Sunday, October 28, 2007

Biology and Art

I love reading bioephemera; Jessica always has interesting things to say about biology and art (and her artwork is amazing). I was impressed at the insight in her latest post. It taught me a thing or two about detachment and human nature. Don't take my word for it, get over there and read it.

Jessica Palmer
Bee and Echinacea
watercolor on Strathmore paper

Friday, October 26, 2007

This Week's Citation Classic

Fraenkel-Conrat H. and Williams R.C. (1955). Reconstitution of active tobacco mosaic virus from its inactive protein and nucleic acid components. PNAS USA 41: 690-698.

This week's citation classic is probably the coolest experiment you've never heard of. Fraenkel-Conrat and Williams literally took a virus apart, separated its components, then put it back together again. Granted TMV is a relatively simple virus, consisting of 2130 molecules of coat protein and one molecule of genomic RNA 6390 bases long. Nonetheless, this experiment caused quite a buzz in the scientific world.

Gunther Stent wrote to Sidney Brenner, "Frankel-Conrat seems to have done the biggest thing with TMV since Stanley crystalized it. He can add soluble TMV protein to soluble TMV RNA, aggregate the whole mess into rods of which 0.1% are infective!!! Naturally, you don't believe it--nor did I or anyone else, but unless he has made up the whole thing it seems that it must be true. You can't beat that for laughs, can you buddy?"

It was true.

First Fraenkel-Conrat and Williams treated TMV with a mild acid. This treatment eliminated the charges that held the virus together. Then they separated and purified the protein. In parallel, they treated TMV with a detergent to strip away the protein, and recovered the RNA. After these steps, the viruses were no longer infective. Then they mixed the whole mess together again, and lo and behold! Reconstituted viruses!

The following year, Fraenkel-Conrat hybridized the viruses by mixing protein from one strain with RNA from another. Not only did he get viable viruses, he also was able to show that progeny viruses always had the same type of protein coats as the parent strain that donated the RNA. Thus proof that RNA was the genetic material for these viruses.

Photo of Tobacco Mosaic Virus from NIH.

Wednesday, October 24, 2007

I'm #1 on Google!

From David Ng: I'd like to suggest a meme, where the premise is that you will attempt to find 5 statements, which if you were to type into google (preferably, but we'll take the other country specific ones if need be), you'll find that you are returned with your blog as the number one hit.

Looks like I've cornered the market in all things Evilutionary.
Was I the first to ask "What has phage done for you?"
How is it that I'm not the number one John Dennehy?
Admittedly bacteriophage art is kind of an exotic interest.
Is there anything bacteriophages cannot do? I dunno. You tell me.

Hat tip Larry Moran

Virus Traps

Hmm my virus traps work seems to be generating quite a bit of interest. I originally thought it was kind of a neat idea, but just a special case of a broader research program I've been involved in: bacteriophage growth in environments containing multiple host types.

However the virus trap idea seems to have captured the popular imagination. First, Carl Zimmer wrote about virus traps for the NY Science Times. Then the we the German public broadcaster ARD contacted my former PI about including a segment about virus traps in a series of documentary films about viruses. (No word yet whether they will go thru with it; as the director mentions, it might be difficult to "find a 'visual' way to explain your work"). Finally, Janet Ginsburg wrote about virus traps for New Scientist. (Unfortunately it is not open access so go buy a copy at your newsstand or get 4 issues for $4.95 if you purchase online). Janet promises to write about it for her excellent blog as well. I, for one, am eagerly waiting the article.

In the meantime, I've copied a quote from the article.

"Tackling the issue from a different perspective is ecologist Paul Turner of Yale University. To him, a virus trap is an example of an 'ecological trap' - a habitat that looks fertile but is actually a blind alley. The classic example is mayflies mistaking asphalt for water and laying their eggs on it. In nature, ecological traps can cause local populations to decline, or even die out if they outnumber fertile habitats. Turner wanted to know under what conditions artificial virus traps could do the same, so he created a mini-ecosystem made up of the bacterium Pseudomonas syringae and a virus called phi 6, which preys on it (Ecology Letters, vol 10, p 230).

He chose this system because it is easy to introduce a trap. To attack Pseudomonas, phi 6 first latches onto telescopic appendages called pili, which the bacterium uses to invade plants. When the pili are retracted, the virus is pulled inside. However, there is a mutant 'superpiliated' strain of Pseudomonas which has more pili than normal but cannot retract them, meaning phi 6 can bind to but cannot enter and infect the bacterium. This is the strain used to trap would-be invaders.

To test its effectiveness, Turner prepared test tubes of the bacterium with varying levels of trap, then introduced the virus. 'We set up a game playing by the simplest rules possible,' he explains. He judged success or failure by viral survival and growth rates. If the trap works, virus levels should decline - which is exactly what happened. A 50:50 mix of traps and normal bacteria vanquished phi 6 completely.

Turner's team is now looking to turn experiment into therapy, removing red blood cells and adding decoy attachment sites for viruses. Their focus right now is HIV. 'All of our drugs against HIV are effective because they keep immune cell counts up,' says Turner. 'That's a very expensive venture that a lot of people can't afford. If you could find a way to protect those cells through a sheer onslaught of traps, that might be another way to achieve the same thing.'"

Photo of HIV budding from a CD4 cell from NIH.

Monday, October 22, 2007

Aging in Bacteria

Previously I posted on aging in bacteria. One question I posed was "is, given an initial population that supposedly contains both old and young cells, are the differences in growth rate between cells sufficient to produce large differences in microcolony sizes when microcolonies are initiated on agar?" If true, this finding would have considerable bearing on the biology of an organism I am interested, the bacteriophage. Eric Stewart, author of the original manuscript I wrote about, responded to my question. Turns out there is not much reason to expect large differences in microcolony size due to cell age. However, other factors, such as whether the cell recently divided or not, could affect microcolony size. Here is what Dr. Stewart had to say:

I did not record the size variation of the microcolonies, but even a two-fold difference is completely expected, based on the fact that some cells should arrive on the agar just after division, and some just before (a two-fold difference in starting biomass). Elio noted little variance in his colony sizes, and you wondered if old and new cells were different enough in growth rate to cause visible size differences in microcolonies. In fact, the very mechanism of how cells age (and rejuvenate) makes this almost impossible. Even a very old cell, as long as it can divide once, will produce one young cell in addition to its even older self. That young cell will have a nearly maximal growth rate, and should divide again relatively quickly, producing one more young cell, in addition to its now slightly older self. This means that as long as one division occurs, the colony is once again quickly populated with young cells, and eventually, at large enough population sizes, the entire 'standard' distribution of ages is recapitulated in every colony.

While the explanation above reduces the microcolony size difference due to
the age of the starting cell, there are other factors at play as well. First, the difference in growth rates is something like 2% per old pole cell division, so if the cells are not extremely different in age, it will be very hard to detect, given the already two-fold variation in microcolony size due to the cell cycle timing of the first cell. Second, old cells are exponentially decreasing in frequency, by the very nature of the division that produces them. Young (first division) cells make up half of any E. coli population, due to the fact that one is produced in every division. The exact same process means that one half of the population is at least one division old, one quarter is at least two divisions old, 1/8th is at least three divisions old, etc. This means that in order to find one arbitrarily old cell, you must examine 2^X cells, where X is the division age you are seeking. As this doubles with each additional division, you can see that truly huge numbers must be examined to find really old cells. For example, examining about one thousand colonies will, on average, reveal one that arose from a ten division old cell; this would then need to be detected in the distribution of nine, eight, seven, etc. division old cells, taking into account the fact that the very first division produces a young cell, as noted above. Finally, there is a large amount of noise; that 2% difference is an average of very many cells. The distribution is quite

For those reasons, it is quite difficult to detect senescence in bacteria.
We accomplished it by examining very large numbers of cells, and measuring their actual individual growth rates (exponential fit to the increase in length over time). It was the automation that allowed us to achieve this; others had come very close in the past, but were limited by the need to measure and record all of the data by hand e.g. Powell EO and Errington FP. 1963. Generation times of individual bacteria: Some corroborative measurements. J Gen Microbiol 31: 315–327.

Dr. Stewart also responded to questions regarding the number of cells dying during the course of the experiments.

Elio Schaechter wrote that he spread Salmonella cells on nutrient agar on a slide, and counted how many didn't form colonies. This type of experiment was also performed by others (e.g. Gallant, J., and Palmer, L. (1979) Error propagation in viable cells. Mech. Ageing Dev. 10: 27-38), as well as repeated by myself before the timelapse experiments in the paper. Counting 17,000 microcolonies, I found a 'failure to grow' rate of about 1 in 400 for E. coli, which agreed with the Gallant and Palmer results as well. I suspect that there may be a 'plating shock' that results in such relatively high levels of non-growth, compared with the different measurement of non-growth during timelapse, which came out at about 1 in 2000. Therefore, this rate probably doesn't indicate much about senescence, but some other cause of 'death' (non-growth).

So there you have it. Cells age. But you have to check quite a few cells before you notice much of an effect.

Photo of Bacillius subtilis by Dr. Leendert Hamoen, Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne.

Friday, October 19, 2007

Extraordinary Sex Ratios

This Week's Citation Classic comes from the venerable W. D. Hamilton. 1967. Extraordinary Sex Ratios. Science 156: 477-488.

Here's a test. Read pgs. 142-143 of R.A. Fisher's Genetical Theory of Natural Selection. Then read the first paragraph of Hamilton's Extraordinary Sex Ratios. Both explain why the sexes usually come in equal numbers. Which is easier to understand? I suggest the latter.

Perhaps now you will understand why so many evilutionary biologists hold Bill Hamilton in such high esteem. I still recall my initial reading of the paper during my first semester of graduate school. My advisor said to me one day, "mumble mumble dominance... mumble mumble sex ratios... mumble mumble foraging....mumble sex ratio... mumble have more males...." In his defense, he was probably speaking clearly. I was just so cowed that I had trouble concentrating. I left his office thinking, "I better read up on sex ratios". I look up "Sex Ratios" in ISI Web of Knowledge. Wow... 8,549 results! OK, sort by times cited. Hmmm... Extraordinary Sex Ratios 1,406 citations. OK, I'll start with that one.

My reaction on reading the first page: WHOA! So that's why the number of males and females are equal. Sex ratio is one of those things that seems obvious until you start to think about it. Darwin himself thought the problem of sex ratios was too difficult to tackle, and left it for future generations (Descent of Man, p. 399). Fisher first figured it out as I mentioned above.

Much of Extraordinary Sex Ratios deals with exceptions from balanced sex ratios, usually cases where females outnumber males, and gives excellent examples of these. One example in particular totally blew my mind: the Pyemotidae. Take Acarophenax tribolii for example. These mites usually occur in broods biased 15-1 in favor of females, and they are quite naughty. The single male will mate with and fertilize all of his sisters. Hang on. Before you get too excited, all this happens in full view of the mother. Are you slackjawed yet? Is your jaw slack? This will make your jaw hit the floor. All this takes place in the mother's womb! That's right. The enormously swollen, gravid, female A. tribolii has~16 full-grown adult mites having a great, big, incestuous orgy in her womb! Eventually these ungrateful offspring burst her open, killing her. Actually not all of them. The poor male completes his life cycle and dies before he is born. At least he isn't a virgin.

The reason the sex ratio is so biased in Pyemotidae is because they engage in incest exclusively (or nearly so). So why make lots of males? One can fertilize all his sisters; a second would be a total waste of energy and effort. The Pyemotidae have evolved further to protect this male as much as possible by having the mating take place within the womb because, if he dies, the females evolutionary life is over. Moreover, you keep all the actors in close proximity, ensuring all offspring are fertilized.

Stephen Jay Gould writes about the Pyemotidae in Ch. 6 of The Panda's Thumb. Olivia Judson also mentions them in her book, Dr Tatiana's Sex Advice to All Creation.

Bill Hamilton died on 7 March 2000 from complications of malaria. A page is dedicated to his memory.

The drawing above is Fig. 53 Progenesis in the mite Siteroptes graminum. A sexually mature female with one male and four females growing within her body. (From Rack, 1972.)

Monday, October 15, 2007

Chilling effect, indeed...

Tara posted a down-right scary article today at at Aetiology. I don't mean Halloween spooky goblins and ghosts scary; I mean scary as in getting sent to PMITA prison scary.

"...a University of Pittsburgh geneticist, Robert Ferrell, plead guilty to charges of failing to follow proper [Material Transfer Agreement] procedures in mailing [microbiological] samples, after being investigated initially for charges related to bioterrorism that were dropped... and another professor awaits trial.... Ferrell violated this [Material Transfer Agreement] agreement by sharing [Bacillus subtilis and Serratia marcescens] strains with Kurtz. Normally, this would be an issue handled between Ferrell (and his university) and ATCC; however, under the broad definitions of mail and wire fraud under the Patriot Act, the government stepped in and charged Kurtz and Ferrell with mail and wire fraud--felonies that, since they're being charged under the Patriot Act, could carry a possible 20-year sentence."

Has the government no sense of decency at long last?

Intellectual Bloggers

Ed Yong at Not Exactly Rocket Science tagged me with an Intellectual Blogger Award. I'm flattered to be considered among such illustrious company as The Loom and Retrospectacle among others! He wrote that my blog "focuses very much on the science, rather than the creationism/ID debate." This is true... there are many other bloggers who can handle the IDiots much more ably than I. I think I will pass on the meme by tagging some other blogs that "focus very much on the science". Also I will try to mention those that I haven't called attention to before.

I only became aware of this blog fairly recently, but I really like some of the posts. The author is Rob Carlson from theUniversity of Washington. Rob is developing new fabrication techniques and microfluidic systems for manipulating and measuring cells and analytes. This is a topic I am very interested in at present.

Sex, Genes and Evolution
John Logsdon is a molecular evolutionary biologist at the University of Iowa. It doesn't hurt that he reads my blog "slightly less than daily". That's ok, I only publish slightly more often than weekly.

Rosie Redfield is a microbiologist extraordinaire at the University of British Columbia. Her blog is highly technical, but I enjoy it because she writes about a lot of the things I like thinking about.

Dan Rhoades is a
a staff scientist for Agave Biosystems in Ithaca NY. His blog is an interesting blend of the macro and the micro.

Microbiology Bytes
Alan Cann is a Senior Lecturer at the University of Leicester. He writes a great blog on all things microbial.

Friday, October 12, 2007

The Most Beautiful Experiment in Biology

This week's citation classic is:

Meselson M, Stahl FW. 1958. The Replication of DNA in Escherichia coli
Proceedings of the National Academy of Sciences USA 44 (7): 671-682.

After Watson and Crick published their structure of DNA in Nature in 1953, the race was on to empirically demonstrate its correctness because, in fact, Watson and Crick's model had precious little going for it other than the fact that it was so damned pretty.

The beauty of the Watson-Crick model is that the structure implies that information can be coded in the sequence of bases and this sequence can be replicated by splitting the double helix in two and constructing new double helixes from the two single strands. But how to prove this?

Enter Caltech grad student Matt Meselson and postdoc Frank Stahl. The two met in a physiology course at the MBL in Wood's Hole: "I partied my way through that course," Stahl confesses. "During the partying, I met Meselson."

Meselson and Stahl decided they could determine how DNA replicated when all the big shots, such as the great Delbruck (see Delbruck, PNAS, 1954), had failed. They spent a couple of years futzing around with phages before hitting upon the idea of using E. coli and heavy nitrogen. 15N contains an extra neutron and molecules made with it would be heavier than molecules containing 14N. So Meselson and Stahl grew E. coli in 15N for many generations, resulting in cells with much heavier than normal DNA. This DNA was extracted, combined with DNA from normal E. coli, and ultracentrifuged in a cesium chloride solution. The photos of the ultracentrifuged DNA showed that the lighter DNA formed one band and the heavier DNA formed another. So far, so good.

Now the clincher. The cells grown in 15N were now transferred to regular 14N media and allowed to grow for one generation. This DNA was then extracted and ultracentrifuged. This DNA showed a band intermediate to that of the heavy DNA and the light DNA. Why? Because the original heavy DNA split in two and a new light DNA chain was constructed to match the parental heavy DNA strain. Semi-conservative replication!

“Stahl credits the beauty and success of their paper to two things. First, the "delightfully clean data" were serendipitous. The clean data peaks they observed resulted from the DNA fragmenting during handling; unfragmented DNA would not have separated as nicely. Stahl likens pipetting DNA to "throwing spaghetti over Niagara Falls." The stress of the pipetting caused tremendous shearing of the DNA, although they did not realize this at the time, nor did they realize how critical this would be to obtaining clean peaks. In addition, Meselson was a "stickler for clarity," said Stahl. "Every single word in that paper was discussed several times before being allowed to keep its position in the sentence." Tinsley Davis. PNAS | December 28, 2004 | vol. 101 | no. 52 | 17895-17896.

Animations explaining the experiment are available here and here.

Bacteriophage Art!

A recent Bioephemera post highlights the work of Holly Wichman, a professor at the University of Idaho who makes models of bacteriophages. When I was at the University of Idaho, Holly was still working on LINE-1 retrotransposons and I was studying pronghorn social behavior. Since then we've both converged on phage research. She has proven far more creative than I in this field.

Thursday, October 11, 2007

(Almost) Friday Funnies...

Here is a collection of anti-cretinist cartoons.

Hat-tip Greg.

Wednesday, October 10, 2007

Cool Science Site of the Day

Mendeleev's Periodic Table is a marvel of an information source. So much data is packed into this fairly simple looking chart, including symbol, atomic number and mass, electron configuration, and valence. I really didn't think it could be improved upon. That is until I found this web version. Clicking on the elements brings up the element's wiki page and all the info contained therein. A sliding bar in the upper right corner shows the temperatures of transition states. You can click on series, properties, orbitals and isotopes to find further information for each element. Sweet!

What is a Gene?

Mark Gerstein and colleagues published a very nice review of the gene in Genome Research this summer, and I missed it. I think I was on vacation in Wyoming. Anyway, I just found it now. If you missed it too, definitely check it out. The review covers how genes were conceptualized since their "discovery" by Mendel, and touches upon all the major milestones in the history of genetics. The authors then discuss issues with the current conception of the gene, and propose a new model. Here is their summary:

A proposed updated definition
There are three aspects to the definition that we will list below, before providing the succinct definition:

  1. A gene is a genomic sequence (DNA or RNA) directly encoding functional product molecules, either RNA or protein.
  2. In the case that there are several functional products sharing overlapping regions, one takes the union of all overlapping genomic sequences coding for them.
  3. This union must be coherent—i.e., done separately for final protein and RNA products—but does not require that all products necessarily share a common subsequence.

This can be concisely summarized as:

The gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products.

We've come a long way from "One Gene, One Protein".

If you have some way of printing it out, there is a fantastic time-line poster of genetics milestones here.

Sunday, October 7, 2007

Trilobite Press

Normally I don't advertise commercial interests on this site; the Evilution Store was an exception, but I'm about to make another one... Marek Eby sent me a note pointing out his Trilobite clothing line. I love this kind of stuff... the geekier the better. I think this kind of advertising does an important service; it increases the visibility of science in general and evolution in particular in popular culture. At any rate , it's a lot better than wearing a shirt with a Nike logo. I'm sure Anne-Marie would love this one. The shirt depicting a Velociraptor wearing a beret a la Che Guevara is my favorite (see above). Oh and Christmas is coming soon. No reason. Just thought I'd mention that.

Friday, October 5, 2007

This Week's Citation Classic

The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. S. J. Gould, R. C. Lewontin Proceedings of the Royal Society of London. Series B, Biological Sciences, Vol. 205, No. 1161, The Evolution of Adaptation by Natural Selection (Sep. 21, 1979), pp. 581-598.

I confess I am not a huge fan of Stephen Jay Gould. Although his extensive science writing is often charming, and has helped popularize evolutionary biology across a much broader spectrum (Wonderful Life was wonderful!), I consider much of his evolutionary thought simply wrong headed and strange. I won't go into specifics here, *cough, cough, punctuated equilibrium*, but some of his work is basically window dressing. I haven't read his latest opus, The Structure of Evolutionary Theory (its size, 5.1 pounds, is quite daunting; I'm waiting for the Reader's Digest version) so I could be wrong here, but I doubt it.

Dick Lewontin, on the other hand, is a great evolutionary biologist and has made many seminal contributions to the field.

Despite my misgivings about Gould, I found the paper on the Adaptationist Programme to be spot on. First off, it has a fantastic title. Not a cutesy punning title, but a novel, eye-catching title with side references and metaphors that actually make sense.

Second, the paper addressed a real concern in evolutionary biology. Despite G.C. Williams tour-de-force, Adapatation and Natural Selection, the study of adaptation in the '70s still suffered from wishy-washy, uncritical thinking (Larry Moran might argue still does today!). The problem was Just So stories (so named after the Kipling kiddie stories about How the Leopard Got His Spots etc.) where anyone can invent reasons, however fanciful, for why certain phenotypic traits exist.

Gould and Lewontin cite experimental work by D.P. Barash as an example of this problem.

Barash mounted a stuffed male near the nests of two pairs of bluebirds while the male was out foraging. He did this at the same nests on three occasions at ten-day intervals: the first before eggs were laid, the last two afterwards. He then counted aggressive approaches of the returning male toward the model and the female. At time one, aggression was high toward the model and lower toward females, but substantial in both nests. Aggression toward the model declined steadily for times two and three and plummeted to near zero toward females. Barash reasoned that this made evolutionary sense, since males would be more sensitive to intruders before eggs were laid than afterward (when they can have some confidence that their genes are inside). Having devised this plausible story, he considered his work as completed.

The explanation misses an obvious alternative. Perhaps the males approached the models a few times, learned that they were fake, and thereafter no longer responded to them. The proper way to conduct this experiment is to expose a male to the model once... either before or after the eggs are laid. The experiment was replicated by Morton et al. (1978) who found no evidence for anti-cuckoldry behavior.

Gould and Lewontin believed that too many biologists were simply making up similar stories for every conceivable trait. Perhaps some organismal traits have no function! Take the belly button. Maybe it evolved to collect lint so that cavemen would have a source of fiber for their diets! Uhhm... not likely. The belly button is an example what Gould and Lewontin would call a spandrel. The San Marco spandrels are so beautifully decorated with mosaics that one could be convinced that they were designed expressly to display mosaics. Not so! Spandrels simply hold up the ceiling; they were painted to make them look pretty. Belly buttons serve no function; they are simply the remnant of the umbilical connection between the mother and fetus.

So how should one determine whether a certain trait is an adaptation? A good adaptive hypothesis will make predictions concerning the trait it seeks to explain. Also several criteria should be met: (1) trait variation must affect fitness or a component of fitness; (2) the hypothesis of adaptive variation must be confirmed by either manipulating the selective environment or the phenotypic trait itself; and (3) the mechanistic link between the trait and fitness must be demonstrated.

Monday, October 1, 2007

Maria Sibylla Merian

James Audubon gets all the press, but Maria Sibylla Merian could give him a run for the money in the artist/naturalist department. In 1699, she traveled from Amsterdam to Surinam, where she explored the Surinam River and its surrounding rainforest. Along the way, she sketched the local fauna and flora for her masterwork, The Metamorphosis of the Insects of Surinam, published in 1705. She is the subject of a new biography by Kim Todd, Chrysalis, Maria Sibylla Merian and the Secrets of Metamorphosis.

A nice flash gallery of selected plates is available here (the above thumbnail does her work no justice). Learn more about her at the National Museum of Women in the Arts.