Thursday, November 27, 2008

Tiktaalik in the Year of Darwin

A great video lecture for the holiday!


Wednesday, November 19, 2008

On Human Evolution

Is our species, Homo sapiens, still evolving? No doubt all of you have wondered about this at some point (unless you don't believe in evolution, in which case you have a different puzzle to scratch your heads over). And with human technology constantly coming up with ways to allay any selective pressures, it is easy to think that we've stopped evolution in its tracks as far as our own species is concerned. But have we, really? Is it even possible to pause evolution? Last month, Seed magazine had an interesting article, "How We Evolve" describing the state of current knowledge about human evolution and how modern genomics tools are helping to shed light on this question:

When the previous generation of life scientists was coming up through the academy, there was a widespread assumption, not always articulated by professors, that human evolution had all but stopped. It had certainly shaped our prehuman ancestors — Australopithecus, Paranthropus, and the rest of the ape-men and man-apes in our bushy lineage — but once Homo sapiens developed agriculture and language, it was thought, we stopped changing. It was as though, having achieved its aim by the seventh day, evolution rested. "That was the stereotype that I learned," says population geneticist and anthropologist Henry Harpending. "We showed up 45,000 years ago and haven't changed since then."

The idea makes a rough-and-ready kind of sense. Natural selection derives its power to transform from the survival of some and the demise of others, and from differential reproductive success. But we nurse our sick back to health, and mating is no longer a privilege that males beat each other senseless to secure. As a result, even the less fit get to pass on their genes. Promiscuity and sperm competition have given way to spiritual love; the fittest and the unfit are treated as equals, and equally flourish. With the advent of culture and our fine sensibilities, the assumption was, natural selection went by the board.

So what can genomics tell us?

John Hawks started out as a "fossil guy" studying under Milford Wolpoff, a paleoanthropologist who is the leading proponent of the faintly heretical multiregional theory of human evolution. Coming to genetics from such a background has perhaps given Hawks the stomach to wield unfashionable hypotheses. In December of last year, he, Harpending, and others published a paper whose central finding, that evolution in humans is observable and accelerating, would have been nonsensical to many geneticists 20 years ago. Up to 10 percent of the human genome appears to be evolving at the maximum rate, more quickly than ever before in human history.

Go read the rest of the story. Especially the frightening scenarios towards the end.


Friday, November 7, 2008

How plastic is your brain? Perhaps you'll find out in the Bio Colloquium today

Well, you will at least learn about neuroplasticity in species that do have more plastic brains then humans. As usual, the seminar will be in Science II, Room 109, starting at 3:00 PM. Be there!

Hormonal and environmental control of neuroplasticity

Dr. Christy Strand

Department of Biological Sciences

California Polytechnic State University


Many people have the incorrect notion that the brain is a relatively static organ or that it can degenerate, but not grow. The study of neuroplasticity encompasses changes in the brain from the cellular and molecular level to the gross anatomical level (e.g. changes in the sizes of brain regions). In adult male songbirds, the brain regions that control singing behavior grow seasonally, providing a means to investigate the regulatory mechanisms and the functional consequences of adult neuroplasticity. Specifically, during the breeding season, these regions are larger than at other times of the year due to increases in neuron number and size or decreases in density. Numerous factors that change during the breeding season have been implicated in regulating the growth of these brain regions, most notably, testosterone (T), photoperiod and singing behavior. I use a comparative approach to investigate the effects of T, photoperiod, singing and other social or environmental factors on song control region growth and new neuron incorporation in the adult male songbird brain. I also investigate how environmental, physiological and hormonal factors affect neurogenesis and neuroplasticity in adult snakes and lizards. This integrative approach provides a more complete analysis of the contributions of various factors to the regulation of neuroplasticity in vertebrate animals.


When a Cutthroat meets a Rainbow

ResearchBlogging.orgSubmitted by Christopher Clapp for the Evolution class.

The introduction of a known species of rainbow trout into a native population of cutthroat trout and the consequences of their contact within their environments is the focus of this study. The interaction of these two species has resulted in their study of subsequent progeny shows hybridization of the two, and thus a decline of the natural populations of cutthroat trout. The implications of this hybridization will show throughout subsequent generations, considering what is known of the native species. Metcalf uses mitochondrial and nuclear markers to determine the levels of crossing of the two species based on the nature of homozygous or heterozygous allele category. These populations of hybridization were evaluated due to the known history of the streams being studied. Trout being separated by natural geographic restrictions such as natural waterfalls or by human chemical treatment conducted in the past forms for a basis of evaluation.

The successful progeny of hybridization between the two locations is evident; however there are differences between the chemically treated streams and the naturally restricted. Interestingly enough, results show that there is a trend of the cutthroat nuclear trout alleles being more prevalent beyond the upstream barrier as expected. The mitochondrial alleles were more prevalent within the hybrid or rainbow species within the areas that direct contact has been introduced within the natural barrier stream. Our study supports the notion that natural waterfall barriers provide a refuge for pure native cutthroat trout genomes across their range (Metcalf et al 2008). In the Cony Creek population, which was subject to chemical treatment in 1984, the nuclear markers were more prevalent within the cutthroat species. This bias toward the pure cutthroat is speculated to be due to the chemical treatment of the streams to eradicate the rainbow trout populations amidst restocking the cutthroat population (Rosenlund et al. 2001). Why is the case? The allele frequency distributions and disequilibrium values suggest that hybridization has been underway for longer in Cony Creek than in Graneros Creek according to Metcalf, et al (2008). I seem to feel that introducing a chemical treatment to an environment that focuses directly on one specific species allows for a re-founding of the native species. However, there findings show the invasiveness nature of the rainbow species. Over time the cutthroat nativity would be eradicated regardless of natural barrier or chemical treatment. This poses two major problems for the environment with regard to the natural species, and the changes of fish populations within streams. The introduction of new fishes for conservation strategies not only directly affect the native population, it affects the ecosystem among other animals within the environment as well. If an aggressive population of trout that is more successful than the native, the impact on resources for the community will also be affected; the environment will be in disequilibrium.

We seem to have two intrusions of the human hand into an environment, one for the introduction of the rainbow, and one to eradicate the rainbow trout species. The study shows that there is greater fitness among the hybrids. The cross between a rainbow trout female and a cutthroat male resulted in a shorter time to hatching and the progeny had a faster growth rate and a greater abundance of yolk at hatch and emergence than the hybrids of the reciprocal cross (Hawkins and Foote, 1998). Nevertheless, the two species form a system of fertility to study the hybrid selection based on natural selection and/or the effects of human based effects in the form of conservation strategies. What is this to say for the natural selection of the hybrid species or the difference between the two, and what are the effects of the introduction on the environment? Historically fishless lakes and streams have been associated with declines in amphibians, changes in invertebrate communities and changes in nutrient cycling (Knapp and Matthews, 2000). However, there is always something to be learned from the development of a new species. The selection and fitness over such a short amount of time is interesting to evaluate within the two species.

It seems to be that the rainbow trout are invading the natural species of cutthroat, and have an effect on the native species. Why are the rainbows so successful at invading this species? What are we to learn of the intrusion of populations by human hands? Either way, I agree with Metcalf in the capacity that the evaluation of the new hybrid species will give insight into long-term conservation strategies. It seems that if we limit the studies and only hold them as individuals there will always be contradiction of the results. Conservation methods and steps may be a bit naïve if you only consider one method to achieve one result. By not considering the whole picture, we are increasing our opportunity cost, and thus the potential for loss.


Denise K. Hawkins, Chris J. Foote (1998). Early survival and development of coastal cutthroat trout (Oncorhynchus clarki clarki), steelhead (Oncorhynchus mykiss), and reciprocal hybrids Canadian Journal of Fisheries and Aquatic Sciences, 55 (9), 2097-2104 DOI: 10.1139/cjfas-55-9-2097

Roland A. Knapp, Kathleen R. Matthews (2000). Non-Native Fish Introductions and the Decline of the Mountain Yellow-Legged Frog from within Protected Areas Conservation Biology, 14 (2), 428-438 DOI: 10.1046/j.1523-1739.2000.99099.x

J. L. Metcalf, M. R. Siegle, A. P. Martin (2008). Hybridization Dynamics between Colorado's Native Cutthroat Trout and Introduced Rainbow Trout Journal of Heredity, 99 (2), 149-156 DOI: 10.1093/jhered/esm118

Rosenlund BD, Kennedy C, Carnowski K. 2001. Fisheries and the Aquatic management of Rocky Mountain National Park. (US Dept. of the Interior).


Tuesday, November 4, 2008

Endorsing a presidential candidate through the lens of Science

How can you argue (rationally) against this?

Far more important is this: Science is a way of governing, not just something to be governed. Science offers a methodology and philosophy rooted in evidence, kept in check by persistent inquiry, and bounded by the constraints of a self-critical and rigorous method. Science is a lens through which we can and should visualize and solve complex problems, organize government and multilateral bodies, establish international alliances, inspire national pride, restore positive feelings about America around the globe, embolden democracy, and ultimately, lead the world. More than anything, what this lens offers the next administration is a limitless capacity to handle all that comes its way, no matter how complex or unanticipated.

Sen. Obama's embrace of transparency and evidence-based decision-making, his intelligence and curiosity echo this new way of looking at the world. And that is what we should be weighing in the voting booth. For his positions and, even more, for his way of coming to them, we endorse Barack Obama for President of the United States.

[read the rest of the endorsement by Seed: Barack Obama for President]

And then, if you haven't already done so, go VOTE!!


Sunday, November 2, 2008

My Inferiority to Scrub Jays

ResearchBlogging.orgRudy Cerda confesses for the Birds & Reptiles class. Elsewhere, Claire Go has blogged about the same study!

Western Scrub Jay with peanutAs much as I like to think that I plan according to future needs, such as time management in order to write papers, study for exams, and even complete this blog, I know I can only operate under pressure. However, when planning for “essential” needs such as food or snacks, I save the best for last or at least hide some away in case I may need or want any later. For example, I’ll always leave my favorite flavor of candy last because I want that flavor to linger for awhile, or I’ll eat the crust first on a slice of pizza because I’d rather wait to take in the gooey, cheesy goodness on the other side of the piece... but enough of my planning for less than crucial things. Aphelocoma californica, better known as the western scrub jay, may exhibit planning for the future in perhaps a more critical way than I do.

According to the Bischof-Köhler hypothesis, only humans are able to disconnect themselves from their current motivation and plan for the future. Apparently other animals do not have crystal balls to predict their future needs and any future-oriented behaviors are due to either patterns of fixed actions or prompted by current motives. There have been previous studies involving rats and pigeons that have that have only supported the Bischof-Köhler hypothesis by the animals solving tasks involving the future, however, the “future” was only a very short time period. Also, primates have also shown the ability to take actions based on future consequences; however, the motives or reasons for the actions have not been differentiated.

Scrub jays are relatively abundant around campus and I frequently observe jays bouncing around with nuts in their beaks. Every so often I’ll see one that is particularly sneaky and decides to stash its food away as if its saying, “You’re not going take this from me,” or preparing for the budget cuts around campus (or perhaps they can sense the inevitable collapse of the economy!) that may take away their beloved seeds. Raby et al also noticed this behavior in western scrub jays and hypothesized that the jays store food based on anticipation of future need. They predicted that the jays would do this in an area in which they have learned they will be hungry and by storing a particular food item in a place where they know it will not be available.

To test this hypothesis, a total of eight western scrub jays were placed in two different compartments on alternate mornings for six days. In one compartment they were given breakfast and the other they were not. After this training, the birds were given food unexpectedly given food to either eat or store in the evening. If the birds were capable of planning for the future, they would store relatively more food if they were in the compartment in which they were not given breakfast because they would anticipate being hungry the next morning… psychics! And the results displayed their fortune-telling abilities as they stored significantly more food (more pine nuts than powdered nuts) in the compartment in which they had not received breakfast.

To ensure the hoarding of the pine nuts was not associated to a specific compartment, two different types of food were given; a specific food was given in a specific compartment and both types in a third compartment. If the jays had a preference of a certain food they would store more of the “other” food rather than the “same” food when offered to store the food away. The results supported the hypothesis of preferential storing food.

Often I find it hilarious when I see a jay hopping around with something in its beak, it hides the food and about 30 seconds later it’s looking for the food it just sneakily stashed away! Some planning if it can’t even remember where it put its food! In the Raby study, it was stated that the birds were slightly hungry, so perhaps those greedy jays around campus are just playing dumb because they aren’t hungry at that moment in order to fool everyone and plot their takeover of campus and my apartment complex! Well, it’s nice to know that my planning skills may be significantly inferior to a scrub jay’s.


C. R. Raby, D. M. Alexis, A. Dickinson, N. S. Clayton (2007). Planning for the future by western scrub-jays Nature, 445 (7130), 919-921 DOI: 10.1038/nature05575


Saturday, November 1, 2008

Convergence of the Death Adder with Viperidae

Common death adder (Acanthophis antarcticus)Submitted by Brandon Williams for the Birds & Reptiles class.

In a study of the Australian death adder (Acanthophis antarcticus), a member of the Elapidae, Richard Shine observes the convergence of the snake with the Viperidae (Shine 1980). There are no vipers that live in Australia, yet the death adder resembles vipers much more so than other members of the elapids. Shine hypothesizes that the sit-and-wait ambush hunting techniques select for similar adaptations in vipers and death adders. Most elapids are more active searching foragers.

In many ways Shine shows how death adders are adapted in similar ways to vipers rather than their elapid cousins. Death adders feed mostly on ectotherms as juveniles and switch to endotherms as adults. Death adders have a shorter stouter body than most elapids and a pronounced head. A. antarcticus have a delayed sexual maturation and a corresponding slow growth rate. The delayed maturation probably evolved after the ambush hunting strategy, which tends to allow for high survivorship because that leaves less opportunity for predation on the snakes. A. antarcticus has a unique adaptation for ambush hunting which is completely absent in all other elapids, yet is found in nine different vipers. This adaptation is caudal luring; using the thin, yellow wriggling tip of their tail as bait for prey. All of these adaptations point to convergence of the death adder with vipers. The reason for this is the ambush hunting technique.

Shine also posits that because just over half of mature females were found not to be reproductive that female death adders reproduce every other year. He was probably correct, however there could be some genetic or another unseen reason why many of the females were non-reproductive. Testing his hypothesis could be done. He could collect live female specimens of mature size during the breeding season, tag them with a number, noting whether they were reproductive or not, and let them go. Then over the next few breeding seasons he could collect female death adders that had been tagged and note whether the ones that were specifically reproductive last season were non-reproductive the following season. Over a few seasons he could see how consistent the data was with his every other year hypothesis.


Shine, R. 1980. Ecology of the Australian Death Adder Acanthophis antarcticus (Elapidae). Pp. 281-289. Evidence for Convergence with the Viperidae. Herpetologists' League.



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