Wednesday, June 27, 2007

This Week's Citation Classic

Birch, LC. 1948. The intrinsic rate of natural increase of an insect population. J. Anim. Ecol. 17: 15-26.

In many of my published papers, one can find a simple equation:

r = ln (nt/no)/t

The equation permits the calculation of "little r", otherwise known as the intrinsic rate of increase, the per capita growth rate, the net reproductive rate, or the Malthusian parameter. Roughly "r" is the natural logarithm of the change in animal's abundance over time. I never really stopped and considered its origin, until recently.

The equation was first described in Elements of Physical Biology by AJ Lotka in 1925, however was not applied to animals until Leslie and Ransom published on voles in 1940. But being first is not always best. While Leslie and Ransom's contribution is valuable, I don't think it really captures the broader evolutionary significance of "little r". By contrast, Birch's paper on grain weevil population biology does introduce the reader to the wider implications of the Malthusian parameter. One of the implications that derived from Birch's research was that external processes such as weather and disturbance, were more important to the regulation of animal numbers than internal processes, such as competition or self-regulation. In addition, Birch suspected that it was likely that population demographic analyses could be important clues to the evolution of major life history traits (e.g. generation time, fecundity). This premonition later proved to be spot on.

Not without difficulty, Birch's work persuaded population geneticists of the utility of using "little r" as a measure of absolute fitness. That is, the genotype with the higher "little r" is going to out-compete and eventually supplant the genotype with the lesser "little r". Much significant work in evolutionary biology and ecology has been built on these foundations.

In 1954 Birch went on to publish with HG Andrewartha, "The Distribution and Abundance of Animals", a classic book which introduced an entire generation of evolutionary biologists and ecologists to the study of population biology.

Painting by Emil Zeck, courtesy of NSW Agriculture.
Description: As with other species of Sitophilus, this species of weevil is a pest of stored grain, in this case, primarily of rice. Zeck shows in this painting, however, that the species can also be found feeding in stored corn and wheat. The small size of the beetle is evident from the background image which has adult beetles with rice grains. The detail in the magnified section is superb given the size of the insect and its legless larvae.

The Helderberg Formation

Just south of Albany lies the Helderberg Escarpment descending from the Allegheny Plateau (visible in the background of the Albany skyline above). It's a fairly geologically interesting area, and I visited John Boyd Thatcher State Park this past weekend for a closer look. Soon I tripping down the Indian Ladder trail and poking around the Manlius and Coeymans Limestone which were deposited during Devonian epoch ~416 to 359 mya.Incidentally this area has been famous since the 1820's as one of the richest fossil beds in the world. Brachiopods, tentaculites and crinoids exist in abundance, and could be found embedded in the rocks. Also the visitor list to this area is virtually a Who's Who of the early American scientific establishment: Agassiz, Dana, Silliman, Marsh, Beecher, Hall, Le Conte, Emmons, Eaton, Walcott, Leidy, Whitney and many others. Walking over this historical ground was, thus, fascinating on two levels: it figures prominently in the history of life (as the Devonian-Silurian epochs follow on the heels of the Cambrian) and prominently in the history of science (as the above mentioned gentlemen were instrumental in the forming the major institutions that later made American science a world class enterprise).

Tuesday, June 26, 2007

Science Times Special Issue: Evolution

This week's Science Times is devoted to the topic of Evolution. There's so much good stuff, I don't know where to start.

Carol Kaesuk Yoon has a fantastic article about Evo-Devo. Turns out the same DNA sequences are tweaked over and over to different body plans and complex forms.

Nick Wade writes about human evolution. Think humans have stopped evolving? Think again. Human evolution continues to surprise and startle evolutionary biologists.

Carl Zimmer from the Loom covers Rich Lenski's Long Term Evolution Experiment. It's up to 40,000 generations now! Lenski is my scientific "grandfather"; my former advisor, Paul Turner, did his Ph.D. under Lenski.

John Nobel Wilford writes about the Human Family Tree. In case you haven't heard by now, "missing links" keep popping up all over the place.

Dennis Overbye ponders DNA encoded messages, a topic I covered earlier in this blog.

Natalie Angier writes about Toxoplasma gondii, every one's favorite mind parasite.

Cornelia Dean reveals that humans are not in a class by themselves.

Finally, now's your chance to pose questions to Sean B. Carroll, evolutionist extraordinaire and author of Endless Forms Most Beautiful.

Stop by Bugmenot and get a username and password, if you don't feel like registering.

Photo: Charles Darwin on the porch of Down House, Kent.

Monday, June 25, 2007

8 Random Facts

Ricardo from My Biotech Life tagged me with the "8 random facts about me" blog meme. OK, you asked for it...

Here are the rules:

  • We have to post these rules before we give you the facts.
  • Players start with eight random facts/habits about themselves.
  • People who are tagged need to write their own blog about their eight things and post these rules.
  • At the end of your blog, you need to choose eight people to get tagged and list their names.
  • Don’t forget to leave them a comment telling them they’re tagged, and to read your blog.
  1. When I was younger I wanted to be a medical doctor. A short stint as a phlebotomist in a hospital convinced me otherwise. Let's just say the glamorous portrayals of medicine in popular culture are somewhat exaggerated.
  2. I've always had a penchant for unusual pets. I suppose the most unusual was my pet leech. Currently my companion animals are more conventional: a dog, Sarah, and a cat, Penelope.
  3. I've held several of the "Worst Jobs in Science". Perhaps one of the worst was mosquito researcher. Does sticking your arm into a cage full of mosquitoes every day so that they can obtain a blood meal sound worth a 15k a year research assistant salary? On the plus side, I soon attained a remarkable lack of sensitivity to mosquito salival antigens.
  4. I did my MS on pronghorn behavioral ecology. My project involved spending hours observing pronghorn through a spotting scope waiting for them to defecate so I could collect their scat for later chemical analysis. To this day, I get a Pavlovian response when I see ungulates defecate.
  5. On the plus side, I did get to capture a several day old pronghorn fawn while ear-tagging. To hold this skinny bag of bones, gaze into its enormous doe-like eyes and feel (and hear!) its thumping heart against my chest is still one of the highlights of my life.
  6. I've got a reading addiction; I'm a compulsive reader. Books, magazines, the backs of cereal boxes etc. I've actually been fired for reading on the job. Twice. Luckily I now work in a field that doesn't discourage reading on the job.
  7. My favorite wildlife encounter occurred on a backpack trip in Yellowstone. My friend and I spotted a grizzly sow and three (!) cubs approximately 100 m away. My friend had to stop me from approaching closer, otherwise I probably would have met the same fate as Timothy Treadwell.
  8. My favorite job was working as an Environmental Education Intern in Northern Minnesota. I taught XC skiing, snowshoeing, wilderness camping, and played "educational" games like tag and hide and go seek with grade school kids. If it wasn't for the $50 a week plus room and board, I might have made a career out of it.
I'm tagging some of my favorite blogs including, Sandwalk, Bioephemera, ERV, Interrogating Nature, Mixotrophy, Science, Politics & Religion, This Week In Evolution, and Twisted Bacteria.

Friday, June 22, 2007

This Week's Citation Classic

Hershey AD & Chase M. 1952. Independent functions of viral protein and nucleic acid in growth of bacteriophage. J. Gen. Physiol. 36: 39-56.

This week's citation classic is cited by practically every undergraduate genetics textbook, with good cause. The experiments they describe, the so-called Blender Experiments, are a marvel of elegance, simplicity and fundamental importance.

Until Alfred Hershey and Martha Chase, there was still debate regarding the nature of the genetic material. Was it DNA or protein? While Avery, MacLeod and McCarty's pneumococcal work ostensibly clinched the case for DNA, but this work was largely ignored and there remained some holdouts (isn't that always the case). Some, including double Nobel laureate Linus Pauling, considered DNA too simple a molecule to play such an important role as the genetic organizing principle for the entire organism. Hershey and Chase provided the final nail for the protein coffin.

Knowing that DNA, but not protein, possesses phosphorus, and protein, but not DNA, possesses sulfur, Hershey and Chase added either radioactive phosphorus or sulfur to cultures of T2 phages and E. coli, and later separated out the phages. Hershey and Chase now had two types of bacteriophages: one with a radioactive external protein coat, the other with highly radioactive DNA. These phages were added to fresh cultures, incubated for a short time, then whirled in a kitchen blender causing the phages to fall off the bacteria. The cultures were then separated using a centrifuge; the heavier bacterial cells fell to the bottom and formed a pellet, the lighter bacteriophages and loose phage parts remained in the liquid (called supernatant).

Hershey and Chase examined the pellet and the supernatant for radioactivity. In the cultures infected by bacteriophages with radioactive sulfur (with labeled protein), most of the radioactivity was in the liquid with the phages. In the cultures infected by bacteriophages with radioactive phosphorus (with most of the label in their DNA), most of the radioactivity was in the pellet of infected bacteria. Thus the radioactive DNA, but not the protein, entered the bacterial cells, clinching the case for DNA as the genetic material.

As further proof, Hershey and Chase found that offspring of the original viruses had radioactive DNA, but not radioactive protein, showing that the DNA was passed down from parent to offspring. It is fair to say that the scientific community, including Pauling, were now convinced of the fundamental nature of DNA.

Tuesday, June 19, 2007

Should Science Speak to Faith?

The July issue of Scientific American contains an interesting debate between Lawrence M. Krauss, theoretical physicist and author of The Physics of Star Trek, and Richard Dawkins, evolutionary biologist and author of The God Delusion. While both agree on the primacy of science in understanding our world, they do not agree about the best ways to counter religiously motivated threats to the scientific endeavor. Krauss favors engaging the faithful, whereas Dawkins, in the quite diplomatic and understated words of the editor, "has generally shown less achieving a peaceful coexistence between science and faith." The exchange makes for an interesting read, as both sides make good points, and it seems that, in the end, they find much common ground. As Krauss says, and Dawkins agrees to, "What we need to try to eradicate is not religious belief, or faith, it is ignorance. Only when faith is threatened by knowledge does it become the enemy." The main difference between the two is that Dawkins advocates "tough love" and Krauss favors a more nuanced approach.

The Creation of Adam. Michelangelo. 1508-1512.

Monday, June 18, 2007

It's a Miracle!

The Flying Spaghetti Monster was photographed in the skies. It can only mean that the Flying Spaghetti Monster exists! Observe the startling resemblance to the cartoon below. At least FSM had the good sense not to show up on toast or bird doo. The Church of the Flying Spaghetti Monster was formed by Bobby Henderson in response to efforts to teach creationism in public schools. Henderson's argument is that his theory and intelligent design theory had equal validity, stating "if the Intelligent Design theory is not based on faith, but instead another scientific theory, as is claimed, then you must also allow our theory to be taught, as it is also based on science, not on faith." Learn more about the Church of the Flying Spaghetti Monster here. Oh and read more about what the image actually depicts here.

Sunday, June 17, 2007

The Causes of Color

Color is fascinating, but we usually don't consider what it is we are seeing. This fantastic website explains the phenomenon of color in wonderful detail. Did you know that all the colors in the universe result from a mere 15 physical causes? How about that diamonds are colorless because they are held together so tightly that they are incapable of absorbing visible light? Or that birds' tetra- or pentachromatic color space is the most complex in nature? This exhibit is a public service of the Institute for Dynamic Educational Advancement (IDEA).

Image: The Turning Road, Lestraque - Andre Derain (1906)

Friday, June 15, 2007

Bacteriophages and Bacterial Virulence

There's a recent article reporting that the bacteriophage YpfPhi contributes to the pathogenicity of the plague bacillus, Yersinia pestis. Virulence factors carried on phage are quite common. Why should this be? It's an interesting question. I don't think anyone has satisfactorily addressed this problem. For further reading, here's a nice open access review.

This Week's Citation Classic

Hamilton, W.D. 1971. Geometry for the selfish herd. Journal of Theoretical Biology 31:296-311.

One of the most difficult things to do in science is come up with an idea that revolutionizes a field. Most biologists fail to do so in their entire careers. I can think of at least six major revolutions inspired by Bill Hamilton: Inclusive Fitness (the so-called Hamilton's Rule; Hamilton 1964), Mate Choice and Good Genes (Hamilton & Zuk 1982), Extraordinary Sex Ratios (Hamilton 1967), the Red Queen Theory and the Evolution of Sex (Hamilton 1980), Tit for Tat and the Evolution of Cooperation (Axelrod & Hamilton 1981) and present paper, Selfish Herds (Hamilton 1971).

Geometry for the Selfish Herd is my personal favorite from Hamilton's oeuvre. With a few pages of text and some simple algebra and geometry, Hamilton explains the behavior of animals wide ranging as elk, herring, starlings, bats, locusts, caterpillars, and sheep. All of these animals, and their brethren, aggregate into groups. Some theorists supposed that this was for the benefit of the species, for better access to mates or to enable members to assess population numbers. Hamilton thought this was nonsense. These animals are aggregating to ensure that their fellows are eaten rather than themselves.

In the first paragraph of the paper, Hamilton writes,

"Imagine a circular lily pond. Imagine that the pond shelters a colony of frogs and a water-snake. The snake preys on the frogs but only does so at a certain time of day-up to this time it sleeps on the bottom of the pond. Shortly before the snake is due to wake up all the frogs climb out onto the rim of the pond. This is because the snake prefers to catch frogs in the water. If it can’t find any, however, it rears its head out of the water and surveys the disconsolate line sitting on the rim-it is supposed that fear of terrestrial predators prevents the frogs from going back from the rim-the snake surveys this line and snatches the nearest one."
So what will the frogs do in such a situation? Will they disperse evenly about the rim of the pond where each frog has an equal chance of being eaten? (See Fig. A).

"No", said Hamilton, "each will have a better chance of not being nearest to the snake if he is situated in a narrow gap between two others." The frogs now bordering a wide gap will have the greatest chance of being eaten (See Fig. B).If the frogs continue to move, they will "quickly collect in heaps", with the outermost individuals selfishly struggling to find a place in the middle. So strong is this urge that animals will experience extreme discomfort at being separated from the herd. Hamilton cites a passage from Sir Francis Galton, Darwin's cousin.

Yet although the ox has so little affection for, or individual interest in, his fellows, he cannot endure even a momentary severance from his herd. If he be separated from it by stratagem or force, he exhibits every sign of mental agony; he strives with all his might to get back again and when he succeeds, he plunges into its middle, to bathe his whole body with the comfort of closest companionship.

So there you have it, a superb theory of animal behavior, exceptionally general, expressed cogently and written with verve and enthusiasm. And such a great title. How cool is that?

Tuesday, June 12, 2007

Further Blurring the Line Between Science and Art

Today's Science Times contains a nice article about Felice Frankel, a senior research fellow at the Initiative for Innovative Computing at Harvard and a research scientist. Frankel's images have been published in over 300 journal articles and/or covers and various other publications for general audiences. Frankel has helped change the visual face of science, and that is helping to engage people with science. Frankel says, "“To me the idea is to engage somebody to look at something, and they don’t even know it’s science,” she said. “People are not intimidated by pictures. It permits them to ask questions.”

Monday, June 11, 2007

Is There Anything Phages Cannot Do?

Beka Solomon of Tel Aviv University reported at the recent American Society of Microbiology meeting that bacteriophages can break up senile plaques in an animal model of Alzheimer's disease. The authors administered non-lytic filamentous phages intranasally to mice, and found that the phages dissolved beta-amyloid plaques. The mice showed, "improved cognitive and olfactory functions, protected neuronal degeneration, reduced brain inflammation and significantly decreased senile plaque load."

It is not clear the mechanism by which the phage engendered this result, nor is it clear whether it would be an effective therapy against human Alzheimer's disease. How will, for example, the human immune system react to the phage? Nonetheless, this is a fairly interesting result and I am amazed that it has not seen greater press coverage (or any at all for that matter).

Sunday, June 10, 2007

'Tis But a Scratch!

Sean Carroll, the estimable author of Endless Forms Most Beautiful and The Making of the Fittest, dismantles Michael Behe's creationist apology The Edge of Evolution in a book review at Science. While taking down Behe is so simple even a research assistant could do it (heh heh just joking ERV:), Carroll does get a hat tip for his Best Use of a Monty Python Metaphor in describing Intelligent Design advocates insistence on showing up at a sword fight armed with sticks. Unfortunately for ID, Behe is about as sharp as a bowl of jello.

"The continuing futile attacks by evolution's opponents reminds me of another legendary confrontation, that between Arthur and the Black Knight in the movie Monty Python and the Holy Grail. The Black Knight, like evolution's challengers, continues to fight even as each of his limbs is hacked off, one by one. The 'no transitional fossils' argument and the 'designed genes' model have been cut clean off, the courts have debunked the "ID is science" claim, and the nonsense here about the edge of evolution is quickly sliced to pieces by well-established biochemistry. The knights of ID may profess these blows are 'but a scratch' or 'just a flesh wound,' but the argument for design has no scientific leg to stand on."

Cartoon Credit: Joe Sutliff, after Monty Python and the Holy Grail

Friday, June 8, 2007

This Week's Citation Classic

d'Herelle, F. 1917. On an invisible microbe antagonistic to the dysentery bacillus. Comptes rendus Acad. Sci. Paris 165: 373-375.

Credit for the discovery of bacteriophages is usually given to Frederick Twort and Felix d'Herelle. I somewhat disagree. While Twort's report preceded d'Herelle's by a year and a half, he was thoroughly misguided about its nature (he thought it was an enzyme and persisted in this view for an unseemly length of time). Moreover, Twort failed to pursue his discovery, did little work of any serious import, and spent much of his career trying to grow viruses on artificial media.

By contrast, d'Herelle understood immediately what he observed, comprehended its implications and set forth a far reaching research program to explore its practical use.

d'Herelle is also a far more interesting character. A high school graduate, self-taught in microbiology, d'Herelle would have been noteworthy for another reason besides discovering bacteriophages: d'Herelle can be credited with originating modern biological pest control through his use of bacterial diseases to control locust infestations.

Here are some of d'Herelle's notable achievements:

-made whiskey from maple syrup
-built a chocolate factory but went out of business
-1st scientific paper "proved" carbon was not an element, but a compound
-made liquor from bananas
-cured coffee rot in Guatemala
-made schnapps from sisal
-destroyed a locust plague in Argentina
-initiated the field of phage therapy

d'Herelle discovered phage while employed at the Pasteur Institute in Paris. In the course of studying bacteria in fecal samples from dysentery patients, he observed that a filterable (i.e. able to pass through a fine filter) microbe caused the complete lysis of of dysentery bacilli cultures. Almost singlehandedly, d'Herelle developed new experimental approaches to study this new microbe and elaborated theories about its nature and role in infectious diseases.

The citation classic I have cited is a marvel of clear thinking, able writing and concise form. It served as the basis not only for d'Herelle's entire subsequent career, but also for much of the 20th century's phage research. d'Herelle's work also presaged experimental evolution, originated Luria and Delbruck's famous Fluctuation Test and anticipated the importance of adaptive evolution. d'Herelle most certainly deserved a Nobel Prize for his discovery. Alexander Fleming received one for discovering penicillin, and that finding did not have a fraction of the import on science as did the discovery of phage. Etienne Wolff, professor on the faculty at Strasbourg, argued that "the existence of a destructive principle of bacteria, which was revealed to be a filterable virus, is very much more important from the general point of view than the discovery of penicillin, a bactericidal substance extracted from an organism....Bacteriophage represent a scientific revolution, while penicillin is a particular case of chemotherapy."

In the 1960s Félix d’Hérelle's name appeared on a list published by the Nobel Foundation of scientists who had been worthy of receiving the Nobel Prize, but did not.

Photo: (left to right) Elena Makashvili, Felix d'Herelle, Georgiy Eliava.

Thursday, June 7, 2007

Julie MacDonald Awarded $9,628 Special Thanks Payment in 2005

Regular readers will know I rarely write about politics (I try to stay positive), but this report was too much for me to ignore.

Julie MacDonald, the recently disgraced deputy assistant secretary for fish, wildlife and parks at the Department of the Interior (DOI), was given a Special Thanks for Achieving Results award of $9,628.

The payment was just short of the $10,000 threshold that would have triggered a review by the Office of Personnel Management. What's more, the current administration's fingerprints are all over it: "The document obtained by ESWR says only 'ERB approval and White House clearance certified by White House Liaison on 2/10/05.'"

That was three weeks after George W. Bush had been inaugurated for a second time. Political appointees are barred from receiving cash awards from June 1 of a presidential election year to the following Jan. 20.

"It is absolutely disgusting that MacDonald was awarded thousands of dollars for suppressing scientific research and trashing endangered species," said Kieran Suckling, policy director of the Center for Biological Diversity. "MacDonald was financially rewarded for breaking the law and driving species to the brink of extinction. I've never seen anything so cynical in my life."

Nature has also picked up the story (unfortunately, not open access).

Emma Marris writes in the Nature article: "The report, by the DOI’s office of inspector general, paints a portrait of a woman determined to minimize the Endangered Species Act’s effect on the economy. It includes evidence from colleagues that she heavily edited science reports from the field despite having no formal scientific training, and bullied and intimidated field scientists into producing documents along the lines she wanted. Observers say the case highlights how appointees of President George W. Bush can and have pushed political agendas within federal agencies."

Later in Marris' article is this stunner: "The report outlines how [MacDonald] sent internal departmental documents to a friend in the game World of Warcraft 'to have another set of eyes give an unfiltered opinion of them'."

To top it all off, MacDonald is being investigated by congress "for her role in removing the Sacramento splittail fish from the endangered species list. MacDonald owns a farm in a floodplain that is a habitat for the fish, according to an investigation by the Contra Costa Times, a newspaper in California." If this isn't a conflict of interest, I don't know what is.

More here at this article from the ESWR newsletter.

Wednesday, June 6, 2007

Tangled Bank

The 81st edition of the web's oldest science blog carnival, "Tangled Bank", has been posted at Behavioral Ecology Blog.

Origins of Life in the Multiverse

Eugene V. Koonin is a Senior Investigator at the National Center for Biotechnology Information (NCBI). He has just published a paper in Biology Direct (Open Access), which is highly speculative, greatly entertaining, and, "vastly metaphysical". The latter comment is from one of the reviewers, Eric Bapteste, who also wrote, heh, "I might be strange but I often like to read Eugene Koonin's papers." I know this because the paper is Open Peer Review which makes for an especially engrossing read since the reader is allowed access to a seldom opened window in scientific publishing (On the other hand, I've never personally seen a review like this one; it reads somewhat like a debate. The reviewers no doubt wrote their reviews with their audience in mind. Alternatively, it could just be due to the nature of the paper itself.).

Anyway the paper is about cosmology and evolutionary biology. Koonin considers the origin of life to be the central problem of biology. More controversially Koonin considers the current RNA world hypothesis for the origin of life unlikely given the traditional laws of physics in a single, finite universe. Koonin proposes that the RNA world is not only likely, but instead probable, if we embrace the cosmological model of eternal inflation. Eternal inflation suggests that all macroscopic histories permitted by laws of physics are repeated an infinite number of times in the infinite multiverse. In other words, Koonin invokes the anthropic selection principle to explain the origin of life itself! The reason why we see life evolve in this universe is because, if there are an infinite number of universes, then chances are at least some of them will evolve life able to reason about the evolution of life. In fact, according to Koonin, the odds of life evolving are so small that an infinite multiverse is needed to explain it. Yes, I realize this sounds like something the 70's Show gang thought up during a circle "session", but I assure you these are some serious scientists considering a serious question.

One last point, Koonin addresses intelligent design and creationism in the final paragraph. "A final comment on 'irreducible complexity' and 'intelligent design'. By showing that highly complex systems, actually, can emerge by chance and, moreover, are inevitable, if extremely rare, in the universe, the present model sidesteps the issue of irreducibility and leaves no room whatsoever for any form of intelligent design." While this comment is well intentioned, I seriously doubt that any creationist is going to be persuaded by the argument that all life derived from an RNA world regardless of how many universes are posited to exist. Creationists possess exceptionally strong self-imposed cognitive barriers preventing such considerations.

Photo credit: JPL.

Tuesday, June 5, 2007

Science Writing

One of the better, but least appreciated, science writers is Mark Ptashne. Ptashne is the author of the finest molecular biology text I have had the pleasure to read: A Genetic Switch. This book explains a difficult subject (the lysis/lysogeny "decision" in phage lambda) in extraordinarily lucid English. I especially like how the book is recursive, and at each repetition, the story becomes more detailed.

Anyway, I raise the subject of Ptashne and science writing because he has just published an essay on science writing at Current Biology (sadly, not open access, but I summarize for those lacking access).

Ptashne begins by opining the state of scientific writing, "I learn from Bill Bryson in his fine “A Short History of Everything” that obscure scientific writing has a well-established history. Newton wrote impenetrably to keep tourists out; the geologist Hutton, with profound things to say, wrote obscurely, and to his detriment, because he was incapable of writing a coherent English sentence."

Fortunately for Ptashne, he had good teachers.

"Watson [yes, that Watson] applied the following method (at least to me): my finely honed draft was sailed back across the table accompanied by an eyebrow-push-up-grimace and the word: 'Unreadable'."

"Max [Delbruck] returned a manuscript, torn to pieces, along with a note that said: 'Please switch fields.'"

"Al Hershey didn't bother to tear up my manuscript. I wrote a 20 page paper for him and got it back with most lines crossed out and the occasional phrase circled and marked 'Good'. So I rewrote and rewrote and it came back with not a mark on the first page! Not a mark on the second! Then the third page: a line through the middle, a penciled-in 'START HERE', and then most lines thereafter crossed out."

So how does one write well when one has to write about technically complex material?

Ptashne serves up the usual advice, "There are some rules that help, I suppose: short sentences, the active voice, as few technical and compound words as possible, and so on. I used to write by hand, read (out loud) into a tape recorder, re-read the typed outcome, throw away, read a page of Nietzsche, and start again."

But this is just a starting point.

"When I am struggling over yet another of my obscurely written drafts I sometimes recall: amateurs play music ‘in general’; professionals play each note. And so I present to a tough-minded friend one paragraph — just one — and when that is reported to be transparent I go on to the rest. But even if I have followed the rules I mentioned above, and even if that first paragraph seemed fine at the time, now, in view of what else I have written, that first paragraph might have to go, or be seriously recast. Each paragraph is an experiment — you might not know for some time whether it is any good."

The point is good writing takes serious effort. It is a process of vision and revision and revision. Giving your piece to others to read provides the proper distance and forgetfulness required to view a piece anew. With a fresh perspective, phrases to be simplified, redundancies to be eliminated, and tangled knots of language to be unwound suddenly appear from the forest of words.

Monday, June 4, 2007

Nature Network

Heh... Larry Sanger, co-founder and chief organizer Wikipedia, and the founder of Citizendium, asked if someone could create a group for Citizendium on Nature Networks. I volunteered. I started poking around a bit and I found a few familiar faces: PZ Meyers (Pharyngula), Carl Zimmer (The Loom), Madhusudan Katti (Reconciliation Ecology), Razib Khan (Gene Expression) Shalini Sehkar (Scientia Natura), Cesar Sanchez (Twisted Bacteria) and Bora Zivkovic (Blog Around the Clock).

There aren't that many people on Nature Network yet... why are so many of them science bloggers? Very interesting....

Grand Prize Winner: 4th Annual Smithsonian Photo Contest

This amazing photo was taken by Joelle Linhoff, who won the Grand Prize of the Smithsonian's 4th Annual Photo Contest. At first glance it looks almost like an impressionistic painting; I can hardly believe it is a photo.

Sunday, June 3, 2007

Is the Web 2.0 Killing Culture?

There is a thought provoking article in the Sunday Times (London) about an upcoming new book by Andrew Keen, The Cult of the Amateur.

Keen "argues that many of the ideas promoted by champions of web 2.0 are gravely flawed. Instead of creating masterpieces, the millions of exuberant monkeys are creating an endless digital forest of mediocrity: uninformed political commentary, unseemly home videos, embarrassingly amateurish music, unreadable poems, essays and novels."

As a case in point, Keen points out that, "Wikipedia, with its millions of amateur editors and unreliable content, is the 17th most trafficked site on the net., a subscription-based service with 100 Nobel prize-winning contributors and more than 4,000 other experts is ranked 5,128. As a result, Britannica has had to make painful cuts in staffing and editorial."

“Once dismantled, I fear that this professional media – with its rich ecosystem of writers, editors, agents, talent scouts, journalists, publishers, musicians, reporters and actors – can never again be put back together. We destroy it at our peril,” says Keen.

The problem is, supposedly, that people, given a choice between "amateur" content at ad-supported free sites and "expert" content pay-for-use sites, will always choose the former.

Keen makes some valid points, however, I think his concerns are overwrought and anecdotal. Talent isn't going to disappear just because TV stations, record companies and publishing houses aren't there to guide it through the creative process. On the contrary, in direct contradiction of Keen's use of the "dictator image" of the democratization of the web (i.e. "dictatorship of idiots", "if the crowd says that two plus two equals five, then two plus two really does equal five.") , the new media abolishes the dictatorship of the few. We are now able to make our own choices regarding talent and value.

Much issue has been made about the unreliability of Wikipedia. However Nature showed that Wikipedia and Britannica were roughly equal in accuracy of scientific content. This is not to say that Wikipedia does not have its issues, but these (i.e. vandalism, differences in opinion) can be resolved through newer alternatives, such as Citizendium, which aims to improve on Wikipedia’s model by adding “gentle expert oversight” and requiring contributors to use their real names.

Image by Ross Mayfield.

Friday, June 1, 2007

Patterns in Nature

Amy Lamb was a biochemist studying protein synthesis; now she's a photographer, and her online studio can be found here. Her work is phenomenal. Dr. Lamb's work is presently being exhibited at the United States Botanic Garden.

"These are purely visual comparisons as opposed to scientific comparisons," she says. "But as a scientist, I looked at the flowers not only for their beauty, but also from [the perspective of] why and how they got to be these forms and colors. My eye is not just about design, it's about science."

There's an article in the Scientist about her as well.

SREL Update: A 30 day reprieve...

Hat tip to Reconciliation Ecology. Brief story there.

This Week's Citation Classic

This week there are actually two citation classics, both published in 1961.

Connell JH. 1961. The influence of interspecific competition and other factors on the distribution of the barnacle chthamalus stellatus. Ecology 42: 710-723.

Connell JH. 1961. Effects of competition, predation by Thais lapillus, and other factors on natural populations of the barnacle Balanus balanoides. Ecological Monographs 31: 61-104.

According to the ISI Web of Knowledge, they have been cited 888 and 593 times respectively, which for Ecology papers, is a considerable sum. Both of these papers result from Joseph Connell's Ph.D. work at Glasgow University.

Connell, fresh from a frustrating M.S. project on rabbits in the Berkeley hills (he was able to capture only 40 rabbits in two years, one of them 19 times), "vowed then to adopt a simple rule of thumb, namely, never again to study anything bigger than [his] thumb."

Inspired by an obscure paper by the French Ecologist Harry Hatton, Connell decided to expand on Hatton's work intertidal invertebrates, particularly on the effects of predation and competition for space. The data Connell was able to collect has significant implications for the study of interspecific competition, recruitment, predation and population dynamics, but their importance transcends their direct scientific relevance. His work can be pointed to as the birth of a major paradigm change in the study of Ecology, the origin of controlled experimental manipulations of natural populations in the field. Although it is almost stunning to consider today, Ecologists, at one point, conducted mainly observational studies, and almost never engaged in direct experimental manipulations.

As Connell said, "Most scientists regard the experimental method as the normal way to do scientific research. But many ecologists still don't do experiments, possibly because they associate them with white coats and indoor laboratories. I did too until I was led by Ed Deevey's review to a paper by a little known French Ecologist, Harry Hatton, who in the 1930s performed a beautiful series of experiments on natural populations of marine animals and plants."

Another interesting thing regarding the Chthamalus stellatus work is that it was a side project from Connell's main dissertation work. In fact, Connell explicitly disregarded a suggestion by his major professor CM Yonge not to spread his study wider. However, since Yonge was in Glasgow and Connell was out of sight on the Isle of Cumbrae, Connell could safely ignore his major professor's instructions and embark on a secret study of interspecific competition.

Deevey ES. 1947. Life tables for natural populations of animals. Quart. Rev. Biol. 22: 283-314.
Hatton H. Essais de bionomie explicative sur quelques especes intercotidales d'algues et d'animaux. Ann. Inst. Oceanogr. Monaco 17: 241-348.

Photo by Brian Teusch.