Good Science Writers: Richard Dawkins

 
Richard Dawkins was not included in Richard Dawkins' book: The Oxford Book of Modern Science Writing. The reason for the omission is obvious, so I rectify the "oversight" by including him in my list of good science writers.

I don't always agree with what Dawkins writes but there's no controversy about his ability to explain biology to the general public. He has a clear, crisp style that's easy to read and his arguments are well constructed. Part of his success is achieved by simplifying difficult concepts but this is also part of the problem since, in some cases, an over-simplification leads to misinterpretations.

Dawkins is also a master of metaphor but, sometimes the metaphors are misleading and can give an incorrect view of evolution (e.g. Climbing Mt. Improbable). I've chosen an excerpt from The Ancestor's Tale to illustrate Dawkins' skill at writing about science. This book is somewhat less polemical than his others, although it still has its fair share of strongly voiced personal opinions about evolution.

The passage below addresses "convergence," a favorite topic of theistic evolutionists such as Simon Conway Morris and Ken Miller. Dawkins has his own spin on the subject. He begins by addressing a question posed by Stuart Kauffman in 1985. Kauffman asked whether there are certain features of life that are easy to evolve. If so, we might expect these features to appear whenever life evolves. On the other hand ....

Those biologists who could be said to take their lead from the late Stephen Jay Gould regard all of evolution, including post-Cambrian evolution, as massively contingent—lucky, unlikely to be repeated in a Kauffman rerun. Calling it "rewinding the tape of evolution," Gould independently evolved Kauffman's thought experiment. The chance of anything remotely resembling humans on a second rerun is widely seen as vanishingly small, and Gould voiced it persuasively in Wonderful Life. It was this orthodoxy that led me to the cautious self-denying ordinance of my opening chapter; led me, indeed, to undertake my backwards pilgrimage, and now leads me to forsake my pilgrim companion at Canterbury and return alone. And yet ... I have long wondered whether the hectoring orthodoxy of contingency might have gone too far. My review of Gould's Full House (reprinted in The Devil's Chaplain) defended the unpopular notion of progress in evolution: not progress towards humanity—Darwin forfend!—but progress in directions that are at least predictable enough to justify the word. As I shall argue in a moment, the cumulative build-up of complex adaptations like eyes, strongly suggests a version of progress—especially when coupled in imagination with some of the wonderful products of convergent evolution.

Convergent evolution also inspired the Cambridge geologist Simon Conway Morris, whose provocative book Life's Solution: Inevitable Humans in a Lonely Universe presents exactly the opposite case to Gould's "contingency." Conway Morris means his subtitle in a sense which is not far from literal. He really thinks that a rerun of evolution would result in a second coming of man: or something extremely close to man. And, for such an unpopular thesis, he mounts a defiantly courageous case. The two witnesses he repeatedly calls are convergence and constraint.

Convergence we have met again and again in this book, including in this chapter. Similar problems call forth similar solutions, not just twice or three times but, in many cases, dozens of times. I thought I was pretty extreme in my enthusiasm for convergent evolution, but I have met my match in Conway Morris, who presents a stunning array of examples, many of which I had not met before. But whereas I usually explain convergence by invoking similar selection pressures, Conway Morris adds the testimony of his second witness, constraint. The materials of life, and the processes of embryonic development, allow only a limited range of solutions to a particular problem. Given any particular evolutionary starting situation, there is only a limited number of ways out of the box. So if two reruns of a Kauffman experiment encounter anything like similar selection pressures, developmental constraints will enhance the tendency to arrive at the same solution.

You can see how a skilled advocate could deploy these two witnesses in defence of the daring belief that a rerun of evolution would be positively likely to converge on a large-brained biped with two skilled hands, forward-pointing camera eyes and other human features. Unfortunately, it has only happened once on this planet, but I suppose there has to be a first time. I admit that I was impressed by Conway Morris's parallel case for the predictability of the evolution of insects.

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Getting Rid of "Darwinism" in New Scientist

 
Last week, Olivia Judson published a controversial article on the New York Time website. She made the case for getting rid of terms like "Darwinism" and "Darwinian" to describe modern evolutionary biology [Let’s Get Rid of Darwinism]. I'm in complete agreement as I've stated on many occasions [see Why I'm Not a Darwinist]. The main point, as far as I'm concerned, is that modern evolutionary biology has gone way beyond Darwin's original ideas and it's no longer appropriate to describe the modern ideas as "Darwinian." In fact, it can be downright incorrect if you're a pluralist, like me.

Let's see how this might work in practice. The latest issue of New Scientist uses the term "Darwinian evolution" once in the lead editorial [Creationists launch cynical attack on school science]. Here's what it says ...

WHEN science education in the US has come under attack from religious critics, it has proved useful in the past to ask the question, what is science? This approach has been key to keeping public-school science lessons free from non-scientific alternatives to Darwinian evolution, such as creationism and intelligent design (ID) - the notion that life is so complex it could not have arisen without an intelligent agency, aka God.

Nothing is gained here by referring to biological evolution as "Darwinian evolution." As a matter of fact, in this context the term is bound to cause confusion. There are many scientists who think there really are legitimate alternatives to "Darwinian" evolution (e.g. random genetic drift) but the editorial implies that all such alternatives are simply attempts to sneak God into the equation.

Getting rid of "Darwinian" would be a good thing in this case since it is much more accurate to depict the conflict as a challenge to "biological evolution" and not just "Darwinian" evolution.

The lead article in the July 12-18th issue is New legal threat to teaching evolution in the US. The term "Darwininan evolution" is used a couple of times, as in ...

The new legislation is the latest manoeuvre in a long-running war to challenge the validity of Darwinian evolution as an accepted scientific fact in American classrooms.

Again, nothing is gained—and something is lost—by referring to biological evolution as "Darwinian evolution." It would be better to drop the term "Darwinian."

But there's a more serious problem with the article. It is accompanied by a photograph of a classroom with some writing on the blackboard. You can see the photo on the New Scientist website but you can't read what's written. Here's what it says on the blackboard ...

Darwin's Theory says:
Anyone who is familiar with the anatomy of man and the apes must admit that no hypothesis other than that of close kinship affords a reasonable ... explanation of the extraordinarily exact identity of structure in most parts of the bodies man and gorilla.

This is not Darwin's Theory. One of Darwin's main contributions was to show that evolution is the best explanation of life as we know it. We now think of this as the fact of evolution—demonstrated to such an extent that it would be perverse to entertain any other explanation. It's the fact of evolution that's described on the blackboard and this is not a theory, and it's certainly not Darwin's Theory.

The mechanisms of evolution are a different story. Darwin proposed that natural selection was an important mechanism of evolution. This is part of evolutionary theory and it can be referred to as Darwin's Theory of Natural Selection. There are other mechanisms (e.g. random genetic drift) that Darwin did not imagine because his understanding of genetics was incomplete. Those mechanisms are non-Darwinian mechanisms.

The blackboard photo in New Scientists is contributing to the general confusion among the public and thus, it is hurting the cause rather than helping it. This is another case were avoiding the terms "Darwin's Theory" and "Darwinian" would be a good idea.

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Monday's Molecule #81

 
Today's molecule is not a specific molecule but rather a type of molecule. You have to identify the type of molecule shown here.

There's a connection between today's molecule and a Nobel Prize. The clue is the red "P" atom in the molecule. The Nobel Prize was awarded for discovering where that red "P" came from and how quickly this type of molecule was produced. Similar studies were done with many other "P"-containing molecules. This was the beginning of a whole new field of study in biochemistry.

The first person to correctly identify the type of molecule and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are four ineligible candidates for this week's reward. You know who you are.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: The molecule is a phosphatidate. It's an intermediate in the synthesis of triacylglycerols or glycerophospholipids. The R₁ and R₂ groups represent strings of -CH₂- groups, usually sixteen or eighteen carbons.

The phosphorus (P) atom is derived indirectly from inorganic phosphate and the incorporation of radioactive phosphorus as phosphate (³²PO₄^2-) into phosphatides was first studied by George de Hevesy. He received the Nobel Prize in 1943 for his work on using radioisotopes to study the synthesis of biological molecules such as phosphatides.

Lots of people knew that the molecule was a phosphatidate but nobody got the Nobel Laureate so there are no winners this week.

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Gene Genie #34

 
The 34th edition of Gene Genie has been posted at ScienceRoll [Gene Genie 34: Summertime].

This is the first time I host Gene Genie since January. Gene Genie is the blog carnival of clinical genetics and personalized medicine. Enjoy the numerous posts and articles focusing on these interesting fields of medicine.

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

Here are all the previous editions .....

1. Scienceroll
2. Sciencesque
3. Genetics and Health
4. Sandwalk
5. Neurophilosophy
6. Scienceroll
7. Gene Sherpa
8. Eye on DNA
9. DNA Direct Talk
10. Genomicron
11. Med Journal Watch
12. My Biotech Life
13. The Genetic Genealogist
14. MicrobiologyBytes
15. Cancer Genetics
16. Neurophilosophy
17. The Gene Sherpa
18. Eye on DNA
19. Scienceroll
20. Bitesize Bio
21. BabyLab
22. Sandwalk
23. Scienceroll
24. biomarker-driven mental health 2.0
25. The Gene Sherpa
26. Sciencebase
27. DNA Direct Talk
28. Greg Laden’s Blog
29. My Biotech Life
30. Gene Expression
31. Adaptive Complexity
32. Highlight Health
33. Neurophilosophy
34. ScienceRoll

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Species-Scape

 
This is a snapshot of an animated picture of a "species-scape." The size of the organisms represent their relative abundance on Earth. See Species-Scape on the Cornell University website.

Another version is shown on Christopher Taylor's blog Catalogue of Organisms [The Species-Scape Picture].

Notice how insignificant mammals are, yet one particular species of mammal has the potential to ruin the entire planet for all other species.

Some groups seem to be missing, bryophytes (moss) for example. Can you find any others?

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Nobel Laureate: George Palade

 

The Nobel Prize in Physiology or Medicine 1974.

"for their discoveries concerning the structural and functional organization of the cell"

George E. Palade (1912 - ) received the Nobel Prize in Physiology or Medicine for his contribution to understanding how proteins are synthesized and secreted in eukaryotic cells. He worked mostly on the secretory (exocrine) cells of guinea pig pancreas using a combination of cytological and cell fractionation techniques. As he says in his Nobel lecture, he was fascinated by the organization of these cells with their complex endoplasmic reticulum studded with ribosomes. Palade was among the first to get good electron micrographs of these structures [see below].

The idea was to track the route of newly synthesized proteins from the ribosomes to the exterior of the cell. Part of the solution came from developing techniques for EM autoradiography. This allowed Palade and his group to show that new proteins were first made by ribosomes sitting on the surface of the endoplasmic reticulum (ER). The labelled proteins were immediately seen to enter into the lumen of the ER. Subsequently they passed through internal vesicles and the Golgi until they reached the plasma membrane.

The photographs below show the results of a typical pulse-chase experiment. In the first panel (A) you can see that that with only a short pulse of radioactive amino acids the radioactive proteins—identified by the black squiggles—are localized to the endoplasmic reticulum. For a complete description of the photograph see The American Society for Cell Biology.

The pathway worked out in the 1950s and '60s is now known to be correct and it's a universal pathway found in all eukaryotes.

Palade is credited with being the first one to describe the small particles that later came to be known as ribosomes.

Palade was born in Romania where he obtained his M.D. degree in 1940. He joined the Rockefeller University shortly after World War II and remained there until he took up a position at Yale in 1973. In 1990 he moved to the University of California, San Diego.

Palade shared the 1974 prize with Albert Claude and Christian De Duve.

The presentation speech was delivered in Swedish by Professor Jan- Erik Edström of the Karolinska Medico-Chirurgical Institute


THEME:
Nobel Laureates

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen,

The 1974 Nobel Prize in Physiology or Medicine concerns the fine structure and the function of the cell, a subject designated Cell Biology. There are no earlier Prize Winners in this field, simply because it is one that has been newly created, largely by the Prize Winners themselves. It is necessary to go back to 1906 to find Prize Winners who are to some extent forerunners. In that year Golgi and Cajal were awarded the Prize for studies of cells with the light microscope. Although the light microscope certainly opened a door to a new world during the 19th century, it had obvious limitations. The components of the cell are so small that it was not possible to study their inner structure, their mutual relations or their different roles. To take a metaphor from an earlier Prize Winner, the cell was like a mother's work basket, in that it contained objects strewn about in no discernible order and evidently, for him, with no recognizable functions.

But, if the cell is a work basket, it is one on a very tiny scale indeed, having a volume corresponding to a millionth of that of a pinshead. The various components responsible for the functions of the cell correspond in their turn to a millionth of this millionth, and are far below the resolving powers of the light microscope. Nor would it have helped if researchers had used larger experimental animals: the cells of the elephant are not larger than those of the mouse.

Progress was quite simply at a standstill during the first few decades of this century, but then in 1938, the electron microscope became available, an innovation that held out great promise. The difference between this microscope and the ordinary light microscope is enormous, like being able to read a book instead of just the title. With such an instrument it should now be possible to see components almost down to the dimensions of single molecules. But the early hopes were succeeded by disappointment. It was found impossible to prepare the cells in such a way that they could be used. The book remained obstinately shut, even though it would have been possible to read it.

Albert Claude and coworkers were the first to get a glance inside the book. In the mid-forties they made a break-through and succeeded in preparing cells for electron microscopy. I say a glance, because much technical development still remained to be done, and George Palade should be mentioned foremost among those who developed electron microscopy further, to the highest degree of artistry.

In addition to form and structure it is necessary to know the chemical composition of the cell components in order to understand their functions. It was hardly possible to analyse whole cells or tissues since these consist of so many different components, and so, one would get a confused picture. Each component has to be studied separately and obviously this is difficult when the components are so small. Here a new art was developed, and again Claude was the pioneer. He showed how one could first grind the cells into fragments and then sort out the different components on a large scale with the aid of the centrifuge. This was an important beginning. Palade made further contributions, but it was above all Christian de Duve who introduced brilliant developments within this field.

The functions of the cell could now be mapped with this armoury of methodology. Palade has taught us which components function when the cell grows and secretes. The Prize Winner of 1906, Camillo Golgi, discovered a cell component, the Golgi complex. Palade has demonstrated its role and he discovered the small bodies, ribosomes, in which cellular protein is produced.

Production of organic material must be balanced by scavenging and combustion of waste, even in the tiny world of the cell. de Duve discovered small components, lysosomes, which can engulf and dissolve, e.g., attacking bacteria or parts of the cell itself which are old and worn out. These are real acid baths, but the cell itself is normally protected by its surrounding membranes. Sometimes, however, the lysosomes are converted into veritable suicide pills for the cells. This occurs when the surrounding membranes are damaged, e.g. by ionizing radiation. The lysosomes play a role in many clinically important conditions and the foundations laid by de Duve are of the greatest significance for the interpretation of these states, and, thus, also for prophylactic and therapeutic measure.

To sum up, the 1974 Prize Winners have by their discoveries elucidated cellular functions that are of basic biological and clinical importance. Thus, they cover both aspects of the Prize, Physiology as well as Medicine.

Albert Claude, Christian de Duve and George Palade. During the last 30 years a new subject has been created, Cell Biology. You have been largely responsible for this development both by creating the basic methodology and by exploiting it to gain insight into the functional machinery of the cell. On behalf of the Karolinska Institute, I wish to convey to you our warmest congratulations, and I now ask you to receive the prize from the hands of his Majesty the King.

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The Ethical Frontiers of Science

 
I'm at the Chautauqua Institution this week where the theme is The Ethical Frontiers of Science.

Today's speaker was Arthur Caplan Professor of Bioethics at the University of Pennsylvania. His topic was "Is it Immoral to Want to Live Longer, Be Smarter and Look Better?" The answer is no, it is not immoral. There's nothing wrong with wanting to take advantage of modern scientific advances to prolong life, enhance intelligence, and look better." I agreed with everything he said.

Caplan looked over the speakers for the rest of the week. Many of them are his friends and he's very familiar with their views. That's why he was able to congratulate us for coming to the first lecture. "It will be the highlight of the entire week," he said, "because all the other speakers are wrong." I suspect he's right but it will be fun, nevertheless, hearing what some of them have to say.

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Monday's Molecule #80

 
Today's molecules are the little black blobs in the photograph. One of them is circled in the lower left-hand corner.

There's a direct connection between today's molecule and a Nobel Prize. In fact, the photograph was lifted directly from the Nobel lecture of the prize winner. The prize was awarded for determining the role of those little black blobs in the type of cell shown in the photo.

The first person to correctly identify the molecule and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are four ineligible candidates for this week's reward. You know who you are.


THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: The photograph is rough ER and the black blobs are ribosomes. George Palade won the Nobel Prize for working out the pathway of protein secretion from the ribosomes on the surface of the ER to the plasma membrane. Many of you got it right but the first one was Charles Peterson of Hofstra University.

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Good Science Writers: Sean B. Carroll

 
Sean B. Carroll is Professor of Molecular Biology and Genetics at the University of Wisconsin in Madison, Wisconsin (USA).¹ His research interests focus on evolution and development, mostly in fruit flies and other insect. Carroll is one of the leading advocates of a new approach to evolution arising out of what we have learned from animal development ("evo-devo"). (See the official Sean B. Caroll website.)

He is co-author on two textbooks: From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design (2nd ed, 2005) with Jen Grenier and Scott Weatherbee; and Introduction to Genetic Analysis (9th ed., 2007) with Anthony Griffiths, Richard Lewontin, and Susan Wessler. Sean B. Carroll has written two trade books: Endless Forms Most Beautiful: The New Science of Evo Devo (2005) and The Making of the Fittest (2006).

Sean B. Carrol was not included in Richard Dawkins' book: The Oxford Book of Modern Science Writing

The excerpts below are from The Making of the Fittest. This is a book that emphasizes the role of natural selection in evolution.

It may be the most remote place on Earth.

Tiny Bouvet Island is a lone speck in the vast South Atlantic, some 1600 miles southwest of the Cape of Good Hope (Africa) and almost 3000 miles east of Cape Horn (South America). The great Captain James Cook, commanding the HMS Resolution, tried to find it on his voyages through the Southern Ocean in the 1770s, but failed both times. Covered by an ice sheet several hundred feet thick that ends in sheer cliffs, which in turn drop to black volcanic beaches, and with an average temperature below freezing, it still doesn't get many visitors.

Fortunately, for both my story and natural history, the Norwegian research ship Norvegia made it to Bouvet Island in 1928, with the principle purpose of establishing a shelter and a cache of provisions for shipwrecked sailors. While on Bouvet, the ship's biologist, Ditlef Rustad, a zoology student, caught some very curious-looking fish. They looked like any other fish in most respects—they had big eyes, large pectoral and tail fins, and a long protruding jaw full of teeth. But they were utterly pale, almost transparent. When examined more closely, Rustad noticed that what he called "white crocodile fish" had blood that was completely colorless.

Johan Ruud, a fellow student, traveled to the Antarctic two years later on the factory whaling ship Vikingen. He thought the crew was pulling his leg when one flenser (a man who stripped the blubber and skin from the whale) said to him, "Do you know there are fishes here that have no blood?"

Playing along, he replied, "Oh, yes? Please bring some back with you."

A good student of animal physiology, Ruud was perfectly sure that no such fish could exist, as textbooks stated firmly that all vertebrates (fish, amphibians, reptiles, birds, and mammals) possess red cells in their blood that contained the pigment hemoglobin. This is as fundamental as, well, breathing oxygen. So when the flenser and his friends returned from a day's efforts without any blodlaus-fisk, Ruud dismissed the idea as shipboard lore.

Of all the scientists in the world today, there is no one with whom Charles Darwin would rather spend an evening than Sean Carroll.

         Michael Ruse

He wasn't looking for a new kingdom.

Microbiologist Tom Brock and his student Hudson Freeze were prowling around the geysers and hot springs of Yellowstone National Park one day late in the summer of 1966. They were interested in finding out what kinds of microbes lived around the pools and were drawn to the orange mats that colored the outflows of several springs.

They collected samples of microbes from Mushroom Spring, a large pool in the Lower Geyser Basin whose source was exactly 163 degreed F, thought at the time to be the upper temperature limit for life. They were able to isolate a new bacterium from this site, a species that thrived in hot water. In fact, its optimal growth temperature was right around that of the hot spring. They dubbed this "thermophilic" creature Thermus aquaticus. Brock also noticed some pink filaments around some even hotter springs, which raised his suspicion that life might occur at even higher temperatures.

The next year, Brock tried a new approach to "fishing" for microbes in the hot springs of Yellowstone. His fishing tackle was simple: he tied one or two microscope slides to a piece of string, dropped it in the pool, and tied the other end to a log or a rock (don't try this on your own—you will be arrested and quite likely scalded or worse). Days later, upon retrieving the slides, he could see heavy growth, sometimes so much that the slides had a visible film. Brock was right that organisms were living at higher temperatures than had previously been thought, but he did not imagine that they were living in boiling water. And they weren't just tolerating 200 degrees F or more—these organisms were thriving in smoky, acidic, boiling pots such as Sulpur Cauldron, in the Mud Volcano area of the park. Brock's Yellowstone explorations opened eyes and minds to the extraordinary range of life's adaptability, identified bizarre but important new species such as Sulfolobus and Thermoplasma, and launched the scientific study of what he called "hyperthermophiles," lovers of superheat.

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1. Sean B. Carroll is the biologist. Sean Carroll is the physicist at the California Institute of Technology and one of the authors on the blog Cosmic Variance.

The Fluctuation Test

John Dennehy of The Evilutionary Biologist continues his almost perfect¹ record of picking important papers for his Citation Classic.

This week's paper is the classic 1943 paper by Luria and Delbrück on the fluctuation test [The Fluctuation test]. This was the paper that proved that mutations arise randomly with respect to their phenotype. As John says, it is one of the most important experiments in biology.

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1. For the exception see It Happens to all of Us Eventually.

Good Science Writers: Eugenie Scott

 
Eugenie C. Scott has been the Executive Director of the National Center for Science Education (NCSE) since 1987. She is a physical anthropologist who taught at several universities prior to becoming director of NCSE.

Scot has published dozens of articles on evolution and creationism in the popular press and she is a frequent guest on television and radio broadcasts. She is one of the world's leading experts on explaining evolution to the general public (and to other scientists).

Although she meets all the qualifications, she was not included in Richard Dawkins' book: The Oxford Book of Modern Science Writing.

The following excepts are taken from her latest book Evolution vs. Creationism: An Introduction.

If a population at the end of a geographic range of a species is cut off from the rest of the species, through time it may become different from other populations. Perhaps natural selection is operating differently in its environment than it is in the rest of the species range, or perhaps the population has a somewhat different set of genes than other populations of the species. Just by the rules of probability, a small, peripheral population is not likely to have all the variants of genes that are present in the whole species, which might result in its future evolution taking a different turn.

No longer exchanging genes with other populations of the species, and diverging genetically through time from them, members of a peripheral, isolated population might reach the stage where, were they to have the opportunity to mate with a member of the "parent" species, they would not be able to produce offspring. Isolating mechanisms, most of which are genetic but some of which are behavioral, can arise to prevent reproduction between organisms from different populations. Some isolating mechanisms prevent two individuals from mating at all: in some insects, for example, the sexual parts of males and females of related species are so different in shape and size that copulation can't take place. Other isolating mechanisms come into effect when sperm and egg cannot fuse for biochemical or structural reasons. An isolating mechanism could take the form of the prevention of implantation of the egg or of disruption of the growth of the embryo after a few divisions. Or the isolating mechanism could kick in later: mules, which result from crossing horses and donkeys are healthy but sterile. Donkey genes thus are inhibited from entering into the horse species and vice versa. When member of two groups aren't able to share genes because of isolating mechanisms, we can say that speciation between them has occurred. (Outside of the laboratory, it may be difficult to determine whether two species that no longer live in the same environment are reproductively isolated.)

The new species would of course be very similar to the old one—in fact, it might not be possible to tell them apart. Over time, though, if the new species manages successfully to adapt to its environment, it might also expand and bud off new species, which would be yet more different from the parent—now "grandparent"—species. This branching and splitting has, through time, given us the variety of species that we see today.

... common to all ID [intelligent design] proponents is the rejection of "Darwinism." In ID literature, "Darwinism" becomes an epithet, though it is not always clear in any given passage exactly what is meant by "Darwinism." In evolutionary biology, "Darwinism" usually refers to the ideas held by Darwin in the nineteenth century. Usually the term is not used for modern evolutionary theory, which, because it goes well beyond Darwin to include subsequent discoveries and understandings, is more frequently referred to as "neo-Darwinism," or just "evolutionary theory." Evolutionary biologists hardly ever use "Darwinism" as a synonym for evolution, though it occasionally is used this way by historians and philosophers of science. In ID literature, however, "Darwinism" can mean Darwin's ideas, natural selection, neo-Darwinism, post-neo-Darwinian evolutionary theory, evolution itself, or materialist ideology inspired by "Godless evolution."

The public, on the other hand, is unlikely to make these distinctions, instead equating "Darwinism" with evolution (common descent). For decades, Creation Science proponents have cited the controversies among scientist over how evolution occured—including the specific role of natural selection—in their attempts to persuade the public that evolution itself—the thesis of common ancestry—was not accepted by scientists, or at least was in dispute. Within the scientific community, of course, there are lively controversies, including over how much of evolution is explained by natural selection and how much by additional mechanisms such as those being discovered in evolutionary developmental biology ("evo-devo"). No one says natural selection is unimportant; no one says that additional mechanisms are categorically ruled out. But these technical arguments go well beyond the understanding of laypeople and are easily used to promote confusion over whether evolution occurred. Intelligent Design proponents similarly exploit public confusion about "Darwinism" to promote doubt about evolution.

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Was Charles Darwin a Good Science Writer?

 
Olivia Judson is a research fellow at Imperial College in London (UK). She studies evolution. Judson is a former pupil of W.D. Hamilton. She is also the daughter of Horace Freeland Judson.¹

Judson writes a weekly article for the New York Times website. This week she tackles the heretical question of whether Charles Darwin was a good science writer [An Original Confession]. Here's a treaser ...

It always happens the same way. A glance around the room to make sure no one else is listening. A clearing of the throat. A lowering of the voice to a conspiratorial tone. Then, the confession.

“I’ve never read ‘On the Origin of Species.’ I tried, but I thought it was boring.”

Thus, a number of eminent scientists — biologists all — have spoken. Or rather, whispered.

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1. Author of The Eighth Day of Creation, the definitive history of the early days of molecular biology.

[Hat Tip: RichardDawkins.net]

Tangled Bank #109

 
The latest issue of Tangled Bank is up at Greg Laden's Blog [The Tangled Bank #109: LOL Evolution!].

Welcome to the One Hundred and Ninth Edition of The Tangled Bank, the Weblog Carnival of Evolutionary Biology. This is the LOL edition of the Tangled Bank....

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If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

A Gene Wiki

 
The prevalence of errors and omissions in sequence databases is one of the ugly little secrets of molecular biology [Errors in Sequence Databases]. We know how to fix the problem; it requires careful annotation by knowledgeable experts. Unfortunately, this is time-consuming and expensive since you have to hire annotators. One other possibility is to allow open access to all existing records in databases such as GenBank, RefSeq, or PDB. This ain't gonna happen because here's no way to verify the changes to make sure they are valid. The people who control these databases are very reluctant to allow open access and the authors of the database entries are uneasy about allowing others to insert annotations into their records.

But there are other models that might work. A recent paper by Huss et al. (2008) in PLoS Biology describes a possible solution. They point out that Wikipedia seems to be a successful model of collaborative effort to ensure accuracy. Why not adopt this model for gene annotation?

Some examples of human genes already had Wikipedia entries and these entries were updated and annotated by various users. In order to stimulate and encourage this process, Huss et al. (2008) created stub entries on Wikipedia for every human gene. Here's how they describe it in their paper.

In principle, a comprehensive gene wiki could have naturally evolved out of the existing Wikipedia framework, and as described above, the beginnings of this process were already underway. However, we hypothesized that growth could be greatly accelerated by systematic creation of gene page stubs, each of which would contain a basal level of gene annotation harvested from authoritative sources. Here we describe an effort to automatically create such a foundation for a comprehensive gene wiki. Moreover, we demonstrate that this effort has begun the positive-feedback loop between readers, contributors, and page utility, which will promote its long-term success.

Today, anyone with access to Wikipedia can contribute to annotating human genes. Two examples of well annotated genes are HSP90 and NF-κB.

Let's look at some examples of stub entries to see how the process might work. I've chosen the human members of the HSP70 multigene family because I'm familiar with these genes. All members of the family function as molecular chaperones, helping to ensure that proteins are properly folded [Heat Shock and Molecular Chaperones].

There are two major inducible genes called HSPA1A and HSPA1B. They are adjacent to one another on chromosome 6. The database entries for these genes are confusing and in most cases it's almost impossible to discern which gene is being referred to.

Here's the Wikipedia stub for HSPA1A. Clearly there's an opportunity to modify this entry in order to make it clear that there are two very similar genes and to point to the proper sequence records for this gene. The second gene, HSPA1B, has its own entry in EntrezGene so I was expecting to find it on Wikipedia. Unfortunately, it's not there. A search for HSPA1B redirects you to HSPA1A. So right away we have a problem. Someone made a decision to merge these entries on Wikipedia making it very difficult to correctly annotate the separate genes.

HSPA1L is an intronless gene closely linked to HSPA1A and HSPA1B. HSPA1L is not heat shock inducible, instead it is developmentally regulated. The gene is expressed exclusively in the testes. The stub entry for this gene [HSPA1L] includes an RNA expression profile that beautifully illustrates the developmental regulation but there's nothing in the annotations that mentions this. This is an excellent opportunity to correct an omission in the existing databases.

Let's look at one more example to see how useful the Wikipedia effort might be. The HSPA4 gene is identified on all databases as a member of the HSP70 gene family. It's usually called "Heat shock 70kDa protein 4." The Wikipedia stub reflects the GenBank annotation [HSPA4]. However, it has been known for a long time that this gene is NOT a member of the HSP70 gene family. The annotation is incorrect. Instead, this gene is Apg-2 an HSP100 homologue not related to HSP70. The original error is due to Fathallah et al. (1993) who sequenced the first example. They mistakenly called it a novel hsp70 gene due, in part, to sequencing errors and partly to an overactive imagination. Mistakes such as these are extremely difficult to remove from the database but we now have an opportunity to correct the error on the Wikipedia entry.

Putting the human genes on Wikipedia is almost as good as allowing open access to the primary sequence databases. The effort will only be successful if scientists make the effort to edit the Wikipedia entries. It's unlikely that most gene entries will be modified but even if only a subset is annotated, it's better than none at all. It would be nice if the RefSeq records could point to the Wikipedia records. That will encourage people to make comments on Wikipedia.

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Huss III, J.W., Orozco, C., Goodale, J., Wu, C., Batalov, S., Vickers, T.J., Valafar, F., and Su, A.I. (2008) A Gene Wiki for Community Annotation of Gene Function. PLoS Biol 6(7): e175 [doi:10.1371/journal.pbio.0060175]

Flatfish

 
Flatfish are strange looking animals that live sideways. One of their eyes has migrated to one side of the fish so that when it lies on its "side" at the bottom of the ocean both eyes point upwards. This is an interesting example of the evolution of a change in development.

Fossil relatives of modern flatfish have recently been described and they confirm much of what was surmised about the evolution of these strange creatures. Several bloggers have written about this and it's well worth the effort to read their postings.

Christopher Taylor at Catalogue of Organisms wrote The Ugly Stick in Action.

Ed Yong at Not Exactly Rocket Science wrote 'Missing link' flatfish has eye that's moved halfway across its head.

GrrlScientist at Living the Scientific Life wrote The Mysterious Origin of the Wandering Eye.

Carl Zimmer at The Loom wrote Dawn of the Picasso Fish.

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[Image Credit: The drawings are by Georgi Pchelarov from The Classification of Fishes.]