Saturday, May 31, 2008

Science Blogs Book Club: Microcosm

Carl Zimmer's new book "Microcosm" is out, and is the inaugural subject of the Science Blogs Book Club. I've been asked to participate, along with Jessica Snyder Sachs and PZ Myers. We will be posting about Zimmer's book in the coming weeks. Feel free to chime in with your own questions as we will be happy to discuss them.

Zimmer has been a favorite writer of mine since I read Parasite Rex. Til then, I had not the gleeful pleasure of reading about the world's nastiest creatures in the popular press.

Microcosm, is a fantastic read, and Zimmer makes the story of Escherichia coli positively gripping. You can read an excerpt from the book at the New York Times.

Tuesday, May 27, 2008

Viruses Being Born

I don't know how long it will be up, but check out the video on the Rockefeller University home page. It shows HIV viruses budding on the surface of a cell, and is the first video ever taken of virus birth.

Using revolutionary microscopy techniques, the Rockefeller team "became the first to document the time it takes for each HIV particle, or virion, to assemble: five to six minutes. “At first, we had no idea whether it would take milliseconds or hours,” says Jouvenet. “We just didn’t know.”

To prove they were observing HIV, the team used fluorescent tagged viral Gag protein.

"Although many different components gather to form a single virion, the Gag protein is the only one necessary for assembly. It attaches to the inner face of the cell’s outer membrane and when enough Gag molecules flood an area, they coalesce in a way that spontaneously forms a sphere.... When enough Gag molecules get close and start bumping into each other, the cell’s outer membrane starts to bulge outward into a budding virion and then pinches off to form an individual, infectious particle."

How cool is that?

Image from the Welcome Trust.

Friday, May 23, 2008

This Week's Citation Classic

This week's citation classic is Clyde A. Hutchison, III, Sandra Phillips, Marshall H. Edge Shirley Gillam, Patricia Jahnke, and Michael Smith. Mutagenesis at a Specific Position in a DNA Sequence. The Journal of Biological Chemistry, 253: 6551-6560.

Nobel Laureate Michael Smith doesn't get enough recognition, and I attribute it to his relatively conventional name. His 1993 co-laureate Kary Mullis seems to get much more attention, perhaps because of his more unusual name*, but the technique that Smith developed, in my opinion, ranks with the PCR in terms of utility. This technique is site-directed mutagenesis (SDM).

Back in the old days, if you wanted to change the genotype of your study organism, you needed to bombard it with chemicals or radiation, then screen the mutants, hoping you might chance upon the right mutation. Obviously this technique is kind of inefficient. Joshua Lederberg once commented, "“The ignis futuus of Genetics has been the specific mutagen, the reagent that would penetrate to a given gene, recognize it, and modify it in a specific way. ”

SDM is this ignis futuus. Where radiation works like a sledgehammer, SDM works like a laser. One can target specific nucleotides for mutation into whatever change is desired.

SDM relies on constructing DNA oligionucleotides that are identical for the sequence of interest, but contain the mutation of interest.

Using the bacteriophage {phi}X174, the study's lead author Clyde Hutchinson "teamed up with Smith, and the pair realized that an obvious route to a mutagenic method was to use a mutant oligonucleotide primer for E. coli DNA polymerase I on a circular single strand template, which would produce a product that could be converted to a closed circular duplex by enzymatic ligation."

Today SDM is coupled with the PCR, and is used widely to study gene regulatory elements, DNA-protein interaction, and protein structure/function are all typical targets for mutagenesis studies, and in my own lab to study life history variation among phage lambda.

A Journal of Biological Chemistry article describing the discovery is available here.

Any connection between a recent Sandwalk post, the fact that Smith is Canadian and that this article is biochemical in bent is purely coincidental.

*I suppose there are other hypotheses, but let's be kind.

Tuesday, May 20, 2008

Epic Fail: Evolution and Creationism in America's Classrooms

It is no exaggeration to call evolution “the central concept of biology.” So why is the fact of evolution denied by half of our population? A new article in PLoS Biology by Michael Berkman, Julianna Pacheco, and Eric Plutzer suggests it might be on account of their lack of education at the high school level. Since only ~25% of the US population obtains a college degree, it is the duty of high school teachers to provide a proper scientific education to our citizens. Model high school curriculum guidelines provided by the National Science Teachers Association, the National Research Council, and the American Association for the Advancement of Science, strongly suggest that teachers “provide evidence that evolution has attained its status as a unifying theme in science.”

However, teachers that don't "believe" in evolution aren't going to teach it in the classroom. In the paper, Berkman et al. describe the results of the polling 939 high school biology teachers. "Roughly one sixth of all teachers professed a “young earth” personal belief, and about one in eight reported that they teach creationism or intelligent design in a positive light. The number of hours devoted to these alternative theories is typically low—but this nevertheless must surely convey to students that these theories should be accorded respect as scientific perspectives."

Why do these teachers fail to contribute proper instruction in evolution? The article suggests, "that high school teachers who completed the largest number of college-level credits in biology and life science classes and whose coursework included at least one class in evolutionary biology devote substantially more class time to evolution than teachers with fewer credit hours. The best prepared teachers devote 60% more time to evolution than the least prepared."

The article concludes that it is incumbent on college educators to provide future high school teachers with a proper education. "Scientists concerned about the quality of evolution instruction might have a bigger impact in the classroom by focusing on the certification standards for high school biology teachers. Our study suggests that requiring all teachers to complete a course in evolutionary biology would have a substantial impact on the emphasis on evolution and its centrality in high school biology courses. In the long run, the impact of such a change could have a more far reaching effect than the victories in courts and in state governments."

Monday, May 19, 2008

First Step to Reviving Extinct Species

The Tasmanian tiger was the largest known carnivorous marsupial of modern times. Unfortunately, the last known Tasmanian tiger died in captivity in the Hobart Zoo in 1936. Now there is new hope for reviving this lost species. In a feat of science akin to that described in the movie Jurassic Park, Scientists from University of Melbourne and University of Texas have successfully extracted genes from an extinct Tasmanian tiger (thylacine) and cloned it into a mouse.

Andrew Pask and Marilyn Renfree of the University of Melbourne's Department of Zoology and Richard Behringer of the MD Anderson Cancer Center in Houston isolated thylacine DNA from 100 year old ethanol fixed museum specimens. The DNA was then cloned into mouse embryos. The thylacine gene Col2a1 was shown to have a similar function in developing cartilage and bone development as the Col2a1 gene does in the mouse.

"I have no doubt the whole creature could be brought back to life in the future,'' said Dr Pask.

“At a time when extinction rates are increasing at an alarming rate, especially of mammals, this research discovery is critical,” says Professor Marilyn Renfree, Federation Fellow and Laureate Professor in the University of Melbourne’s Department of Zoology, the senior author on the paper. “For those species that have already become extinct, our method shows that access to their genetic biodiversity may not be completely lost.”

The research article appears in PLoS One.

Painting from Lycee Condorcet.

Thursday, May 15, 2008

This Week's Citation Classic

Dawkins R and Krebs JR. Arms races between and within species. Proc. R. Soc. Lond. B 205, 489-511 (1979)

Back in the old days before Richard Dawkins was an atheist gadfly, he did some interesting work in behavioral ecology, particularly among digger wasps. One of my favorite (and most cited) Dawkin's paper is Arms Races Between and Within Species, which he published with the estimable Lord Krebs. (There was a time when Behavioural Ecology was my favorite book in the world). The paper is very accessible, even for someone not schooled in the jargon-dense field of biology.

"Arms races" are evolutionary short hand for the coevolutionary adaptation, counter-adaptation struggles that occurs between competing entities. The term derives from the Cold War struggle between the US and the USSR where every move by the US (deploying missiles say) was countered by a similar move by the USSR.

Dawkins and Krebs's paper was one of the first to popularize the metaphor in an evolutionary context. It was, and still is, an exceptionally powerful idea and can be applied to a great number of contexts. The crux of their argument is that organisms do not respond to the physical environment alone, but rather to all the abiotic and biotic components of their habitat.

Dawkins and Kreb's cite Darwin as one of the first progenitors of the idea,

"'. . .the structure of every organic being is related, in the most essential yet often hidden manner, to that of all the other organic beings, with which it comes into competition for food and residence, or from which it has to escape, or on which it preys. This is obvious in the structure of the teeth and talons of the tiger; and in that of the legs and claws of the parasite which clings to the hair on the tiger's body. But in the beautifully plumed seed of the dandelion, and in the flattened and fringed legs of the water-beetle, the relation seems at first confined to the elements of air and water. Yet the advantage of plumed seeds no doubt stands in the closest relation to the land being already thickly clothed with other plants; so that the seeds may be widely distributed and fall on unoccupied ground. In the water-beetle, the structure of its legs, so well adapted for diving, allows it to compete with other aquatic insects, to hunt for its own prey, and to escape serving as prey to other animals.'"

An important point made by Dawkins and Krebs is that arms races are often asymmetrical, as epitomized by the Life-Dinner principle. In this metaphor, the Rabbit runs faster than the Fox since the Rabbit is running for its Life whereas the Fox is running only for Dinner. Dawkins and Krebs suggest that this can lead to species extinction. As they write in the conclusion,

"...the arms race concept may help to resolve the old controversy over whether lineages drive themselves to extinction through progressive evolution. The orthogenetic idea that evolution has its own inexorable internal momentum forcing lineages beyond the limits of natural selection is obviously absurd. Rut orthodox natural selection, if there is an arms race, can generate the kind of runaway process that looks like orthogenesis, and which might eventually hasten extinction of the lineage."

I find it interesting that Dawkins, one of the most prominent proponents of genic selection, appears here to be advocating for species selection.

Monday, May 12, 2008

Science Debate 2008

There probably won't be a science debate between McCain and Obama.

Shawn Otto, CEO of Science Debate 2008, writes

Part of the problem, from our perspective, is a perception in the media, particularly the political editors, that this is a niche debate. We have saturated coverage in the science community, but have had a very difficult time getting the mainstream national media to cover this effort at all, despite numerous and frequent attempts; they believe that issues like religion loom far larger in this election and science simply doesn't sell papers. Science has also been somewhat nonvocal and under political attack over the last several years, and this has helped to create the inaccurate perception of an uninfluential minority.

Science Debate 2008 commissioned Research America to poll American attitudes towards a science debate. The results?

85% of Americans Want a Presidential Debate on Science!!!

Ask Obama and McCain to debate science issues today.

I sent an email to each.

Given that the past 8 years have been disastrous from a science policy perspective, I'm very concerned as to where the next president stands on important science issues such as climate change, habitat protection and stem cell biology. Why won't Mr. ___ agree to participate in the Science Debate 2008?

Full list of results here. - Science Connected

There is a new facebook for Scientists. It's called SciLink. I recently signed up and noticed Carl Zimmer and PZ Myers have profiles. Those guys are EVERYWHERE :)

It looks pretty interesting. I was able to upload some, but not all, of my publications. Hopefully that bug will be worked out.

I particularly like the Tree of Science feature

Friday, May 9, 2008

This Week's Citation Classic

I've finally read Darwin's The Voyage of the Beagle. I put it off since I figured it was mostly of historical interest, and I wouldn't learn anything new. I was wrong. The work is certainly remarkable for its insight and breadth of knowledge.

While the evolutionary ideas are nascent, the book does show the progression of Darwin's thoughts on biological change via natural selection. Most of these thoughts came to Darwin thru revelations from geology.

First is his realization of the age of the Earth. On viewing the granitic formations on the coast of Brazil, Darwin remarks, "Can we believe that any power, acting for a time short of infinity, could have denuded the granite over so many thousands of square leagues?" and later considering the basaltic lava at the Narrows of the Strait of Magellan "we must confess it makes the head almost giddy to reflect on the number of years, century after century, which the tides, unaided by the heavy surf, must have required to have corroded so vast and area and thickness of solid basaltic lava".

Darwin also found a fossilized horse tooth in the Pampas, and commented, "Certainly it is a marvelous fact in the history of Mammalia, that in South America a native horse should have lived and disappeared, to be succeeded in after-ages by the countless herds descended from the few introduced with the Spanish colonies." Darwin was quite aware of the vast number of extinct species whose fossilized remains had been found.

Numerous times Darwin observes slight variations between species spread over geographic areas such as 12 different species of planariae in the southern hemisphere, mice in Chiloean archipelago and, of course, the finches of the Galapagos.

Time plus variation plus extinction must have been a major insight for Darwin. The idea of natural selection must be fermenting when Darwin writes, "When pasture is tolerably long, the niata cattle feed with the tongue and palate as well as common cattle, but during the great droughts, when so many animals perish, the niata breed is under a great disadvantage, and would be exterminated if not attended to; for the common cattle, like horses, are able just to keep alive, by browsing with their lips on twigs of trees and reeds; this the niatas cannot so well do, as their lips do not join, and hence they are found to perish before the common cattle. This strikes me as a good illustration of how little we are able to judge from the ordinary habits of life, on what circumstances, occurring only at long intervals, the rarity or extinction of a species is determined."

The idea of natural selection is crystallized in this paragraph, "The most curious fact is the perfect gradation in the size of the beaks in the different species of Geospiza, from one as large as that of a hawfinch to that of a chaffinch, and (if Mr. Gould is right in including his sub-group, Certhidea, in the main group) even that of a warbler....Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends."

Most of all I was impressed at his vision, even at an early age. "This small family of birds [Tinochorus] is one of those which from its varied relations to other families, although at present offering only difficulties to the systematic naturalist, ultimately may assist in revealing the grand scheme, common to the present and past ages, on which organized beings have been created."

Map from Darwin Day Celebration.

Evolution and Faith

In this week's issue of Science, there are a couple of letters to the editor on a news article from earlier this year: "Crossing the divide". One of the letters is sympathetic to Stephen Godfrey's struggle; the other is less empathetic. I for one am fairly empathetic of those making the transition. It must be very difficult to turn your back on your family, your friends and your community. What do you think?

Sunday, May 4, 2008

Human Shields

The term human shield has a bit of a bad connotation for humans, but not for moose. In a paper published in Biology Letters, Joel Berger reports that in Yellowstone moose birth sites have shifted "away from traffic-averse brown bears and towards paved roads."

Berger goes on to write, "The decade-long modification was associated with carnivore recolonization, but neither mothers in bear-free areas nor non-parous females altered patterns of landscape use. These findings offer rigorous support that mammals use humans to shield against carnivores and raise the possibility that redistribution has occurred in other mammalian taxa due to human presence in ways we have yet to anticipate."

The reason I found this interesting is that I observed similar behavior in a mule deer during a backpacking trip to the same location. My friends and I noticed that this deer (whom we nicknamed Homie) followed us to our campsite, hung around camp all evening, and was even spotted the next day. That evening and the next morning we saw no fewer than four grizzly bears, and I later found out that this area was one of the most heavily grizzly trafficked areas in all of Yellowstone. We jokingly suggested Homie was using us to fend off the grizzlies. At the time I thought it was more likely that the Homie was looking for handouts, but now I have to wonder!

Astronomy Picture of the Day?

This science nerd gets alerts from google when bacteriophages appear in the news. That's how I found out about the 21 April 2008 NASA Astronomy Picture of the Day. The short article is, for the most part, on the money. It's estimated that there are 10^31 phages on earth. That's more numerous than stars in the universe (~10^21). However, phage therapy is a bit more advanced than they let on. You can read more about phage therapy here.

Credit: Wikipedia