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Zoology 206

Fall, 2012


Posted by Bruce on October 20, 2011
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This site contains supplementary material for students in my section of Zoology 206 at Miami University.  It is designed to allow them to explore some of the most recent developments in evolutionary biology and to easily access material that may provide further insight into the topics covered in class. Comments are welcome throughout.

Note that this  is not the official site for the course.  Announcements, assignments, etc. will be posted on the course site in Niikha.

In this video from TEDMED 2012, Franziska Michor of Harvard University describes how very simple evolutionary processes apply to the etiology and treatment of cancer. The crux of the talk involves use of computer modeling of cancer as an evolutionary process can be used to infer drug dosing regimes that minimize the probability of resistance to the drug developing in tumor cells. As such, this is nothing new in evolutionary biology. However, she makes a more intriguing point, describing cancer as an evolutionary reversion to a single-cell paradigm within the context of a multicellular organism. At this point, such thinking may or may not have practical significance, but if nothing else, it is a nice intellectual connection between a fundamental development in evolutionary history (the rise of multicellularity) and modern disease processes.

Jerry Coyne on Evolution

Posted by Bruce on May 11, 2012
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Jerry Coyne, a long-time leader in evolutionary genetics, has become a public voice for evolution, particularly since the publication of Why Evolution in True . He also has a very active blog of the same name. This is a video of a lecture on the subject he recently gave at the Harvard Museum of Comparative Zoology, where he did his Ph. D. work under Richard Lewontin in the late 70’s.

Small Mammoth

Posted by Bruce on May 10, 2012
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The smallest mammal fossils, found on Crete.

Dick Lewontin on Biology

Posted by Bruce on May 9, 2012
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I haven’t viewed this one yet, but Dick is always provocative. Comments?

Svante Paabo on TED

Posted by Bruce on May 8, 2012
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If ever a Nobel prize is awarded for evolutionary biology, Svante Paabo should be a recipient.

Love Song of a Jurassic Cricket

Posted by Bruce on February 7, 2012
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Pretty cool – Gu et al., in the Proceedings of the National Academy of Sciences, have been able to infer the sound of a Jurassic katydid, based on microscopic examination and reconstruction of fossilized wings.

Lunar Video

Posted by Bruce on February 2, 2012
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OK, this has nothing to do with evolution, but it is neat – NASA video from the side of the moon we don’t see.

In 2008-9, Case Western Reserve University put on a series of lecture entitled “The Year of Darwin”. Speakers included such eminent scientists as Neil Shubin and Sean Carroll. It also included speakers from other areas, including Judge Jones, who presided over Kitzmiller vs. Dover School Board of Education in Pennsylvania in 2006. This was the first legal test of the constitutionality of Intelligent Design in public education. His decision was, I think, a remarkable one, which very clearly addresses and rules on the scientific and religious freedom issues that underlay the case.

Evolutions Top 10 for 2011

Posted by Bruce on January 1, 2012
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Tis the season for top 10 lists, and since I’ve been spending much of the past several months getting caught up on the current state of evolutionary biology, I thought I’d take a stab at producing such a list.  As I did so, some rough guidelines were

  1. The list is derived first and foremost from the peer reviewed literature of 2011
  2. A secondary concern is the extent to which reports in the literature were covered in the world of science journalism.
  3. The list does not include developments regarding the popular acceptance or rejection of evolutionary science.  To do so would take it out of the realm of established science (wherein I have a few qualifications) and into the domains of theology and belief (where I do not).

Finally, I did ask a few of my friends from the world of science for a few suggestions.  That generated one surprise, which is noted below.

So here goes:

  1. Neanderthals, Denisovans, and Modern Humans.  This story has been emerging for the past few years, involving the sequencing of the Neanderthal genome by Svante Paabo and colleagues, as well as their genetic analysis of the Denisovan thumb from Siberia, showing the existence of yet another homonid species that was contemporaneous with Homo sapiens.  The two major stories that put this at the top of the list for 2011 are the demonstration by Abi-Rached et al. that immune system genes from both Neanderthal and Denisovan man have introgressed into the genome of Homo sapiens, and the demonstration of extensive gene flow from Denisovans into modern man by Reich et al.
  2. Deciphering the Cambrian.  As all students of evolutionary history know, the sudden appearance of animals with backbones (indeed all of the biletaria) in the fossil record durning the Cambrian vexed Charles Darwin (and many others) tremendously.  This year saw two fascinating new developments, as well as a reasoned synthesis of where we stand in our understanding.  First, Paterson et al. provided evidence regarding the origin of compound eyes, showing that Anomalocaris, a stem group to the Arthropods, possessed compound eyes with over 16,000 facets.  Then, in a story that has received much attention (and is the subject of another post) Huldtgren et al. argue that early Edicaran fossils thought previously  to be developing animal embryos are in fact encysting protists.  Finally, Doug Erwin and colleagues gave us an outstanding overview of where we stand vis-a-vis the fossil record and the molecular clock, and provided an intriguing hypothesis regarding the role of micro-RNA’s in bilaterian evolution.
  3. Australophithecus sebida  An unreconstructed fly geneticist like me ventures into the world of human origins at his peril.  However, Science saw fit to highlight the work of Lee Berger and colleagues, who make the case that Australopithecus sediba is in fact a lineal ancestor of Homo sapiens.  Given the norms in physical anthropology, it is safe to say that we haven’t heard the last of this.
  4. The genome of the black plague  I may have missed things from the world of microbial evolution, but this one does stand out.  By sequencing the genome of plague bacteria recovered from remains of victims from the 1300’s, Bos et al. were able to show that the causative strain lies at the base of the phylogenetic tree of modern Yersinia pestis, both confirming that bacterium’s role as the causative agent of the medieval plague and suggesting that it is indeed ancestral to all modern strains.
  5. The human brain, the genome and repetitive DNA  Those of us who were trained in another era either did not learn about mobile and/or repetitive DNA or thought about it as an annoying distraction from the real meat of genetics (Barbara McClintock’s use of the term “controlling elements” notwithstanding).  We now know better.  Mark Batzer and his associates have continued their groundbreaking work on transposable elements in primates, showing that in fact nearly 2/3 of the human genome is transposon-related, my old friend John McDonald and his colleagues have provided evidence that the insertion and deletion of transposons has played an important role in the divergence of humans and chimpanzees, and Baillie et al. showed that somatic transposition of retroposons plays an important role in normal and abnormal brain function.
  6. Fine-tuning the end-Permian mass extinction  In my mind, the end-Permian mass extinction is one of the most fascinating events in evolutionary history, right up there with the Cambrian explosion.  As Doug Erwin argued in his wonderful 2008 book, it defies simple explanation (unlike the Cretaceous/Tertiary event).  Shen et al. have now narrowed the timing of the extinction to a period of less than 200,000 years and have shown conclusively that it occurred simultaneously in the terrestrial and marine worlds.  Their data are consistent with rapid warming due to carbon and/or methane release as the primary causative factor.
  7. Have we entered the Anthropocene?  OK, this moves into the science/society realm, and as we enter an election year in the United states, its inclusion on this list may be seen by some as political.  Nevertheless, I would argue that the question of whether human alteration of the global environment has in fact propelled the Earth into a new geological era.  The Economist, hardly a bastion of liberal journalism, did a very thoughtful piece on the subject, and The Philosophical Proceedings of the Royal Society A devoted a theme issue to the subject.  For those of you teaching paleontology, what would you think of asking your students to speculate on what the geological signal of the past several thousand years might look like a million or so years in the future?
  8. Origins of feathers and birds  No list like this would be complete without at least one mention of dinosaurs.  So here goes.  The dispute rages on as to the ancestry of birds – while it was clearly reptilian, whether it was Archeopteryx or something else remains to be determined. A report from Xu et al. suggested Xiaotingia as an alternative, however Lee and Worthy disputed that claim.  And fossils in amber have revealed more about dinosaur feathers, including evidence regarding color and the evolution of their function for flight as early as the late cretaceous.  Once again, since dinosaurs are involved, I’m sure we’ll be hearing more
  9. Not your dinosaurs’ cycads  I’m not a botanist, but one thing that stuck from my time in Florida was that cycads are in fact “living fossils”, a taxon that has dwindled since its heyday in the Jurassic/Triassic period of ca. 165 million years ago.  Now Nagalingum et al. have shown that in fact the last common ancestor of living species dates to only about 12 MYA, suggesting a rediversification of the taxon beginning in the late miocene.
  10. How the penis lost its spine(Courtesy of Yoshi Tomyasu) OK, this is the one that was suggested to me by a colleague  McLean et al. turned what seemed to be a rather arcane subject, losses of regulatory sequences in humans relative to chimpanzees, when they found that one such loss was that of a sequence necessary for the formation of a penile spine.  They further demonstrated that the potential for such formation may still exist in the human genome, and they speculate that the loss is associated with increased pair bonding and paternal care in humans.  Sociobiology lives on!

Well that’s it.  Please feel free to tell me what I’ve missed (or what really doesn’t belong here).  All told, it’s been a good year.  Darwin and Wallace would be proud of their legacy.

Happy New Year!

Search for Precambrian Animals

Posted by Bruce on December 27, 2011
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It’s been a good month of December for devotees of the Cambrian “explosion”. First, Doug Erwin and his colleagues published an excellent paper, bringing together the paleontological record, sophisticated molecular clock analyses, and the latest in Evo-Devo research (including analysis of both mRNA and miRNA in the developmental toolkit of metazoa) to create a fascinating (albeit somewhat speculative) overview of the current state of our understanding of evolution during the Ediacaran and early Cambrian. Then, as a Christmas treat, Science, in its December 23 issue, published this paper, by Therese Huldtgren and colleagues, in which they use advanced microscopy to reach the conclusion that some fossils from China, hitherto believed to be examples of early metazoan embryos, are in fact much more likely to be clusters of protist cells, thus moving them outside of the metazoan crown group.

N. J. Butterfield, in a Perspective piece accompanying the paper, summarizes the significance of the paper as follows:

Wherever the Doushantuo fossils eventually end up, it will clearly not be within “crown-group” Metazoa. Does this then mean there were no early Ediacaran animals? Not at all. No fossil assemblage, however well preserved, provides a full account of past diversity, particularly when the local conditions are so extraordinary as to fossilize nuclei and other intracellular constituents. The “exceptional” fossil record is, by any measure, woefully unrepresentative and incomplete (15). When it comes to assessing the first appearance of early, difficult-to-preserve animals, the most reliable signal will be found in the conspicuous coevolutionary features that they have induced in other organisms with higher preservation potential (16). Early Ediacaran microfossils—with or without included “embryos”—may no longer include animals, but their dramatic radiation clearly marks the arrival of this revolutionary new clade.

So how does this get translated into the popular media?

The first is from an online site devoted to state politics; the second from the Voice of America. I invite you to read one or both of these articles – they are actually not bad. However, both headlines no doubt suggest to some that the new findings in some way threaten the entire theory of evolution. Quite the contrary – what the authors did was to test a very specific hypothesis – that the Doushantuo fossils are the remains of early metazoans – by applying new methods, and in so doing appear to have disproven that specific hypothesis. This is in fact what happens in the normal course of science. Most experimental scientists (including me) have had similar experiences. However, we also recognize that to a great extent, scientific progress is dependent on such testing, and as it occurs, many hypotheses will be found wanting.

So again, it’s been a great month for the Cambrian. And no, the theory of evolution has not been upended.