because it should be a constructive process. Rather than nit-picking the details of the proposals it was mostly pointing out areas that weren't clear or suggesting expanding in some directions in the proposal to strengthen it. There was some debate among the three of us on a few points but it was always easily resolved. The most important part of this process is that it is done in a respectful and objective manner so that nobody feels they are being targeted or branded and so that the author can then edit their proposal for the better.
The Last Day of Classes for Spring '10
In all the rush, papers, projects and tests of the last weeks of class I've neglected to update this blog in several weeks. Today is the last day of classes and the final proposal was due earlier today so Geology 390 is now complete with the exception of this blog. I'll try to give a full account of how things have progressed since the last post in the first week of April and hopefully give some insight into how to keep everything under control. To keep the posts from becoming excessively long I'm going to split it up over three posts as it originally should have been.
After the first draft of our proposal was due on the 5th the best effort first draft was due on the 14th. While working in small bits and pieces on projects sounds ideal it never really seems to work well for me. If I can get myself into the right mood to work and dive into something I just keep going until I've exhausted my thoughts or am forced to by some other obligation usually a growling stomach. So when I worked on the final draft it was in chunks of time greater than four hours at least. I also find that it's useful to change the environment your working in to focus on work. Trying to write in places that I am intimately familiar with makes me more prone to distractions and procrastination. Some of the most productive work on both the drafts was done in the geology lab of Smith 101, it's not the friendliest room but it's quiet devoid of distractions and there are vending machines with drinks and food to keep me working (popcorn seems to work really well for me).
When I got the first draft back in class it was not surprising that comments about the description of research section were the strongest and most consistent. The bullet-form I had needed to be rewritten into paragraph form and explain more clearly how I actually will go about accomplishing my research. It was a relatively easy edit because the bullet-form acted as a detailed outline. I also felt that my introduction and background section was scattered but I had a hard time finding a good way to organize my thoughts. So since Emily is also doing biological research I asked if she would be willing to let me look over her proposal to see how she organized it. It was very different from how I had written in my first draft and having a different angle of approach was extremely helpful in pulling together a cohesive introduction.
With new ideas floating around in my head I picked apart my first draft into sections that I thought all the bits fell under; placoderms in general, ecology and geology. From these topics I melded together different parts of the first draft, expanded where I thought it was important and removed information that no longer belonged. I ended up writing another outline just for the introduction and background section. Organizing my thoughts where I could see them helped keep things from getting overwhelming and organized I would suggest this to anybody else writing any paper.
April 06, 2010
First Draft Completed
So this is much later than I was hoping to post again on here but it was a long busy Easter Weekend. First off the proposal was due yesterday and though I got it done I found that it was difficult for a variety of reasons.
When I began to write the report I was just planning on going in the order that it would be presented in the proposal. So I began with the abstract which was surprisingly difficult because I wasn't entirely sure how I was going about the proposal. I did get it done first but it was altered after the whole draft was written when I had a better understanding of my focus. My suggestion to those writing a proposal is not to start with the abstract because summing up your entire proposal in a few sentences succinctly requires you to have a complete understanding of what your doing.
I then tried to continue on to the introduction and background information section but had a very difficult time trying to start it and establish a logical and clear order. After a few unsuccessful attempts I moved to some of the more monotonous sections such as budget, facilities, personnel and statement of convicition. These sections were all very easy for me to do because describing the fish from the museum makes the facilities and support clear and the museum is only a short walk from my dorm room as well. All these things have no budget so that section of my proposal was very very short.
In the personnel section though I did not think to incude myself because I thought the person writing the proposal is the one who would do the remainder of the work. Professor Hauck pointed out that this is not always the case. It is not uncommon for restrictions on submitting proposals to be placed on students by universities or institutions and so a faculty or employee would submit the proposal in their stead to circumvent these restrictions. So in effect the person who submits the proposal might do nothing else for the actaul research.
When these sections were done I reluctantly moved back to the introduction and background section of the proposal. I did find though that just writing the other section had cleared some things up in my head about the project and I could at least begin writing. I started rewriting the Intro/Background section several times but always kept the previous attempts to draw from them later and what I ended up with was a composite of all these attempts. I had a lot of trouble trying to write and introduce the material in such a way that it was always relevant to my question and linked back to it but I still kind of feel that at least some sections were merely information dumps. Some feedback from Monday and tomorrow should help in focusing that section meaningfully.
Once that part had been finshed the remaining section was the explanation of the research process itself. I now had a very good idea of where and how I wanted to go about my project so this section came very naturally to me as a sequential list of step that were broken down into smaller and smaller sections. Where applcable papers or particular difficulties to overcome in the research were noted under the appropriate section. My main problem with this section was that it turned out to be a kind of bullet-point breakdown and didn't flow well or look pretty. I would like to figure out how to retain the rigid order detailed in the draft but perhaps replace most of it with descriptive text.
The final draft is due in a week and then the week after that the final proposal is due and the end of the semester is upon me. Time to get back to work.
March 29, 2010
The Crunch Begins
There is a little more than a month left in the semester and that means that deadlines are approaching fast for a number of projects, reports, papers, housing, summer courses and a host of other things. Geology 390 is no exception as the first draft of our proposal is due in a week. So it's time to put all the papers I've been reading and the discussions in class to use but I have also continued my actual research as well.
At the museum this past Thursday I spoke with my advisor Dr. Ryan about some quesitons I had. The first was if there was a traditional sequence for describing bones in paleontology in general. Apparently the traditional method is to start with the head region and the move back along the spine(this only applies to vertebrates obviously), and then finally to the extremities. In the case of the specimen I will be studying this means that I would probably start from the dorsal part of the head shield and then move ventrally and then into the thoracic shield in the same pattern.
Professor Hauck suggested the idea of a 3D reconstruction using a CT scan on the specimen. I talked about this with Dr. Ryan and he said that the specimen was too compressed and the plates too flat for any CT scan to be really meaningful or revealing. The plates might possibly be thin because according to some theories of placoderm evoltuion heavy plates are primitive while a trend to reduce armor is a derived characteristic of many groups. This loss is theoretically to increase mobility and expand beyond benthic life habits.
A random thought that just struck me that is a tangent to my project. Since placoderms were thought to be at least primitively benthic and went almost entirely extinct at the end of the Devonian which was is also around the time of oceanic anoxic events that would have depleted the bottom waters of oxygen and could have contributed to the downfall of the group.
Back on track now, I also began taking rough measurements of the specimen and comparing it to those from the original descriptions by Newberry as well as the illustrations of his specimens with my own. The measurements along the longest axes of the head shield are roughly the same but the jaw to head shield length ratio appears to be very different. The specimen I am studying also appears to have some traits more in common with one of the described species than the other but I'll need to examine more bits and pieces of Titanichthys in the museum to check for size and shape variation. The specimen may be an intermediate between Newberry's two species which would be very exciting.
Dr. Ryan is also helping me set up a photo shoot with the museum's photographer, hopefully this week. Based on the papers that I have read and examined it seems like a dorsal and ventral veiw of the head and thoracic shields is the most important and standard in descriptions.
I hope to put up another post on this blog by Saturday to give an update on the progress of the draft for my proposal.
March 22, 2010
Gone for Break, Back for Fish
It's been quite a while since this blog was last updated unfortunately. Spring Break in Death Valley has come and gone and the last month and a half of classes are going fast. In fact, the outline for the project proposal was due earlier this morning already and the 1st draft is due in early April.
So in the light of the ever-shortening semester I've been trying to read up on more papers and refine the specific things that I will need to answer those questions. I was finally able last Thursday to find the original description of Titanichthys and found that there were two species originally both described by Nebwerry, though I don't know if both are still valid. The description was in a USGS Monograph from 1889, The Paleozoic Fishes of North America and was in the museum's library. The terminology is understandably archaic so translating it for comparison to my specimen could be a challenge.
I've also managed to find additional papers for modeling jaw motion and bite force of placoderm fishes. Fortunately for my research a group came to the Cleveland Museum of Natural History late last year to measure the jaws of Dunkleosteus to estimate it's bite force and published a paper on their methods and results. Since my specimen is closely related to Dunkleosteus the model should be applicable to it as well. If I can find the theoretical force of the jaw it may be able to tell me whether the specimen might have fed by gulping water in and pumping it through gills for filtering(like modern whale sharks) or used passive filtering(some sharks) or it may have swallowed prey whole.
When I go to the museum this week I need to talk to Dr. Ryan about a few things. The first is how to go about putting in illustrations or photographs of the specimen in the proposal and the the paper. I'm not much of an artist and I don't have any experience with software that is used to create images either. Professor Hauck mentioned today in class that a CT scan might be a possibility is showing inner details of the specimen and possible getting some of the 3D dimensions more clearly. I'm not sure if this is feasible with the specimen or if I would be able to get access to the necessary equipment so I'll have to ask about that. I also want to see if I might be able to get into the lab on the weekends when it would otherwise be closed, more in preperation for next semester when I should have a little more time to get down there and study my specimen.
As the semester moves on there is of course a multitude of projects that are being piled on so it's more important than ever to stay on top of all my studies and not push things until the last minute.
February 28, 2010
The Papers Come Marching On
So this week I've been continuing to plow my way through paper after paper, expanding to the geology of the Ohio region and some environmental ones on the period as well. In addition to the phylogenies of the fishes I also have diagrams of placoderm skeletons and phylogenies of the placoderms themeselves, I suspect it will soon look like I have some sort of placoderm wallpaper. As I said before the phylogeny of the basal fishes is just mind-boggling in how much it jumps around and within the placoderms themselves the relationships are even more inconsistent often because they examine a single or only a few traits such as teeth. Some papers from the last few years have revealed an amazing discovery about these ancient fish. At least some, if not all, placoderms gave live birth! Specimens from the Australian Gogo are so pristinely perserved in three dimensions that embryos, umbilical cords, and perhaps even a yolk sac have been preserved for over 400 million years!!!
Unfortunately that fact has very little to do with my specimen since part of what makes the Gogo placoderms amazing is that the rock around them can be literally melted away by submerging them in an acid bath. The fossils preferentially take up minerals that are resistant to acid, such as silicates, while they rest in carbonate rock that reacts strongly with acid to melt away. In the Cleveland Shale there is insted mudstone and, unfortunately for people trying to clean the fossils, pyrite. All the rock is resistant to acid about eaqually so you would end up destroying the fossils just as much as the rock with an acid bath.
Speaking of the area I made my way down to the museum this past Thrusday to continue my work. I brought my camera along for the first time and took pictures of the entire specimen from mostly the dorsal and ventral views articulated as they would have been in life, althought the specimen was lying on a table instead of in three-dimensions as in life. Even in these past few days I've made a point of trying to become more familiar with the names of the bones present in placoderms, but on Thursday I really didn't have a clue so my pictures aren't particularly focused or oriented on particular bones. Some of the papers I had been reading though noted the presence of sensory lines on the headshields of placoderms as being somewhat diagnostic. I have seen these sensory lines before when cleaning specimens but had never really looked into how they were organized so I also took specific pictures of obvious sensory lines.
After I was satisfied with my pictures I decided to really try a first and very rough attempt at identifying the bones. I grabbed a diagram of a typical dinicthys headshield, a very close relative of Titanichthys, and began to sketch where I thought the bone boundaries were. I first tried sketching it as a whole but the seperate pieces were not to scale so on the second time I drew each physical piece of the specimen individually. The boundaries between the bones are a lot less clear then I was expecting, being a different pattern of rough bumps than the rough bumps on rest of the bone. These boundaries are suture lines, places where the bones have fused together early in the individuals life which makes sense for armor.
I've sketched a little less than half of the specimen's headshield but already it looks like some bones have significantly different proportions than the dinichthys skull that I was looking at. How much variation is found within a species of genus I'm not sure, but within placoderms they apparently vary widely. I also have come to realize that as far as I am aware right now there is a single species of Titanichthys named and described, the original by Newberry in 1885. I really need to track down the original paper on this and find out where the original specimen is, if not in the Cleveland Museum of Natural History already. Considering the number of specimens in the museum labeled as Titanichthys it seems unlikely they are all a single species. I have a very unique oppurtunity here to describe and possibly name a new species that has not really been studied in over 100 years.