Epigenetics Revisited

I'm still struggling with the concept of epigenetics [see Epigenetics]. Most of the modern definitions are so broad that they become meaningless. It's impossible to distinguish between epigenetics and plain old regulation of gene expression.

One of my colleagues, Craig Smibert, was so annoyed by my questions about epigenetics that he pointed me to a series of articles in Nature in the hopes it would shut me up. The relevant article is Perception of Epigenetics by Adrian Bird (Bird 2007).

It's not going to help. After describing several examples like methylation and histone modifications, Bird then points out that these modifications are not necessarily stable ...

So how accurately transmitted should an epigenetic mark be? Variation due to faulty copying is compounded by current evidence that all histone modifications, as well as DNA methylation itself, can be abruptly removed during development, thereby preventing the persistence of these modifications in a heritable epigenetic sense.

In other words, an epigenetic phenomenon doesn't really need to be heritable in order to qualify as epigenetic.

Furthermore, an epigenetic phenomenon doesn't even have to be passed on to progeny to qualify.

The restrictiveness of the heritable view of epigenetics is perhaps best illustrated by considering the brain. A growing idea is that functional states of neurons, which can be stable for many years, involve epigenetic phenomena, but these states will not be transmitted to daughter cells because almost all neurons never divide.

That's not very helpful. It's beginning to look like any activation or repression of eukaryotic genes will count as epigenetics. (According to some, it doesn't have to be eukaryotes. There is epigenetic regulation in bacteria as well, Casadesús and Low (2006).)

Here's the definition ...

Given that there are several existing definitions of epigenetics, it might be felt that another is the last thing we need. Conversely, there might be a place for a view of epigenetics that keeps the sense of the prevailing usages but avoids the constraints imposed by stringently requiring heritability. The following could be a unifying definition of epigenetic events: the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states.

Does this include simple activation and repression of genes during development in the manner of control of lac operon expression? You betcha.

Bird may be thinking mostly of histone modifications and DNA methylation but he's well aware of the fact that these are often consequences, not causes, of activation and repression. He says,

For example, transcriptional activation through sequence-specific DNA-binding proteins brings in histone acetyltransferases, which then epigenetically adapt the promoter region for transcription (for histone acetyl groups, although ephemeral, would now be epigenetic).

So we're right back where we started, Craig will not be happy. Just about anything that modifies or regulates gene expression in eukaryotes (multicellular?) counts as epigenetics.

One could ask, what's the point? Why create a special word to describe regulation of gene expression in eukaryotes (and prokarotes) using mechanisms that we've known about for thirty years?

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Bird, A. (2007) Perceptions of epigenetics. Nature 447:396-398. [doi:10.1038/nature05913]

Casadesús, J. and Low, D. (2006) Epigenetic Gene Regulation in the Bacterial World. Microbiology and Molecular Biology Reviews 70:830-856. [doi:10.1128/MMBR.00016-06

What Breed of Liberal Are You?

 

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[Hat Tip: Mike Dunford (Social Justice Crusader)]

Monday's Molecule #82

 
Today's molecule isn't exactly a molecule. Your task is to figure out what's going on in the photograph. Be as specific as possible using proper terminology—remember, this is a family blog.

There's a connection between today's molecule and a Nobel Prize. Sometimes I just can't identify a molecule that points to a Nobel Laureate so I have to use something else. This is going to get harder and harder as I run out of "easy" Nobel Prizes.

The first person to correctly identify what's happening in the photo 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 three 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 winner is Steve Matheson who knew that the photograph represented conjugating bacteria (group sex) and the Nobel Laureate is Joshua Lederberg (1958). Congratulations Steve!

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[Photo Credit: Researchers Trade Insights About Gene Swapping by Elizabeth Pennasi Science 305:334 - 335. DOI: 10.1126/science.305.5682.334]

Postmodernism and the Two Cultures

John Wilkins at Evolving Thoughts has some comments about the "two cultures" debate [see Cocktail Parties and the Two Cultures].

While most scientists see the problem as a lack of respect for science, John examines the other side of the coin. Noting that the Sokal Affair often comes up in these discussion, John reacts to the criticism of postmodernism implicit in that reference. It's true that most scientists agree with Alan Sokal that the worst form of postmodernism is an embarrassment to all disciplines, not just the humanities. However, it's also true that humanities (e.g. English, Sociology, Psychology) have been far more lax than the sciences when it comes to intellectual rigor. In that sense, the humanities have lost respect.

John attempts to explain the good things about postmodernism. I understand his point, although I think might be protesting just a bit too much. He concludes with,

There is a cultural divide between the humanities and the sciences, but it is not a simple one. It has to do, ultimately, with respect. The division is between those who respect science, and those who respect the humanities (and the other human-related subjects, like social science, political science and so on). Yes, we in the humanities treat science like a text. This is because, as we are not doing science, we interface with that vibrant tradition via the texts of science, mostly. And we are being, as philosophers, very "meta" about science - that is, we are discussing its discussions, and reflecting upon its reflections. Textualisation is impossible to avoid, although one can correct for it. But some of us respect science. We respect it for the same reason that Locke, Hume, Kant and Mill respected science - it is where the knowledge is gathered (or made, or constructed out of data, etc.), so it is the single most important part of human cognition and social organisation to a philosopher.

Anyone who has spent much time wading through the pious, obscurantist, jargon-filled cant that now passes for 'advanced' thought in the humanities knew it was bound to happen sooner or later: some clever academic, armed with the not-so-secret passwords ('hermeneutics,' 'transgressive,' 'Lacanian,' 'hegemony,' to name but a few) would write a completely bogus paper, submit it to an au courant journal, and have it accepted . . . Sokal's piece uses all the right terms. It cites all the best people. It whacks sinners (white men, the 'real world'), applauds the virtuous (women, general metaphysical lunacy) . . . And it is complete, unadulterated bullshit – a fact that somehow escaped the attention of the high-powered editors of Social Text, who must now be experiencing that queasy sensation that afflicted the Trojans the morning after they pulled that nice big gift horse into their city.

Gary KamiyaYes, it's all about respect. However, I still think scientists are feeling more like Rodney Dangerfield¹ than the average sociologist or philosopher. The way I see it, philosophers and others in the humanities often have a very narrow view of science. It's not that they treat science as just another human endeavor, which is bad enough, it's that they treat science as something that's not a part of their disciplines. This exact point is addressed in a lecture Alan Sokal gave earlier this year [What is science and why should we care?]. "Science" is not just about rocket ships and natural selection, it's a way of thinking. A way of thinking that people in the humanities would be wise to adopt. Sokal says,

At a superficial level you could say that my topic is the relation between science and society; but as I hope will become clear, my deeper theme is the importance, not so much of science, but of the scientific worldview—a concept that Ishall define more precisely in a moment, and which goes far beyond the specific disciplines that we usually think of as "science"—in humanity's collective decision making. I want to argue that clear thinking, combined with a respect for evidence—especially inconvenient and unwanted evidence that challenges our preconceptions—are of the utmost importance to the survival of the human race in the twenty-first century.

Of course, you might think that calling for clear thinking and a respect for evidence is a bit like advocating Motherhood and Aple Pie (if you'll pardon this Americanism)—and in a sense you'd be right. Hardly anyone will openly defend muddled thinking or disrespect for evidence. Rather, what people do is to surround these practices with a fog of verbiage designed to conceal from their listeners—and in most cases, I would imagine, from themselves as well—the true implications of their reasoning.

Sokal has it right, as far as I'm concerned. The war between the two cultures is not just about whether you've read Shakespeare or Einstein, it's about how you think. Either you adopt the scientific worldview that values evidence and rationality, or you practice some form of superstition. In this sense, the humanities are just a part of science and not a separate way of knowing.

Sokal emphasizes this point again and again.

I stress that my use of the term "science" is not limited to the natural sciences, but includes investigations aimed at acquiring accurate knowledge of factual matters relating to any aspect of the world by using rational empirical methods analogous to those employed in the natural sciences.

I don't think John Wilkins would agree with this perspective since it makes philosophy—and all other humanties—just a part of a scientific worldview.²

John continues with his analysis of the two cultures problem.

Scientists often do not respect humanists, either. It is a running gag that PZ or Larry Moran will tweak me and others for being mere philosophers, but the gag is that most scientists really do think philosophy is a waste of funds and office space. Likewise they think the same thing about literary studies, history, social sciences, and in fact everything that is not their own speciality. It's not hard to see this as special pleading, but if scientists want respect, they had better show some. It's not impossible: Ed Wilson and Stephen Jay Gould are just two examples of scientists who - for all their faults - respect the humanities. Nobody has the time or energy (or mental capacity) to become experts in both fields; there's barely enough time to become expert in one subspeciality of one discipline of one field); but we can respect those who do learn those limited domains even if they are not our own. This is a plea for respect too, between the analytic and continental styles of philosophy. Neither is totally stupid nor totally on track. Rather than reject the other styles, perhaps what we should do is mutually support each other to do what we do well.

For the record, I'm much closer to Gould on this issue that it appears. I have a great deal of respect for philosophy, provided that it's done correctly. I would strongly support making philosophy and the study of logic a mandatory course in every university. Similarly, there is much to be learned about human behavior—and, let's face it, we are all interested in ourselves even if we know that we are just one species out of ten million—by studying sociology, English literature, and art history. The problem isn't lack of respect for the subject matter as much as lack of respect for the way the subjects are studied.

I'd also like to point out that I'm an equal opportunity curmudgeon—the best kind, in my opinion. While I don't hesitate to point out the muddle-headedness of philosophers like Michael Ruse and Daniel Dennett who pretend to be scientists, I also don't hesitate to make fun of scientists like Ken Miller and Francis Collins who abuse science to support religion.

In the war between rationalism and superstition there are many in the humanities who are on the wrong side. But there are lots of scientists who are wrong as well. I still think that, as a general proposition, there's more respect for the humanities out there than for science. Our society is educating an entire generation of scientific illiterates who are not only unknowledgeable about basic concepts in science but, in most cases, still quite proud of their ignorance.

The next time you hear someone say that science or math is way too hard for them, you should express your sympathy by saying, "Gee, I'm sorry you're too stupid to understand these things. What can I do to help?"

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1. or Aretha Franklin

2. To put it even more bluntly. All of the humanities is simply concerned with the behavior of one particular species on this planet. It's just one tiny part of life on this planet, which, in turn, is an infinitesimally small part of the universe. Those who think that the philosophy of Plato is more important than understanding evolution have their priorities all screwed up.

Cocktail Parties and the Two Cultures

I can't tell you how many times I've been in the company of "intellectuals" who can discuss at great length their operatic preferences or how many novels by Gabriel García Márquez they've read, but who don't know what DNA is or which planet is closest to Earth. In many cases these "intellectuals" seem to be downright proud of the fact that they "can't do math." Scientific ignorance is not a only acceptable among this group but seems to be almost a badge of honor.

Imagine the response if one were at a cocktail party and admitted that you didn't know who Gabriel García Márquez was, and what's more, you don't care.¹ The concept of two cultures, science and humanities, isn't new—it dates from the time of the scientific revolution almost 500 years ago. The conflict is almost always characterized as the lack of respect shown by humanities toward science. Here's how C.P. Snow put it in his writings on The Two Cultures.

A good many times I have been present at gatherings of people who, by the standards of the traditional culture, are thought highly educated and who have with considerable gusto been expressing their incredulity at the illiteracy of scientists. Once or twice I have been provoked and have asked the company how many of them could describe the Second Law of Thermodynamics. The response was cold: it was also negative. Yet I was asking something which is the scientific equivalent of: Have you read a work of Shakespeare's?

I now believe that if I had asked an even simpler question -- such as, What do you mean by mass, or acceleration, which is the scientific equivalent of saying, Can you read? -- not more than one in ten of the highly educated would have felt that I was speaking the same language. So the great edifice of modern physics goes up, and the majority of the cleverest people in the western world have about as much insight into it as their neolithic ancestors would have had.

Much has been written on this topic including a book by Stephen Jay Gould (The Hedgehog, the Fox, and the Magister's Pox) that has to be the most useless contribution to the debate that has ever been published. (I say this as an unabashed fan of Gould.)

Two bloggers have recently re-opened the debate. Chad Orzel at Uncertain Principles got the ball rolling with The Innumeracy of Intellectuals and Janet Stemwedel (Adventures in Ethics) picked up on the discussion with Fear and loathing in the academy. The latest contribution from Janet is Assorted hypotheses on the science-humanities divide, in which she offers several hypotheses to explain the two cultures problem.²³

The comments on both sites are interesting. They bring up related issues such as why do we have courses like "Astronomy for Dummies" and "Science for Poets" while all science majors take pretty much the same courses as the humanities students. You don't usually find examples of dumbed down philosophy courses for biologists.

What's so amazing is that Janet even has one commenter (Shawn) who's willing to defend the superiority of the humanities over the sciences. Here's part of his comment ...

As for the topic generally: it really speaks to the elitism in the hard sciences that everyone from the "science side" is more than happy (either implicitly or explicitly) to lump the soft sciences in with fine arts and literature without batting an eye. It's also rather ironic that many people on the "science side" of this debate seem to have no problem with trotting out tired cliches, culture war bugaboos, and fourth hand anecdotes to shore up their, frankly childish, arguments regarding the irrelevancy of the humanities.

Everything from ascot-ed and monocled patricians, to post-modern mandarins, to smug artsy conformists, a rouges gallery of stereotypes and cartoons presented as if it were actual evidence. But I guess what do you expect from a bunch of nerds who have no knowledge of real life. (See? It's such an easy game to play.)

Yes, of course science saves lives and makes life better, but the actual business of living, 90% of the lifespan of the overwhelming majority of humans is dominated by subjects connected to the realm of humanities. The internet is the product of science and engineering (and massive government/tax-payer funded research), but in the end it's merely a vehicle for people to conduct their lives and maybe (or maybe not) enrich their lives. Science certainly can save your life, but the humanities make it worth living.

The humanities IS civilization and civilization is the sciences' natural habitat. Science is in fact inconceivable without the humanities.

This could be fun.

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1. That doesn't apply to me. I know who he is, and I just don't care. His main claim to fame is that he got his Nobel Prize the same year as Bergström, Samuelsson, and Vane and Aaron Klug.

2. As you might have guessed, this debate was way too tempting for John Wilkins. He has weighed in with philosopher's take on the subject: What philosophy of science and "postmodernism" have in common. John has some interesting things to say but I'll deal with them in a separate posting.

3. Razib at Gene Expression contributes: Humanities "vs." science.

[Image Credit: The cartoon is by Serge Bloch from The New York Times via Can the “Two Cultures” Become One Again?]

Good Science Writers: Stephen Jay Gould

 
Stephen Jay Gould is far too good a writer to have been ignored by Richard Dawkins in his book: The Oxford Book of Modern Science Writing. According to Dawkins, he and Gould "... enjoyed—or suffered—a kind of love/hate relationship on opposite sides of the Atlantic and opposite sides of several schisms in the broad church of Darwinian theory."¹ Dawkins selected an essay by Gould on Charles Darwin's book on worms.

I think Gould deserves a better hearing so I've selected two excerpts that show where he differs from Dawkins. The first is from Wonderful Life (1989). Here Gould is discussing the Burgess Shale and notes that there were many diverse species, most of which have not left modern ancestors. If you represent this diversity—or disparity as Gould prefers—as a tree, it has a rapidly expanding bushiness and out of that wide base only a few branches extend upwards to modern times. This is very unlike the traditional tree that looks more like an inverted cone with steadily increasing diversity. Gould draws certain conclusions from this data—conclusions that have been widely misinterpreted. If you're going to engage in the "evolution wars" it's a good idea to get the views of your opponents right.

This inverted iconography, however interesting and radical in itself, need not imply a revised view of evolutionary predictability and direction. We can abandon the cone, and accept the inverted iconography, yet still maintain full allegiance to tradition if we adopt the following interpretation: all but a small percentage of Burgess possibilities succumbed, but the losers were chaff, and predictably doomed. Survivors won for cause—and cause includes a crucial edge in anatomical complexity and competitive ability.

But the Burgess pattern of elimination also suggests a truly radical alternative, precluded by the iconography of the cone. Suppose that winners have not prevailed for cause in the usual sense. Perhaps the grim reaper of anatomical designs is only Lady Luck in disguise. Or perhaps the actual reasons for survival do not support conventional ideas of cause as complexity, improvement, or anything at all humanward. Perhaps the rim reaper works during brief episodes of mass extinction, provoked by unpredictable envirnonmental catastrophes (often triggered by impacts of extraterrestrial bodies). Groups may prevail or die for reasons that bear no relationship to the Darwinian basis of success in normal times. Even if fishes hone their adaptations to peaks of aquatic perfection, they will all die if the ponds dry up. But grubby old Buster the Lungfish, former laughing stock of the piscine priesthood, may pull through—and not because a bunion on his great-grandfather's fin warned his ancestors about a coming comet. Buster and his kin may prevail because a feature evolved a long time ago for a different use has fortuitously permitted survival during a sudden and unpredictable change in rules. And if we are Buster's legacy, and the result of a thousand other similar happy accidents, how can we possible view our mentality as inevitable, or even probable?

We live, as our humorists proclaim, in a world of good news and bad news. The good news is that we can specify an experiment to decide between the conventional and the radical interpretations of extinction, thereby settling the most important question we can ask about the history of life. The bad news is that we can't possibly perform the experiment.

I call this experiment "replaying life's tape." You press the rewind button and, making sure you thoroughly erase everything that actually happened, go back to any time and place the past—say, to the seas of the Burgess Shale. Then let the tape run again and see if the repetition looks at all like the original. If each replay strongly resembles life's actual pathway, then we must conclude that what really happened pretty much had to occur. But suppose that the experimental versions all yield sensible results strikingly different from the actual history of life? What could we then say about the predictability of self-conscious intelligence? or of mammals? or of vertebrates? or of life on land? or simply multicellular persistence for 600 million years? (pp. 48-50)

Note the contrast between Gould's views and those of theistic evolutonists such as Ken Miller and Simon Conway Morris. Those writers emphasize that the replay of the tape of life would still produce intelligent beings with a soul. They claim that the evidence of convergence favors such a view.

The second excerpt comes from The Structure of Evolutonary Theory. Here Gould is discussing the demise of the hardened version of the Modern Synthesis. He claims that this version, entrenched in the 1950's, is no longer correct. It needs to be expanded to include other modes of evolution.

I choose this example to illustrate two things about Gould: first, the reason why he makes such a claim and, second, how he addresses his critics. The necessity of responding to other points of view is exactly what one expects from a scientist but, unfortunately, few scientists exhibit this characteristic.

Gould is referring to an article he published in Paleobiology back in 1980. In that article he quoted Ernst Mayr's definition of the Modern Synthesis² and then pronounced it "effectively dead."

Given the furor provoked, I would probably tone down—but not change in content—the quotation that has come to haunt me in continual miscitation and misunderstanding by critics: "I have been reluctant to admit it—since beguiling is often forever—but if Mayr's characterization of the synthetic theory is accurate, then that theory, as a general proposition, is effectively dead, despite its persistence as textbook orthodoxy" (Gould, 1980). (I guess I should have written the blander and more conventional "due for a major reassessment" or "now subject to critical scrutiny and revision," rather than "effectively dead." But, as the great Persian poet said, "the moving finger writes, and having writ ..." and neither my evident piety nor obvious wit can call back the line—nor would tears serve as a good emulsifier for washing out anything I ever wrote!)

Yes, the rhetoric was too strong (if only because I should have anticipated the emotional reaction that would then preclude careful reading of what I actually said). But I will defend the content of the quotation as just and accurate. First of all, I do not claim that the synthetic theory of evolution is wrong, or headed for complete oblivion on the ashheap of history; rather, I contend that the synthesis can no longer assert full sufficiency to explain evolution at all scales (remember that my paper was published in a paleobiological journal dedicated to the studies of macroevolution). Two statements in the quotation should make this limitation clear. First of all, I advanced this opinion only with respect to a particular, but (I thought) quite authoritative, definition of the synthesis: "if Mayr's characterization of the synthetic theory is accurate." Moreover, I had quoted Mayr's definition just two paragraphs earlier. The definition begins Mayr's chapter on "species and transspecific evolution" from his 1963 classic—the definition that paleobiologists would accept as most applicable to their concerns. Mary wrote (as I explicitly quoted): "The proponents of the synthetic theory maintain that all evolution is due to the accumulation of small genetic changes, guided by natural selection, and that transspecific evolution is nothing but an extrapolation and magnification of the events that take place within populations and species."

Second, I talked about the theory being dead "as a general proposition," not dead period. In the full context of my commentary on Mayr's definition, and my qualification about death as a full generality, what is wrong with my statement? I did not proclaim the death of Darwinism, or even of the strictest form of the Modern Synthesis. I stated, for an audience interested in macroevolutionary theory, that Mayr's definition (not the extreme statement of a marginal figure, but an explicit characterization by the world's greatest expert in his most famous book)—with two restrictive claims for (1) "all evolution" due to natural selection of small genetic changes, and (2) transspecific evolution as "nothing but" the extrapolation of microevolutionary events.—must be firmly rejected if macroevolutionary theory merits any independent status, or features any phenomenology requiring causal explanation in its own domain. If we embrace Mayr's definition, then the synthesis is "effectively dead" "as a general proposition"—that is, as a theory capable of providing a full and exclusive explanation of macroevolutionary phenomena. Wouldn't most evolutionary biologists agree with my statement today?

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1. It's interesting that even when describing their differences, Dawkins puts it in the context of "Darwinian theory." Anyone familiar with the conflict knows that it was really about additions to, or conflicts with, strict "Darwinism."

2. Gould discuss this again in his 1980 Science article on "Darwinism and the Expansion of Evolutionary Theory." In that article he quotes Mayr's definition of the Modern Synthesis ...

The term "evolutionary synthesis" was introduced by Julian Huxley ... to designate the general acceptance of two conclusions: gradual evolution can be explained in terms of small genetic changes ("mutations") and recombination, and the ordering of this genetic variation by natural selection: and the observed evolutionary phenomena, particularly macroevolutionary processes and speciation, can be explained in a manner that is consistent with the known genetic mechanisms.

[Image Credit: Photograph of Stephen Jay Gould by Kathy Chapman from Lara Shirvinski at the Art Science Research Laboratory, New York (Wikipedia)]

Tangled Bank #110

 
The latest issue of Tangled Bank was supposed to appear on Blue Collar Scientist but circumstances intervened¹ and PZ Myers has kindly filled the gap on Pharyngula [Tangled Bank #110].

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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.

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1. The blog owner was recently diagnosed with cancer.

Good Science Writers: Douglas J. Futuyma

 
Douglas J. Futuyma is Distinguished Professor in the Department of Ecology and Evolution at the State University of New York at Stony Brook [Douglas Futuyma]. He is best known for his textbooks on evolution, Evolutionary Biology, beginning with the first edition in 1979. The latest version is a shorter textbook entitled Evolution (2005).

Futuyma has also published a trade book on the evolution/creation controversy. The first edition of Science on Trial: The Case for Evolution was published in 1983 and the second edition was published in 1995. Since Futuyma is a professional scientist, he meets all the qualifications for inclusion in Richard Dawkins' book: The Oxford Book of Modern Science Writing. But he is not there.

Douglas Futuyma is a brilliant textbook author. This kind of science writing is not usually recognized, but it should be. Futuyma's ability to accurately explain complex ideas is head-and-shoulders above that of most other textbook authors—no matter what their subject. I've chosen two excerpts from Evolution (2005) to illustrate this ability. You may find them familiar—that's because they have been widely quoted and paraphrased to the point where they seem trivial. Let's not forget that it is Futuyma who first began to explain evolution in this manner.

What Is Evolution?
The word evolution comes from the Latin evolvere, "to unfold or unroll"—to reveal or manifest hidden potentialities. Today "evolution" has come to mean, simply, "change." It is sometimes used to describe changes in individual objects such as stars. Biological (or organic) evolution, however, is change in the properties of groups or organisms over the course of generations. The development or ONTOGENY, or individual organisms is not considered evolution: individual organisms do not evolve. Groups of organisms, which we may call populations, undergo descent with modification. Populations may become subdivided, so that several populations are derived from a common ancestral population. If different changes transpire in the several populations, the populations diverge.

The changes in populations that are considered evolutionary are those that are passed via the genetic material from one generation to the next. Biological evolution may be slight or substantial: it embraces everything from slight changes in the proportions of different forms of a gene within a population to the alterations that led from the earliest organism to dinosaurs, bees, oaks, and humans. (p. 2)

Good Science Writers

Good Science Writing
David Suzuki
Helena Curtis
David Raup
Niles Eldridge
Richard Lewontin
Steven Vogel
Jacques Monod
G. Brent Dalrymple
Eugenie Scott
Sean B. Carroll
Richard Dawkins

Evolution as Fact and Theory
In The Origin of Species, Darwin propounded two major hypotheses: that organisms have descended, with modification, from common ancestors; and that the chief cause of modification is natural selection acting on hereditary variation. Darwin provided abundant evidence for descent with modification, and hundreds of thousands of observations from paleontology, geographic distributions of species, comparative anatomy, embryology, genetics, biochemistry, and molecular biology have confirmed this hypothesis since Darwin's time. Thus the hypothesis of descent with modification from common ancestors has long had the status of a scientific fact.

The explanation of how modification occurs and how ancestors gave rise to diverse descendants constitutes the theory of evolution. We now know that Darwin's hypothesis of natural selection on hereditary variation was correct, but we also know that there are more causes of evolution than Darwin realized, and that natural selection and hereditary variation themselves are more complex than he imagined. A body of ideas about the causes of evolution, including mutation, recombination, gene flow, isolation, random genetic drift, the many forms of natural selection, and other factors, constitute our current theory of evolution or "evolutionary theory." Like all theories in science, it is incomplete, for we do not yet know the causes of all of evolution, and some details may turn out to be wrong. But the main tenets of the theory are well supported, and most biologists accept them with confidence. (pp. 13-14)

I've also chosen an excerpt from Science on Trial (1995). In order to appreciate it, you will need a bit of background. The passage below comes from a chapter on "Chance and Mutation." The chapter opens with a brief description of a play by Tom Stoppard celled Rosencrantz and Guildenstern Are Dead. For those of you not intimately familiar with Shakespeare's Hamlet, Rosencrantz and Guildenstern are two minor characters who are tricked by Hamlet and end up sailing to England where, contrary to their expectations, they will be executed. Stoppard's play is about fate and inevitability.

But just as gravity and Brownian movement may both affect the motion of an airborne particle, chance and natural selection often work simultaneously, and certain evolutionary phenomena can be understood only if we take both into account. Many populations of houseflies throughout the world have evolved a resistance to DDT—an adaptation that has come about by natural selection. In some populations, however, the adaptation is provided by a dominant gene; in some by a recessive gene; in some by a number of genes, each with a small effect. The physiological mechanism by which the genes act also varies: flies can be resistant, for example, either by having developed an enzyme that degrades DDT or by having altered the cell membrane so that DDT is less able to penetrate the tissues. These are alternative adaptive mechanisms. Which one developed in a particular population must have depended on which mutations happened to be present in the population when it became exposed to DDT—and this is very much a matter of chance. Thus, chance initially determines what genetic variations will be acted on by natural selection to develop an adaptation.

When we extrapolate this principle of indeterminacy to long-term evolution, we can understand why different organisms have evolved different "solutions" to similar adaptive "problems." By chance, they had different genetic raw materials to work with. It is doubtless adaptive for male frogs to have a vocal sac that enables them to produce resonant calls that attract females. But whether a frog developed a single sac in the middle of the throat, as in the bullfrog, or a pair of sacs on either side, as in the leopard frog, may have been affected by what mutations first occurred by chance in the ancestor of each species.

If chance is a name for the unpredictable, them almost any historical event is affected by chance. Would Hamlet's mother, watching him stab Polonius through the arras, have predicted that this would be one in a chain of events leading to the death of Rosencrantz and Guildenstern? If you had been on the island of Mauritius in the mid-Tertiary, would you have predicted that the pigeons there would evolve into flightless dodos and then become extinct in the seventeenth century because they were easy prey for sailors? If you had seen a bipedal ape on the plains of Africa in the Pliocene, could you have predicted that this feature would prove crucial in the evolution of a larger brain and the development of human culture? Probably not; for in all such instances, the event that we recognize in hindsight as a "cause" might have been followed by other events leading to a different outcome. All of evolution, like all of history, seems to involve chance, in that very little of what has happened was determined from the beginning.

The mind that cannot abide uncertainty is troubled by the idea that the human species developed by "chance." But whether we evolved by chance or not depends on what the word means. We did not arise by a fortuitous aggregation of molecules, but rather by a nonrandom process—natural selection favoring some genes over others. But we are indeed a product of chance in that we were not predestined, from the beginning of the world, to come into existence. Like the extinction of the dodo, the death of Rosencrantz and Guildenstern, or the outbreak of World War I, we are a product of a history that might have been different. (pp. 146-147)

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WikiPathways

Find a website with a correct citric acid cycle and win $1,000,000 or equivalent!NatureNews has an article on the growth of biological Wikis as a way of involving the molecular biology community in annotating genes, proteins, etc. [Molecular biology gets wikified]. I strongly support the work of Huss et al. (2008) as I described in a previous posting [A Gene Wiki].

Now Pico et al. (2008) have tried to do for metabolic pathways what Huss et al. did for genes. Unfortunately, WikiPathways isn't going to be successful for a number of reasons.

The idea is to create a Wiki for various pathways and allow the biological community to update and comment on the various entries. However, whereas Gene Wiki did the right thing by adding the human genes to Wikipedia, WikiPathways creates its own separate database. This makes it much less accessible since not only do you have to make an effort to find the Wiki, you also have to create an account to make changes.


That's not the only problem. Let's look at a familiar metabolic pathway on WikiPathways, the citric acid cycle. Right away you can see that there are no visible chemical reactions. Instead, you just see a pathway created by lines between boxes with the names of molecules. You don't even see that CO₂ and reducing equivalents are produced by this pathway! That's not going to be very useful.

Contrast the WikiPathways entry with the existing entry on Wikipedia [citric acdi cycle]. The Wikipedia entry is much more useful and, as it turns out, reasonably accurate. I'd be tempted to correct the Wikipedia entry but I'm not interested in doing all the work required to make the WikiPathways entry useful.

Speaking of corrections, when I teach my biochemistry course in the winter I challenge my students to find a single website that shows the citric acid cycle correctly. By that I mean a website where every single reaction is correctly balanced and all reactants and products are shown. The Wikipedia reactions are not correct and the sum of all reactions is incorrect, although in this case the only errors are in balancing the number of hydrogen atoms. Can anyone find the mistakes? Can anyone find a website that's correct? (You can't count any website that shows a figure from my textbook and you can't count the IUBMB website (e.g., citrate synthase). (The most serious error is in getting the products of the succinate dehydrogenase reaction wrong.)

The prize for finding a correct website is seeing your name in print on Sandwalk or $1,000,000 (one million dollars), whichever I think is the most valuable.

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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]

Pico, A.R., Kelder, T., van Iersel, M.P., Hanspers, K., Conklin, B.R., and Evelo, C. (2008) WikiPathways: Pathway Editing for the People. PLoS Biology, 6(7), e184. [DOI: 10.1371/journal.pbio.0060184]

Epigenetics

Epigenetics is one of those words that means entirely different things to different people. P.Z. Myers has put up a nice description of the term on his blog [Epigenetics]. Here's how he defines epigenetics ...

Epigenetics is the study of heritable traits that are not dependent on the primary sequence of DNA.

In fairness, he then goes on to explain that this is an unsatisfactory definition. That's an understatement.

Now, as it turns out, those scientists who work on animal development employ a definition of epigenetics that looks very much like what we used to call developmental regulation of gene expression. That's why PZ can say ...

... developmental biology basically takes epigenetics entirely for granted — development is epigenetics in action! Compare an epidermal keratinocyte and a pancreatic acinar cell, and you will discover that they have exactly the same genome, and that their profound morphological, physiological, and biochemical differences are entirely the product of epigenetic modification. Development is a hierarchical process, with progressive epigenetic restriction of the fates of cells in a lineage — a dividing population of cells proceeds from totipotency to pluripotency to multipotency to a commitment to a specific cell type by heritable changes in gene expression; those cases where there is modification of the DNA, as in the immune system, are the exception.

Here's the problem. If this is epigenetics then what's the point? When I was growing up we had a perfectly good term for these phenomena—it was regulation of gene expression. Why is there a movement among animal developmental biologists to use "epigenetics" to refer to a well-understood phenomenon?

I've been bugging my colleagues today by asking them to tell me whether certain examples of gene regulation are epigenetic or not.¹ The answers are mixed so I thought I'd submit the questions to Sandwalk readers. Which of the following are "epigenetic"?

1. Consider an E. coli cell that grows and divides for hundreds of generations in the absence of any exogenous β-galactosides (e.g. lactose). Under those conditions the lac operon is repressed and this state is heritable from generation to generation due to the presence of lac repressor.
2. Consider mating type in yeast. In an α cell the a gene is suppressed from generation to generation. This is heritable regulation of gene expression. All daughter cells inherit the ability to express the α gene and suppress the a gene.
3. During a bacteriophage infection certain genes are turned on in a definite sequence. In the simplest cases there is a set of "early" genes that are expressed as soon as the 'phage DNA enters the cell. After a few minutes the expression of the "early" genes triggers the expression of the "late" genes. Note that the "late" genes are not transcribed initially even though they are present.
4. Right now your major heat shock genes (e.g. Hsp70 genes) are transcriptionally silent. However, if you are stressed by heat those genes will become active and will be transcribed at a very high rate.
5. During oogenesis in fruit flies the bicoid gene is expressed in nurse cells and bicoid mRNA is deposited in the egg. In males, the bicoid gene is never expressed.
6. One of the nucleotides at an EcoR1 restriction endonuclease site in E. coli is methylated. This blocks cleavage at that site, thus protecting the bacteria from degrading its own genome. The methylation pattern is inherited from generation to generation by the action of a methylase enzyme.
7. Globin genes are expressed in erythroblasts but not in brain cells. During development the globin genes are activated in erythroblast stem cells because certain activator proteins are synthesized. The globin genes are not activated in any other tissues.
8. During development in mammalian females one of the X-chromosomes is randomly inactivated [Calico Cats]. Once this occurs the pattern is inherited in (almost) all cells that descend from the initial embryonic cell where the inactivation first occurred. The same X-chromosome is inactivated in all daughter cells.

I'm interested in two questions. First, is it possible to define epigenetics in a rigorous manner so that we can decide whether certain cases are "epigenetic" or not? Second, what, if anything, is the difference between "epigenetics" and "developmental regulation of gene expression"?

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1. And they are quite annoyed about it. Many of them are avoiding me because they don't know how to answer the questions.

[Image Credit: The cartoon is from Mark Hill's website at the University of New South Wales, Australia. It appeared originally in Nature. The figure represents a different definition of "epigenetics"—one that focuses on modifications to DNA and histones.]

Climbing Mount Improbable as Metaphor

 
One of my postings, Good Science Writers: Richard Dawkins, has been re-posted on RichardDawkins.net. This doesn't happen very often—in fact this may be the very first time. I can't imagine why they would have selected this particular posting.

I mentioned that some of the Dawkins metaphors are misleading and I suggested that Climbing Mount Improbable was one example. That prompted a comment from Richard Dawkins so I replied on his website. In case anyone is interested, I'm reproducing it here.

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Richard Dawkins asks,

I am interested in the suggestion that Climbing Mount Improbable might not be an ideal title.

Richard, we've been over this ground before but for the benefit of the lurkers let me explain why I think the metaphor is inappropriate.

To begin with, you use the Mt. Improbable image as a metaphor for evolution. This is misleading since evolution encompasses more than just adaptation. It would be difficult to apply the "Climbing Mt. Improbable" metaphor to the organization of our genome, for example, since it's clearly not well-designed and could never be characterized as the peak of an adaptive landscape.

But even as a metaphor for adaptation the image is less than perfect. Most readers will see the peak of Mt. Improbable as a goal of adaptation, implying that evolution somehow recognizes that there is an ultimate perfection that all organisms seek to achieve by reaching the summit. As you well know (I hope) there are very few (any?) species that are perfectly adapted to their environment. If this were true, adaptation would cease because the species resides on the summit of Mt. Improbable.

Thus, in the real world, species tend to move about in the foothills rather than attempt to scale the highest peak. As long as they are good enough to survive and reproduce that's all that's required.

Yes, some individuals within the population might acquire a mutation that makes them a little more fit but in most cases the selective advantage will be too small to make much of a difference. I don't believe there's any great pressure to get to the top of Mt. Improbable. That's why we usually don't see perfection in nature. And it explains why most organisms do not look as though they have been designed by some intelligent being. If anything the "design" looks more like a Rube Goldberg creation, and I doubt that anyone would say that those creations represent the peak of perfection.

I prefer a different view of evolution, one that emphasizes chance and accident [Evolution by Accident]. For me, the metaphor of "Climbing Mt. Improbable" is quite wrong as a metaphor of evolution.

Now, I understand that you disagree about the role of chance and accident. You say, for example, on page 326 of Climbing Mt. Improbable, "It is all the product of an unconscious Darwinian fine-tuning, whose intricate perfection we should not believe if it were not before our eyes" (referring to the evolution of figs and fig wasps). For someone who believes that such a description is characteristic of most evolution (adaptation) the "Climbing" metaphor may seem quite appropriate.

BTW, I agree with you that your case for adaptationism is much stronger in Climbing Mt. Improbable than in The Blind Watchmaker. I especially like the chapter you mention, The Museum of All Shells, where you discuss - among other things - the contrast between your view of evolution and the mutationist view. Ironically, you begin that discussion by pointing out that this is a sophisticated controversy, "... and Mount Improbable, even in its multiple-peaked version, isn't a powerful enough metaphor to explore it."

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Nobel Laureate: George de Hevesy

 

The Nobel Prize in Chemistry 1943.

"for his work on the use of isotopes as tracers in the study of chemical processes"


George de Hevesy (1885 - 1966) received the 1943 Nobel Prize in Chemistry for his work on tracing the synthesis of biological molecules using radioactive isotopes, such as ³²P.

He was able to show, for example, that ³²P is readily incorporated into phosphatides (lipids) in chickens and mammals (including humans) but that incorporation into nucleic acids was much slower unless the tissues were growing rapidly. de Hevesy also showed that ³²P from labeled ATP could be incorporated into fructose-1,6-bisphosphate during glycolysis. This was the beginning of studies using radioisotopes to elucidate biochemical pathways.

The presentation speech was delivered by Professor A. Westgren, member of the Nobel Committee for Chemistry of the Royal Swedish Academy of Sciences in a radio address on December 10, 1943. The situation in Europe at the time made travel to Sweden quite difficult so there was no formal awards ceremony, even though de Hevesy was at Stockholm University.

When, in 1913, de Hevesy was working with Rutherford in Manchester, this young scientist had been commissioned to isolate radium D from radioactive lead. His efforts were unsuccessful. It had in fact become apparent that radioactive radium D differed so little from inactive radium G, the last of the series of descendants of radium, that all attempts to isolate them from each other seemed destined to failure. The reason for this was at the same time discovered. Radium D and radium G are isotopes and constitute different species of lead. They differ in their atomic weight whilst their atoms have the same nuclear charge. The shells of their electrons, shells which determine their chemical properties, are therefore more or less identical.

Although unsuccessful, de Hevesy's efforts were not wasted. They gave him the idea for a new method of chemical research.

If it is impossible to isolate chemically a radioactive isotope from an element of which it is part, it must be possible to use this peculiarity to follow in its details the behaviour of this element during chemical reactions and physical processes of different kinds. The active atoms are recognized by their radiation and, being faithful companions of the inactive atoms of an element, they serve as markers for them. Since the intensity of radiation can be determined with such precision that imponderable quantities can be measured in this way, extremely small quantities of a marker of this kind are sufficient.

By using radium D as a marker, de Hevesy determined the solubility of highly insoluble lead compounds. He succeeded in determining exactly the quantity of lead sulphide or of lead chromate taken up under different conditions from solvents of different types. He studied the exchangeability of lead atoms into the dissolved substances and was able to confirm that it corresponded to the behaviour of the lead atoms as ions. The movements of the atoms in solid lead, i.e. the self-diffusion which occurs in this metal, would be determined; it had previously been impossible to measure this process. By precipitating thorium B, a very active isotope of lead, on the surface of a lead crystal and by following the reduction in radiation intensity brought about by the changes in place of the active atoms with the inactive lead atoms of the lower layer, and hence with the penetrations which took place in the crystal, he was able to measure the energy needed to liberate an atom from the crystallised part of the lead, in other words the dissociation energy of the crystal lattice. This energy was found to be of the same order of magnitude as the heat of vaporisation of lead. This latter research is particularly interesting from the physico-chemical point of view.

The new method has also enabled biological processes to be studied. Beans placed in solutions containing lead salts with a mixture of active lead atoms absorbed a part of these salts but the distribution of the metal was not the same in the root, the stem and the leaves. Most of the lead, which does not favour natural biological development but on the contrary acts as a poison, stays in the root. Relatively more lead was extracted from dilute than from more concentrated solutions. Absorption and elimination of lead, bismuth and thallium salts by animal organisms was studied in this way. A knowledge of the distribution of bismuth compounds introduced into an animal organism is valuable from the medical point of view, since some of these compounds, as we know, are used therapeutically.

So long as natural radioactive elements only were used as markers, use of the new method was inevitably very limited. In fact the method could be applied only in the case of heavy metals - lead, thorium, bismuth and thallium - and their compounds. The situation was to be very different when Frédéric and Irène Joliot-Curie, and Fermi succeeded in producing radioactive isotopes from any element by bombarding it with particles. This discovery was made some ten years ago and the study of chemical processes by means of radioactive markers has since then been carried to such a point that it is now widely used in laboratories throughout the world. De Hevesy has remained the prime mover in this new field of activity and much first-class and important research has been carried out by him and his co-workers.

Exceptionally valuable results have thus been obtained in biology. An isotope of radioactive phosphorus, which can be obtained by exposing sulphur to neutron radiation or ordinary phosphorus to radiation from nuclei of heavy hydrogen, has mostly been used. This radioactive phosphorus is sufficiently long-lasting for tests of this nature. It has a half-life of approximately 14.8 days. De Hevesy produced physiological solutions of sodium phosphate containing this marker and injected them into animals and humans. The distribution of the phosphorus was determined at certain intervals. A study of blood samples showed that the phosphorus thus introduced quickly left the blood. In human blood the radio-phosphorus content had fallen after only 2 hours to a mere 2% of its initial value. It diffuses into the extra-cellular body fluid and gradually changes places with the phosphorus atoms of the tissues, organs and skeleton. After some time it can even be found, though in very small quantities, in the enamel of the teeth. Exchanges small and slow as they may be, therefore occur between the outer hard parts of the teeth and the inner tissues of the bones and the lymph. Most of the phosphorus introduced, finds its way into the skeleton, muscles, liver and gastro-intestinal organs. Elimination of phosphorus from living organisms has also been studied by this method.

Phosphorus is an extremely important element in biological processes. The knowledge of its functions in living organisms which has been acquired thanks to the use of radioactive markers is therefore of the very greatest interest. De Hevesy succeeded in detecting where and at what speed the various organic compounds of phosphorus are able to form and the paths which they take in the animal organism. In order to form from a phosphate which has been injected into the blood they must first penetrate into the cells. Acid-soluble compounds of phosphorus form rapidly, whereas phosphatides closely related to fatty substances are slower-forming. These latter form mainly in the liver, whence they are carried by the blood plasma to the places where they will be consumed. De Hevesy showed that the phosphatides of the chicken embryo are produced in the embryo itself and that they cannot be extracted from the egg yolk.

De Hevesy also carried out several investigations with radioactive sodium and potassium. He studied how physiological saline containing radioactive sodium which was injected into a human subject first spread into the blood and then slowly penetrated into the cells; he also studied the manner in which it is excreted. After 24 hours the blood corpuscles had lost approximately half their sodium content.

In addition to the above-mentioned markers, several other active isotopes, such as magnesium, sulphur, calcium, chlorine, manganese, iron, copper and zinc, have been used for this type of research. In the case of the lighter elements it has also been possible to use inactive isotopes such as heavy hydrogen, with an atomic weight of 2, nitrogen, with an atomic weight of 15, and oxygen, with an atomic weight of 18. It is of course less easy to determine the content of an inactive than of an active marker, but this can be done by determinations of density or mass-spectrographically. To determine the concentration of deuterium, or heavy hydrogen, which is twice as heavy as ordinary hydrogen, is a relatively easy matter. De Hevesy used deuterium as marker in many tests. He then noticed that a person who has drunk water containing heavy hydrogen excretes deuterium in the urine after only 26 minutes. Frogs and fishes swimming in water containing deuterium absorb it and, after about 4 hours, are in equilibrium with the medium as far as the deuterium is concerned. Heavy nitrogen and heavy oxygen have also been used in many investigations.

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The Goal of a Science Education

We've recently been debating the purpose of our undergraduate program in biochemistry. There are some who think that the main goal is to teach students how to do biochemistry. Those biochemists want as many lab courses as possible and they want to provide plenty of opportunities for students to carry out research projects in a research lab. In some cases, they want to minimize the number of formal lectures. These are the biochemists who want undergraduates to read the primary literature instead of textbooks.

On the other hand, there are biochemists who want to emphasize the basic concepts and principles of biochemistry. They want to teach student about biochemistry. They believe that students need the latest knowledge of how cells work at the molecular level before they learn how to do research at the frontiers.

The first group wants to train students for a career in biochemistry while the second group tends to think that most students will not go on to be biochemists.

Eva Amsen, a graduate student in our department, has some comments. You should read her posting on her Nature Network blog [What will you be?]. Here's some of the interesting part ...

The problem is not that a science undergraduate degree is not a career-oriented degree. It shouldn’t be. History, English, Philosophy, and some of the social sciences aren’t career paths either. But for those fields people seem to know that, and yet people associate science with something that leads to a job. They picture a scientist in a lab somewhere, and don’t realize that the people at the bench are either lab techs with a degree from a technical college or university students or -graduates at some point in their training. It’s all training, it never ends. A select few will eventually have their own lab, and if their grandmother lives to experience this they can tell her that they now are a scientist. Finally, at the age of 35-40 they have what the family would consider a job. And then they spend the next few decades struggling to get grants and write papers just to be able to keep that job.

The problem is that science programs pretend to be career-oriented. They train you for the job of research scientist, but there are way more students than ever needed to fill these jobs. I’d guess that about 10% of PhD students end up with their own lab. Everyone else has to find an alternative career. But if 90% of the graduates of a science program need to find an alternative career, is it still alternative, or is that just what people do with their degrees?

I agree with Eva. Science programs often pretend to be career oriented but they should be knowledge oriented. The main goal should be to teach students how to think and not how to work at a bench. Thus, students who graduate from an undergraduate—or graduate—program will have valuable skills that they can use in any career they choose.

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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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