Wednesday, October 29, 2008

A Bite of Beta-Carotene for Better Twitterpation

Submitted by Pedro Garcia for Evolution

House Finch.jpgScarlet Macaw.jpgPink Flamingo.jpgAmerican Kestrel.jpg

ResearchBlogging.orgBirds, birds, and more birds, with over 10,000 species of birds well known and classified, one can get an array of different colors which would make even the most non-bird lover’s staring in awe. With some species having such intricate combinations of reds, yellows, greens, and blues, (such as the scarlet macaw of South America) one might ask, “Why do they have such vibrant and magnificent plumage?” (or something along those lines). It’s a well known fact that skin and feather color (yellows and reds) is linked with carotenoids in the body. One well known example is the Caribbean flamingo, known for its brightly reddish/pink color. This species of bird gets its color from the high intake of beta-carotenes obtained from its diet of crustaceans and algae. But why? What good is it to be so brightly colored? One might even think that such bright colors would be a sort of bull’s eye for predators as if saying “Hey, you…the one with the sharp teeth…I’m over here!” Well, in short, it can all be explained by loosely quoting the hip hop song… “it’s all about sex, baby!”

That’s right, ongoing research has been linking brightly colored plumage in birds to…well, sex! This is the not-so-PG stuff that Darwin didn’t really talk about in his book (at least not directly), however it is merely the process of evolution at work. Researchers Negro, et al, (2002), have gone even more in depth concerning the correlation of plasma carotenoid-dependent skin color in relation to sexual selection. Their work consisted of analysis of brightness of color, not in the feathers, but, in the cere, lores, and tarsi of the small falcon the American Kestrel (Falco sparverius) along the time scale of mating season to hatching of offspring. As stated in the article, research has shown that color of plumage in birds does have an effect on sexual selection in brightly colored birds (Negro, 2002). As stated earlier, the brightness of plumage (specifically reds and yellows) is dependent on the amount of carotenoids found in the body; and beta-carotene is taken in directly from food source. Simply put, female birds choose the male with the brightest plumage because he is the one that can successfully obtain the most food, thus passing on the “better” genes to the offspring. As said before, it’s the process of natural selection at work.

Although there has been much research on sexual selection and plumage color, this article delves in even further and tries to find a correlation with skin color in birds as a function of sexual selection. It seems that, as hypothesized before, there is a brighter skin hue during the mating season. However, what came next seemed to be of even greater interest. It seems that, at least among American Kestrels, the “brightness” of the skin color began to fade as soon as the mating season ended. This was directly linked with a reduction in plasma-carotenoid levels (Negro, 2002). It is believed that the reduction occurs as a trade-off between sexual selection (during mating season) and maintaining better health (post-mating season). Since the bright coloration is no longer needed after mating, it would seem that a reduction in plasma-carotenoids would allow for the carotenoids to assist in other health-related body functions (such as anti-oxidants aiding in the reduction of oxidative damage by free radicals).

One concern I have with research is the methodology used for the experiments. All subjects were captive Kestrels from the “Avian Science and Conservation Center of McGill University, Canada…” which were fed a consistent diet of “…day-old cockerels” which were carotenoid-rich (Negro, 2002). This brings up my concern that the Kestrels were not mimicking natural processes, thus adding, in my eyes, a great amount of tolerance and bias to the results. It should be noted that the author does state that they have “previously shown that variation in plasma carotenoids during the mating period (April) was not attributable to diet, parasites or androgen levels” (Negro, 2002). Ideal settings that would eliminate this tolerance would include plasma collection of marked Kestrels in the wild throughout a series of mating and fledging seasons.


J. J. Negro, G. R. Bortolotti, J. L. Tella, K. J. Fernie, D. M. Bird (1998). Regulation of integumentary colour and plasma carotenoids in American Kestrels consistent with sexual selection theory Functional Ecology, 12 (2), 307-312 DOI: 10.1046/j.1365-2435.1998.00176.x


On McCain/Palin's appalling contempt for science and learning

Trust Christopher Hitchens to lay it out in choice words:

In an election that has been fought on an astoundingly low cultural and intellectual level, with both candidates pretending that tax cuts can go like peaches and cream with the staggering new levels of federal deficit, and paltry charges being traded in petty ways, and with Joe the Plumber becoming the emblematic stupidity of the campaign, it didn't seem possible that things could go any lower or get any dumber. But they did last Friday, when, at a speech in Pittsburgh, Gov. Sarah Palin denounced wasteful expenditure on fruit-fly research, adding for good xenophobic and anti-elitist measure that some of this research took place "in Paris, France" and winding up with a folksy "I kid you not."

It was in 1933 that Thomas Hunt Morgan won a Nobel Prize for showing that genes are passed on by way of chromosomes. The experimental creature that he employed in the making of this great discovery was the Drosophila melanogaster, or fruit fly. Scientists of various sorts continue to find it a very useful resource, since it can be easily and plentifully "cultured" in a laboratory, has a very short generation time, and displays a great variety of mutation. This makes it useful in studying disease, and since Gov. Palin was in Pittsburgh to talk about her signature "issue" of disability and special needs, she might even have had some researcher tell her that there is a Drosophila-based center for research into autism at the University of North Carolina. The fruit fly can also be a menace to American agriculture, so any financing of research into its habits and mutations is money well-spent. It's especially ridiculous and unfortunate that the governor chose to make such a fool of herself in Pittsburgh, a great city that remade itself after the decline of coal and steel into a center of high-tech medical research.


With Palin, however, the contempt for science may be something a little more sinister than the bluff, empty-headed plain-man's philistinism of McCain. We never get a chance to ask her in detail about these things, but she is known to favor the teaching of creationism in schools (smuggling this crazy idea through customs in the innocent disguise of "teaching the argument," as if there was an argument), and so it is at least probable that she believes all creatures from humans to fruit flies were created just as they are now. This would make DNA or any other kind of research pointless, whether conducted in Paris or not. Projects such as sequencing the DNA of the flu virus, the better to inoculate against it, would not need to be funded. We could all expire happily in the name of God. Gov. Palin also says that she doesn't think humans are responsible for global warming; again, one would like to ask her whether, like some of her co-religionists, she is a "premillenial dispensationalist"—in other words, someone who believes that there is no point in protecting and preserving the natural world, since the end of days will soon be upon us.

Go read the rest. Then VOTE (sorry I can't) to make sure these people aren't in charge of your country for much longer!

Note, however, that common usage of names notwithstanding, Drosophila are not fruit flies (as you should know even if Hitchens doesn't - if you've taken Entomology). Palin was referring to a study of the olive fruit fly (pictured above), which is a true fruit fly (Tephritid), as well as a serious crop pest right here in California. Which makes her remarks even more bizarre because she was attacking applied research of considerable economic significance - research that many a farmer might care about even more than us urban elites pursuing basic research!! Clueless in so many ways...

[Hat-tip: onegoodmove and Evolgen]


Monday, October 27, 2008

Marking a quarter century of living and fighting with HIV

Scientific American has a special report out on: HIV--25 Years Later]. Check it out! Here's the editor's introduction:

In 1983 and 1984 scientists established that HIV (the human immunodeficiency virus) causes AIDS, which had recently begun cropping up in gay men in California and New York. The discovery quickly led to predictions that a preventive vaccine would soon be on tap. Similarly, in 1996, after powerful drug combinations began forcing HIV down to undetectable levels in the blood, prominent HIV researcher David D. Ho of the Rockefeller University voiced optimism that attacking the virus early and hard could prove curative.

Yet neither a vaccine nor a cure has materialized. Indeed, the most promising vaccine prospects have failed. And when aggressive treatment stops, the wily virus comes roaring back.

Where do we go from here? Scientific American asked two leading HIV researchers to address the biggest scientific challenges facing the field today: Is finding a vaccine even possible? And what, exactly, would it take to rid a person’s body of HIV and thus effect a cure? Their frank, thought-provoking answers follow.

And if you want to read a first hand account from the early days of what it was like to deal with the beast in the field, my favorite is Abraham Verghese's memoir of the period he spent as a doctor in the South (not those coastal cities) when HIV first hit small-town communities: My Own Country: A Doctor's Story.


Darn those scientists, confounding our politics again!

Unbelievable!! This is the leadership we are supposed to look forward to?!

As someone who came to the US because of the opportunities this country offered to pursue scientific research, and having seen science get bipartisan lip service (at least) over the past 4 presidential election cycles (when I have been here), despite the decline in science funding over the past 8 years, I find it really bizarre to see this "team of mavericks" tilting against the windmills of science in this fashion! First it was McCain railing against "pork-barrel" earmark funding to study the genetics of grizzly bears (a very successful project, btw, that he had actually voted for, before turning it into a convenient flogging-horse on the campaign trail), and now Palin takes on the iconic model organism of modern genetics, Drosophila!! Talk about clueless chutzpah, bashing research on the very organism which has yielded, among myriad other insights, important clues about autism, the cause she claims she would fund by cutting off these "earmark" projects!! But, as has been clear from the day she joined the ticket, and as Rachel Maddow demonstrates yet again, this hockey-mom continues to operate in a completely irony-free zone - how can one make fun of her when she embodies the joke so completely? (remember how people chuckled when someone initially suggested that she had foreign policy expertise because of Alaska's proximity to Russia; until she actually took that line seriously and ran with it?)

Science - cutting-edge basic science - has surely been one of the defining characteristics of this country's global leadership over the past half-century or more, no?! Why do these "mavericks" now suddenly think it is ok to throw that away, and that they will win more votes if they bash science and scientists? I've wondered about the curious dichotomy in this culture, where science and technology provide the basis of so much of everyday life, yet science and scientists, and intellectuals in general, are feared/reviled as nerds/dangerous elitists. Is the anti-intellectual strain in this society so strong that McCain/Palin can drum up a few more votes to win this election by continuing to bash science, and further entrench the age of american unreason? Please tell me that is not the case, that things haven't gone that far wrong... or should I be packing my bags as another soon-to-be-unwanted scientist who has been wasting his life and taxpayer money studying birds??!! While remaining a foreigner, to boot!!


Sunday, October 26, 2008

On the early evolution of cells

ResearchBlogging.orgSubmitted by Brandon Williams for the Evolution class.

In this article, Carl Woese provides a theory on the early evolution of cells. Woese posits that it is necessary to go beyond classic Darwinian thinking of Vertical Gene Transfer (parent to offspring). He believes that Horizontal Gene Transfer (HGT) played a more crucial role in the early development of cells; that is until each of the three branches of life (Bacteria, Archaea and Eucarya) reached their Darwinian Thresholds. This threshold is a point where the cells of random RNA and proteins have finally reached a level of complexity that they have become a “species” and Vertical Gene Transfer can take over. Before that, cells traded genetic material with each other, evolving as a community.

I commend Woese for attempting to push us past the thought of endosymbiosis. While endosymbiosis may have occurred, the two cells that combined had to have been fully evolved cells that functioned without each other before the joining. Careful consideration to his theory needs to be taken to understand how much of translation and transcription was evolved before bacteria, archaea, and eukaryotes emerged. The wide spread similarities and differences point to some truth in this.

Woese may have a better explanation than endosymbiosis as to how archaea, bacteria and eukaryotes evolved past their Darwinian threshold through HGT; however, he still cannot explain how those cells could initially evolve the genomes (albeit small) to trade parts with in the first place. He posits that translation existed before transcription or genome replication. RNA dominated and proteins were made, transcription completed evolution after each Darwinian threshold, and genome replication came third. I find it interesting yet hard to believe that nucleotides formed by themselves, without a metabolic pathway already in place, and in enough numbers to form RNAs capable of translating proteins. Enough amino acids would have to exist also and Woese gives no explanation for their appearance or the fact that they are conveniently in close proximity to the RNAs. I also find it hard to believe that such an incredible amount of nucleotides and amino acids existed to support enough primitive cells containing RNA and protein that were able to trade with each other, and that these ancient cells would survive long enough to reach a Darwinian threshold.

In conclusion, Carl Woese’s theory could have serious implications on our idea of the early evolution of cells when before we were content to recite “endosymbiosis” and leave it at that. However it still leaves us glaring at what we don’t know and may never know.


C. R. Woese (2002). On the evolution of cells Proceedings of the National Academy of Sciences, 99 (13), 8742-8747 DOI: 10.1073/pnas.132266999


Socially learned foraging behaviors in wild black bears

ResearchBlogging.orgAndrew Mora offers a review of the Biology department seminar by Rachel Mazur.

The American Black Bear, Ursus americanus, is currently the only species of bear in the state of California. In a fascinating presentation by Rachel Mazur, pictures and videos were used to depict the beauty of these bears in their natural and not so natural environments; the latter being bears foraging for food in developed areas of the national parks including getting food out of trash cans, cars, etc.

DSC_4100.jpgAccording to Mazur, these bears are especially hungry during the months of March and April. During this time, a bear is either termed by Mazur to be a wild foraging bear, which consists of eating grasses, roots, insects from shredding logs etc., or they can be food conditioned bears, which consist of getting their nutrition from developed areas, or humans.

Research by Mazur finds that bears have traits for social learning and the most critical times of a bears learning process is during the first year when they are in constant contact with their mother (Mazur, 2008). Three separate hypotheses were compared to describe how these bears are learning to become food-conditioned to developed areas. The first is that bears inherit these behaviors from their mothers and can be predicted (Mazur, 2008). The others include bears learning individually (that is, without the help of the mother) and transmitted learning from sow to cub (Mazur, 2008).

The methods used for this experiment were efficient in that homogeneity was taken into consideration. Therefore five variables were taken into consideration including park, sow identity, sow behavior, rearing method and cub outcome (Mazur, 2008). The two national parks which Mazur encouraged everyone to visit include Sequoia National Park and Yosemite National Park. From showing clips of a movie on this research, it was evident that many years of hard work by numerous staff was done to work with these bears and monitor their statuses.

Mazur stated that she was very pleased with the results that they came across. An easy to read table of her results shows the number of sows that they started with (23 food conditioned and 9 wild), the rearing methods of these sows (rearing in wild or food-conditioned rearing), and the outcome of the cubs once separated from their mothers (Mazur, 2008).

Conclusions made by Mazur asserted that rearing method had a highly significant effect on the cub outcome (Mazur, 2008). If a cub was reared food-conditioned, it was much more likely to be food-conditioned once separate from its mother. That being said, the last hypothesis stated by Mazur was seen to be the most accurate: that bears become food-conditioned through social learning.

In both seminar and paper, Mazur stated that there are numerous implications for the work that has been done. She posed a question to the room regarding the bear’s possibility of creating culture and even tradition in our national forests with these new food-conditioned characteristics (Mazur, 2008). What I found beneficial in this work is the implication that food-conditioning in developed areas in our national forests do not necessarily imply adaptive strategies of these Ursus americanus, but may very well be falling into an ecological trap (Mazur, 2008). I also found it interesting for her to note that science and management have recently become less taboo as a pair in the scientific world.


R MAZUR, V SEHER (2008). Socially learned foraging behaviour in wild black bears, Ursus americanus Animal Behaviour, 75 (4), 1503-1508 DOI: 10.1016/j.anbehav.2007.10.027


Passing gas relieves pressure...

Blood pressure, that is! Yes! Who knew:

A smelly rotten-egg gas in farts controls blood pressure in mice, a new study finds.

The unpleasant aroma of the gas, called hydrogen sulfide (H2S), can be a little too familiar, as it is expelled by bacteria living in the human colon and eventually makes its way, well, out.

The new research found that cells lining mice’s blood vessels naturally make the gas and this action can help keep the rodents’ blood pressure low by relaxing the blood vessels to prevent hypertension (high blood pressure). This gas is “no doubt” produced in cells lining human blood vessels too, the researchers said.

“Now that we know hydrogen sulfide’s role in regulating blood pressure, it may be possible to design drug therapies that enhance its formation as an alternative to the current methods of treatment for hypertension,” said Johns Hopkins neuroscientist Solomon H. Snyder, M.D., a co-author of the study detailed in the Oct. 24th issue of the journal Science.

[via The Stink in Farts Controls Blood Pressure | LiveScience]

I wonder if this provides any basis for the use of black salt as recommended in Ayurvedic medicine for lowering blood pressure. Black salt contains H2S, and does help relieve intestinal gas and heartburn, but I don't know if it can actually get into blood vessels where the above effect seems to work. Maybe the ancients (my ancestors!) were on to something after all? Even if they had no clue how it actually worked, classifying it as a "cooling" element, they did link it to lowered blood-pressure. Either way, black salt sure tastes good in my chaat!

And sorry guys, this still doesn't give us any easy excuse for passing gas...

[Hat-tip: Smoke Signals]


Friday, October 24, 2008

Lizards Showing Some “Leg”

ResearchBlogging.orgSubmitted by Cindy Hua for Evolution

Most of us think that evolution in species take several generations to thousands of years to occur. However, how about if I say in one generation’s time there is a significant change in morphology? Jonathan Losos and his team of researchers from Washington University, St. Louis has found a peculiar lizard that is evolving in a tremendous rate. The brown anole, a Caribbean native lizard, spends most of its day hunting on the ground. One of its main predators is the curly-tailed lizard.

As we all know from our evolution class, a chain of islands sets up a great opportunity for parent species to change significantly. Since the Bahamas are home to the brown anole, natural selection will most likely to occur if there is a change in predator population. Losos has tested his hypothesis that with the introduction of more curly-tailed lizards into the main island, the brown anoles are under the influence of selection pressure change (Losos, et. al, 2006). When brown anoles sense danger of increasing populations of curly-tailed lizards, it flees towards trees and stay away from the ground activities for a few generations.

After a year’s experiment, Losos discovered that the brown anoles are experiencing a change in leg morphology. In the first six months of his study, the anoles originally had long legs, which enable them to outrun the predators. However, six months later, the survivors had drastically shorter legs, which permit them to hide in narrow crevices and climb in trees. Losos noticed that within a single generation, the anoles went to quick reversals in selection pressure (Losos, et. al). The behavior of the lizards changed, as they prefer treetops than the ground. Here we see natural selection at its finest.

Over several generations down, the continuing threat of curly-tailed lizards will force the anoles population to evolve shorter and shorter legs. However, I find it hard to believe that brown anoles can evolve in one generation at such a fast pace. Perhaps through time the longer legged anoles died off and Losos found mostly shorter legged since it was able to survive and reproduce.

The quick reversal of evolution by means of selection pressure is quite interesting. The brown anoles started with long legs to outrun its predators but discovered it to be a hindrance as it cannot bend its legs to hide in crevices. It preferred to have shorter legs to save energy and it is easier to live in trees away from the main predator. The anoles do not have a use of long legs anymore so it does not have to evolve back. For example, ostriches, emus, and kiwis all are flightless birds yet they have small wings. Their ancestors were flying species, but, through time, with fewer predators to run away from, they probably foraged on the ground more. Over generations, they most likely could adapt better on land and did not need developed wings for flight. That is why they evolved long, strong legs for running and scratching for food. I believe this is similar to what is occurring to the brown anoles. Their ancestors must have evolved longer legs to run away from predators. however, current species reverted to shorter legs when selection pressure changed. Although I believe the leg lengths did change because of pressure, I find it hard to believe this had all occurred in one generation.


J. B. Losos, T. W. Schoener, R. B. Langerhans, D. A. Spiller (2006). Rapid Temporal Reversal in Predator-Driven Natural Selection Science, 314 (5802), 1111-1111 DOI: 10.1126/science.1133584


Development and Divergence of Canid Morphology, A Critical Review

ResearchBlogging.orgSubmitted by Tara Clever for the Evolution class.

When considering the comparison, it is astonishing that toy poodles belong to the same family as wolves: Canidae. Even more interesting is the observation of the divergence of domestic dogs from wolves. Robert K. Wayne approaches this topic with his paper “Limb Mophology of Domestic and Wild Canids: The influence of Development on Morphologic Change.” His primary objective was to determine whether allometry as an index of development and function is the same in domestic and wild canids. (Wayne 1986)

Bivariate Analysis

Domestic dog breeds have wider long bones than their wild counterparts of the same femur length. When comparing relative long bone width, there was little difference between domestic dogs and wild canids. Metapodial, scapula, and olecranon length difference were ovbious between dogs and wild canids. Long bone width and development reflect that fact domestic dogs do not need to hunt or escape predation.

Discriminate Analysis

General size of all canidae family members, domestic and wild, was analyzed to determine similarity of morphologic patterns. Despite diversity in limb size and proportion, domestic dogs are highly distinguished from all except wolf-like canids. Morphologic separation of wild canids among each other and of domestic dogs and wild species depends on difference in metatarsal and olecranon morphology. This suggested that morphologic evolution abides by phylogenetic boundaries (Wayne 1986).

Ontogenetic Analysis

Similarity of dog-intraspecific and dog-ontogenetic analysis showed that small dog breeds are paedomorphic whereas large dog breeds are hypermorphic. This assumes that diversity of limb diversity is predetermined and reflected in the development of an individual as breeders artificially select domestic dogs for favorable traits.


Wayne’s study indicated that allometry can be utilized as an index of devlelopment and function in both domestic dogs and wild canids. Morphological and bone differences were apparent amongst all members of the canidae family. However, some differences were not as distinguishable between domestic dogs and closely related wolves. As domestic dogs are bred for entertainment value, these differences will become more apparent.

Literature cited

Wayne, R. K. (1986). "Limb Morphology of Domestic and Wild Canids: The influence of Development on Morphologic Change." Journal of Morphology 187: 301-319.


Thursday, October 23, 2008

Cellular scaling rules and primate brains - revisited

ResearchBlogging.orgKelsey Faria blogs about a paper, earlier reviewed here, for her contribution to the Evolution class.

The order of Primates is known for a variety of species that are energetic, inquisitive, social, and intelligent. Whereas the order of Rodentia typically lack the range or number of skills that primates encompass. Theses differences seem to put these two orders in completely different categories, although species in each order have relatively similar brain sizes. So the question arises what could be different about their brains that it affects their behavior? The question raises the possibility that primate brains differ from rodent brains in their cellular composition (Herculano-Houzel et al 2006).

The authors examined the cellular scaling rules for primate brains and show that brain size increases isometrically as a function of cell numbers. This isometric function is in contrast to rodent brains. Rodent brains have the ability to increase faster in size than in numbers of neurons. As a result of the linear cellular scaling rules, primate brains have a larger number of neurons than rodent brains of similar size (Herculano-Houzel et al 2006). In all probability this would give primates an advantage over the rodents which may explain the richer behavioral repertories and better cognitive abilities (Herculano-Houzel et al 2006).

Brain size fluctuates across mammalian species, and several studies have focused on finding any shared regularities behind brain morphology and cellular composition across species with different brain sizes. With these regularities this leaves room to discover new hypothesis about the underlying development and evolution of the brain. Studies have proven that animals from different species differ in their behavioral repertoires, and one would assume differences in cellular composition of the brain

The authors conducted an analysis in which cellular scaling rules were applied to rodents and primate brains. They concluded that the average neuronal size is larger in larger brains, whereas the average non-neuronal cell size remains comparatively stable. They also discovered that the neuron ratio increases with increasing brain size (Herculano-Houzel et al 2006).

With the information collected through this analysis the authors were interested in applying the scaling rules to other mammalian orders. There main goal was to set rules that can be applied to all brains and possibly reflect characteristics from a common ancestor which would conclude why there is a phylogenetic variance across orders. They were particularly interested in cellular scaling differences that might have arisen in primates. If the same rules relating numbers of neurons to brain size in rodents also applied to primates, a brain comparable to ours, with approximately 100 billion neurons, would weigh approximately 45 kg and belong to a body of 109 tons, about the mass of the heaviest living mammal, the blue whale (Herculano-Houzel et al 2006).

Inevitably their study indicates that there must be scaling differences between rodent and primates due to their behavior relative to similar brain size. The authors used the isotropic fractionators, which is a non-stereological method, which estimates the total number of neuronal and non neuronal cells in the cerebral cortex, cerebellum, and remaining structures of the brain (Herculano-Houzel et al 2006). They examined across six species of the order Primata, from Callithrix to Macaca, and in the closely related tree shrew, which is in the order Scandentia.

From the results gathered the authors concluded that the cellular scaling rules for primate brains differ from those of rodents. There was a distinct difference between the primate brains and rodent brains, primate brains do not hyper scale as they gain neurons, as rodent brains do. Primate brains also increase in size according to their number of neuronal cells which means that the average neuronal cell remains constant. The rodent brains increase in size faster than they gain neurons, which results in a increasing in the average neuronal cell size. When looking at neuronal densities they remain stable in primates and they tend to decrease in rodent brains. Primate ratios of non-neuronal neuronal cells to Mbr (brain mass) do not correlate although rodent’s ratios do.

The authors also included the tree shrews included in the experiment did not alter the results. Therefore the tree shrews are in fact a close relative of the primates and they to conform to the primate scaling rules.

Some implications for humans according to the data are that larger brains do not have a larger relative number of neurons in the cerebral cortex. From their results both the cerebral cortex and the cerebellum represent fractions of brain mass but do not differ significantly with an increase in brain size. Although, relative cortical size is seen to increase significantly with increasing brain size when larger species, such as great apes and humans, are considered (Herculano-Houzel et al 2006). It will be interesting to see if these scaling rules will apply if and when the addition of apes and humans are included in the experiment. A primate brain containing 100 billion neurons would be expected to weigh about 1,450 g and belong to a body of 72.7 kg, values that match the average mass of a human’s brain and body. This would conclude that humans and their brains are in fact isometrically scaled up versions of a common primate plan (Herculano-Houzel et al 2006).


Suzana Herculano-Houzel, C. E. C., Peiyan Wong, and Jon H. Kaas (2006). "Cellular scaling rules for primate brains." Proceedings of the National Academy of Sciences 104(9): 3562–3567. doi: 10.1073/pnas.0611396104.


On glaciations, climate change, and pleistocene isolated fish

ResearchBlogging.orgRaj Kotagiri offers his perspective on a Biogeography class discussion.

This is a review of our discussion several weeks ago about the Glaciation and Pleistocene periods. There were four major periods in the history of Earth during glaciation period and probably the most important of these is the second period that occurred some millions of years ago between 850 Ma to 635 Ma during the late Proterozoic Age. It was suggested that during this age Earth was covered completely in ice and then led to the Cambrian Explosion which has been responsible for diversification of multi-cellular life during this era.

The current period of constant glaciations in Pleistocene epoch from 1.8 million years to 10,000 years BP where the present continents were positioned and the plates on which these continents rested have not rotated more than 100 km since the start of this period. Repeated glacial cycles have described the climate of Pleistocene period pushed to 40th parallel in some places. 30% of the surface of the Earth has been covered by ice at its highest extent. Also, there was a zone of permafrost that extended from southern edge of glacial sheet of North America to Eurasia. The average annual temperatures of the ice and permafrost were -6˚C and 0˚C respectively.

One of the papers we discussed in class was “Global heat budget, plate tectonics and climate change” (Harris, 2002). This paper stimulated curiosity and discussion among the students in class. We arrived to the following conclusions about climate change on Earth from the paper and discussion.

  1. The Earth’s surface temperature has fluctuated since past 2000 Ma.
  2. Individual locations on Earth have undergone long-term change in temperature at different times and in different places.
  3. We discussed new evidences concerning the difference in heat absorption by land and water; such as, the transport of excess heat pole ward from the tropics and the change in distribution of land and sea resulting from plate tectonics. These evidences explain the major fluctuation in the geological record-setting temperatures measured during last 350 Ma. However, these evidences create confusion since they are not supported by sufficient background data.
  4. he paper also dealt with various controls which resulted in the climate change on the Earth’s surface.
    1. First control dealt with changes in the distribution of land and sea due to plate tectonics. This explains the major temperature fluctuation (>25˚C) around the globe in the last 350 Ma.
    2. Second order control was large scale changes in ocean currents and thermohaline circulation (15-25˚C).
    3. Third order control was Milankovitch orbital cycle producing variations in the air temperature by order of 10˚C.
    4. Fourth order control was massive volcanic eruptions and how changes in carbon dioxide production caused minor perturbations (<5˚C).

The take home message of our discussion was: the Earth's climate change was influenced by many factors; some of which act independently, while others acted interdependent with each other. The process of climate change was a gradual process which took many millions of years to see any significant change in climate. This change in temperature and climate, at different locations of the Earth, resulted in the geological distribution of various types of habitats on Earth.

The second paper we discussed in class was “Pleistocene isolation in the northwestern pacific marginal seas and limited dispersal in marine fish, Chelon haematocheilus (Temminck and Sclegel, 1885)” (Liu et al, 2007). This paper deals with three marginal seas: the Sea of Japan, East China Sea and South China Sea. During the period of Pleistocene glaciation when the whole earth was mostly covered by ice, the populations of living organisms were isolated in the seas.

We discussed the hypothesis that the rise of post glacial sea level resulted in the homogenization of the population by high disperse potential. To test this hypothesis, researchers used Chelon haematocheilus as the model organism. This fish belongs to the Mugilidae family, and is present in shallow coast water as well as freshwater regions in north Japan through the Korean Peninsula, and to the coast of China South. The early life history characteristics indicate that potential larval dispersal of C. haematocheilus is high. If C. haematocheilus larvae could travel on the currents, the connectivity should be high among populations within this region. The distribution and biological characteristics of C. haematocheilus make it a good subject to test the homogenization hypothesis.

Molecular analysis revealed three lineages which might have diverged in the three marginal seas during Pleistocene low sea level. Analysis of molecular variance and population statistics revealed significant differences in genetic structure among populations of the marginal seas. The outcome of the above analysis revealed that gene flow in C. haematocheilus is far more restricted spatially than predicted by the potential dispersal capabilities of this species. These results provide evidence for strong genetic divergence among these fishes in the marginal seas of the Northwestern Pacific, which coincides with expected pattern of vicariance due to sea level changes during the Pleistocene.

In order to support the above hypothesis further investigation should be done on other species of the same region.

Stuart A. Harris (2002) Global Heat Budget, Plate Tectonics and Climatic Change. Geografiska Annaler. Series A, Physical Geography, 84:1-9

JIN-XIAN LIU, TIAN-XIANG GAO, SHI-FANG WU, and, YA-PING ZHANG. (2007) Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haematocheilus (Temminck & Schlegel, 1845). Molecular Ecology 16:275-288. DOI: 10.1111/j.1365-294X.2006.03140.x


Monday, October 20, 2008

This won't help your grades...

... even if you think the gambit might win you some votes!



Thursday, October 9, 2008

Loss of Diversity

ResearchBlogging.orgMichael Rosenzweig’s article predicts our planet’s future loss of diversity. He argues that by decreasing the area available for wildlife, it not only decreases habitat, but also actually causes a decrease in the rate of speciation for all organisms. Essentially, his argument rests on how the size of a species range affects its rate of speciation. Although somewhat controversial, large range sizes are thought to have higher rates of speciation as well as lower rates of extinction, and Rosenzweig’s article looks at the other end of that equation. With habitats decreasing, range sizes must decrease as well and that in turn depresses the number of future new species. Eventually this leaves us with fewer and fewer species of life forms.

So where does this leave us? Rosenzweig acknowledges that due to the reality of human population needs large productive areas of landscape may not be able to be set aside solely for wildlife. He proposes a new paradigm of comprise he terms Reconciliation Ecology, which he describes as the modification of human habits and habitats to accommodate species diversity. His solutions often require complex relationships between government, business and the private sector. While, when possible, conservation of land for wildlife is often the best solution Reconciliation Ecology provides a new framework to increase habitat that is accessible to both humans and other species. Accordingly, this would provide larger habitat ranges for species, which, in turn, would cause a decrease in the loss of speciation.

Rosenzweig sees this as a win/win solution, which happens to be part of the title of one of his books on the topic. While some might argue, myself included, that it seems more like a win for us and a lose, although less of one, for wildlife. Many environmentalists, and others, want more and more lands set aside for pure conservation and see Reconciliation Ecology as a sell out. I can see their reasoning, however, I also think they may be missing an important point. The key word in his proposal is “compromise”. I believe he intended his idea would be a way that would take land that humans need for whatever purpose and try to make as many accommodations we can to allow it to be somewhat useful habitat. Those areas would most likely not be available for traditional conservation. That being said, I think the label sell out doesn’t quite fit, however, I’m not sure I would call it a win/win solution either.
M. L. Rosenzweig (2001). Loss of speciation rate will impoverish future diversity Proceedings of the National Academy of Sciences, 98 (10), 5404-5410 DOI: 10.1073/pnas.101092798


Of squirrels and conifers coevolving

ResearchBlogging.orgA review submitted by Jordan Anderson for the Evolution class.

The feeding preferences of pine squirrels (Tamiasciurus) on conifers lead to two separate patterns of evolution; one of divergence and one of convergence. Squirrels first forage indiscriminately, and then switch to discriminate feeding when supplies run short. This causes selective pressure on the species that is least easily used and results in divergence (Smith, 1970). This selection also produces a divergence between the two tree species in regards to defense mechanisms, such as early shedding of seeds. An example of convergence results, when part of the prey is temporarily inaccessible to the squirrels, thus resulting in energy withheld. Squirrels tend to feed the most on individual trees that are different from the rest in that they are producing more cones, or more seeds per cones (Smith 1970).

The study conducted by Smith took place in the Cascade Mountains of southwestern British Columbia, which is significant, because the Cascade Mountains create a rain shadow with the forests to the east being very dry and prone to burning. In this area, lodgepole pines are ubiquitous and their cones are serotinous, they remain closed for years after maturation to enable them to reseed areas after frequent burns (Smith, 1970). Douglas-firs are also common in this area and will alternate between years of crop failures and years of crop masts; large production. The squirrel population in this area is very stable, they first feed on Douglas-firs but switch to lodgepole pines during crop failures (Smith, 1970). The lodgepole pines serve as a nearly constant food source. On the west side of the Cascade Mountains, the situation is quite reversed. Lodgepole pines are rare, are nonserotinous, and may have cone crop failures (Mowat 1960). This results in a fluctuating squirrel population exerting less selection pressure on lodgepole pines, as they do not exploit as much of the cones. The squirrels in the east exert a selection pressure for harder lodgepole pine cones, and less seeds per cone in the Douglas-firs. Thus, the lodgepole pines exert a selection pressure for squirrels with stronger jaws, those that can eat the stronger cones (Smith, 1970). This change in squirrels is evident as the squirrels in the east have stronger jaw muscles than those in the west.

Another study, explored other information of populations of red squirrels Tamiasciurus, and found that they are territorial. An individual will have its specific area that it maintains year-round. The individual will forage in autumn to assemble a cache of food items. The cache will be located near the center of the individuals’ territory (Larsen et al, 1997). During periods of shortage, squirrels depend on cached food (Vander Wall, 1990). The squirrels will leave their midden to forage on their territory only if the environment happens to be milder on that particular day (Larsen et al, 1997). The squirrels are then foraging the cones that still remain on the trees. Unfortunately, winter foraging does have some drawbacks. It may be more energetically costly to forage than to feed on the food already stored in their midden. It also increases the risk of predation (Larsen et al, 1997).

A study conducted by Lindsay inadvertently tested Smith’s hypothesis about squirrel size relative to cone morphology or cone anatomy. More specifically, Lindsay tested whether squirrel size was influenced by pressure in maintaining efficiency within foraging for a cone cache. He observed that changes in cone morphology selected for squirrel size (Lindsay, 1986). Small squirrels were found in areas dominated by spruce, hemlock, and redwoods (all of which have small cones with little energy per cone). Conversely, large squirrels were found in forests that had larger cones with a greater energy per cone (Lindsay, 1986). His study showed that discriminatory feeding tactics based on the individuals’ size could minimize loss of energy from the food source as they became more efficient in handling time. Efficiency, was calculated by measuring the amount of energy in a particular food while taking into consideration the energy used to process the food. This relationship is noted by Palmer, who expressed the total energy as “net energy” with the energy lost in processing known as “handling time.” Thus, minimizing handling time is a highly efficient tactic for feeding discrimination and efficiency (Palmer, 1981). This is particularly applicable to squirrels, because they need to obtain lots of energy to store up for winter; they need to be efficient in their foraging techniques in order to survive.

Lindsay noted more evidence in support of Smith’s research by observing T. douglasii in association with small cones. This makes sense as douglasii has weak jaw muscles and can manipulate the smaller cones. T. hudsonicus was found in association with large, thick cones, suitable for hudsonicus as it has strong jaw muscles (Larsen, 1986).

I found Smith’s experiment to be exceptionally thorough. This is evident by many authors who have cited Smith’s work within their own studies. However, he was unable to discern if any animal was exerting a selection pressure to maintain thick seed coats (as a defense mechanism by the conifers). I have not yet found an article exploring this important topic. More research needs to be conducted to discover if insects or birds are inhibited by the thick seed coats of ponderosa pine, western white pine, and Douglas-fir (Smith, 1970). If animals are selectively choosing seeds with a thinner coat, then they are creating a selective pressure for the conifers to produce a thicker seed coat in order to escape predation.


K. W. Larsen, C. D. Becker, S. Boutin, M. Blower (1997). Effects of Hoard Manipulations on Life History and Reproductive Success of Female Red Squirrels (Tamiasciurus hudsonicus). Journal of Mammalogy, 78 (1), 192-203

S. L. Lindsay (1986). Geographic size variation in Tamiasciurus douglasii: Significance in relation to conifer cone morphology Journal of Mammalogy, 67 (2), 317-325

E. L. Mowat (1960). No serotinous cones on central Oregon lodgepole pine Journal of Forestry, 58, 118-119

A. Richard Palmer (1981). Predator Errors, Foraging in Unpredictable Environments and Risk: The Consequences of Prey Variation in Handling Time Versus Net Energy The American Naturalist, 118 (6), 908-915 DOI: 10.1086/283883

Christopher C. Smith (1970). The Coevolution of Pine Squirrels (Tamiasciurus) and Conifers Ecological Monographs, 40 (3), 349-371 DOI: 10.2307/1942287

Wall, V. 1990. Food hoarding in animals. University of Chicago Press.


Friday, October 3, 2008

Seminar today on the evolutionary ecology of becoming urban

Its my own turn at bat in our departmental colloquium today. Here's the blurb on what I'll talk about:

Becoming urban: behavioral and evolutionary implications of living in the city

Dr. Madhusudan Katti, Department of Biology, California State University, Fresno


DSC_2294.NEF (1).jpgThe city may be the ultimate expression of the human effort to control our environment: in evolutionary ecological terms, it represents a strategy to minimize the risks of starvation and predation by creating habitats which dampen natural variability in climate and food availability, and provide shelter from predators. Simultaneously, humans also generate a considerable surplus of food, making cities attractive habitats to many other wild species. Recent theoretical work by myself and colleagues shows that typical changes in spatio-temporal patterns of food availability (higher and more predictable) and predation regimes (may be lower) accompanying urbanization can alter competitive dynamics such that weak competitors survive better in urban than in more natural habitats. This has several implications for species that are able to invade the novel urban habitat: higher population densities, potentially reduced selection pressures, and in turn, greater vulnerability to sudden environmental changes. In this presentation, I explore consequences for the evolution of commensalism and the continued coexistence of other species with humans, using recent work on house sparrows (the ultimate commensal now at risk in urban habitats), corvids (suburban Scrub Jays), and south Asian primates (urban Macaques and Langurs). I will also present an overview of several projects currently ongoing in my laboratory focusing on different effects of urban environments on bird behavior, ecology, and diversity, and describe opportunities for students to get involved!

On: Friday, October 3, 2008, At: 3:00-4:00 PM, In: Science II, Room 109


Thursday, October 2, 2008

Darwin Quote of the Day

"I had, also, during many years followed a golden rule, namely, that whenever a published fact, a new observation or thought came across me, which was opposed to my general results, to make a memorandum of it without fail and at once; for I had found by experience that such facts and thoughts were far more apt to escape from the memory than favourable ones. Owing to this habit, very few objections were raised against my views which I had not at least noticed and attempted to answer."

-- Charles Darwin, in Darwin, Francis ed. 1887. The life and letters of Charles Darwin, including an autobiographical chapter. vol. 1. London: John Murray.


Wednesday, October 1, 2008

Carl Zimmer on a career among the Galapagos finches

grants220.jpgAbout two months ago I was fortunate enough to attend Rosemary Grant's plenary lecture at the 2008 meeting of the American Ornithologists' Union. It was one of the most deeply impressive lectures I've heard in the 20 years that I've been attending scientific conferences. I've known Peter and Rosemary Grant for 10 years now, and consider myself extremely fortunate in being able to claim a personal connection with such greatness: they are my academic grandparents! If you've taken my classes (any of them!), you've probably heard me talk about them at some point. What I meant to do, but haven't had the time to do, is write more about Rosemary's wonderful talk here. Well, at this point in the semester, the prospects of finding time for something like that is slipping farther away. Fortunately, however, Carl Zimmer (who is way better with the written word / blog than me), happened to attend a joint lecture by them yesterday, and gives us an excellent account on his new blog at Discover. An absolute must read for the week!

Thanks, Carl!


Tomorrow, I dine with a rationalist!

Yes, I am one of the group of faculty members invited to a reception with James Randi tomorrow night, before he gives his public lecture on campus. Here's the announcement:

The University Lecture Series

Proudly Presents

James Randi

“Pseudo-Technology in the New Millennium”

Thursday, October 2, 2008

7:30 p.m. ~ Satellite Student Union

James Randi has an international reputation as a magician and escape artist, but today he is best known as the world’s most tireless investigator and demystifier of paranormal and pseudoscientific claims. He has pursued “psychic” spoonbenders and exposed the dirty tricks of faith healers. He appears frequently on US television shows and in the late 1960’s was host of “The Randi Show” on WOR-Radio.

To read more about James Randi visit our website

For Ticket Information: please call the University Student Union Information Center at 278-2078 or visit them in the University Student Union.


Carnivals new and old

It seems a new forthnightly carnival focused on evolution has been going around for the past month, and I only just noticed. Well, you can start by reading The Carnival of Evolution #3 at Greg Laden's blog.

And, btw, the venerable Tangled Bank is also online in its 115th incarnation at Evolved and Rational. Check it out.

And students, don't tell me you can't find inspiration to write something about evolution here!


Zotero: an open source alternative to Endnote

If you haven't tried the campus site-licensed Endnote software to manage your reference collection yet - (or perhaps because you have and didn't like it) and if you'd prefer an open-source alternative with some apparently nifty online features (esp. for firefox users), consider Kevin Zelnio's advice: Screw EndNote, Try Zotero. You can download it here.



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