Thursday, November 29, 2007

Way Cool Post

Frequent readers may know that a prominent sub-theme of this blog is the relationship between science and art, a subject of considerable interest to myself. Scientist/Artist Jessica Palmer at Bioephemera has an excellent post on the subject.

Although the article is mostly about whether art can inform science, I found it jarring at some points because my view of art and science is so conflated, namely that science IS art (note this doesn't make the reverse also true). I don't know if Jessica would agree with me on that point, I was struck by this sentence from her post:

"Even in the simplest botanical print, or inventory of a wonder cabinet, the artist always “frames” the science - it can’t be helped! Choice of medium, choice of angle, choice of context - all of these are choices. The line between representation and story-telling is very fuzzy indeed...."

Now substitute scientist for artist. Science, then, is a way of constructing a world-view from our experiences. This does not imply that science is making stuff up and passing it off as "truth". In fact quite the opposite; fiction is abhorrent in science as, I would argue, it is in art. Look at the following depiction of three molecules. Which one looks "real" to you?
My gut reaction on looking at the picture (before reading the text) was that there was something wrong with the one on the right. The one on the left was better, but there was still something weird about it. The middle one looked "right". As it turns out, "#3, the DNA cube, is a fictitious structure - but a real (though synthetic) molecule; #1, a nanotube synthase, is the one that’s entirely made up. #2, the rotary motor, is the real structure." Now I am totally not a structural biologist and I spend very little time looking at molecular structures. Why then did the middle one just "feel" right to me? I have no clue.

But I suspect that it's because science is art and beauty is our guide. "Beauty is truth, truth beauty", right?

Queen of Decay
watercolor on paper
Jessica Palmer 2005

Wednesday, November 28, 2007

Bug Art

This week's issue of Nature has an interesting review of an exhibition, The Art of Arthopods. California entomologist Steven Kutcher uses insects as living paintbrushes to generate his "paintings". Read more about it here.

Kutcher's bug art is on display at the Entomological Society of America meeting in San Diego (9–12 December) and at the Lancaster Museum (15 December–13 January 2008), in California.

Incidentally I used to have a couple of Madagascan hissing cockroaches (above), but I failed to think of using them to create art work.

Tuesday, November 27, 2007

Quorum Sensing or Diffusion Sensing?

I'd like to call attention to an interesting couple of posts at one of my favorite science blogs, RRResearch. I find them interesting because they highlight two opposing views of the function of small signaling molecules (autoinducers). One view (Quorum Sensing) suggests that microbes secrete these molecules in order to estimate population density and predict the utility of investing in secreting molecules that can be used by the whole population. In this view, secreting shared molecules is an inherently cooperative behavior, and as such is exploitable by cheating.

Rosie Redfield has suggested an alternative explanation: diffusion sensing. Her paper in Trends in Microbiology hypothesized that "bacteria instead secrete and detect autoinducers as a method of determining whether the benefits of secreting more expensive effector molecules will limited by diffusion and mixing." This is an inherently selfish behavior because "it would be a waste of resources to secrete degradative enzymes such as proteases if they are going to immediately wash away."

The whole issue hearkens back to George Williams classic, Adaptation and Natural Selection. If that book is to be summarized in one sentence, it might be "Thou Shalt Not Invoke Group Level Adaptations When Individual Level Adaptations Will Suffice!" That is, don't claim an adaptation benefits a group of organisms when plausible explanations invoking benefits to individuals are available. By this rule, quorum sensing might be a valid explanation for autoinducer secretion, but only after diffusion sensing explanations are ruled out.

I share Rosies' frustrations. Every time someone tells me about this wonderful new experiment showing that bacteria cooperate (which, in some cases, they no doubt do), I always groan and ask if they read Rosie's paper. Invariably they haven't.

The series of posts is interesting in another light. It shows the process of science in action, which is usually an opaque process to most people. Here we have two opposing "schools of thought" arguing about the proper way to interpret ambiguous data. In the long run, it will be the hypothesis that best explains the data that "wins". In this case, the debate plays out in the blogosphere and not behind the august pages of Nature (available by subscription only).

Update: I missed this earlier, but Ford Denison of This Week in Evolution wrote a nice post about the original Diggle et al. Nature paper here.

Photo: Vibrio fischeri growth on Petri dishes after incubation in nano CuO suspension. V. fischeri is a putative case of quorum sensing. Photo from KBFI.

Thursday, November 22, 2007

This Week's Citation Classic

Olsen MW & Mardsen SJ. 1954. Natural parthenogenesis in turkey eggs. SCIENCE 120 (3118): 545-546.

Almost all vertebrates reproduce sexually, i.e. the sperm and egg join to form an embryo. Vertebrates that reproduce asexually are exceptionally rare, however turkeys are one such species that can do so. Many explanations are given as to why turkeys reproduce asexually on occasion (as high as 40% of offspring are products of parthenogenesis): low sperm count, male unavailability etc. I'll offer one of my own. Female turkeys see males (photo above) and think, "No way in hell am I having sex with that!"

Here is a quote from the Ohio State University 4H site:

Dr. M. W. Olsen working for the United States Department of Agriculture extensively studied the development of parthenogenesis in turkeys. He worked with a small variety of turkeys called Beltsville Small Whites. He found that the onset of parthenogenetic development in turkeys takes place three or four hours prior to ovulation or soon after ovulation of the ovarian follicle from the ovary. In Dr. Olsen’s early studies, the parthenogenetic development in eggs from nonmated hens would only proceed though the development of membranes and early blood formation by the embryo. He bred a strain of Beltsville Small Whites for a higher incidence of parthenogenesis in unfertilized eggs. As selection continued, the incidence of the condition increased and parthenogenic development proceeded to more advanced stages until an embryo that developed parthenogenetically from an unfertilized egg. The first poult that hatched by this method was moved, for safe keeping, from the research farm to Dr. Olsen’s basement. Unfortunately, his dog killed the turkey.


Happy Thanksgiving!!!

Saturday, November 17, 2007

Rivers and Tides

I just finished watching Rivers and Tides, a film about Andy Goldsworthy, one of my favorite artists. Goldsworthy creates ephemeral art sculptures from materials found in nature. The film is amazing. Here is a clip.

More images are available from the Andy Goldsworthy Digital Catalog, the Met, Morning Earth and WebShots.

Time interviewed Goldsworthy earlier this year.

This Week's Citation Classic

Volkin E & Astrachan L. 1956. Phosphorus incorporation in Escherichia coli ribonucleic acid after infection with bacteriophage T2. Virology 2 (2): 149-161.

After the discovery of DNA structure by Watson and Crick, the way seemed paved to a quick resolution of how proteins were made. Unfortunately, both theory and experiment quickly stalled at an impasse. Data from several labs was extremely difficult to interpret, namely findings that 1) for several bacterial species, DNA bases varied widely, but the cytoplasmic RNA did not (Belozersky & Spirin 1958) and 2) the cytoplasmic RNA was exceptionally stable (Davern & Meselson 1960). These findings seemed to suggest it was impossible for RNA to be a template for protein synthesis.

The problem was that this cytoplasmic RNA was not what later came to be known as messenger RNA (mRNA), but rather a relatively "inert" form of RNA associated with ribosomes (i.e. rRNA)(Note: rRNA is now thought to carry out key reactions during translation).

On Good Friday 1960, Sidney Brenner, Francis Crick and Francois Jacob were hanging out at Brenner's rooms at King's College when they put together some anomalous data and created a theory to explain protein synthesis. These data were 1) Hershey et al.'s (1953) discovery of a small fraction of RNA that was synthesized rapidly just after phage infection, 2) Pardee et al.'s observation of extremely rapid enzyme synthesis following mating between two bacterial types and 3) a report from two relative unknowns, Eliot Volkin and Lazarus Astrachan, from Oak Ridge National Laboratory.

Volkin and Astrachan infected E. coli with phage, then exposed the culture to radioactive 32P for a few minutes. What they found was a "DNA-like RNA" that did not resemble the previously found RNAs (i.e. rRNA and tRNA) and turned over very rapidly. The main difference was that it had similar bases to the DNA of phage.

f DNA labelled f RNA E. coli DNA E. coli RNA
A 32 33 25 26
U or T 32 29 25 19
C 18 20 25 25
G 17 18 25 19

What Volkin and Astrachan did not realize is that they discovered the key to solving the protein synthesis mystery.

Crick describes the Good Friday Meeting in What Mad Pursuit, "What the PaJaMo [i.e. Pardee et al. 1959] type of experiment showed was that the ribosomal RNA could not be the message.... Where, then, is the message? At this point Sydney Brenner let out a loud yelp -- he had seen the answer. (So had I, for that matter, though nobody else had). One of the peripheral problems of this confused subject had been a minor species of RNA [found by Volkin and Astrachan] that occurred in E. coli ... [Volkin and Astrachan's] result had hung in midair, surprising but unexplained.... What Sydney had seen was that the Volkin-Astrachan RNA was the messenger RNA for the phage-infected cell... It is difficult to convey two things. One is the sudden flash of enlightenment when the idea was first glimpsed. It was so memorable that I can recall just where Sydney, Fran├žois, and I were sitting in the room when it happened. The other is the way it cleared away so many of our difficulties. Just a single wrong assumption (that the ribosomal RNA was the messenger RNA) had competely messed up our thinking, so that it appeared as if we were wandering in a dense fog."

Paul Berg, winner of the 1980 Nobel Prize in Chemistry, calls Volkin and Astrachan's research an "unsung but momentous discovery of a fundamental mechanism in genetic chemistry" and a "seminal discovery [that] has never received its proper due."

What happened? Everybody knew of Volkin and Astrachan's findings at the time. In an interview at his Oak Ridge home in late 2003, Volkin recalled his conversation with Sydney Brenner at Cold Spring Harbor Laboratory in New York, where Volkin conducted research on the hot topic of bacterial viruses during the summers in the late 1950s. "I can well remember sitting on the lawn at Cold Spring Harbor and telling Sydney Brenner about our experiments," Volkin says. "I gave a presentation on our RNA research to the group there." In a 1977 issue of Nature, renowned biophysicist T. H. Jukes wrote that in 1956, "I had squeezed my way into a doorway of a packed room to hear a paper by Volkin and Astrachan on DNA-like RNA." (ORNL).

The problem was that Volkin and Astrachan's data was self-admittedly "sloppy", Volkin and Astrachan weren't well known, ORNL wasn't highly regarded and the data simply did not fit with the dominant paradigm at the time. Brenner, Crick and Jacob ended up getting recognized with "discovering" mRNA, while Volkin and Astrachan were never properly credited. Many scientists felt Volkin and Astrachan deserved Nobel recognition.

Belozersky AN & Spirin AS. 1958. A correlation between the compositions of the deoxyribonucleic and ribonucleic acids. Nature 182: 11–112.

Hershey AD, Dixon J & Chase M. 1953.Nucleic acid economy in bacteria infected with bacteriophage T2 .1. Purine and pyrimidine composition. Journal of General Physiology 36 (6): 777-789.

Davern CI & Meselson M. 1960. Molecular conservation of ribonucleic acid during bacterial growth. Journal of Molecular Biology 2: 153.

Pardee AB, Jacob F & Monod J. 1959. Genetic control and cytoplasmic expression of inducibility in the synthesis of Beta-galactosidase by E. coli. Journal of Molecular Biology 1 (2): 165-178.

Photo: One of the early RNA electron micrographs scanned with the vidicon/RTPP system (Jacob Maizel, Bruce Shapiro, and Lewis Lipkin). The sample was adenovirus type 2 messenger RNA. Bruce developed boundary segmenters and boundary shape descriptors that could map electron micrograph data to the secondary structure.

Friday, November 16, 2007

Welcome Gastrolith

Christopher Boynton was recently accepted at Columbia AND started a cool new blog, Gastrolith.

Congrats and Welcome, Chris!

Thursday, November 15, 2007

First Direct Evidence of Flying Spaghetti Monster!

A recent report found first fossilized evidence of the Flying Spaghetti Monster.

The resemblance is uncanny!
Ha! Just kidding, this is a report of exceptionally well preserved jellyfish from the Middle Cambrian i.e. ~505 mya. This finding sets the origins of jellyfish back ~200 mya. Previously fossilized jellyfish were found in Pennsylvanian shale ~320 mya. This is an exceptional find because the fossils are so pretty and jellyfish are, of course, soft bodied, thus difficult to find preserved.

Tuesday, November 13, 2007

Star-nosed Moles

I mentioned Star-nosed moles in a previous post. The illustration doesn't really do it justice. I suppose the illustrator toned down the drawing because, in RL, its just too freaky. Nobody would believe him.

Here's a nice post on Star-nosed moles.

Addenum: Ed Yong pointed out this post. Holy crap! That's awesome! Moles rock!

Sunday, November 11, 2007

Evilution sucks...

Heh.. this gave me a chuckle.

Comic by Rosemary Mosco of Bird and Moon.

Saturday, November 10, 2007

This Week's Citation Classic

Haig D. 1993. Genetic Conflicts in Human Pregnancy. The Quarterly Review of Biology, 68 (4): 495-532.

I suppose most people think the bond between a mother and her child is the strongest among all human relations. In a Darwinian sense, this is generally true; mothers and their offspring share ~50% of their genes. Moreover, unlike father-offspring relationships, mothers can be absolutely certain of the relatedness between themselves and their children by virtue of giving birth.

Perhaps this is why the internecine warfare that occurs between the mother and the fetus during pregnancy is so shocking.

The existence of parent-offspring conflicts was first popularized by Robert Trivers in the early 1970s. However the examples proffered of parent-offspring conflicts were animals such as caribou, baboons and macaques. The connection to humans was rarely made explicit.

David Haig changed this. He pointed out that the interests of the fetus differed from that of the mother. The offspring can best increase its evolutionary fitness by taking all it can get from the mother because it values itself (100% relatedness) over that of potential future sibs (50% relatedness). The mother on the other hand can best increase her fitness by spreading her reproductive resources over several offspring.

Some medical implications of the mother offspring conflict include:

Gestational diabetes--the mother loses control of her blood sugar levels to the offspring. As wiki notes, this can lead to a "large baby" or macrosomia.

Pre-eclampsia--the fetus induces high blood pressure in the mother in order to access more resources.

Beckwith-Wiedemann syndrome--fetus overgrowth syndrome

I previously wrote about Mother-Offspring Conflict here.

Carl Zimmer has a great article here.

"Mother & Child" by Gustav Klimt (1862-1918).

Friday, November 9, 2007

Blog Readability Test

Uh, I guess regular readers should be proud... but maybe I should make an effort to broaden my audience.

Level of education required to understand this blog: Genius

Find out what your blog's readability level is here.

I'd be interested in finding out what level of education readers have!

Hat tip: Larry and Bora

Wednesday, November 7, 2007

Get Ready for Judgement Day!

PBS is airing at two hour special on 2005's Kitzmiller v. Dover Area School District trial, otherwise known as Scopes II. Science won a deserved victory when, on December 20, 2005, Judge Jones issued his 139-page findings of fact and decision, ruling that the Dover mandate was unconstitutional, and barring intelligent design from being taught in Pennsylvania's Middle District public school science classrooms.

I, for one, will be TiVo-ing this one.

In defense of Matt Kaplan

Recently I responded negatively to an article in the Economist about research in my former lab. My complaints were, 1. sensationalistic title, 2. oversimplification, 3. sexing up the subject matter, and 4. failure to credit first author. Several respondents convinced me I was being too harsh, so I've retracted the post and apologized to Matt. The problem is that the Economist's Editors, not authors, choose titles, and Editors also have a significant influence on the tone and content of the article. The issues are not really Matt's fault.

The issues I raise are actually part of a dilemma for many science writers: what is an acceptable level of detail in an article? Naturally not all readers can be expected to understand science writing at the level of Science and Nature, but does science writing in the Economist need to be dumbed-down? The editors apparently think so. The sad thing is that they are probably right. Many people have a difficult time understanding even rudimentary science. Take for example the recent experience of the British National Lottery. In their game, Cool Cash, players scratch away a window to reveal a temperature. If that temperature is lower than temperature on the card, the player wins. The problem is that many players could not determine which number was smaller: -7 or -8.

Matt wonders, "if sacrificing some detail [is] acceptable to reach a wider audience? Is it right that editors have total control of titles to popularise complex science? Do they really know better than the journalist?"

My opinion is that there is that, beyond a certain level, sacrificing detail is counter-productive because the science itself is mis-represented, giving the reader a false understanding of science and the state of scientific knowledge. Easy to say, of course, but what is that level. I don't think there are any easy answers. Publishers know that if their readers cannot understand the material, they probably won't buy the work. Ultimately the consumer is responsible for the content because they exercise choice in the marketplace.

I, and Matt, would be very interested in what others have to say.

Photo from the Onion.

Tuesday, November 6, 2007

What would you improve?

Mark Hoofnagle at Denialism has a neat article on what would you improve if you could redesign the human body. I'm fine with an appendix, I'm not female so I don't really care about childbirth, and I'm still fairly young so I am not really concerned with my prostate. However, I would like to upgrade my senses. I'd like eyes like a hawk, ears like an owl, touch like a star-nosed mole, and a nose like bloodhound.

Birds have acute vision, but also can see ultraviolet light. Their world must be especially colorful. How cool is that?

Besides having rather keen hearing, Owls have asymmetrical ear openings permitting it to precisely locate things even in the absence of visual cues. My hearing isn't so great so this would be nice for me.

Star-nosed moles have rather exquisite senses of touch since they are functionally blind.

Bloodhounds have exceptionally sensitive noses. Imagine being able to figure out where your partner is in the grocery store by following their scent? I guess the drawback is that garbage will smell pretty bad...

Presumably it is possible for humans to evolve all these traits given enough time and the proper selective forces. In fact, it is likely that many of our senses have degenerated via relaxed selection over the millennia.

I'd also like to be able to jump higher than four inches, but let's leave that for another time...

Drawing from WikiCommons.

Monday, November 5, 2007

Author Order

EMBO Reports Science and Society section has an interesting note about author position in publications. Wren et al. 2007 note that a prominent publication trend is "author inflation", where the number of authors per paper is growing. This is probably linked to the increase in complexity of biological research and the trend towards greater collaboration across disciplinary boundaries. Naturally everyone wants the coveted first or last author spots, but those are in short supply, so more researchers are listed in the middle author spots. Given that there are, on average, more authors, what happens to those in the middle? Wren et al. report that the perception is that the more authors there are, the less each middle author contributed.

Wren et al. provide some valuable advice for untenured faculty and grad students: if possible, become corresponding author.

"Respondents reduced last-author credit when the corresponding author was the middle author. This suggests that candidates for promotion or tenure would be well advised to highlight publications on which they acted as corresponding author, especially if they were not the last author."

I found this surprising since I thought that nobody paid attention to who was corresponding author. At any rate, I am in favor of clearly delineating contributions in the paper itself, preferably on the first page, but not many journals require this.

Sunday, November 4, 2007

Night on the Town

Friday night a couple of friends and I received an after-hours tour of one of my favorite places in the world, the American Museum of Natural History. It's really nice to tour the museum when there are no screaming kids running around. One of the highlights was a trip to the roof where we had a view much like the one above (I was kicking myself for not bringing my camera). The other highlight was viewing the hominan phylogeny now including the purported newest member, Homo floresiensis in the Hall of Human Origins. Since the first reports of the little man; some have suggested that it is a clear cut case of microcephaly and over-eager anthropologists. There has been a lot of back and forth on this hypothesis, but if in fact the skull is that of a new human species, it doesn't look anything like that of the more recent hominids. Actually you have to go back to Australopithecus before you really see something that looks similar to H. floresiensis. Now wouldn't that be stunning; a new genus of hominids contemporaneous with Homo ~20k years ago!

John Hawks has a superb series of posts on H. floresiensis.

Top photo by ezola.

Thursday, November 1, 2007

This Week's Citation Classic

Readers of this blog may notice that my choices for classic papers come mainly from the evolution, ecology and molecular biology literature. This is not to imply that findings in other fields are less important, but rather that my command of the literature in other fields such as phylogenetics, developmental biology and cellular biology is less apt. However, even a caveman such as myself is familiar with the Homeobox discovery.

McGinnis W, Levine MS, Hafen E, Kuroiwa A, Gehring WJ. 1984. A conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes. Nature 308: 428-33.

Homeotic genes determine when, where and how animal body segments develop. In other words, they tell cells in the developing embryo what kind of structures to make, i.e. legs, head, arms etc. Mutations in homeotic genes can result in dramatic changes in animal body plans, such as the antennapedia in the fruit fly that causes legs to develop instead of antennae (see photo). These genes, as the Nobelist Edward B. Lewis discovered, usually are co-linear in space and time with their segments of activity.
Many homeotic genes contain a common motif, a region termed the homeobox. This 180bp sequence encodes a 60 amino acid transcription factor, a protein that switches on and off other genes by binding to the relevant regions of DNA. The awesome thing about the Homeobox is that they are evolutionarily highly conserved, as McGinnis et al. discovered. The homeobox of the fruit fly is nearly identical to that of a wide variety of animals including the mouse and even humans! This is extraordinarily strong proof of common descent. Next time you see a fly, think about how you and she share a very similar stretch of DNA, the Rosetta Stone of life.

The master himself, PZ Meyers, covers Homeobox

Top photo from NIH. Fruit fly head showing the effects of the Antennapedia gene. This fly has legs where its antennae should be. Embryo cartoon from