Oh, to be free of biology lab

30 03 2007

There has been quite a lively discussion going on lately (see here, here, here, here, here, and here for some of the highlights) over science labs for undergraduates, and being that I’m an undergrad myself (and have 2-3 lab courses every semester) I thought I would weigh in on the subject.

First, I should be honest and say that I’m none too happy with my undergraduate education up to this date. There have been some high points and some low, but especially since I started reading more scientific books and papers on my own, I don’t feel like I’m getting much from any of my classes. It may sound arrogant, but half the time I feel I could teach some classes better than my professors (becoming that insufferable know-it-all everyone hates in the process), and at this point college has merely become the institutional meat-grinder that I have to go through if I want to get my degree and some amount of respect. Darwin had publish a massive work on barnacles that took 8 years, I have to spend 8 years avoiding the BS; means to an end as far as some amount of academic respect.

Before I go off on my rant, I have had some positive experiences with lab work. Although my actual paleontology lab involved little more than looking at fossils and taking notes, the class did take a trip to the Inversand marl pit in southern New Jersey, where I was able to collect some bone material (there’s too little to ascertain from what, but likely a marine reptile) including a crocodile scute and mosasaur vertebrae. Certainly, neither was a big scientific acheivement but I felt utterly exhilarated uncovering part of an animal that lived over 65 million years ago right around where I was standing (the area was about 100 feet underwater during the end-Cretaceous). Another such positive experience occurred last summer when I spent one week in Stokes State Forest and another in Barnegat Bay, learning techniques for birding, forestry, etc. While I have to say I wasn’t particularly excited about the forestry/botany aspects of the first week, it felt good to actually be outside practicing methods used to determine various aspects of ecology rather than sitting in lecture.

If I had any other good labs experiences, however, I have long since forgotten them. Most labs I have taken have been horribly constructed and leave the student with little new information, certainly not reinforcing the concepts learned in lecture. Indeed, for some classes “Lab” merely means “video time,” where ancient National Geographic programs are shown without further discussion or comment. Others, however, involve monitored viewing/experience with materials, such is my current biology 102 lab. Each lab starts off with a quiz and .ppt presentation, followed by viewing of ancient Turtox-brand slides and then a final wrap-up where each group is assigned a question. The past week has been an exception being that we’ve been dissecting a fetal pig, but it seems more about just being able to name the anatomy than understanding about how the systems work in the organism. Indeed, often it feels like the course is designed with future med-students in mind, important aspects of biology like behavior, evolution, and ecology getting little mention or being pushed to the end of the semester.

Part of the problem with biology courses, and labs specifically, is that lack of enthusiasm shown by instructors. What grad student really wants to get up early and set up 20 microscopes with slides and herd undergraduates for 3 hours? I have yet to be through the system myself, but from what I understand if you cannot pay for grad school on your own, you need to get a GA or TA-ship, meaning if you can’t get a grant and you can’t pay on your own, you have to be a TA. I don’t want to paint all TA’s with too wide a brush (maybe it’s just Rutgers) but most of the ones I have encountered aren’t particularly happy about their situation and do little to inspire undergrads. Indeed, there are professors as well that seem like they would much rather be doing their own research than teaching an introductory course, and this apathy (and even contempt) comes across quite clearly.

Like I said, I don’t want to say that all labs are worthless or that every college is like mine, but as far as my own experience, I feel that I’m merely paying for my degree in yearly installments. There’s little that I’ve learned through my classes that I actually remember, and whenever I’ve shown an interest in a particular field or a desire to get involved, I’ve been brushed aside or looked down upon. When I switched my major to ecology & evolution, my adviser told me she didn’t think I could do it, and I’ve magically been reassigned to someone else (although it’s probably for the better). I’m tired of sitting in cramped lecture halls and listening to dispassionate professors stumble through lessons, I actually want to LEARN something and become a professional, but it doesn’t seem like I can do so at college. While gaining a “well-rounded” education is important, I think things are made more difficult on students by having to balance biology, chemistry, physics, math, history, etc. all in the same semester through much of their undergraduate work; if the classes had a common theme, were integrated, or even fed into each other, I think the acquiring and retention of information would be much greater, but I know that I have chosen my classes poorly in the past and now am stuck playing “clean up” in order to get my degree in the next year.

Sometimes I wonder if I’ll ever make a good scientist at all, not for lack of interest or passion, but because I simply can’t stand the Ivory Tower of academia. I would absolutely love to go to Africa and study ecology and evolution there, but no one will take me seriously or even support me without having gone through the collegiate initiation process first, even though it has really done little to spur my intellectual development. There must be a better way.


What’s bad for sharks is bad for all

30 03 2007

We’ve known for some time that large species are being eliminated at a rate that could essentially wipe them out, and yet little has been done to mitigate this problem. After Jaws came out, sharks were primarily hunted as trophies or as symbols of manhood, but during the 1980’s commercial fishermen were told to turn to sharks as an alternative for other fish on the decline. This, of course, backfired and sharks continued to suffer, all the while the atrocious practice of finning (cutting a sharks fins off and dumping the rest of the body back into the ocean, often still alive) went on to supply traditional remedies/cuisine to Asia. According to this LiveScience article, we’ve now reached the point were large sharks are no longer effective as apex predators in some areas (primarily the East Coast of the US), and smaller sharks and rays are no longer kept in check. In addition to the sick and dying fish, sharks eat other sharks and rays regularly, and now that the large sharks are gone the smaller ones are not kept in check and decimating their food supply, which will in turn lead to a population crash when their food runs out and a large swath of major marine predators will be gone.

Part of the problem is that we can detect the effects of reduced shark populations, but we have no idea how many there really are. Sure, sharks get some protection and we know their numbers are declining, but management plans are exceedingly lacking in population studies. Beyond the difficulty of figuring out a marine organisms population size, there doesn’t seem to be that much interest in sharks. Last fall, I went to one of the “big wheels” of the marine science department telling him I wanted to get involved with shark ecology and population studies, to which he replied “What are you ever going to do studying sharks?” There seems to be a realitively small group of scientists who study sharks, but not nearly enough to gather the type of data needed to protect the many species that are now in trouble.

Oodles of confusion, part II

30 03 2007

Yesterday I posted about a new paper in Nature which, through phylogenetic study, suggests that modern mammal lineages diversified earlier than once thought and the extinction of non-avian dinosaurs did not increase the lineages diversity. PZ, Larry Moran, and Mike Dunford have all covered this story as well, but there is one important facet of the study that I think is missing from many of the discussions about it popping up around the blogosphere. If the paper does accurately reflect what occurred to lineages that would lead to modern monotreme, marsupial, and placental mammal groups, this does not mean that there was no diversification of mammals after non-avian dinosaurs went extinct. Indeed, the paper itself states the following;

The supertree therefore contains no evidence that the diversification rate of the extant mammalian lineages increased soon after non-avian dinosaurs went extinct. Although there is strong palaeontological evidence that mammalian diversity, driven by a massively elevated rate of speciation, generally rose rapidly immediately after the K/T boundary, there is in fact no conflict between the palaeontological and neontological interpretations of the known facts. Most diversifications immediately after the K/T boundary were in groups such as multituberculates, plesiadapiforms and ‘archaic’ ungulates, as plots of the numbers of genera known in each sub-epoch indicate. These groups declined or went extinct early in the Cenozoic era and so are barely, if at all, represented in the phylogeny of living species. The continuing low rates of extant mammalian diversification through this period imply that the dearth of Palaeocene crown-group fossils is a real reflection of the low diversity of those clades. The low rates are also consistent with (but not direct evidence for) the hypothesis that extant lineages were inhibited in some manner by the diversity of the predominantly Palaeocene groups, and only started to diversify with the decline of the latter. However, like most other proposed competitive exclusion scenarios (for example, see refs 24, 25), this conjecture is based purely on the negative correlation of taxon diversities rather than direct evidence of exclusion.

While this may be a “minor” theme of the paper, I find this aspect of it particularly exciting. If the study is correct, then extant mammal lineages diversified once before the K/T extinction, but did not do so again until later when many of the other “archaic” mammal groups became extinct. Indeed, it almost seems like modern mammal groups could not catch a break, and if this holds up it would be extremely interesting to find out why now-extinct mammal groups were so successful while extant groups were not, and what caused such a reversal in fortune. Even forgetting about the K/T extinction for a moment, if mammals diversified long before the extinction, what led to this diversification? These are questions that certainly beg answers.

While the idea that extant mammals like opossums crawled out of the ash a little after the K/T extinction and led an unstoppable march of progress towards you and I is preposterous, I can’t see how the extinction of many groups of animals would not “set the stage” for further diversity and evolution. The process was likely more chaotic than previously thought, but it seems apparent that some (now extinct) mammal groups did diversify in the wake of the K/T extinction, although the reasons for this will require further investigation. I’m sure that there will be some debate over this paper for a long time to come, but hopefully paleontologists, paleoecologists, and those undertaking phylogenetic studies will be able to communicate each other to make sense of the fossil and genetic data. Either way, the extinction of the dinosaurs did mark a major landmark for mammals, and how all members of that group responded to the changes around them is something that will require much more study to ascertain.

Bininda-Emonds ORP, Cardillo M, Jones KE, MacPhee RDE, Beck RMD, Grenyer R, Price SA, Vos RA, Gittleman JL, Purvis A (2007) The delayed rise of present-day mammals. Nature 446:507-511.

Photo of the Day: Amur Leopard

30 03 2007

Here’s another one of my favorite shots of the Philadelphia Zoo’s Amur Leopard;

Amur Leopard

The leopard, as usual, was resting right in front of the glass, perfect to get some good profile shots. Unfortunately for me, however, there was a much more serious photographer (or at least his equipment looked much more serious) trying to get some photos as well, so I had to defer. The leopard wasn’t sure what to do with all this attention, however, and every so often would look from the other cameraman to me almost as if to say “Are you done bothering me yet?”

Giraffes: The next Icon of IDiocy

29 03 2007

There are few animals as utterly charming as the giraffe, but the question of just how it got its neck (and internal systems to support such an adaptation) has been a vexing one. I’ve been planning to write something on giraffe evolution for some time now, but I didn’t have the impetus to do so until I popped over to UD today and saw Dembski had posted a screed proclaiming that the question of how the giraffe got its next must lead us to “alternatives” to evolution. The article is wrong from the onset, and (as seems to nearly always be the case) Stephen Jay Gould already addressed this issue years ago.

Unfortunately, I returned Gould’s collection of essays Leonardo’s Moutain of Clams and the Diet of Worms to the library so I can’t quote directly from the article, but in the latter part of the book there is an essay dealing specifically with giraffes. As Gould correctly notes, many have used giraffes as a symbol of false Lamarckian evolutionary principles, the classic textbook treatment stating that Lamarck thought over generations the giraffe stretched its neck further and further to reach delicious leaves, thus passing on this trait to its offspring, but this treatment is far from accurate. The book Tall Blondes chronicles how the giraffe was (and even still is) an enigma while other creatures become more well-known, and thus few scientists gave it detailed treatments in their writings or used it as an example; too little was known about giraffes to make such a tactic prudent. From what I remember of the Gould essay, Lamarck only mentioned the giraffe in passing and Darwin initially referred to it not about its neck, but about the use of its tail as a flyswatter. Indeed, giraffes tails are so wonderful as flyswatters that at times they were hunted for their tails, which made traditional wedding gifts, and Darwin considered how such an anti-pest adaptation may allow animals like giraffes to inhabit more infested landscapes. Again, if I remember correctly, Darwin did discuss the giraffe in more detail in later writings, but primarily in response to criticisms from another scientists and not as a triumphant proof of evolution.

The short preview suggests that evolutionists either have to figure out exactly how the giraffe got its neck and other essential internal organs (sounds like the flagellum argument all over again) or embrace saltation, which would certainly not work given the necessity for integrated systems to be in place to allow the giraffes head to be up so high. Thus, the writer procliams, the intelligent design “alternative” wins out, and I would not be surprised if the giraffes neck was the next attempted “Icon of IDiocy”. For my own part, I’ve still got plenty of reading to do on extinct and extant giraffes, but hopefully soon I’ll have something more substantial here for you all.

Oodles of confusion

29 03 2007

There’s been quite a few news reports over the past 24 hours involving a new paper in the upcoming issue of nature entitled “The delayed rise of present day mammals.” The conventional wisdom is this; modern mammal groups were generally prevented from evolving and diversifying into the forms we would see post K/P extinction by the presence of dinosaurs. Once the dinosaurs were out of the picture, the mammals had lots of space and resources to evolve into a variety of forms. The new paper, however, suggests that modern mammal groups were already relatively diverse during the time of the dinosaurs (the paper states that this diversification occurred about 93 million years ago), but then placental mammal group diversity fell off, not to rise again until well after the K/P extinction.

While there is some amount of controversy surrounding the paper (being based on phylogenetic supertrees and some palentologists pulling the emergence dates for the mammal groups into question), the popular articles covering this story have certainly made things confusing. While many of the articles do mention that some mammal groups did diversify (only to lead to dead ends), the articles sport titles like “Dinosaur demise didn’t lead to new species” and don’t give readers the requisite background information as to what mammal groups existed during the time to get a good picture of what this study says occurred. This study also brings to mind something my paleontology professor discussed last semester (I wish I knew what paper/study he was referring to), in which the diversity of North American fauna dropped dramatically across the K/P boundary, warm-blooded and large animals (even mammals) faring worst of all. If I remember correctly, the professor stated there was only one surviving mammal group in North America, although until I find the study he was citing for myself I won’t put this forward as absolute fact. Even so, it does make sense; if North America was flash-fried by the impact of a meteor in the Yucatan, very little would survive. As I said, I am not an expert in these matters (so please correct me if I’m wrong), but in order to fully understand what happened to evolution through the K/P extinction we need not only to know what existed, but where and when (i.e. biogeography) and always be comparing the fossil evidence with the phylogenetic evidence.

I was also a bit puzzled by this inclusion into the ScienceDaily article on the topic;

The tree of life shows that after the MEE, certain mammals did experience a rapid period of diversification and evolution. However, most of these groups have since either died out completely, such as Andrewsarchus (an aggressive wolf-like cow), or declined in diversity, such as the group containing sloths and armadillos.

Andrewsarchus has long been a media-darling, despite the fact that the actual fossil material we have is exceedingly limited (the primary part being a skull, on display at the American Museum of Natural History). This beast (almost always striped like a tiger in life reconstructions) belonged to the Order Mesonychia (or Mesonychids, once thought to be the ancestors of whales), and was an angulate (hoofed-mammal), although there has been much debate over how closely related ungulate groups really are. While the Order Andrewsarchus belonged to became entirely extinct, the “agressive wolf-like cow” description does nothing but confuse. Andrewsarchus was not a cow, nor a wolf, but a variety of large carnivore that cannot be shoehorned into modern placental mammal groups, and referring to it as some sort of meat-eating cow certainly doesn’t do Andrewsarchus justice.

Like I said, while the study is interesting, I believe the treatment that it has gotten from many media outlets has been a little confusing (such is what you have [I’m assuming] non-scientists trying to cover such a story). Rather than a big paradigm shift, this study poses some new questions; why did placental mammal groups diversify, decline, and then diversify once more long after the dinosaurs became extinct? What sort of competition was there? Were modern mammal groups “held down” by other groups in the same way they weren’t allowed to diversify under the dinosaurs? If so, what caused this change that allowed the rise of modern mammal groups? Hopefully as more fossil material is collected and fine-tuning of phylogenetic study occurs, more on the oscillation of modern-mammal diversity will be illuminated, but until then it still is clear that the extinction of non-avian dinosaurs did leave the door open for mammal diversity to rise, even if it wasn’t among the lineages that would lead to extant taxa.

If I could talk to the animals….

29 03 2007

Zoos can be wonderful institutions of education and conservation, but more often than not it’s merely about entertainment, and this sentiment is nothing new. Check out this old short from Nick Park (of Wallace & Gromit fame) entitled “Creature Comforts”

The short has also been turned into a new(ish) series, featuring the same theme of real audio + claymation, and the trailer for it is below;