Saturday, September 29, 2007

Evilution Store SoHo

I was walking around SoHo this afternoon when I came across this store. Evilution eh? Science and art, eh?
Well no self-respecting evilutionary biologist would pass up an opportunity to shop in an Evilution Store. The shop carried all manner of fossils, stuffed animals, shells, geodes etc. Not to mention a complete line of hominid skulls.
Oh and many skeletons. Including this pair of children's skeletons. Other gifts included fruit bats in a frame, stuffed weasels, shark in a jar, penis bones, rattlesnake head, worm lollipops (I bought a couple for my nieces. They love candy). I happened to be wearing my Evilution Concert T-shirt (i.e. Stony Brook U, June 23-27, 2006). The girls behind the counter thought it was pretty amusing to meet a real live evilutionary biologist. The vibe of the whole store was decidedly creepy. I couldn't help thinking, I bet Bioephemera would love this.

Friday, September 28, 2007

This Week's Citation Classic

One of the expensive, but worthwhile, book purchases I have every made was Sambrook and Russell's Molecular Cloning, 3rd ed. I figured if I was going to be a professional biologist, I needed this because I haven't visited a good wet lab that doesn't have a dog-eared copy lying around somewhere. Clocking in at $259, it has a hefty price tag, but for sheer utility I don't think it can be beat. For pretty much anything you want to do in molecular biology, you can find clear, lucid instructions here.

Joseph Sambrook is a tumor virologist internationally renowned for his studies of viruses and the molecular biology of normal and cancerous cells, which effectively changed the ways in which scientists now approach cellular development of many forms of human cancer. In 1969, he was hired by James Watson to work at Cold Spring Harbor Laboratories, where his group developed much of the technology which was later used to produce genetic and physical maps of the entire human genome. For that, he got a building named after him at CSHL.

David Russell is t
he Eugene McDermott Distinguished Chair in Molecular Genetics at UT Southwestern. Dr. Russell's research interests are in cholesterol metabolism, in particular the enzymatic pathways that dispose of cholesterol. His laboratory has isolated over a dozen genes that encode enzymes involved in cholesterol breakdown, and has identified the molecular bases of six human genetic diseases characterized by abnormal cholesterol metabolism.


Animal Meme

I've been tagged by Anne-Marie at Pondering Pikaia. She has a very cool German Shepard and writes an excellent blog.

An interesting animal I had:
This is difficult because there is no shortage of candidates: Madagascan Giant Hissing Cockroaches, Praying Manti, Walking Sticks, tarantulas, frogs, lizards, rodents etc. I suppose for sheer strangeness, however, my leech would take the prize. To forestall the inevitable questions, I fed it snails.

An interesting animal I ate:
Again there is no shortage of candidates; among animals, I've knowingly eaten from eight phyla (Cnidaria, Uniramia, Chelicerata, Crustacea, Mollusca, Annelida, Echinodermata, & Chordata). Unknowingly, who knows... I'd have to guess at least half of the phyla. The most recent unusual organism was a jellyfish. How was it? Kind of like chewy noodles.

An interesting animal in the Museum:
One of my favorite animals went extinct quite some time ago: Opabinia regalis (depicted above). It derives from the Cambrian Explosion ~530 mya. Its reconstructed image was greeted with laughter as a pretty good joke when first presented at a scientific meeting in 1972. We are still not sure what exactly it is.

An interesting thing I did with or to an animal:
I held a 3 day old pronghorn fawn while it was weighed and tagged. It was a bag of bones with giant eyes and a furiously beating heart. I don't think any wild animal has so touched me before or since.

An interesting animal in its natural habitat:
My favorite wild animals encounter was with a mom Grizzly and her three cubs in Yellowstone NP. To this day, Ryan Monello, wildlife biologist par excellence at the University of Missouri: Columbia, believes he saved my life by preventing me from trying to get closer. He is probably right.

I'm tagging Larry, Cesar, Matt, Jessica and Carl. I'm guessing they will have interesting responses.

Photo from the Smithsonian National Museum of Natural History collection.

Thursday, September 27, 2007

Evolution of Cooperation

Ford Denison at This Week in Evolution posted today on two interesting new papers dealing with the evolution of cooperation.

The original view of evolution was epitomized by the phrase "Nature, red in tooth and claw." (I'm not sure how popular it was with scientists, but it was undoubtedly popular with the public). This view dovetailed nicely with the concepts of "survival of the fittest" and "natural selection."

In the 30s, 40s and 50s, old-school ecologists, such as W.C. Allee and Alfred Emerson, sort of rebelled against this paradigm, claiming that animals often behaved altruistically, particularly to their peers. This period marked the apex of the Group Selectionist school of ecological thinking.

The pendulum swung back the other way in the 60s, when a young post-doctoral associate at the University of Chicago, G.C. Williams, left lecture by Emerson muttering "Something must be done...." (Perhaps apocryphal, from Sober & Wilson's Unto Others). The result was Adaptation and Natural Selection (1966). This marked the rise of the Selfish Gene movement in evolutionary biology, culminating with Richard Dawkins classic, The Selfish Gene. This is not to say that the concept of cooperation was totally abandoned. Actually, it was placed on a more substantial theoretical foundation, particularly by W.D. Hamilton, who developed the notion of kin selection and Hamilton's Rule. Nonetheless the emphasis was definitely on selfish behavior.

More recently cooperation has been making a comeback. Many papers are being published in the field and there are quite a few labs devoted to the subject. To Ford's two papers, I'd like to add one of my own, reporting on work from the Currie Lab at UW: Madison. The paper has just appeared in PLoS One so all can access. Here Poulson et al. (2007) look at the evolution of cooperation using a really neat study system: the fungus-farming ants.

The attine ants are really Earth's first farmers because they began to cultivate fungus by providing it food and protection over 50 million years ago, with the domestication of a fungus in the family Lepiotaceae. As any farmer knows, it's hard work to keep your crop free of pests and disease. This is true too for the ants; their fungal crop often suffers infestation from the parasitic microfungi, Escovopsis.

Fortunately for the ants, they have help, from the actinomycetous bacteria, Pseudonocardia no less. (For more on actinomycetes, check out Twisted Bacteria; he also posted on this system earlier). Specifically, the Pseudonocardia are the third partners in the mutualism; they produce antibiotics that inhibit Escovopsis growth. Poulson et al. (2007) write "The antibiotic-producing bacteria are typically housed in elaborate structures on the cuticle of workers, connected to exocrine glands that appear to provide nutrients to support the growth of Pseudonocardia." So, in other words, these ants maintain little bottles of pest spray on their backs. How cool is that?

Educational materials can be found here and here.

Incidentally, the phrase, "Nature, red in tooth and claw" derives from canto 56 in the poem, In Memoriam A.H.H., by the English poet Alfred, Lord Tennyson. It's a wonder anyone found it; the poem is quite long :P

Photo: Bridge forming ants from Mark Ridley's Evolution.

Friday, September 21, 2007

This Week's Citation Classic

This week's citation classic is Avery OT, MacLeod CM & McCarty M. 1944. Studies on the chemical nature of the substance inducing transformation of pneumonococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. Journal of Experimental Medicine 79: 137-158.

From the time scientists began thinking about the physical nature of the genetic material, the leading candidate was protein. Nucleic acid, first discovered by Frederick Miescher in 1869, was well known, but was considered too regular, too monotonous to encode something as fantastic as life itself. Nucleic acid was thought instead to be a structural molecule, like scaffolding. Protein, by contrast, was known to be considerably complex, hence was thought to be the information bearing molecule.

Avery and colleagues changed all that. Through a simple and ingenious set of experiments, Avery demonstrated unequivocally that DNA was the genetic material. The Dolan DNA Learning Center, Cold Spring Harbor Laboratory has a marvelous animation sequence describing the actual experiments.

The paper itself is a tour de force model of clarity. Unlike many of today's papers, it reads something like a mystery novel where the clues accumulate until there is no choice but to be borne along inexorably towards an exciting conclusion.

"The data obtained by chemical, enzymatic, and serological analyses together with the results of preliminary studies by electrophoresis, ultracentrifugation, and ultraviolet spectroscopy indicate that, within the limits of the methods, the active fraction contains no demonstrable protein, unbound lipid, or serologically reactive polysaccharide and consists principally, if not solely, of a highly polymerized, viscous form of desoxyribonucleic acid.... The evidence presented supports the belief that a nucleic acid of the desoxyribose type is the fundamental unit of the transforming principle of Pneumococcus Type III."

However, it was some time before Avery et al.'s results were generally accepted. Some scientists thought there must have been contamination; others thought it was a neat trick, but specific just to Pneumoncoccus.

Horace Freeland Judson, author of the Eighth Day of Creation, wrote "some papers are great, of course, because they establish, define, settle their issues. This great paper did something else: Avery opened a new space in biologists' minds--a space that his conclusions, so carefully hedged, could not at once fill up."

Not everyone was resistant to the notion of DNA as the genetic material. Chargaff immediately changed fields upon reading Avery et al. 1944, and went on to make important discoveries on the ratios of the various bases. Hershey and Chase were convinced. Watson and Crick obviously spent little time worrying whether the transforming principle was protein or DNA.

One of the great travesties of 20th century science is that Avery, MacLeod and McCarty did not receive the Nobel Prize for their achievement. No less a giant than Joshua Lederberg claimed that theirs was "(t)he pivotal discovery of 20th-century biology."

There's a nice collection of documents at the National Library of Medicine.

Avery during a lighter moment...Photos from National Library of Medicine.

Thursday, September 20, 2007

Video of Enzyme Unraveling DNA

For the first time, scientists have videotaped the interaction of an enzyme and DNA. Researchers from the University of Cambridge have used a revolutionary Scanning Atomic Force Microscope in Japan to produce amazing footage of a protective enzyme unraveling the DNA of a virus trying to infect a bacterial host. The footage shows a bacterial type III restriction enzyme attaching itself to the DNA of a virus, in order to break the DNA before the virus has the chance to infect the bacterium.
video
Dr Robert Henderson, who led the Cambridge research, explains:

“This is the first time that such a process has been seen in real time. To be able see these nano-mechanisms as they are really happening is incredibly exciting. We can actually see the enzyme ‘threading’ through a loop in the virus’s DNA in order to lock on to and break it, a process known as DNA cleavage."


This film was originally published online on July 23, 2007 in the journal The Proceedings of the National Academy of Sciences (PNAS), 10.1073/pnas.0700483104

Original press release here.

Tuesday, September 18, 2007

Ernst Haeckel Archive

Wikimedia is a fantastic resource; I love to browse it in my spare time (sadly limited at present). Here is a set of plates from Ernst Haeckel's Kunstformen der Natur (Artforms of nature) (1904).

This description of Kunstformen der Natur is abridged from Wikipedia.

Kunstformen der Natur (Art Forms of Nature) is a book of lithographic and autotype prints by German biologist Ernst Haeckel. According to Haeckel scholar Olaf Breidbach (the editor of modern editions of Kunstformen), the work was "not just a book of illustrations but also the summation of his view of the world." The over-riding themes of the Kunstformen plates are symmetry and organization. Kunstformen der Natur was influential in early 20th century art, architecture, and design, bridging the gap between science and art. In particular, many artists associated with Art Nouveau were influenced by Haeckel's images, including René Binet, Karl Blossfeldt, Hans Christiansen, and Émile Gallé. One prominent example is the Amsterdam Commodities Exchange designed by Hendrik Petrus Berlage, which was in part inspired by Kunstformen illustrations.

Monday, September 17, 2007

Bacteriophage Lysogeny


There's a great new post over at Microbiology Bytes about bacteriophage lysogeny.

Usually bacteriophages lyse their hosts following infection, however a few so-called "temperate" phage undergo lysogeny. In lysogeny, the bacteriophage integrates its genome into that of its host. The phage, then, is replicated each time the bacterial cell divides. In the lysogenic state, the bacteriophage can have considerable influence over host physiology.

Check out this page for the full details!

Photo from Viruses (Scientific American Library) by Arnold J. Levine

Breath-taking Stupidity

Via the Tiny Frog.

Notes from a Creationist class...

Instructions to Class: In the first chapter of the Book of Genesis is an amazing statement, coming from 3,500 years ago, of the divine creation of the universe. It is impossible to combine evolution and the Bible. Not only has science not proven evolution, famous evolutionists laugh at those who try to “marry” evolution with the Bible. There are a number of problems that evolutionists have not solved. Let’s look a several of them.

[S]cientists have computed that to provide a single protein molecule by chance combination would take 10262 years. Take thins pieces of paper and write “1” and then zeros after them – you would fill up the entire known universe with paper before you could write that number.

100000000000000000000000000000000000000000000000000000000000000000
000000000000000000000000000000000000000000000000000000000000000000
000000000000000000000000000000000000000000000000000000000000000000
00000000000000000000000000000000000000000000000000000000000000000

Whoa, that's 10^262. It didn't even take up the full page!

Friday, September 14, 2007

This Week's Citation Classic

Publish PostHurlbert S H. Pseudoreplication and the design of ecological field experiments. Ecol Monogr. 54:187-211, 1984.

It's not often a paper claiming that half of all papers published in ecology are crap is cited more than 2,880 times. But that's exactly what Stewart Hurlbert did. He pointed out that a significant fraction of papers published in ecology suffered from poor experimental design and inappropriate statistical analysis.

The main problem is pseudoreplication, which is non-independent measurements of any phenomena.

As Hurlbert (1984) puts it:

“Pseudoreplication is defined as the use of inferential statistics to test for treatment effects with data from experiments where either treatments are not replicated (though samples may be) or replicates are not statistically independent.”

For example, lets say you want to see if there is a relationship between diet and weight in frogs. You feed 10 frogs either 1 gram or 2 grams of flies a day. Over the next month, you weigh the frogs once a week. Then you analyze your data via an analysis of variance (ANOVA) with weight as the dependent variable, food level as a treatment and find that the high food frogs gained more weight than the low food frogs. So it must be the treatment right? Wrong! This is pseudoreplication. Weighing the same frog four times violates the assumption of non-independence in an ANOVA. Therefore, this ANOVA may underestimate your probability value (P-value or the probability of obtaining a result at least as extreme as a given data point, assuming the data point was the result of chance alone) by an order of magnitude or more. Thus you may be claiming there is a relationship between the two variables when in fact none exists.

If you read the old literature, or even some of the new literature, you see pseudoreplication over and over again. However, the problem is easily correctable by conducting a repeated measures ANOVA or by "nesting' your measurements.

Hurlbert had this to say about writing the paper:

"Some minor additional revision and expurgationwas requested. Prompted by a reviewer's charge that I used "private language and humor by misstatement," the managing editor, Lee Miller, questioned some of my metaphors such as "demonic intrusion" and "biting the bullet as well as the apple," and the copy editor, Sarah Gagnon, thought I was pushing matters by acknowledging the helpful comments of colleagues and then saying that "Any errors that remain are their responsibility and theirs alone." In the end, they kindly relented and let me have my fun."

Ahhh the good ole days. I seriously doubt anyone could get away with such humor today.

On a personal note, I was first introduced to this paper in my first semester in grad school in a seminar taught by Ed Garton, Advanced Population Biology. Never mind that I had never taken Intermediate Population Biology or even Population Biology for Dummies, I signed up thinking, how hard could it be? My cheeky attitude soon turned to outright fear and trembling as I gawked at the foot high stack of required literature readings and I gaped at the comments by one of my classmates, the long-haired Ryan J. Monello, during our first class. What was I doing in this class of ubermenschen such as Monello and John Pearce? Obviously I better tuck my tail between my legs and back out of this mess. Turns out Monello was bluffing; he didn't know anything about population biology (some would argue he still doesn't :P ). I ended up learning a lot of great biology, doing fairly well in the class (A or A- I think) and Monello became one of my best friends.

Photo: Hurlbert rafting on Laguna Colorada, Bolivia via his website.

Tuesday, September 11, 2007

Darwin Day Petition

The grad students at Portland State University have created a petition to reclassify non-science books currently classified in the science category.

To quote from the first paragraph of their petition:

"As scientists, we feel strongly that categorizing Intelligent Design ("ID") as science is both inappropriate and misleading. Local bookstores and libraries unintentionally exacerbate this misleading categorization when they shelve ID books and legitimate science texts in the same section . Our goal is to convince the U.S. Library of Congress to re-classify ID books into sections other than the science section."

The petition stems from a visit to the famous Powell's Book Store in Portland. I love Powell's, but they should know better than to put ID books on the Science shelves. Ultimately the goal is not have ID books removed from stores and libraries, but rather to have them placed in more appropriate categories, such as Pseudoscience or Fantasy.

The above petition is intended for scientists. Informed citizens can also sign a petition here.

Monday, September 10, 2007

100th Post Blogoversary: XKCD and Dating

XKCD, the famous webcomic for nerds, has a new comic up about "dating pools". I've heard the (age/2)+7 rule a few times before, but I've never considered plotting it out to see what it implies. Someone found some census data, and reports that the results are less promising than XKCD suggests. This figure shows that, given the (age/2)+7 rule, available singles peaks at 27.
Another figure suggests that XKCD was basically right...
Here the number of available partners does show a concave shape. Even though I am too lazy to do the graphing, I am inclined, based on intuition, to believe the latter curves rather than the former. I wonder if anyone out there cares to clear up this controversy. I am sure your paper would fly thru peer review at the venerable Annals of Improbable Research. Just make sure you credit me as a co-author in keeping with the guidelines for giving credit where credit is due:

Anyway, back to the graph. The situation is poor for single women past 35 yrs of age; they far outnumber single men of a similar age. Interestingly the sex ratio at birth is 1.05:1 in favor of men. (The genetics of sex ratio are a very interesting story, which I will cover at some point). However, men are stupid, risk-taking fools whose bodies tend to degenerate faster, thus women tend to live, on average, six years longer than men. Men, that is those that haven't offed themselves in some ridiculous stunt, will enjoy less competition for mates once they are past the age of 35.

On the other hand, there are some folks who can mathematically demonstrate that they will remain single for all time.

Friday, September 7, 2007

This Week's Citation Classic


This week's citation classic is Gunther Stent's Molecular Biology of Bacterial Viruses (WH Freeman, 1963). Stent is a polymath, currently a professor emeriti in the MCB Department at UC: Berkeley. He started his career by obtaining a Ph.D. in Physical Chemistry in 1948 from the University of Illinois, then joined Max Delbruck's lab at the California Institute of Technology, before joining the University of California, Berkeley faculty as an Assistant Research Biochemist in 1953. Stent soon left his mark on fields as diverse as bacterial genetics to DNA structure to neurobiology and even the history and philosophy of science. His published books include, the classic, Phage and the Origins of Molecular Biology (1966, 1992), the textbook, Molecular Genetics: An Introductory Narrative, The Neurobiology of the Leech (1981), Mind from Matter: An Evolutionary Epistemology (1986), and his autobiography, Nazis, Women and Molecular Biology.

Molecular Biology of Bacterial Viruses
is part textbook, part memoir, part history, part lab manual and thoroughly entertaining. I still use it and cite it in my own work. Dedicated to Max Delbruck, it opens with a stunning photo of the DNA of phage T2 liberated from the phage's capsid. It proceeds then to discuss phage history, morphology, growth, life cycle, genetics and theory. Anyone with even a cursory interest in phage cannot help being educated and entertained by this book.

Here is a poetic tribute to Gunther Stent on the occasion of his 80th Birthday.

Sunday, September 2, 2007

What I did last summer (and year)....

Earlier in these pages I gave a brief background of what I've been doing for the past year. I've been interested in how differences in mRNA production and differences in holin structure led to variability in lysis timing. Max Delbruck was the first to consider this question; he looked at variation in the number of babies a single phage produces and found a great deal of variation in this important life history trait. Delbruck's method, diluting a suspension of infected bacteria such each dilution contained on average less than one bacterial cell, and then plating all the (hundreds of) dilutions, is especially onerous, and perhaps explains why his work was not followed up.

(i.e. production rate, and observe the changes in Moreover, his work leaves open the questions of what causes the variation and whether it is evolutionarily significant. My work follows up on Delbruck's, except that I chose to look at a different, but closely related life history trait, lysis time. Earlier work has shown that there is a direct correlation between lysis time and burst size: the longer the phage waits to lyse the cell, the more babies it can produce. So it makes a good proxy for burst size, as well as an interesting life history trait in its own right. Plus, we now have the genetic techniques to manipulate the phage's genome and dissect the causes of variation: to wit, the ability to manipulate the holin protein structure and to alter the strength of the promoter that controls holin production. All we need is a way of observing lysis time for individual cells. Enter the microscope-mounted perfusion chamber! Here is the setup:

The way this works is you place a glass cover slip on the bottom, a cell-binding agent (poly-lysine) and some E. coli infected with lysogenic phage, then place another cover slip on top. The cells form a single layer on the bottom cover slip. The whole unit is placed on a heating platform, under a normal light microscope, and tubes are attached to allow a flow of nutrient broth thru the chamber. The heating platform generates a heat spike, inducing the phage to begin the lysis process. With a microscope mounted camera, I filmed the bound cells following the heat spike until they lysed, then recorded the time of lysis for each cell.

Given are the variation in lysis time for the wild type (JJD3), the most variable altered holin sequence genotype (JJD9) and the most variable altered promoter genotype (SYP028). This histogram (below) clearly shows the greater variability (standard deviation, SD, in lysis time for the latter two genotypes.

In general, SD increases with the mean lysis time (below, P = 0.0087). This result is consistent with the idea that, on average, it takes a longer time for a weak holin-holin interaction to attain the critical holin raft size that is necessary for hole formation. Furthermore, the the timing of attainment also varies widely among individual infected cells. That is, we should expect to observe a positive relationship between the mean lysis times and their standard deviations.
Greater promoter strength leads to a shorter lysis time (P = 0.0065). Interestingly, the lysis time variation seems to show a threshold effect. Within a range of promoter strength (between 150 to 250), different mean lysis times showed a similar stochasticity (P = 0.9593). However, once the promoter strength was dropped to a low level, the stochasticity increased dramatically.
Finally I showed an environmental component to lysis time stochasticity by reducing the nutrients provided to the host cells. Expression of the phage holin protein requires the host synthesis machinery, including the RNA polymerases (RNAPs) for transcription, ribosomes for translation, and many other raw materials for protein synthesis and enzymes for modifications. In general, cells growing at a higher rate will have a higher concentration of the synthesis machinery. Here as growth rate increases, the stochasticity (SD) decreases (P = 0.0346), demonstrating that host physiology can greatly influence the outcome of a viral infection.
The commonly invoked causes for cellular stochasticity are the random events of gene transcription, translation, and degradation of the expressed protein. Besides the usual causes, there is another layer of random event for holin hole formation, namely, the association and disassociation of holin raft on the cell membrane. However, in this preliminary study, I was not able to attribute the relative importance of each cause for the observed lysis time stochasticity. If the main cause is due to host biochemistry and physiology, then it would be difficult for the phage to reduce stochasticity. On the other hand, if the main cause is due to the amount of holin production or holin-holin interaction, then it is possible for mutations to change the promoter strength or holin sequence to increase or reduce the level of stochasticity.

Whether the observed lysis time stochasticity is evolutionarily significant remains to be determined; however it is conceivable that selection can favor genotypes with greater or lower levels of phenotypic stochasticity depending on the circumstances. Future experiments will address (1) whether variation in lysis time stochasticity translates into variation in fitness; (2) whether genotypes expressing greater or lower levels of lysis time stochasticity can be selected for; (3) whether similar patterns of stochasticity exist for different phage species.

Saturday, September 1, 2007

Cartoons from Evolution: a journal of nature, 1927-1938

A charming archive of anti-creationist cartoons.
Noted:

Evolution:
a journal of nature

This page provides information about this otherwise lost journal in the 1920s and 1930s devoted to promoting the teaching of evolution in US public schools.

Maintained by:

Dr Joe Cain, Department of Science and Technology Studies, University College London

Senior lecturer in history and philosophy of biology. His current research interests include the history of evolutionary studies, history of American science, and history of natural history.