Summary of origin of life research

I like to write things about abiogenesis. Go here for some great peer-reviewed publications on the origin of the genetic code and the evolution of the chemical processes underlying metabolism.

In a reply to Gordy Slack, Nick Matzke wrote something great at the Panda's Thumb on the same topic and I want to paste in the relevant portion below:

Origin of Life (OOL)

Slack lists a “few worthy points” creationists make. Here is the first:

First, I have to agree with the ID crowd that there are some very big (and frankly exciting) questions that should keep evolutionists humble. While there is important work going on in the area of biogenesis, for instance, I think it’s fair to say that science is still in the dark about this fundamental question.

Minor point first: Shallit points out that “biogenesis” means production of life from life, whereas Slack is talking about the origin of life (OOL). Oops.

Major points: PZ says that sure, big exciting unanswered questions like the origin of life exist in science, but scientists said this first, and furthermore consider them research opportunities, not flaws. Shallit separates OOL from evolution, specifying that evolution is what occurs after you have life; Shallit does this in the face of Slack asserting that this response is disingenuous. Shallit also argues a little over whether or not we’ve made only “little progress” in understanding the OOL, but says even if we’ve only made a little progress, it’s better than ID.

This mini-debate points out what I think, and have often said in conversations, is a major flaw in how we respond to creationists. All too often, when the OOL comes up in popular discussions (reporters, online debates, etc.), the anti-creationist will reply with some variation of “sure, it’s a tough unsolved problem, but we’re working on it”, or the wizened statement “actually, the OOL is outside of the domain of evolutionary biology”, or finally, “we’re pretty much in the dark about the OOL, but at least what we have is better than the creationists giving up and saying a miracle occurred.”

My take: It is high time all of these statements be discarded or highly modified. They are basically lazy, all-too-easy responses relying on hair-splitting technicalities or nearly philosophical assertions of the “even if the creationists were empirically correct on this point, which they aren’t but I’m too busy to back it up right now, it wouldn’t matter” variety. And the worst part is that these sorts of statements mis-describe the actual state of the science among the people who work in the field. It is simply not true that we, the scientific community, know almost nothing about the OOL (what an individual who spent a career working on fossils or fruit flies or speciation might know personally is a different question).

Here is a short list of things we have discovered or confirmed in the last 50 years or so pertaining to the origin of life. In my opinion all of these points have reached high enough confidence that they are unlikely to change much with future discoveries, and our confidence in them does not depend in uncertainties in the remaining unanswered questions.

OOL Discovery #1. All known life can be traced back to a single common ancestor which, compared to what most people think of as present-day life (i.e. plants and animals), was relatively simple – microscopic, single-celled, perhaps as complex as an average bacterium or perhaps somewhat less so.

Because a lot of creationists, and sometimes others, are a bit thick in the head on correctly understanding this point, let me bash away at some common misconceptions. The phrase “single common ancestor” does not, and never has for people who were paying close attention, referred to a literal single individual organism. Think about a phylogenetic tree with humans and chimps on the branches. When you trace the tree back to the “common ancestor” of chimps and humans, does that node represent a literal single individual? No, of course not! Everyone (well, everyone paying attention) realizes that that ancestral node represents a species or population sharing genes in a gene pool. Ditto for all of the other ancestral nodes in a phylogenetic tree, including the Last Common Ancestor of known life.

With this understood, the debate initiated by Ford Doolittle and others over the precise nature of the Last Common Ancestor – they argue that it was a population of unicells that were rampantly trading genes – can be put in the correct context. It’s basically a debate about how wide or narrow the bottleneck the Last Common Ancestor represents, and whether (for example) modern life might contain some genes derived by lateral transfer from pre-LCA lineages that are now extinct. These debates are fascinating and highly technical, but they don’t undermine at all Point #1. Somewhat ironically and counterintuitively, those who say that there was rampant lateral transfer – this is supposed to be the “radical” position that “uproots the Tree of Life” when its proponents get their blood up – are actually pushing the LCA to something more and more like a traditional gene pool, i.e. species, i.e. what every other node in a phylogenetic tree represents.

Any way you slice it, all known life (with minor derived exceptions, and excepting viruses) shares a suite of protein and RNA genes, a DNA-RNA-protein system and a mostly standard genetic code (again with minor derived exceptions), etc. Even if various other bits of modern life came from other ancestral lineages (unlikely for most features in my opinion but there may be some exceptions), this shared system indicates that all known life, i.e. all the stuff that’s not extinct, descends from a pretty good bottleneck where these features were fixed in the “population.” And this reconstructed ancestor is maybe as complex as a typical bacterium and probably less so. It could be that in the last 50 years science discovered that known life had for-real multiple origins, or that at the root of the tree was a complex multicellular organism with 30,000 genes and huge, elaborately regulated, genome, but instead we get a unicell with a relatively small & simple genome. Various caveats, important to scientists but irrelevant to beginner-level education and dealing with creationists (e.g., somewhat more genes may have been passed through the bottleneck in some but not all organisms if the LCA was more of a gene-trading community) should not be allowed to distract from the Main Point: science has confirmed the hypothesis, going back at least to Darwin, that the ancestor of modern life was much less complex than life today.

OOL Discovery #2. The Last Common Ancestor itself was the product of evolution from an even simpler ancestor. The simplest piece of evidence for this is that a number of the genes found in the Last Common Ancestor are homologous, thus derived from a single common ancestor by duplication and modification. An example is the F1Fo-ATPase of bacteria, which interconverts proton gradients (or sometimes sodium ion gradients, which are chemically very similar) and ATP, the main energy currency of cells. It has relatives in all branches of life: the V1Vo-ATPases in eukaryotes (and some prokaryotes), and the A1Ao-ATPases of archaea, and phylogenetic analysis indicates that this membrane-embedded system was found in the LCA (this also confirms that the LCA had membranes, which is useful although already very likely on multiple grounds).

Anyway, the bit of the V/F/A-ATPases that deals with ATP is a heterohexamer, i.e. complex of six proteins (that’s the “hexamer” bit) of two different types (thus “hetero”), cleverly named alpha and beta. The alphas and betas alternate in the six-protein ring, and the betas interact with ATP. The key point here is that the alpha and beta subunits share statistically strong sequence similarity. The simple explanation is that the heterohexamer was descended from a homohexamer made up of six identical proteins forming a ring. Thus we know – as strongly as we know that two people are related by ancestry based on DNA sequence similarity – that long before the last common ancestor of life there was a cellular organism that had something like the F1Fo-ATPase, but a simpler version with a homohexameric ATPase complex instead of a heterohexamer.

This may seem like a trivial point by itself but it is just an example; there are dozens, perhaps hundreds, of others. The evolution of ATPases can be traced much further back: the next closest relative is a homohexamer found in, of all things, the core of the bacterial flagellum and the nonflagellar type 3 secretion systems. Thus the V/F/A-ATPases and the flagellar/nonflagellar type 3 secretion systems can be traced back to an ancestral membrane-associated complex with multiple shared proteins (because the V/F/A-ATPases and type 3 secretion systems shared not just the ATPase protein but also an associated external stalk protein, FliH/Fo-b, which by the way is something I pretty much predicted in 2003 in the Big Flagellum Essay and which Mark Pallen and colleagues nailed down for real in the peer-reviewed literature in 2006).

Even more distant relatives are known: the homohexameric rho (involved in bacterial RNA processing) and homohexameric RecA (DNA processing). And there are even more distant hexameric sister groups; the whole related set of proteins is known as the AAA ATPases if you want to look them up. And if memory serves there are yet more distant non-hexameric relatives.

In other words, the Last Common Ancestor had a suite of ATPase proteins which had already evolved from a single protein ancestor by duplication and divergence events which are still strongly statistically detectable in the present day. And there are a number of other genes for which the same can be said, and undoubtedly many others which occurred but are not statistically detectable billions of years later due to the decay of the signal.

So far we’ve established that anyone, creationist, evolutionist, or whomever, who says that the scientific understanding of the origin-of-life is chemicals –> mystery –> modern-complexity life doesn’t know the first thing about what they’re yapping about. At the very least we’ve got chemicals –> mystery –> quite simple precursor to the LCA –> LCA –> modern life. But there is yet more that we know

OOL Discovery #3. DNA/RNA/protein-based life was preceded by something even simpler, an RNA world or at least an RNA-heavy world.

The RNA world has gotten better press attention than OOL Discoveries #1 and #2 so I will spend less time on it. Read the wikipedia page for an introduction and particularly the EvoWiki page for some of the main supporting evidence.

There are two points worth making about the RNA world that should be made every time this issue is discussed in popular or remedial creationism-related discussions. First: there was a time, not too long ago, when the fact that DNA coded for proteins, and proteins were necessary for making DNA, seemed like the ultimate intrinsically unsolvable problem in the study of the origin of life. It’s the ultimate chicken-and-egg problem, or, if you like, the ultimate “irreducible complexity” problem. And yet, scientists worked on it for a few decades and discovered a workable, surprisingly simple solution.

Second, surprisingly enough (well, surprising to creationists or the naive), this solution, the RNA world, hasn’t just sat around as a purely theoretical just-so story. A highly productive research program has been built on the RNA World concept. Areas that have experienced substantial success in the last decade or two include: the discovery of increasingly diverse catalytic capabilities of RNA; the evolution new capabilities in replicating, evolving RNAs; the evolution of the genetic code which translates DNA to RNA to protein; and the prebiotic origin of RNA components.

Each of these areas has developed into a subfield which has experienced major research discoveries in recent years. For example, on the origin of the genetic code, this paper assembles dozens of indicators on the order in which amino acids were added, step-by-step, to the genetic code and shows that the evidence strongly supports a fairly specific scenario (which shares many similarities with early, more speculative scenarios built on the basis of just a few lines of evidence).

Ergo, we don’t just know that the Last Common Ancestor of Life was simple, and that it’s ancestor was simpler, and that it’s ancestor was an even simpler RNA-dominated critter; we even have a decent idea about the order of the steps by which the genetic code itself evolved.

OOL Discovery #4. The increasingly simple ancestors of modern life weren’t made out of just anything, they were made out of chemicals that just happen to be generated by plausible abiotic mechanisms found in early solar systems. This area is also better known, but many, both creationists and scientists and journalists who haven’t thought about it enough, tend to think of prebiotic chemistry as the beginning and ending of origin-of-life studies, and for some extremely foolish reason which I can’t fashion, probably simple carelessness, tend to think that until chemists pop life out of a test tube then we “know nothing” about the origin of life.

Here’s a short list of discoveries about prebiotic chemistry, all of which increase our confidence in the idea that the origin of life was a gradual process, from abiotic chemicals to simple replicators to the simple ancestors of modern life which were discovered above. I’ll include some subtleties that I’ve seen lead people astray on occasion.

* Water is one of the most common compounds in the universe, and was/is common in the solar system (subtlety: most of it is frozen, but remember that on any planet with hot stuff inside and cold frozen stuff outside will have a just-right region in-between where water will be liquid)

* Earthlike planets are likely reasonably common (subtlety: we haven’t discovered them directly yet, but this is isn’t because they aren’t there, it’s because our instruments are at present only sensitive enough to detect big, close-in planets around other stars. Nevertheless, the distribution of the stuff we can detect strongly indicates that there are plenty of earthlike planets in earthlike orbits which will be discoverable in the near future. That’s a prediction, scientists will test it, that’s science for you. Remember that back in the 1990s, ID proponent William Dembski was skeptical of the whole idea of extrasolar planets. Whoops!)

* Amino acids are easy to generate by a variety of processes, and this is not only supported by experiment, but by observation of amino acids in meteorites and other extra-terrestrial material. (Subtlety: There is a body of serious scientific thought which suggests that the Earth’s early atmosphere was more neutral and less reducing than was thought a few decades ago, but (1) this isn’t for sure, the redox chemistry of the Earth’s rocks and atmosphere is a complex business (and I wonder if the impact which produced the moon, removing much of the mantle but leaving the Earth enriched in heavy iron might have made the Earth’s atmosphere more reducing, at least early on – comments?); (2) even in a neutral atmosphere/ocean system there will be locally reducing conditions – heck, there are local reducing conditions here on earth right now even with our heavily oxidized crust and atmosphere; (3) as it turns out, even neutral atmospheres can produce amino acids in respectable yields anyway; and (4) this whole sub-debate is somewhat moot since we have direct evidence of amino acids forming in the solar system e.g. in meteorites.)

* RNA precursors are somewhat tougher, but there has been progress in that area also, and anyway there is no requirement that the first replicator must have been RNA; various other simpler “worlds” have been suggested and are being explored (PNA, peptide nucleic acids; other NAs of various sorts; and lipid worlds, which have the distinct charm of instant replication ability and statistical inheritance, with daughter bubbes containing a subsample of the chemicals making up the mother bubbles, and growth occuring by incorporation of lipids from the environment and other bubbles; so maybe the first “replicators” were even simpler than some have thought).

* The main energy source of present life is ATP and other energized phosphate molecules. So, what was the prebiotic source of those? It turns out that inorganic polyphosphates (chains like phosphate-phosphate-phosphate-phosphate) have energetic bonds very similar to those of ATP (which is adenine-phosphate-phosphate-phosphate), and yet can be formed by the simple heating of certain rocks.

* Less well-known is the fact that prebiotic origins of many cofactors and other universal small biotic compounds have also been reconstructed

What is actually being worked on. The above should convince you that the idea that we know nothing or very little about the OOL is just uninformed foolishness. The field has made major progress. There are some famous puzzles remaining, but they do not add up to “we know nothing about the origin of life.” Furthermore, some of the puzzles that creationists, and sometimes others, consider to be major hangups, are not necessarily so. For example:

* The origin of chirality (the left-handedness of amino acids). This is a major puzzle if you make the extremely foolish and unthinking assume (like creationists do, but sometimes others) that the first use of amino acids in early life was supposed to be in long amino acid chains made up of 100+ amino acids randomly assembled from an even mixture of 20+ different amino acids with an even mixture of right- and left-handed amino acids. But over here in the real world, where the origin of the genetic code has been reconstructed in some detail, we know the following: the first primitive genetic code used just one or a few amino acids, and one of the first was glycine, which is the simplest amino acid, the most common amino acid produced in prebiotic experiments, and which is achiral (no left-hand/right-hand difference) to boot. If, as has been proposed, the first use of amino acids was as something relatively prosaic, i.e. a short chain of hydrophobic residues to insert into an early membrane, then (a) the odds of getting 10 or so amino acids at once that were either left-handed or glycine were not small at all, and (b) it wouldn’t have mattered much if the occasional right-handed amino acid was incorporated, because the crude chemical property of hydrophobicity is all that is really important, and (c) therefore the origin of a preferred chirality could have been more or less random. There is some very interesting work indicating that nature has various processes which might increase the proportion of left-handed amino acids, but it’s not at all clear that these will be necessary to explain chirality.

* The origin of the first replicator. This really is the big cahuna of the OOL discussion, and where the big and contentious debates are still occurring within science, but again I find that many discussants operate with very crude and naive assumptions about what early replicators “should” have been like and what prebiotic experiments “should” be able to produce to “solve” this problem. It’s a mini-version of the “produce a modern cell in a test tube for me or you haven’t solved the OOL” silliness, i.e., “produce a self replicating RNA World, with duplicating ‘informational genetic sequences’ in the test tube, and until you do you can’t say we know anything about the origin of replicators.”

Again, over here in reality-land the distinctions between replicators and nonreplicators are not so clear. I have already mentioned “lipid-world” ideas and the concept of “statistical inheritance”, where overall chemical properties are transmitted or accumulated, without the need for exact inheritance of a sequence. Similar concepts have been applied by OOL workers to amino acid and nucleic acid “sequences”, where before exact inheritance of sequence is acheived, there might have been a stage where inexact incorporation of a range of chemically similar bases was occurring.

Another subtlety is the difference between “self-replication” and processes where prebiotic compounds go through a series of chemical processes, and differences in chemical kinetics increase the frequency of compounds that have more rapid kinetics; if these compounds are auto-catalytic, they can begin a feedback system where chemicals with higher kinetics take over in a proto-selection system. Strangely, although everyone who takes college chemistry learns that the product of chemical reactions is a combination of thermodynamics and kinetics, many discussions of the OOL from scientists, and all of the derivative critiques by creationists, have focused on thermodynamics. This is particularly odd since self-replication is the ultimate example of kinetics overwhelming thermodynamics.

What’s the point of this sub-discussion? Well, if it is the case that the origin of the first “replicator” was, like everything else we’ve discovered in the study of OOL, a slow, gradual (meaning step-by-step), cumulative process, then it is pretty foolish to have in our heads the idea that OOL experiments should produce full-on replicators in one go to be successful experiments. This is basically a strawman expectation that expresses conceptual confusion about what an evolutionary origin of life “should” look like.

(As an aside, I think biology education would be a lot better off if the above points were consistently made in science curricula and textbooks at the high school and college level. Teaching OOL as a story from simple to complex, rather than a detective story from complex to simple, is probably a mistake if the goal is to get students to understand why scientists think the way they do about these issues.)

The Main Point

Now that we’ve briefly reviewed the OOL field and discussed the major discoveries and some of the common misconceptions, let’s return to the statements I quoted at the beginning. Is it really true that “science is still in the dark” on the OOL, as Slack said? Not a chance. If we lived in a world where it actually looked like the first living things were as complex or more complex than life today, or where the last common ancestor contained absolutely no evidence of an evolutionary history, or where big obvious puzzles like the interdependency of DNA/RNA/protein had no hint of solution, or where the building blocks of life were completely unrelated to those produced in prebiotic experiments – all of these things would be true, say, on a robotic planet without microscopic life, where robots were replicated by macroscopic assembly performed by other robots, and powered by hooking up to a grid of fusion-fueled power plants – then we could say “science is still in the dark” on the origin of this robotic biosphere. But instead, we have numerous lines of evidence all pointing towards the notion that current life descends from a relatively simple ancestor, and that ancestor descends from a series of even simpler ancestors. Why should any of this evidence exist, if life was poofed into existence all in one step, which is what the creationists/IDers think happened even when they won’t admit it, because they are not brave enough to defend what they actually think? Additionally, why should the remaining puzzles, particularly about the origin of the first replicator, cause any unusual amount of discomfort for scientists? Whether or not that puzzle is solved, the gap between prebiotic experiments and the first replicators (or better yet, pseudoreplicators with statistical inheritance) is a drastically reduced vestige of a gap compared to what the gap looked like in, say, 1950. When you think about it, the creationists’ attempt to insert miraculous divine intervention into this tight little gap which is left is actually pitiful, and a pretty sad commentary on the state that creationism/ID has been reduced to. The verse “And God said, let the NA precursors link together into a short noncoding kinetically favored chain and pseudoreplicate approximately statistically after their kind” just doesn’t have the same ring to it.

Similarly, if my characterization of the state of the science is accurate, then it is highly irresponsible for scientists to address creationist arguments about the origin of life with statements like, “even if the creationists were empirically correct on this point, which they aren’t but I’m too busy to back it up right now, it wouldn’t matter” or “actually, the OOL is outside of the domain of evolutionary biology.” The first statement surrenders without argument a favorite bogus creationist talking point, and so confirms and passes on their misinformation, even if the evolution “wins” the argument in his own head on some broader philosophical point. Instead of putting the creationist back on his heels with a wave of contradictory evidence, that sort of response, even if the philosophical point is valid, leaves the creationist and any of his sympathetic readers irate that the empirical point is not being addressed, and that the creationist/ID position is being excluded by the rules of the game. The fact that this sort of response is a lot easier and faster to put together does not make it the best one.

The second statement, splitting the OOL from evolutionary theory, is only technically correct in a sort of legalistic, hairsplitting way. Sure, it’s true that technically, “evolution” only happens once you have life, or at least replicators, but getting from replicators to the last common ancestor is most of what most people think about when they’re thinking about the origin of life, i.e., “where did the evolutionary ancestor of all life today come from?” and all of that is evolution all the way. Furthermore, even the origin of the first classical “replicator” was itself very likely an evolutionary process, in that it occurred in stepwise fashion and not all-at-once, and that the first replicator was likely preceded by various sorts of pseudoreplication, statistical inheritance and kinetic biases. If you remove evolution from your thinking about the origin of the first replicator then it is very likely you will never understand how it happened, or what the current research on the question is about. Finally, even apart from these detailed considerations, “evolution” reasonably has a broader meaning – the evolution of the universe, the solar system, the planet, and the planet’s geochemistry, and the origin of life and the origin of the first replicator must be understood as part of that larger evolutionary history.

One other telling point is that the statement “but the OOL is outside of evolutionary theory” response also has the problem of simply dodging the hard work of describing the discoveries and work of modern science, a problem I have already described. In conclusion, if it were up to me, I would completely scrap this statement from the rhetorical toolkit of evolution defenders.

The OOL topic turned into an essay on its own, but we still have another few of Slack’s points to address.

An excellent summary, if I may say so. He left out a few things that I've mentioned before, like the discovery of the role of borate in natural ribose synthesis by a colleague of mine at UF, and upstairs neighbors, Alonso Ricardo and Fabianne Frye. Go here for some great peer-reviewed publications on the origin of the genetic code and the evolution of the chemical processes underlying metabolism.

Exploring Life's Origins

I like to write things about abiogenesis.

The Boston Museum of Science has a wonderful new online exhibit called Exploring Life's Origins on the topic, so check it out!

The History Channel will air a show, How Life Began, tonight at 9 PM...the show's schedule:

1. Monday, June 16 09:00 PM
2. Tuesday, June 17 01:00 AM
3. Saturday, June 21 10:00 PM
4. Sunday, June 22 02:00 AM
5. Sunday, June 29 02:00 PM

Also, Youtube has a couple of good videos on the topic as well: 1, 2.

Intelligent Design: Evolution = Holocaust!

The upcoming creationist propaganda piece, Expelled, has been exposed. Now, SciAm takes a turn, and it isn't pretty:

April 9, 2008
Expelled: No Intelligence Allowed--Ben Stein Launches a Science-free Attack on Darwin
In a new documentary film, actor, game show host and financial columnist Ben Stein falls for the pseudoscience of intelligent design
By Michael Shermer

Editor's note: This story is part of a series "Expelled: No Intelligence Allowed--Scientific American's Take."

In 1974 I matriculated at Pepperdine University as a born-again Christian who rejected Darwinism and evolutionary theory—not because I knew anything about it (I didn't) but because I thought that in order to believe in God and accept the Bible as true, you had to be a creationist. What I knew about evolution came primarily from creationist literature, so when I finally took a course in evolutionary theory in graduate school I realized that I had been hoodwinked. What I discovered is a massive amount of evidence from multiple sciences—geology, paleontology, biogeography, zoology, botany, comparative anatomy, molecular biology, genetics and embryology—demonstrating that evolution happened.

It was with some irony for me, then, that I saw Ben Stein's antievolution documentary film, Expelled: No Intelligence Allowed, opens with the actor, game show host and speechwriter for Richard Nixon addressing a packed audience of adoring students at Pepperdine University, apparently falling for the same trap I did.

Actually they didn't. The biology professors at Pepperdine assure me that their mostly Christian students fully accept the theory of evolution. So who were these people embracing Stein's screed against science? Extras. According to Lee Kats, associate provost for research and chair of natural science at Pepperdine, "the production company paid for the use of the facility just as all other companies do that film on our campus" but that "the company was nervous that they would not have enough people in the audience so they brought in extras. Members of the audience had to sign in and a staff member reports that no more than two to three Pepperdine students were in attendance. Mr. Stein's lecture on that topic was not an event sponsored by the university." And this is one of the least dishonest parts of the film.

At the Crossroads of Conspiracy

Ben Stein came to my office to interview me about what I was told was a film about "the intersection of science and religion" called Crossroads (yet another deception). I knew something was afoot when his first question to me was on whether or not I think someone should be fired for expressing dissenting views. I pressed Stein for specifics: Who is being fired for what, when and where? In my experience, people are usually fired for reasons having to do with budgetary constraints, incompetence or not fulfilling the terms of a contract. Stein finally asked my opinion on people being fired for endorsing intelligent design. I replied that I know of no instance where such a firing has happened.

This seemingly innocent observation was turned into a filmic confession of ignorance when my on-camera interview abruptly ends there, because when I saw Expelled at a preview screening at the National Religious Broadcasters's convention (tellingly, the film is being targeted primarily to religious and conservative groups), I discovered that the central thesis of the film is a conspiracy theory about the systematic attempt to keep intelligent design creationism out of American classrooms and culture.

Stein's case for conspiracy centers on a journal article written by Stephen Meyer, a senior fellow at the intelligent design think tank Discovery Institute and professor at the theologically conservative Christian Palm Beach Atlantic University. Meyer's article, "The Origin of Biological Information and the Higher Taxonomic Categories," was published in the June 2004 Proceedings of the Biological Society of Washington, the voice of the Biological Society with a circulation of less than 300 people. In other words, from the get-go this was much ado about nothing.

Nevertheless, some members of the organization voiced their displeasure, so the society's governing council released a statement explaining, "Contrary to typical editorial practices, the paper was published without review by any associate editor; Sternberg handled the entire review process. The council, which includes officers, elected councilors and past presidents, and the associate editors would have deemed the paper inappropriate for the pages of the Proceedings." So how did it get published? In the words of journal's managing editor at the time, Richard Sternberg, "it was my prerogative to choose the editor who would work directly on the paper, and as I was best qualified among the editors, I chose myself." And what qualified Sternberg to choose himself? Perhaps it was his position as a fellow of the International Society for Complexity, Information, and Design, which promotes intelligent design, along with being on the editorial board of the Occasional Papers of the Baraminology Study Group, a creationism journal committed to the literal interpretation of Genesis. Or perhaps it was the fact that he is a signatory of the Discovery Institute's "100 Scientists who Doubt Darwinism" statement.

Meyer's article is the first intelligent design paper ever published in a peer-reviewed journal, but it deals less with systematics (or taxonomy, Sternberg's specialty) than it does paleontology, for which many members of the society would have been better qualified than he to peer-review the paper. (In fact, at least three members were experts on the Cambrian invertebrates discussed in Meyer's paper). Meyer claims that the "Cambrian explosion" of complex hard-bodied life forms over 500 million years ago could not have come about through Darwinian gradualism. The fact that geologists call it an "explosion" leads creationists to glom onto the word as a synonym for "sudden creation." After four billion years of an empty Earth, God reached down from the heavens and willed trilobites into existence ex nihilo. In reality, according to paleontologist Donald Prothero, in his 2007 magisterial book Evolution: What the Fossils Say and Why it Matters (Columbia University Press): "The major groups of invertebrate fossils do not all appear suddenly at the base of the Cambrian but are spaced out over strata spanning 80 million years—hardly an instantaneous 'explosion'! Some groups appear tens of millions of years earlier than others. And preceding the Cambrian explosion was a long slow buildup to the first appearance of typical Cambrian shelled invertebrates." If an intelligent designer did create the Cambrian life forms, it took 80 million years of gradual evolution to do it.

Stein, however, is uninterested in paleontology, or any other science for that matter. His focus is on what happened to Sternberg, who is portrayed in the film as a martyr to the cause of free speech. "As a result of publishing the Meyer article," Stein intones in his inimitably droll voice, "Dr. Sternberg found himself the object of a massive campaign that smeared his reputation and came close to destroying his career." According to Sternberg, "after the publication of the Meyer article the climate changed from being chilly to being outright hostile. Shunned, yes, and discredited." As a result, Sternberg filed a claim against the Smithsonian National Museum of Natural History (NMNH) for being "targeted for retaliation and harassment" for his religious beliefs. "I was viewed as an intellectual terrorist," he tells Stein. In August 2005 his claim was rejected. According to Jonathan Coddington, his supervisor at the NMNH, Sternberg was not discriminated against, was never dismissed, and in fact was not even a paid employee, but just an unpaid research associate who had completed his three-year term!

Who Speaks for Science?

The rest of the martyrdom stories in Expelled have similar, albeit less menacing explanations, detailed at www.expelledexposed.com, where physical anthropologist Eugenie Scott and her tireless crew at the National Center for Science Education have tracked down the specifics of each case. Astronomer Guillermo Gonzalez, for example, did not get tenure at Iowa State University in Ames and is portrayed in the film as sacrificed on the alter of tenure denial because of his authorship of a pro–intelligent design book entitled The Privileged Planet (Regnery Publishing, 2004). As Scott told me, "Tenure is based on the evaluation of academic performance at one's current institution for the previous seven years." Although Gonzales was apparently a productive scientist before he moved to Iowa State, Scott says that "while there, his publication record tanked, he brought in only a couple of grants—one of which was from the [John] Templeton Foundation to write The Privileged Planet—didn't have very many graduate students, and those he had never completed their degrees. Lots of people don't get tenure, for the same legitimate reasons that Gonzalez didn't get tenure."

Tenure in any department is serious business, because it means, essentially, employment for life. Tenure decisions for astronomers are based on the number and quality of scientific papers published, the prestige of the journal in which they are published, the number of grants funded (universities are ranked, in part, by the grant-productivity of their faculties), the number of graduate students who completed their program, the amount of telescope time allocated as well as the trends in each of these categories, indicating whether or not the candidate shows potential for continued productivity. In point of fact, according to Gregory Geoffroy, president of Iowa State, "Over the past 10 years, four of the 12 candidates who came up for review in the physics and astronomy department were not granted tenure." Gonzales was one of them, and for good reasons, despite Stein's claim of his "stellar academic record."

For her part, Scott is presented in the film as the cultural filter for determining what is and is not science, begging the rhetorical question: Just who does she think she is anyway? Her response to me was as poignant as it was instructive: "Who is Ben Stein to say what is science and not science? None of us speak for science. Scientists vary all over the map in their religious and philosophical views—for example, Francis Collins [the evangelical Christian and National Human Genome Research Institute director], so no one can speak for science."

From Haeckel to Hitler

Even more disturbing than these distortions is the film's other thesis that Darwinism inexorably leads to atheism, communism, fascism, and could be blamed for the Holocaust. Despite the fact that hundreds of millions of religious believers fully accept the theory of evolution, Stein claims that we are in an ideological war between a scientific natural worldview that leads to Stalin's gulag archipelago and Nazi gas chambers, and a religious supernatural worldview that leads to freedom, justice and the American way. The film's visual motifs leave no doubt in the viewer's emotional brain that Darwinism is leading America into an immoral quagmire. We're going to hell in a Darwinian handbasket. Cleverly edited interview excerpts from scientists are interspersed with various black-and-white clips for guilt by association with: bullies beating up on a 98-pound weakling, Charlton Heston's character in Planet of the Apes being blasted by a water hose, Nikita Khrushchev pounding his fist on a United Nations desk, East Germans captured trying to scale the Berlin Wall, and Nazi crematoria remains and Holocaust victims being bulldozed into mass graves. This propaganda production would make Joseph Goebbels proud.

It is true that the Nazis did occasionally adapt a warped version of social Darwinism proffered by the 19th-century German biologist Ernst Haeckel in a "survival of the fittest races" mode. But this rationale was only in the service of justifying the anti-Semitism that had been inculcated into European culture centuries before. Because Stein is Jewish, he surely knows that the pogroms against his people began ages before Darwin and that the German people were, in Harvard University political scientist Daniel Goldhagen's apt phrase (and book title), "Hitler's willing executioners."

When Stein interviewed me and asked my opinion on the impact of Darwinism on culture, he seemed astonishingly ignorant of the many other ways that Darwinism has been used and abused by political and economic ideologues of all stripes. Because Stein is a well-known economic conservative (and because I had just finished writing my book The Mind of the Market, a chapter of which compares Adam Smith's "invisible hand" with Charles Darwin's natural selection), I pointed out how the captains of industry in the late 19th and early 20th centuries justified their beliefs in laissez-faire capitalism through the social Darwinism of "survival of the fittest corporations." And, more recently, I noted that Enron's CEO, Jeffrey Skilling, said his favorite book in Harvard Business School was Richard Dawkins' The Selfish Gene (first published in 1976), a form of Darwinism that Skilling badly misinterpreted. Scientific theorists cannot be held responsible for how their ideas are employed in the service of nonscientific agendas.

Questioning Darwinism

A final leitmotif running through Expelled is inscribed in chalk by Stein in repetitive lines on a classroom blackboard: "Do not question Darwinism." Anyone who thinks that scientists do not question Darwinism has never been to an evolutionary conference. At the World Summit on Evolution held in the Galapagos Islands during June 2005, for example, I witnessed a scientific theory rich in controversy and disputation. Paleontologist William Schopf of the University of California, Los Angeles, for instance, explained that "We know the overall sequence of life's origin, that the origin of life was early, microbial and unicellular, and that an RNA world preceded today's DNA–protein world." He openly admitted, however, "We do not know the precise environments of the early earth in which these events occurred; we do not know the exact chemistry of some of the important chemical reactions that led to life; and we do not have any knowledge of life in a pre-RNA world."

Stanford University biologist Joan Roughgarden declared that Darwin's theory of sexual selection (a specific type of natural selection) is wrong in its claim that females choose mates who are more attractive and well-armed. Calling neo-Darwinians "bullies," the University of Massachusetts Amherst biologist Lynn Margulis pronounced that "neo-Darwinism is dead" and, echoing Darwin, she said, "It was like confessing a murder when I discovered I was not a neo-Darwinist." Why? Because, Margulis explained, "Random changes in DNA alone do not lead to speciation. Symbiogenesis—the appearance of new behaviors, tissues, organs, organ systems, physiologies or species as a result of symbiont interaction—is the major source of evolutionary novelty in eukaryotes: animals, plants and fungi."

Finally, Cornell University evolutionary theorist William Provine (featured in Expelled) presented 11 problems with evolutionary theory, including: "Natural selection does not shape an adaptation or cause a gene to spread over a population or really do anything at all. It is instead the result of specific causes: hereditary changes, developmental causes, ecological causes and demography. Natural selection is the result of these causes, not a cause that is by itself. It is not a mechanism."

Despite this public questioning of Darwinism (and neo-Darwinism), which I reported on in Scientific American, Schopf, Roughgarden, Margulis and Provine have not been persecuted, shunned, fired or even Expelled. Why? Because they are doing science, not religion. It is perfectly okay to question Darwinism (or any other "-ism" in science), as long as there is a way to test your challenge. Intelligent design creationists, by contrast, have no interest in doing science at all. In the words of mathematician and philosopher William Dembski of Southwestern Baptist Theological Seminary and a key witness in Stein's prosecution of evolution, from a 2000 speech at the National Religious Broadcasters convention in Anaheim, Calif.: "Intelligent design opens the whole possibility of us being created in the image of a benevolent God…. And if there's anything that I think has blocked the growth of Christ as the free reign of the spirit and people accepting the Scripture and Jesus Christ, it is the Darwinian naturalistic view."

When will people learn that Darwinian naturalism has nothing whatsoever to do with religious supernaturalism? By the very definitions of the words it is not possible for supernatural processes to be understood by a method designed strictly for analyzing natural causes. Unless God reaches into our world through natural and detectable means, he remains wholly outside the realm of science.

So, yes Mr. Stein, sometimes walls are bad (Berlin), but other times good walls make good neighbors. Let's build up that wall separating church and state, along with science and religion, and let freedom ring for all people to believe or disbelieve what they will.

Michael Shermer is Publisher of Skeptic (www.skeptic.com) and the author of Why Darwin Matters: The Case Against Intelligent Design. His new book is The Mind of the Market.

Evolution = Hitler. Hmmm...sounds familiar to me for some reason.

Science Debate 2008

This is probably old news to some/most, but I wanted to highlight the Science Debate 2008 site and cause, as it's definitely in line with my reasoning for my YouTube question and the link to firstfreedomfirst's "Sound Science" ad.

Here's a nice argument from an op-ed in the Wichita Eagle that I think summarizes the issues well:

Presidential race needs science debate

Science and technology are central to many of America's most pressing challenges and controversies: Climate change. Energy independence. Stem cell research. Nuclear proliferation. And on and on.

You wouldn't know that, though, by listening to the presidential debates so far.

If these questions do come up, they're often swiftly dispatched with a boilerplate answer or two.

Too often, science is pushed to the sidelines of presidential debates to make way for presumably weightier topics, such as whether Hillary Clinton is really likable or whether Dennis Kucinich saw a UFO.

In one forum, Mike Huckabee responded to a question about a proposed Mars mission by suggesting that Clinton should be the first passenger.

OK. But can we get serious for a moment?

The next president faces difficult, historic decisions in science and technology that will shape our country's future for decades to come.

That's why voters should support a bipartisan effort now gaining steam to hold a presidential science debate.

A grassroots group called Science Debate 2008 is pushing for a televised debate sometime after the Feb. 5 primaries to plumb the candidates' views on energy and the environment, technological and scientific innovation, and medicine.

Organizers say the purpose is simply to acknowledge the overriding importance of science and technology to our nation's prosperity and future.

That future is hardly assured.

A recent report from the National Academies of Science, "Rising Above the Gathering Storm," reported that the "scientific and technological building blocks critical to our economic leadership are eroding at a time when many other nations are gathering strength."

Just a few examples:

• The United States is now a net importer of high-technology products.

• In 2003, American 15-year-olds ranked 24th out of 40 countries in an examination of students' ability to use mathematical skills to solve real-world problems.

• China and India are leaving the United States behind in producing new engineering doctorates.

For the most part, the candidates have offered few specifics about science policy or they've dodged the questions altogether.

Why? Because science isn't one of the issues the bases of either party are fired up about right now. And candidates aren't always eager to talk about these complex issues.

No one expects them to be experts on nuclear physics or the intricacies of evolutionary theory. But voters deserve to know whether a candidate has some scientific literacy, is comfortable discussing and evaluating technological issues, and employs good science and standards of evidence in decision-making.

Among the questions that could be asked at a debate:

Is it realistic for the United States to achieve energy independence? How do we get there?

What is the government's role in fostering innovation and the new generation of alternative energy technology?

How can our schools better prepare students to compete in science and mathematics?

Should creationism and intelligent design be taught in our schools?

How do you assess the evidence for climate change, and are specific measures needed to control greenhouse gases?

What is the future of NASA's manned space program?

How can we continue to attract the world's best and brightest scientists to study and live here?

Democrats charge that under President Bush, scientists' advice has been censored and politicized. Is that true? If so, what would you do to restore the integrity of science?

Americans deserve clear, specific answers to these and a host of other questions.

Admittedly, a science debate will be difficult to pull off amid the tight election-year schedule. Don't expect the candidates to jump at the opportunity. But a growing number of leading science organizations, university presidents, business leaders and politicians are endorsing the idea.

The timing is right for citizens to make a difference.

To get involved, check out the group's Web site at sciencedebate2008.com and sign the petition. At the very least, let the candidates and media know you want a more meaningful discussion of science policy.

We can't afford not to talk about science and innovation. America's future depends on it.

Randy Scholfield is an Eagle editorial writer. His column appears on Fridays. Reach him at 316-268-6545 or rscholfield@wichitaeagle.com.

Indeed.

Papers on information & evolution

Pim van Meurs, frequent contributor to the Panda's Thumb, recently wrote about the incessant lies on the part of ID-creationists regarding (among other things) evolution and information, and he referenced some papers that I have compiled from a few posts that I've written on the topic:

1. Natural selection as the process of accumulating genetic information in adaptive evolution, M. Kimura, Genetic Research Cambridge, 2 (1961) 127-140
2. Rate of Information Acquisition by a Species subjected to Natural Selection, D.J.C. MacKay, open-source @ http://arxiv.org/ (1999)
3. Evolution of biological information, T.D. Schneider, Nucleic Acids Research, (2000), 2794-2799
4. The fitness value of information, C.T. Bergstrom and M. Lachmann, open-source @ http://arxiv.org/ (2006)
5. Review of W. Dembski’s No Free Lunch, J. Shallit, BioSystems, 66 (2002) 93-99
6. The Evolution and Understanding of Hierarchical Complexity in Biology from an Algebraic Perspective, C.L. Nehaniv and J.L. Rhodes, Artificial Life, 6 (2000) 45–67
7. On the Increase in Complexity in Evolution I, P.T. Saunders and M.W. Ho, Journal of Theoretical Biology, 63 (1976) 375-384
8. On the Increase in Complexity in Evolution II: The Relativity of Complexity and the Principle of Minimum Increase, P.T. Saunders and M.W. Ho, Journal of Theoretical Biology, 90 (1981) 515-530

In addition to these papers, I wanted to highlight six other recent reviews that give a great overview of the present scientific thinking towards the origin of the genetic code:

1. "Selection, history and chemistry: the three faces of the genetic code.", Trends in Biochemical Sciences, Volume 24, Issue 6, 1 June 1999, Pages 241-247 (full-text .pdf)
2. "Genetic code: Lucky chance or fundamental law of nature?", Physics of Life Reviews, Volume 1, Issue 3, Dec 2004, Pages 202-229 (full-text .pdf) [low-quality pub, but expansive overview of the subject]
3. "Stepwise Evolution of Nonliving to Living Chemical Systems.", Origins of Life and Evolution of the Biosphere, Volume 34, Issue 4, Aug 2004, Pages 371–389 (full-text .pdf)
4. "The Origin of Cellular Life.", Bioessays, Volume 22, Issue 12, Dec 2004, Pages 1160-1170 (full-text .pdf)
5. "The Origin of the Genetic Code: Theories and Their Relationships, A Review.", Biosystems, Volume 80, Issue 2, May 2005, Pages 175-184 (full-text .pdf)
6. "The Origin and Evolution of the Genetic Code: Statistical and Experimental Investigations.", Robin D. Knight, Ph.D. Dissertation, June 2001.

And three more about evolution and complexity:

1. Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons, Human Mutation, 28(2):99-130, Oct 2006, Download PDF (also see: this article)
2. The origin of new genes: Glimpses from the young and old, Nature Reviews Genetics, 4(11): 865-875 Nov 2003, Download PDF
3. Evolution of biological complexity, PNAS, 97(9):4463-4468, April 2000, Download PDF

See a few of my posts for context with these papers:

1. http://blog.danielmorgan.name/2007/05/cameron-and-comfort-hit-new-low-with.html
2. http://blog.danielmorgan.name/2007/05/something-ive-been-slow-to-realize-re.html
3. http://blog.danielmorgan.name/2007/03/broken-record-that-is-creationism.html
4. http://blog.danielmorgan.name/2007/03/on-origin-of-genetic-code-and.html
5. http://blog.danielmorgan.name/2007/02/destroying-yet-another-creationist-myth.html
   

New piece in the insect evolution puzzle

I wrote a piece a while back on insect evolution. Today, a new study has been reported on which shows 2.5 meter Eurypterids existed during the Devonian period. This shows that giant ancestors of modern land insects still existed in the sea long after other insects had already taken to land.

If you're a fan of invertebrates, check out the 8th edition of the Circus of the Spineless I hosted in April '06.

Conservative weighs in on the fall of the GOP

Respected former Republican John Cole explains why he is voting out the GOP come November:

For starters, people got tired of being associated with these drooling retards. Then, when they realized that these drooling retards had ideological allies running the show in the Bush administration and then began to experience their idiotic policies, they moved from disgusted to outright hostile.

Like me. It had nothing to do with Burke, and everything to do with what the party had become. A bunch of bedwetting, loudmouth, corrupt, hypocritical, and incompetent boobs with a mean streak a mile long and no sense of fair play or proportion.

Seriously- what does the current Republican party stand for? Permanent war, fear, the nanny state, big spending, torture, execution on demand, complete paranoia regarding the media, control over your body, denial of evolution and outright rejection of science, AND ZOMG THEY ARE GONNA MAKE US WEAR BURKHAS, all the while demanding that in order to be a good American I have to spend most of every damned day condemning half my fellow Americans as terrorist appeasers.

And that isn’t even getting into the COMPLETE and TOTAL corruption of our political processes at every level. The shit is really going to hit the fan after we vote these jackasses out of power in 2008.

Screw them. I got out. They can have their party. I will vote for Democrats and little L libertarians and isolationists until the crazy people aren’t running the GOP. The threat of higher taxes in the short term isn’t enough to keep me from voting out crazy people and voting for sane people with whom I merely disagree regarding policy. Hillarycare doesn’t scare me as much as Frank Gaffney having a line to the person with the nuclear football or Dobson and company crafting domestic policy.

That is why the Republican party is in shambles. The majority of us have decided that the movers and shakers in the GOP and the blogospheric right are certified lunatics who, in a decent and sane society, we would have in controlled environments in rocking chairs under shade trees for most of the day, wheeled in at night for tapioca pudding and some karaoke.

The new skepticism

I was reminded this morning in thinking about things like climate change and evolution how starkly different the certitude level on issues in "pure" politics (like war, foreign policy and economic policy) is from scientific issues. I was thinking about how King W will come out and feign cautious, wise skepticism to reserve judgment on things like whether humans are causing global warming and on ID-creationism. The way these issues are framed appeals to American's sense of fairness and objectivity - "let's sit down and discuss all the rational possibilities, and at the end of it, since these issues are so complicated, we'll still have uncertainty, and thus cause for further debate," this frame says. And conservatives love to toe the party line on this in all discussions about climate change and evolutionary biology.

But look how starkly different these conservatives are when asked to discuss the realities of the Iraq war and our general muscular, hawkish foreign policies, or economic policies. Then, "debate" is not so welcome, and instead you become a terrorist sympathizer or a limp-wristed sissy whose idealitistic notions deserve the label of "flower child"...

Scientists have always been promoters of skepticism. The scientific method is conducive to doubt, as its goal is to provide explanations for natural phenomena which have been thoroughly tested in an effort to debunk their validity. Most of the progress we make in science, contrary to public misconception, is based on what we prove wrong. For example, if I have a hypothesis about how a cell regulates its own MAPK proteins, and I test it and falsify it, then we have progress in the form of eliminating possible rational answers. Cumulatively, these falsifications build up until there are only so many rational alternatives left, and these become, if you will, scientific orthodoxy. But even the most hardened orthodoxy, it is understood, is still subject to modification: that's the beauty of scientific knowledge -- it can always be improved and progress is the goal, not just a possibility.

All that said, I want to point out that it is this very tentative nature of science which those who want to exploit the lack of dogma seize on. Any "controversy" in science, real or imagined, can be created because people understand that a white lab coat is not the same thing as a Roman collar -- our lack of dogma makes it easy to challenge the status quo and current thinking. We eschew rigidity and faith in favor of evidence and questioning.

Those with agendas have exploited this feature of science to no end, emphasizing the fact that "all the facts are never in" -- that it is always possible to find new data that would modify our current interpretations of existing data. Sharon Begley explores this theme in climate change at length in an August Newsweek article, "The Truth About Denial". She carefully chronicles the years-long efforts on the part of energy and oil companies to inject doubt into the mainstream American consciousness about the science behind climate change. It is a powerful strategy, and difficult to overcome.

Just yesterday, I had a surprising conversation with the physics teacher at our school, Mary Peterson, who told me that both she and her husband are "climate skeptics". I started a conversation with her, and she told me that the sorts of scientific issues she feels are unresolved involve such things as Mars warming and the decay of the magnetic field of the earth. What was amazing to me was that, although her degree and background are in mathematics and not physics, she certainly had the available faculties to look up and investigate the veracity of these objections for herself, but hadn't. I found out that she had heard this somewhere (Faux News, probably), and had simply believed her source enough not to even go check it out. Little did she know that scientists have addressed all these possible alternative explanations for years, and that they have all been found lacking in merit for various technical reasons.

I really recommend the following index and "guides" for point-by-point refutations of the common objections to man-made climate change:

• The IPCC AR4 report FAQ section (pdf)
  
• Coby Beck's How to talk to Global Warming Skeptic
• New Scientist: Climate Change: A guide for the perplexed
• RealClimate: Response to common contrarian arguments
• NERC (UK): Climate change debate summary
• UK Met Office: Climate Change Myths
• Brian Angliss A Thorough Debunking
• John Cross Skeptical Science

These are all excellent resources with scientific references that should be shared amongst all your friends and colleagues, especially those with whom you think contentious discussions on climate change could take place.

What is so amazing to me is how easily duped people are who feign prudent skepticism towards scientific consensus, but display credulity by swallowing and mindlessly repeating talking points in politics (such as "if we fight them there, we won't have to fight them here" &c.). Is it just that people self-select their news sources in accordance with their pre-determined policy positions, and refuse to budge? Am I the same way? Is it possible to be that way (ignore one side's perspective) if there are actual facts which we can analyze to determine who is right and who is wrong?

Upon further analysis, the president's rationale for invading has been shown a farce and a lie, and every single rationale for the surge and every claim and metric used to support that "the surge is working" falls apart. The central issue of, "Even if we make Iraq 100% safe militarily, that doesn't solve the ethno-sectarian conflict and magically create a unified central government," is continually ignored now, even though Cheney admitted this kept them out of Iraq in 1994.

The numbers get spun in order to keep current policies in place, and people get shuffled when they are no longer willing to spin the right way. As Greenwald recently noted, when Bush is unable to find generals who tell him what he wants to hear, he simply replaces them with those who will. And now, as war with Iran is planned by the right, precipitated by lack of diplomatic progress, and with Faux News dutifully banging the war drums, we need skepticism and cynicism more than ever before. Will it manifest itself? God I hope so.

Why is it that the new skepticism is strongly directed towards scientists, but not towards politics with the same intensity and fervor?

There must be a misunderstanding, here

Dishonest creationists? No way! I don't believe a word of it.

September 27, 2007
Scientists Feel Miscast in Film on Life’s Origin
By CORNELIA DEAN

A few months ago, the evolutionary biologist Richard Dawkins received an e-mail message from a producer at Rampant Films inviting him to be interviewed for a documentary called “Crossroads.”

The film, with Ben Stein, the actor, economist and freelance columnist, as its host, is described on Rampant’s Web site as an examination of the intersection of science and religion. Dr. Dawkins was an obvious choice. An eminent scientist who teaches at Oxford University in England, he is also an outspoken atheist who has repeatedly likened religious faith to a mental defect.

But now, Dr. Dawkins and other scientists who agreed to be interviewed say they are surprised — and in some cases, angered — to find themselves not in “Crossroads” but in a film with a new name and one that makes the case for intelligent design, an ideological cousin of creationism. The film, “Expelled: No Intelligence Allowed,” also has a different producer, Premise Media.

The film is described in its online trailer as “a startling revelation that freedom of thought and freedom of inquiry have been expelled from publicly-funded high schools, universities and research institutions.” According to its Web site, the film asserts that people in academia who see evidence of a supernatural intelligence in biological processes have unfairly lost their jobs, been denied tenure or suffered other penalties as part of a scientific conspiracy to keep God out of the nation’s laboratories and classrooms.

Mr. Stein appears in the film’s trailer, backed by the rock anthem “Bad to the Bone,” declaring that he wants to unmask “people out there who want to keep science in a little box where it can’t possibly touch God.”

If he had known the film’s premise, Dr. Dawkins said in an e-mail message, he would never have appeared in it. “At no time was I given the slightest clue that these people were a creationist front,” he said.

Eugenie C. Scott, a physical anthropologist who heads the National Center for Science Education, said she agreed to be filmed after receiving what she described as a deceptive invitation.

“I have certainly been taped by people and appeared in productions where people’s views are different than mine, and that’s fine,” Dr. Scott said, adding that she would have appeared in the film anyway. “I just expect people to be honest with me, and they weren’t.”

The growing furor over the movie, visible in blogs, on Web sites and in conversations among scientists, is the latest episode in the long-running conflict between science and advocates of intelligent design, who assert that the theory of evolution has obvious scientific flaws and that students should learn that intelligent design, a creationist idea, is an alternative approach.

There is no credible scientific challenge to the theory of evolution as an explanation for the complexity and diversity of life on earth. And while individual scientists may embrace religious faith, the scientific enterprise looks to nature to answer questions about nature. As scientists at Iowa State University put it last year, supernatural explanations are “not within the scope or abilities of science.”

Mr. Stein, a freelance columnist who writes Everybody’s Business for The New York Times, conducts the film’s on-camera interviews. The interviews were lined up for him by others, and he denied misleading anyone. “I don’t remember a single person asking me what the movie was about,” he said in a telephone interview.

Walt Ruloff, a producer and partner in Premise Media, also denied that there was any deception. Mr. Ruloff said in a telephone interview that Rampant Films was a Premise subsidiary, and that the movie’s title was changed on the advice of marketing experts, something he said was routine in filmmaking. He said the film would open in February and would not be available for previews until January.

Judging from material posted online and interviews with people who appear in the film, it cites several people as victims of persecution, including Richard Sternberg, a biologist and an unpaid research associate at the National Museum of Natural History, and Guillermo Gonzalez, an astrophysicist denied tenure at Iowa State University this year.

Dr. Sternberg was at the center of a controversy over a paper published in 2004 in Proceedings of the Biological Society of Washington, a peer-reviewed publication he edited at the time. The paper contended that an intelligent agent was a better explanation than evolution for the so-called Cambrian explosion, a great diversification of life forms that occurred hundreds of millions of years ago.

The paper’s appearance in a peer-reviewed journal was a coup for intelligent design advocates, but the Council of the Biological Society of Washington, which publishes the journal, almost immediately repudiated it, saying it had appeared without adequate review.

Dr. Gonzalez is an astrophysicist and co-author of “The Privileged Planet: How Our Place in the Cosmos Is Designed for Discovery” (Regnery, 2004). The book asserts that earth’s ability to support complex life is a result of supernatural intervention.

Dr. Gonzalez’s supporters say his views cost him tenure at Iowa State. University officials said their decision was based, among other things, on his record of scientific publications while he was at the university.

Mr. Stein, a prolific author who has acted in movies like “Ferris Bueller’s Day Off” and appeared on television programs including “Win Ben Stein’s Money” on Comedy Central, said in a telephone interview that he accepted the producers’ invitation to participate in the film not because he disavows the theory of evolution — he said there was a “very high likelihood” that Darwin was on to something — but because he does not accept that evolution alone can explain life on earth.

He said he also believed the theory of evolution leads to racism and ultimately genocide, an idea common among creationist thinkers. If it were up to him, he said, the film would be called “From Darwin to Hitler.”

On a blog on the “Expelled” Web site, one writer praised Mr. Stein as “a public-intellectual-freedom-fighter” who was taking on “a tough topic with a bit of humor.” Others rejected the film’s arguments as “stupid,” “fallacious” or “moronic,” or described intelligent design as the equivalent of suggesting that the markets moved “at the whim of a monetary fairy.”

Mr. Ruloff, a Canadian who lives in British Columbia, said he turned to filmmaking after selling his software company in the 1990s. He said he decided to make “Expelled,” his first project, after he became interested in genomics and biotechnology but discovered “there are certain questions you are just not allowed to ask and certain approaches you are just not allowed to take.”

He said he knew researchers, whom he would not name, who had studied cellular mechanisms and made findings “riddled with metaphysical implications” and suggestive of an intelligent designer. But they are afraid to report them, he said.

Mr. Ruloff also cited Dr. Francis S. Collins, a geneticist who directs the National Human Genome Research Institute and whose book, “The Language of God: A Scientist Presents Evidence for Belief” (Simon & Schuster, 2006), explains how he came to embrace his Christian faith. Dr. Collins separates his religious beliefs from his scientific work only because “he is toeing the party line,” Mr. Ruloff said.

That’s “just ludicrous,” Dr. Collins said in a telephone interview. While many of his scientific colleagues are not religious and some are “a bit puzzled” by his faith, he said, “they are generally very respectful.” He said that if the problem Mr. Ruloff describes existed, he is certain he would know about it.

Dr. Collins was not asked to participate in the film.

Another scientist who was, P. Z. Myers, a biologist at the University of Minnesota, Morris, said the film’s producers had misrepresented its purpose, but said he would have agreed to an interview anyway. But, he said in a posting on The Panda’s Thumb Web site, he would have made a “more aggressive” attack on the claims of the movie.

Dr. Scott, whose organization advocates for the teaching of evolution and against what it calls the intrusion of creationism and other religious doctrines in science classes, said the filmmakers were exploiting Americans’ sense of fairness as a way to sell their religious views. She said she feared the film would depict “the scientific community as intolerant, as close-minded, and as persecuting those who disagree with them. And this is simply wrong.”

Paper: "From Dayton to Dover"

A thorough summary of the history of education-related court cases involving the teaching of evolution and creationism in public schools:

• Radan, Peter, "From Dayton to Dover: The Legacy of the Scopes Trial" (September 2007). Macquarie Law Working Paper No. 2007-6 Available at SSRN: http://ssrn.com/abstract=1012221

HERE is the download link. The paper explores the cultural backdrop against which the Scopes trial played out, including important immigrational considerations that are often neglected in such analyses. It is both a legal commentary and a philosophical one.

Museum Dedicated to Proving Unicorns Walked The Earth

Based on Job 39:9-12 (KJV), Bible believers have now spent another $30M on a museum dedicated to one of Jesus' favorite creatures, the unicorn. This museum will be located alongside her sister museum, the Creation Museum, in Petersburg, KY.

read more | digg story

New NAS Report on Astrobiology & Abiogenesis

**Update: Carl Zimmer remarks on this in the NYT
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A new National Academies of Sciences publication, The Limits of Organic Life in Planetary Systems, can be read for free in HTML at the site, or downloaded as a .pdf after login. The executive summary may be downloaded here as a .pdf (and the entire book here as a .pdf (1.1MB), if you're too lazy to login and do it yourself). I'm reposting some earlier material on abiogenesis, evolution and the origin of the genetic code below, with updated links that were previously broken.

Repost:

I have compiled a very useful list of papers (continually revised), covering abiogenesis, the evolution of genetic information, the origin of the genetic code, and human evolution. I will list some of those papers below.

For more on the evolution of information in the genome:

1. Natural selection as the process of accumulating genetic information in adaptive evolution, M. Kimura, Genetic Research Cambridge, 2 (1961) 127-140
2. Rate of Information Acquisition by a Species subjected to Natural Selection, D.J.C. MacKay, open-source @ http://arxiv.org/, (1999)
3. Evolution of biological information, T.D. Schneider, Nucleic Acids Research, (2000), 2794-2799
4. The fitness value of information, C.T. Bergstrom and M. Lachmann, open-source @ http://arxiv.org/, (2006)
5. Review of W. Dembski’s No Free Lunch, J. Shallit, BioSystems, 66 (2002) 93-99
6. The Evolution and Understanding of Hierarchical Complexity in Biology from an Algebraic Perspective, C.L. Nehaniv and J.L. Rhodes, Artificial Life, 6 (2000) 45–67
7. On the Increase in Complexity in Evolution I, P.T. Saunders and M.W. Ho, Journal of Theoretical Biology, 63 (1976) 375-384
8. On the Increase in Complexity in Evolution II: The Relativity of Complexity and the Principle of Minimum Increase, P.T. Saunders and M.W. Ho, Journal of Theoretical Biology, 90 (1981) 515-530

In addition to these papers, I wanted to highlight six other recent reviews that give a great overview of the present scientific thinking towards the origin of the genetic code:

1. "Selection, history and chemistry: the three faces of the genetic code.", Trends in Biochemical Sciences, Volume 24, Issue 6, 1 June 1999, Pages 241-247 (full-text .pdf)
   
2. "Genetic code: Lucky chance or fundamental law of nature?", Physics of Life Reviews, Volume 1, Issue 3, Dec 2004, Pages 202-229 (full-text .pdf) [low-quality pub, but expansive overview of the subject]
   
3. "Stepwise Evolution of Nonliving to Living Chemical Systems.", Origins of Life and Evolution of the Biosphere, Volume 34, Issue 4, Aug 2004, Pages 371–389 (full-text .pdf)
4. "The Origin of Cellular Life.", Bioessays, Volume 22, Issue 12, Dec 2004, Pages 1160-1170 (full-text .pdf)
5. "The Origin of the Genetic Code: Theories and Their Relationships, A Review.", Biosystems, Volume 80, Issue 2, May 2005, Pages 175-184 (full-text .pdf)
6. "The Origin and Evolution of the Genetic Code: Statistical and Experimental Investigations.", Robin D. Knight, Ph.D. Dissertation, June 2001.
   

And three more about evolution and complexity:

1. Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons, Human Mutation, 28(2):99-130, Oct 2006, Download PDF
2. The origin of new genes: Glimpses from the young and old, Nature Reviews Genetics, 4(11): 865-875 Nov 2003, Download PDF
3. Evolution of biological complexity, PNAS, 97(9):4463-4468, April 2000, Download PDF

No one pretends that all questions are sufficiently answered within the complex topics surrounding abiogenesis and the evolution of life. But to pretend that there are no answers is to engage in self-deception.
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Technorati tags: Abiogenesis, Intelligent Design, Evolution, Creationism

Tom Short & Haldane's Dilemma

A letter I just sent to Tom Short (one of my featured campus preachers) and his son on Haldane's (non)dilemma follows. Remember that Tom and I had a dispute on Hitler and evolution which he promised to clarify, but never did? I'm not hoping for much better when it comes to this, either...

TO: "tomshort@columbus.rr.com" Tom Short, "pilgrim3@gmail.com" Tim Short

Hey guys,

This a guy from UF that had a lot of conversation with you when you last visited. I won't be at UF the next time you're slated to return, I see, by the schedule you guys have posted. You may or may not remember me from the "Nazi and Hitler" thing...?

That's why I'm writing you. I know that you visit a lot of places and bring up a lot of different arguments, so it's probably impossible to expect either of you to remember this, but we had a discussion about evolution that I wanted to point out on specific thing about: Haldane's Dilemma. We spoke for a while about it, but you probably don't recall the specifics, and they don't really matter.

The long and short of it is that this is often brought up (as it was by you) as an argument that evolution couldn't account for common descent because the rate of mutations is not fast enough. I was just reading an article and I thought it was a very good resource to share with you about this topic.

http://www.pandasthumb.org/archives/2007/07/haldanes_nondil.html

First, recent genomic studies have proven that there is *much* less difference between humans and chimps at the genetic level than previously thought -- of the 14,000 genes studied, only 154 had any phenotype-affecting changes in them whatsoever, and of those, the vast majority were simple point mutations or frame shifts. Second, using Haldane's own work, creationist Walter Remine surmised that only 1,667 phenotype-impacting mutations could occur within the 10M years since we shared a common ancestor with chimps. Third, Haldane was quite misinterpreted by creationists: he never rejected common ancestry, and instead argued brilliantly for it. This should tell you that there is a major problem in citing him to "refute" evolution. Fourth, and most important of all, Haldane's assumptions were undermined by later work.

However, let's assume that you can still validly cite Haldane. Now, being generous, Ian goes through in the article I linked and shows that just using 6M years instead of 10M, and giving up all sorts of ambiguities to favor the creationist accounting, there is still plenty of evidence showing the rate of evolutionary change is perfectly compatible with the observed genomic disparities between ourselves and chimps.

Basically I'm writing you in the hopes that you will consider revising your arguments to make them a bit more intellectually honest. I know you aren't a scientist, and that many of your arguments are prima facie appeals to design, rather than detailed critiques of evolutionary biology. Given both of these two things, and the above-explained problems with using Haldane's work as a "refutation" of evolution, I simply hope you'll stick with integrity and use other appeals and arguments for theism.

Really it's too bad I can't see you again this year; I enjoyed our exchanges.

All the best.

Warmly,
D
http://www.gatorfreethought.org

Don't hold your breath waiting and expecting him to issue a retraction and a promise not to repeat this canard.

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Technorati tags: God, Religion, Intelligent Design, Evolution, Creationism