Five Myths (?) About Intelligent Design Creationism

Melissa Travis writes for a blog called Hard-Core Christianity. Her latest post is: Top Five Myths Christians (and Non-Christians) Often Believe About Intelligent Design. It's interesting because it reveals the standard myths that Intelligent Design Creationists believe about themselves.

Here's the list of "myths" along with what Mellisa Travis has to say about them.

MYTH #1: Intelligent Design (ID) is just a fancy name for Creationism.

The true story: Intelligent Design theory is not a form of, nor is it synonymous with “creationism.” Rather, it is an over-arching scientific theory that disputes wholly naturalistic/materialistic accounts of the origin of the universe and the origin of life. As such it is an indispensable ally for those who espouse various creation models. ID makes NO CLAIM about the age of the earth.

FACT: Modern Intelligent Design Creationism evolved from the creationist movement in the 1980s as was proven conclusively in the Dover trial. Intelligent Design Creationism is not a scientific theory. Instead, its a hodgepodge of criticisms of evolution and of scientists and materialism. Just look at the posts on Evolution News & Views (sic) to see what it's all about. Count the number of posts promoting a "scientific" view of Intelligent Design Creationism as opposed to disjointed helter-skelter criticisms of evolution that often contradict each other.

There's no "over-arching" scientific theory in sight.

What Drives Darwinian Scientists to their Fury

In spite of what they promised earlier, the Evolution News & Views (sic) blog does not allow comments. That's why I'm posting a quotation from today's piece by David Klinghoffer: What Drives Darwinian Scientists to their Fury

You may have wondered why Darwinists in academia get so worked up about intelligent design. Reading what they write about our scientists and their work, you picture these guys turning red and sweating a lot. Alternatively, they try to mask their rage by getting all sarcastic and pseudo-witty -- a man of mature age like Larry Moran, for example, calling other adults "IDiots."

I get "worked up" about Intelligent Design Creationism because it's anti-science and one of my issues is the promotion of scientific literacy (and rationalism). It's wrong to describe my feelings as "rage." My feelings about Intelligent Design Creationists are more akin to my feelings about people who believe they were abducted by aliens, or people who believe in bigfoot. "Bemused," "flabbergasted," and "sad" are more appropriate terms to describe how I react when I read the name "David Klinghoffer."

I'm very picky about who I call an IDiot. It's restricted to that subset of adults (and those who wish they were adults) who believe in Intelligent Design Creationism. It's a useful term, just as the terms "Darwinist" and "pompous professor" seem to be useful to David Klinghoffer [see hypocrisy].

A guy like Professor Pompous or any of the better known Darwinian-scientist writers you can think of aren't driven to their fury directly by the scholarly work of Michael Behe, Doug Axe or Stephen Meyer, but rather indirectly every time a student brings it up in class. Every year a new cohort of young people comes through the lecture hall and some number of them -- probably a growing number -- have been exposed somewhere to ID's critique and alternative to neo-Darwinism. Every time a student puts her hand up and politely asks something along the lines of, "But what about irreducible complexity?" it throws the class discussion down a totally different corridor of the mind than the professor meant it to go.

I hate to be the bearer of bad news, David, but the vast majority of students in my classes have never heard of Intelligent Design Creationism. In my Fall course we discuss Jonathan Wells' book Icons of Evolution as an example of anti-science writing but I have to explain to the class what Intelligent Design Creationism is all about. It never comes up in other classes.

In my own writings on the subject, I concentrate mostly on what the minor IDiots are writing on their blogs and on what the bigger names are saying in their books. That's why I've been spending so much time lately discussing Jonathan Wells' new book The Myth of Junk DNA. I've also written about Michael Behe, Stephan Meyer, and Doug Axe.

So, David, you are dead wrong about almost everything you write if it refers to me. I suspect it doesn't apply to most other professors who oppose the IDiots. We're not troubled—and certainly not "enraged"—by what students are saying. We prefer to make fun of the "big guns" but even those targets aren't much of an intellectual challenge.

Instead of constantly acting like a crybaby over perceived insults to your intelligence, why don't you try responding to the rational, scientific arguments we're making? You might learn something.

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You can buy the T-shirt at Endangered Outlaw.

The Mind of James Shapiro

I recently read Evolution: a View from the 21st Century by James Shapiro. It was a very annoying and frustrating experience. I do not recommend this book. I've already posted a rebuttal of his silly claim that the Central Dogma of Molecular Biology needs to be revised [Revisiting the Central Dogma in the 21st Century ]

The really frustrating part was trying to figure out Shapiro's agenda. He clearly has one. Is it just that he's against "conventional evolutionary theory"—whatever that is? Or, is he laying the groundwork for introducing God and intelligent design?

Shapiro denies that he's a supporter of intelligent design yet he published several papers with Richard Sternberg, one of the darlings of Intelligent Design Creationism. Furthermore, he (Shapiro) uses many of the same anti-evolution arguments used by Intelligent Design Creationists.

This prompted Bill Dembski to accuse James Shapiro of "dancing in the DMZ between Darwin and design" [Is James Shapiro a Design Theorist?].

For proponents of intelligent design, James Shapiro's constant dancing in the DMZ between Darwin and design can be frustrating. On the one hand, Shapiro is as dismissive of Darwinism as any ID proponent. On the other, he constantly gives public notice that he is not on the side of ID. And yet, methinks he protests too much.

This got a response from Shapiro that has now been posted on Evolution News & Views ["Is James Shapiro a Design Theorist?": James Shapiro Replies]. Here's what Shapiro says ...

What is wrong with "dancing in the DMZ" between intelligent design (as articulated by Michael Behe and others) and neo-Darwinism? Are these two positions the only alternatives? I doubt it. That is why my 1997 article in Boston Review on evolution debates was called "A Third Way." What Dembski calls the "DMZ" (i.e. a zone free of futile conflict) is the place where the real evolutionary science is taking place. I am proud to be there, and I see that an increasing number of people are joining me when they realize that natural genetic engineering, horizontal DNA transfer, interspecific hybridization, genome doubling and symbiogenesis provide solutions to problems recognized to be intractable under the limitations of conventional evolutionary thinking.

Clear as mud. There's one thing I know for sure: horizontal DNA transfer etc. are perfectly compatible with today's evolutionary thinking. If Shapiro is wrong about this—and he is— then maybe he's also misleading us about his belief in intelligent design creationism.

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IDiots and Incivility

 

This is just a heads-up to let you know that Casey Luskin is about to post a series of examples of bad behavior by ID critics [The Uncivil Style of Intelligent Design Critics]. Apparently it's going to be a long series ....

I'm going to let ENV readers in on a little secret: When many of us in the intelligent design (ID) movement read the arguments coming from our critics, we're surprised at their low quality and style. We don't rejoice at this -- we'd much rather see a robust, civil, and fruitful scientific debate over the relevant questions. But the incivility, basic inaccuracy, and unserious tone characteristic of so many criticisms of ID all make you wonder: If the critics had stronger rebuttals to offer, wouldn't we be hearing them?

...

There are so many examples of incivility among ID-critics that it's hard to know where to start. And I'm not just talking about the usual Internet suspects, like PZ Myers, Jerry Coyne, or Larry Moran.

On a completely unrelated topic that has nothing to do with Darwinist incivility ...

While you're checking out Evolution News & Views you might want to read a fascinating article by Richard Weikart defending his books From Darwin to Hitler: Evolutionary Ethics, Eugenics, and Racism in Germany and Hitler's Ethic: The Nazi Pursuit of Evolutionary Progress [Robert J. Richards and the Historical Record]. It even has a photo to illustrate the point about Darwin (see below).

This is a follow-up to a very civil article posted last month: Can Darwinists Condemn Hitler and Remain Consistent with Their Darwinism?.

I threw down the gauntlet to many of my Darwinian opponents by telling her that if Darwinism is indeed a purposeless, non-teleological process, as many evolutionists and biology textbooks proclaim, and if morality is the product of these mindless evolutionary processes, as Darwin and many other prominent Darwinists maintain, then "I don't think [they] have any grounds to criticize Hitler."

According to Flam, these are "fighting words." However, I have spoken with intelligent Darwinists who admit point-blank that they do not have any grounds to condemn Hitler, so I am not just making this up. Many evolutionists believe that since evolution explains the origin of morality -- as Darwin himself argued -- then there is no objective morality. The famous evolutionary biologist and founder of sociobiology, E. O. Wilson, and the prominent philosopher of science Michael Ruse co-authored an article on evolutionary ethics in which they asserted, "Ethics as we understand it is an illusion fobbed off on us by our genes to get us to co-operate."

Anyway, let's not forget the important point and that's Casey Luskin's upcoming series on the incivility of ID critics.

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A Dishonest Intelligent Design Proponent?

Most IDiots are ignorant about evolution and they let their religious biases interfere with the proper interpretation of scientific data. We excuse their mistakes on the grounds that they don't know any better.

However, some IDiots clearly should know better. They have advanced degrees in relevant fields and they have received considerable feedback on the claims they post or the books they write. We know they have read the critiques so when they persist in repeating falsehoods, there must be another explanation. They must be lying.

Jonathan Wells has a Ph.D. in molecular biology. He has posted numerous articles about junk DNA and he was written a book on the subject (The Myth of Junk DNA). Lots of people have made comments about his blog posts and his book has been widely critiqued. Many of his claims have been shown to be false.

So what do we make of his recent post on Evolution News & Views) (sic) entitled Why All the Fuss Over Some Junk?. We are forced to conclude that Wells is dishonest. Perhaps with the caveat expressed by Peter Medawar many years ago in his review of Père Teihard's The Phenomenon of Man.

Yet the greatest part of it, I shall show, is nonsense, tricked out with a variety of metaphysical conceits, and its author can be excused of dishonesty only on the grounds that he has taken great pains to deceive himself.

IDiots discover that RNA has secondary structure

I suppose we should be happy whenever some IDiots manage to educate themselves but somehow I find it quite sad when it takes thirty or forty years. Here's an example of a somewhat late-blossoming IDiot who posts on Evolution News & Views (sic): RNA Shows Design, Too. She doesn't sign her name to the post—I think I know why.

Here's what she just discovered ...

RNA differs from DNA in one of the sugars that makes up its backbone and one of the bases that makes up its side branches (uracil instead of thymine); it is also usually found in single strands instead of DNA's double helix. New discoveries, though, are showing RNA does far more than passively transfer DNA's information to other places. It, too, is a masterpiece of intelligent design and function.

A paper in Nature describes how information is stored not only in RNA's base sequence, but in its folds. Because RNA has more degrees of freedom, it can take on a wide variety of forms not possible for DNA. "RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA's ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational and experimental efforts for determining RNA structures," the authors begin (emphasis added). In their conclusion, they say, "We identify hundreds of specific mRNA regions that are highly structured in vivo, and we show for three examples that these structures affect protein expression."

The paper by Rouskin et al. (2014) reports on the development of new software to detect secondary structure in RNA. This is news for IDiots who think that "new discoveries" show that RNA is capable of catalysis and other functions.

Think about that for a minute. This is 2014, it's 25 years since Sidney Altman and Tom Cech were awarded the 1989 Nobel Prize in Chemistry and more that 30 years since undergraduates were routinely taught about catalytic RNAs in introductory biochemistry courses. Those IDiots sure are slow learners.

In other words, the structure, not just the sequence, carries functional information.

Amazing. Sounds like they've never heard of the idea that ribosomal RNA catalyzes peptide bond formation and that it does so through secondary structure. They've never heard of self-splicing introns. All they have to do is read an introductory textbook of biochemistry or molecular biology.

Now if you connect this amazing new bit of information to the equally astonishing (not!) news that some lincRNAs have a function, you get this ....

More design found in what was formerly called junk; more information found parallel to existing information in RNA; more power found in the collective energy of intelligent agents. Why are you not surprised?

The real question is why are IDiots surprised by routine information that even high school students know?

And what does this have to do with intelligent agents? Has this person answered the quiz?

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Nature opposes misinformation (pot, kettle, black)

The lead editorial in last week's issue of Nature (Dec. 8, 2016) urges us to Take the time and effort to correct misinformation. The author (Phil Williamson) is a scientist whose major research interest is climate change and the issue he's addressing is climate change denial. That's a clear example of misinformation but there are other, more subtle, examples that also need attention. I like what he says in the opening paragraphs,

Most researchers who have tried to engage online with ill-informed journalists or pseudoscientists will be familiar with Brandolini’s law (also known as the Bullshit Asymmetry Principle): the amount of energy needed to refute bullshit is an order of magnitude bigger than that needed to produce it. Is it really worth taking the time and effort to challenge, correct and clarify articles that claim to be about science but in most cases seem to represent a political ideology?

I think it is. Challenging falsehoods and misrepresentation may not seem to have any immediate effect, but someone, somewhere, will hear or read our response. The target is not the peddler of nonsense, but those readers who have an open mind on scientific problems. A lie may be able to travel around the world before the truth has its shoes on, but an unchallenged untruth will never stop.

I've had a bit of experience trying to engage journalists who appear to be ill-informed. I've had little success in convincing them that their reporting leaves a lot to be desired.

I agree with Phil Williamson that challenging falsehoods and misrepresentation is absolutely necessary even if it has no immediate effect. Recently I posted a piece on the misrepresentations of the ENCODE results in 2007 and pointed a finger at Nature and their editors [The ENCODE publicity campaign of 2007]. They are responsible because they did not ensure that the main paper (Birney et al., 2007) was subjected to appropriate peer review. They are responsible because they promoted misrepresentations in their News article and they are responsible because they published a rather silly News & Views article that did little to correct the misrepresentations.

That was nine years ago. Nature never admitted they were partly to blame for misrepresenting the function of the human genome.

Dark Matter Is Real, Not Just Noise or Junk

UPDATE: The title is facetious. I don't believe for one second that most so-called "dark matter" has a function. In fact, there's no such thing as "dark matter." Most of our genome is junk. I mention this because one of the well-known junk DNA kooks is severely irony-impaired and thought that I had changed my mind.

A few hours ago I asked you to evaluate the conclusion of a paper by Venters and Pugh (2013) [Transcription Initiation Sites: Do You Think This Is Reasonable?].

Now I want you to look at the Press Release and tell me what you think [see Scientists Discover the Origins of Genomic "Dark Matter"].

It seems pretty clear to me that Pugh (and probably Venters) actually think they are on to something. Here's part of the press release quoting Franklin "Frank" Pugh, a Professor in the Department of Molecular Biology at Penn State.

The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.

"These non-coding RNAs have been called the 'dark matter' of the genome because, just like the dark matter of the universe, they are massive in terms of coverage -- making up over 95 percent of the human genome. However, they are difficult to detect and no one knows exactly what they all are doing or why they are there," Pugh said. "Now at least we know that they are real, and not just 'noise' or 'junk.' Of course, the next step is to answer the question, 'what, in fact, do they do?'"

Pugh added that the implications of this research could represent one step towards solving the problem of "missing heritability" -- a concept that describes how most traits, including many diseases, cannot be accounted for by individual genes and seem to have their origins in regions of the genome that do not code for proteins. "It is difficult to pin down the source of a disease when the mutation maps to a region of the genome with no known function," Pugh said. "However, if such regions produce RNA then we are one step closer to understanding that disease."

I'm puzzled by such statements. It's been one year since the ENCODE publicity fiasco and there have been all kinds of blogs and published papers pointing out the importance of junk DNA and the distinct possibility that most pervasive transcription is, in fact, noise.

It's possible that Pugh and his postdoc are not aware of the controversy. That would be shocking. It's also possible that they are aware of the controversy but decided to ignore it and not reference any of the papers that discuss alternate explanations of their data. That would be even more shocking (and unethical).

Are there any other possibilities that you can think of?

And while we're at it. What excuse can you imagine that lets the editors of Nature off the hook?

P.S. The IDiots at Evolution News & Views (sic) just love this stuff: As We Keep Saying, There's Treasure in "Junk DNA".

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Venters, B.J. and Pugh, B.F. (2013) Genomic organization of human transcription initiation complexes. Nature Published online 18 September 2013 [doi: 10.1038/nature12535] [PubMed] [Nature]

On Re-reading the Origin of Species

 
It's been a great pleasure to read the Origin of Species in preparation for my talk tonight and for our book club meeting last Monday. I had forgotten how clever Darwin was and how he carefully weighs his arguments for evolution.

I had also fallen prey to several myths about the book. For example, I didn't realize that Origin of Species is all about speciation and the difference between species and varieties.

The editors of Current Biology asked several scientists to re-read Origin of Species in honor of Darwin's 200th birthday. The results are published on the journal's website [(Re)Reading The Origin].

I've already mentioned Jerry Coyne's defense of the term "Darwinism" [Jerry Coyne on Darwinism. The contribution from Christiane Nüsslein-Volhard is excellent—she points out one of Dawin's most important arguments and reminds us that it has been largely forgotten because it now seems so obvious.

Many of the scientists comment on the wonderful prose in Origin and on Darwin's delightful style of writing. I agree with them. Mark Ptashne doesn't. He couldn't read the book when he was younger and even today he had to read a condensed version because the original is too difficult! ("Who has the patience to dig through the convoluted sentences, extracting the buried nuggets?")¹

At my book club meeting, and in many discussions with non-scientific friends, the dominant impression is that Darwin is a very humble man who almost apologizes for having a good idea. That's not the Darwin I see. Simon Conway Morris isn't fooled either ....

But what suddenly became clear is that this is a book haunted by the ghost of William Paley the grandfather of creationist thinking and exponent of seemingly irrefutable arguments for organic design. The Origin is Darwin's riposte. Its metaphorical power depends on suspense and a scattering of clues, but significantly Paley himself is mentioned only once. And cleverly not in the context of his ideas on organic design but in an oblique dig at the question of natural evil. First and foremost, The Origin is an exorcism of the doctrine of special creation, and conducted by one of the most skilled exorcists science has ever seen. The brief crescendo in the last chapter is preceded by repeated and sudden flashes of disdain, a quick insertion of the knife before the narrative calmly continues in its ostensibly more objective purpose of piling up the evidence. Darwin knew his enemy intimately, but was far too astute to engage in a head-on clash.

Darwin was right, and he knew it. His expressions of doubt are largely rhetorical and how seamless—at least from a distance—is the edifice upon which he constructs his theory. Yet, it is equally intriguing how he conceals his intellect: the carefully marshalled facts are allowed to speak for themselves and the implications introduced with restraint and circumspection—a sotto voce naturalist. Darwin never doubted his abilities.

Why are so many people not able to see this? I think it's because they aren't familiar with the typical English style of understatement and well-disguised sarcasm.

Darwin's contemporaries weren't fooled. You should read Brian Switek's posting on Darwin's Heartache to see how Darwin's friends responded to the book in November 1859. His old Cambridge mentor, Adam Sedgwick, was not happy.

Andrew Berry and Hopi Hoekstra didn't comment on their own reading of Origin of Species; instead they listed the comments of their students in the course evaluations! The good news is that some students actually liked the book.

My favorite review is by Peter Lawrence who, I must confess, is one of my favorite scientists. Peter noticed something that I also noticed; namely, that Darwin's style of argument is very much a lost art. Here's how Peter puts it ...

I had only dipped into this wonderful book in my student days. But what a revelation for a somewhat jaded scientist to read it now! It is not only the brilliance, farsighted and original nature of the ideas, there is the sheer diversity of knowledge, the pervading presence of thought, of simple direct experiments, of debate, of argument, the consideration of other views and the style. In writing and reading scientific articles nowadays, we become imprisoned, constrained in what is considered appropriate and our vocabulary is reduced. Also our sentences are stifled by fashion and by journals that kill invention and independence with their strict word limits and their 'house style.' Just one example: punctuation. Darwin used everything, even the long dash and the exclamation mark. In my scientific writing I have been frequently told that these are not allowed—OK for great literature, but banned from scientific usage. I don't know why, but dulling down our scientific writing is not in our best interest. By contrast, in Darwin's time, Victorian fashion encouraged a flowery style as well as intellectual freedom; he took full advantage of both. He could write explorative and educative prose. He could spend many pages explaining narrow but important distinctions between different viewpoints and, time and again, one can see the outcome of careful reading and deep reflection. Our data-dominated publications, pared down to fit them into limited space, would be much more comprehensible if there were more argument, more explanation and more justification; indeed, if we reflected more, I think we could make big reductions in our published pages by making sure they carry and convey at least one message of note.

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1. I suspect he hasn't read The Structure of Evolutionary Theory , either.

Jonathan Wells Weighs in on Alternative Splicing

You can read his contribution at Evolution News & Views (sic): The Fact-Free “Science” of Matheson, Hunt and Moran: Ridicule Instead of Reason, Authority Instead of Evidence.

What I find so interesting is the willingness of Wells and Sternberg to believe whatever they find in the scientific literature. (Yeah, right.) In this case, they've found a few papers claiming that the vast majority of human genes exhibit alternative splicing. They claim this refutes the idea that introns are mostly junk.¹

Do they really believe everything that's published in the scientific literature? I don't think so. They are very selective in what they believe. They only believe the papers that criticize evolution or support their belief in intelligent design. That's why they have no credibility. That's why they deserve ridicule. That's why reasoning with an Intelligent Design Creationist is a waste of time.

Don't believe me? Try reading Icons of Evolution by Jonathan Wells. It's the example we use in my course to illustrate how NOT to do science.

Here's Wells standing up for his friend ...

So why are Matheson and Moran so sure that huge portions of introns don’t have functions? According to Matheson, it’s because “Larry Moran and I clearly know a whole lot more about molecular genetics” than Sternberg.

A more naked appeal to authority would be hard to find. It sounds like an undergraduate trying to score points in a late-night bull session (“I know all about that; I took a course in it…”), not a college professor engaged in a scientific debate.

But Matheson didn’t stop there. He demeaned Sternberg by calling him “poor Richard.” He also claimed that Sternberg is “disastrously clueless” because he doesn’t understand “the important and very basic distinction between a transcript and an intron.” Since every undergraduate biology student learns that an intron is a segment of DNA, while a transcript is a segment of RNA encoded by DNA, this last jibe is on a par with Moran’s insult that Sternberg can’t do elementary arithmetic. And it is equally unjustified.

Here's what undergraduates learn when they read what I wrote in my textbook. Maybe I should send copies to Wells and Sternberg?

Internal sequences that are removed from the primary RNA transcript are called introns. Sequences that are present in the primary transcript and in the mature RNA molecule are called exons. The words intron and exon also refer to the regions of the gene (DNA) that encode corresponding RNA introns and exons. Since DNA introns are transcribed, they are considered part of the gene.

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1. I'm ignoring the fact that Sternberg's calculation assumed that every intron in a gene must be alternatively spliced. That assumption is/was not based on anything in the scientific literature but it's unlikely that Sternberg will admit his error.

A paradigm shift in the making

Paradigm shifts are happening all over the place (NOT!). If you look closely you can watch them happening because, as we all know, it's so obvious that the paradigm is shifting (NOT!). Apparently it's even more obvious if you don't have a clue what the paradigms are in the first place.

That's the situation for Mary Poplin, a Professor of education at Claremont Graduate University. She's a brand new contributor to Evolution News & Views (sic) and her first post is the text of the forward she wrote to Bill Dembski's new book [A Paradigm Shift in the Making: William Dembski's Revolutionary Breakthrough].

This is part of the standard hype on the IDiot blogs whenever a new book is about to appear. For the next few weeks we are going to be subjected to incessant, sycophantic, praise of Bill Dembski and his "revolutionary" work. Then comes the publication, the negative reviews, and the complaints that the reviewers don't understand Dembski and don't understand IDiots.

Here's the first two paragraphs of the forward. Doesn't this just make you want to pre-order the book (at 34% of the regular price) (NOT!)?

Scholars have long acknowledged that scientific revolutions, along with their paradigm shifts, happen in human history. Yet rarely do we have an opportunity to witness such a shift first hand or to have such a clear and careful explanation of one. William Dembski's painstakingly detailed explication of the shift from the material age to the information age in science and philosophy is a brilliant and rare example. As both a philosopher and a mathematician, Dembski is metaphysically and methodologically able to delineate this shift, having previously written in both areas as well as developed a statistical method for inferring intelligent causation.

This book extends his earlier work and asks the most basic and challenging question confronting the 21st century, namely, if matter can no longer serve as the fundamental substance of reality, what can? While matter was the only allowable answer of the past century to the question of what is ultimately real (matter's origin, on its own terms, remaining a mystery), Dembski demonstrates there would be no matter without information, and certainly no life. He thus shows that information is more fundamental than matter and that intelligible effectual information is in fact the primal substance.

I'd like to welcome Mary Poplin to the land of IDiots. I think she'll fit right in.

I wonder what Jeffrey Shallit thinks of the idea that information is the primal substance? He recently demonstrated that most IDiots don't understand information [Barry Arrington's Silly Misunderstanding] and that prompted a post on Uncommom Descent proving that Shallit was correct and IDiots really don't understand information [Darwinian Debating Devices: Fail Files 2014-09 – Jeffrey Shallit]. Shallit's response is here.

You know what's coming next? The IDiots are going to tell us that Dembski's new book will address all of the criticisms and we'll just have to go out and buy it ASAP. Meanwhile, nobody is allowed to criticize Dembski until they have read the book.

Oh, BTW, it should take several days to read the book and anyone who publishes a review before then must be lying.

This is getting soooooo boring.

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Nessa Carey doesn't understand junk DNA

Nessa Carey is a science writer with a Ph.D. in virology and she is a former Senior Lecturer in Molecular Biology at Imperial College, London.

She has written a book on junk DNA but it's not available yet (in Canada). Judging by her background, she should be able to sort through the controversy and make a valuable contribution to informing the public but, as we've already noted Nessa Carey and New Scientist don't understand the junk DNA debate.

Casey Luskin has a copy of the book so he wrote a blog post on Evolution News & Views. He's thrilled to find someone else who dismisses junk DNA and "confirms" the predictions of Intelligent Design Creationism. I hope Nessa Carey is happy that the IDiots are pleased with her book [New Book on "Junk DNA" Surveys the Functions of Non-Coding DNA].

More misconceptions about junk DNA - what are we doing wrong?

I'm actively following the views of most science writers on junk DNA to see if they are keeping up on the latest results. The latest book is DNA Demystified by Alan McHughen, a molecular geneticist at the University California, Riverside. It's published by Oxford University Press, the same publisher that published John Parrington's book the deeper genome. Parrington's book was full of misleading and incorrect statements about the human genome so I was anxious to see if Oxford had upped it's game.¹, ²

You would think that any book with a title like DNA Demystified would contain the latest interpretations of DNA and genomes, especially with a subtitle like "Unraveling the double Helix." Unfortunately, the book falls far short of its objectives. I don't have time to discuss all of its shortcomings so let's just skip right to the few paragraphs that discuss junk DNA (p.46). I want to emphasize that this is not the main focus of the book. I'm selecting it because it's what I'm interested in and because I want to get a feel for how correct and accurate scientific information is, or is not, being accepted by practicing scientists. Are we falling for fake news?

Some Questions for IDiots

Here's a short quiz for proponents of Intelligent Design Creationism. Let's see if you have been paying attention to real science. Please try to answer the questions below. Supporters of evolution should refrain from answering for a few days in order to give the creationists a chance to demonstrate their knowledge of biology and of evolution.

The bloggers at Evolution News & Views (sic) are promoting another creationist book [see Biological Information]. This time it's a collection of papers from a gathering of creationists held in 2011. The title of the book, Biological Information: New Perspectives suggests that these creationists have learned something new about biochemistry and molecular biology.

One of the papers is by Jonathan Wells: Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information. Here's part of the opening paragraphs.

James Watson and Francis Crick’s 1953 discovery that DNA consists of two complementary strands suggested a possible copying mechanism for Mendel’s genes [1,2]. In 1958, Crick argued that “the main function of the genetic material” is to control the synthesis of proteins. According to the “ Sequence Hypothesis,” Crick wrote that the specificity of a segment of DNA “is expressed solely by the sequence of bases,” and “this sequence is a (simple) code for the amino acid sequence of a particular protein.” Crick further proposed that DNA controls protein synthesis through the intermediary of RNA, arguing that “the transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein may be possible, but transfer from protein to protein, or from protein to nucleic acid, is impossible.” Under some circumstances RNA might transfer sequence information to DNA, but the order of causation is normally “DNA makes RNA makes protein.” Crick called this the “ Central Dogma” of molecular biology [3], and it is sometimes stated more generally as “DNA makes RNA makes protein makes us.”

The Sequence Hypothesis and the Central Dogma imply that only protein-coding DNA matters to the organism. Yet by 1970 biologists already knew that much of our DNA does not code for proteins. In fact, less than 2% of human DNA is protein-coding. Although some people suggested that non-protein-coding DNA might help to regulate gene expression, the dominant view was that non-protein-coding regions had no function. In 1972, biologist Susumu Ohno published an article wondering why there is “so much ‘ junk’ DNA in our genome” [4].

1. Crick published a Nature paper on The Central Dogma of Molecular Biology in 1970. Did he and most other molecular biologists actually believe that "only protein-coding DNA matters to the organism?"
2. Did Crick really say that "DNA makes RNA makes protein" is the Central Dogma or did he say that this was the Sequence Hypothesis? Read the paper to get the answer—the link is below).
3. Is it true that, in 1970, the majority of molecular biologists did not believe in repressor and activator binding sites (regulatory DNA)?
4. Is it true that in 1970 molecular biologists knew nothing about the functional importance of non-transcribed DNA sequences such as centromeres and origins of DNA replication?
5. It is true that most molecular biologists in 1970 had never heard of genes for ribosomal RNAs and tRNAs (non-protein-coding genes)?
6. If the answer to any of those questions contradicts what Jonathan Wells is saying then why do you suppose he said it?

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Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227:561-563. [PDF]

A physicist tries to understand junk DNA: Part II

Yesterday I posted some comments on a blog post by physicist Rob Sheldon [A physicist tries to understand junk DNA ]. My comments were based on what I had seen on Uncommon Descent but it turns out that was only a summary of a longer post that appeared on Evolution News & Views (sic): More on Junk DNA and the "Onion Test".

The longer post doesn't add very much to the argument but it does have something interesting at the bottom. Here's what Rob Sheldon says about the Onion Test and junk DNA.

IDiots Make a Falsifiable Prediction

The Intelligent Design Creationists, otherwise known as IDiots, are getting desperate. They have been relentlessly promoting Stephen Meyer's upcoming book Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design but so far they have pretty much failed to trick evolutionary biologists into trashing the book before it's published.¹ That must be a major disappointment to them.

The baiting continues with an article by David Klinghoffer on the Evolution News & Views (sic) site: What Darwin's Enforcers Will Say About Darwin's Doubt: A Prediction. Here's what he predicts ....

Among possible lines of attack against Stephen Meyer's forthcoming book, Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design, I foresee some critics trying to argue that it's not fair game for Dr. Meyer to invite the general reading public to consider what's going on in peer-reviewed technical literature pertaining to evolution.

After all, biologists should have the opportunity to air their views in a semi-private professional setting without "creationists" barging in and telling the unwashed masses that many scientists have already given up on the Darwinian paradigm and are seeking post-Darwinian alternatives. Even though it's true, still it's wrong to publicize the fact, thereby leading the common folk astray and confirming their prejudice in favor of seeing life and the universe as reflecting some purpose.

This time I will rise to the bait if only for the purpose of preserving this prediction so we can revisit it in the future.

I'd also like to note, for the record, that the IDiots have published a number of books in the past and I don't recall anyone making the argument that Klinghoffer predicts. Can anyone out there point me to an article where scientists criticized the IDiots for pulicizing controversy within the evolutionary biology literature? It would be quite hypocritical for most bloggers to do so since criticizing the scientific literature is what we do.

Is it just my imagination or have evolutionary biologists also published books where they "expose" the controversies within evolution. If scientists do it routinely then why in the world would they criticize an IDiot for doing it? That doesn't make any sense, does it? (Oops, I inadvertently made the false assumption that IDiots are supposed to be rational.)

Finally, Udo Schüklenk alerted me to this creationist article because he is mentioned. Klinghoffer refers to a discussion about the ethics of infanticide and he thinks that his creationist² buddy Wesley Smith is being attacked for exposing a debate within the bioethics community. You should read the papers he links to along with Udo Schüklenk's paper [In defence of academic freedom: bioethics journals under siege] if you want to catch up on that discussion. As usual, the IDiots get it all wrong. Are you surprised?

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1. That's mostly because we don't care. We are not anticipating anything we haven't heard many times before although, I suppose, we could be surprised.

2. Smith is a lawyer and a Senior Fellow at the Discovery Institute. I don't know what kind of creationist he is.

Science Journalism: A Bias in Favour of Truth

 
Peter McKnight is a science journalist who writes for The Vancouver Sun. Don't hold that against him, he's actually one of the most thoughtful science journalist around. Readers may recall that we had a discussion about his views concerning Marus Ross and his Ph.D. in geology [Peter McKnight of the Vancouver Sun Weighs in on the Marcus Ross Incident and Peter McKnight on the Marcus Ross Issue].

I disagreed with Peter back then but I agree with his latest column from last Saturday [what we need here is a bias in favour of truth]. McKnight argues that the tendency toward balance and fairness in journalism is hurting science journalism. When it comes to science there aren't always two legitimate sides to every story. For example, in the evolution vs. creationism controversy, journalists do not have an obligation to give equal time to creationist nonsense.

Similarly, when I write about evolution and creationism, I am invariably accused of bias -- a lack of balance -- for explaining that evolution is a scientific theory and creationism is not. To repair this problem, certain letter writers tell me that I should simply present both positions equally, without editorial comment, and let my readers decide the truth.

Doing that would amount to an abdication of my role as a columnist, since I have a responsibility to offer an opinion. It would also represent an affront to science, but I understand where my letter writers are coming from; journalism has long promoted the view that journalists ought to present both sides in a dispute and keep their opinions to themselves.

I agree. Science journalists should not be simple reporters of fact. They need to interpret those facts and put them in context. They need to contribute a certain added value to their reports, otherwise we might just as well read the original press releases or the abstract of the paper.

Despite this evidence from more than a century ago, false balance came to dominate journalism and still exists today. Many reasons for this have been identified: In our increasingly partisan era, journalists are ultra-sensitive to accusations of bias, so they ensure balance to ward off such allegations; some journalists don't have the time -- and some are too lazy -- to conduct a thorough investigation of an issue, so it's easier to just present competing opinions; and some journalists don't have the expertise to filter through various opinions and determine which ones are based on solid evidence.

This last reason is particularly common in science journalism, since few journalists outside of publications like Scientific American have backgrounds in science. Yet, remarkably, former New York University sociologist Dorothy Nelkin noted in her book Selling Science that some journalists are hostile to science reporters who have science backgrounds, because "journalists trained extensively in science may adopt the values of scientists and lose the ability to be critical."

I can understand why average journalists are afraid of real science journalists. It's because good science journalists can do something that the typical non-science journalist can't do. That goes against the fundamental credo of the profession; namely, that journalists can cover any story because they're trained to report the facts. (Are they also hostile to those journalists who are knowledgeable about the law, medicine, or business—or is it just science?)

I agree with Peter McKnight about the need for science journalists to inject their own (informed) opinion into their articles. But I want to take it one step further. From my perspective, the most annoying science articles are not the ones that give inappropriate "balance" to the ideas of kooks. The worst ones are those that show no informed skepticism at all but merely report whatever the scientific paper says. I want my science journalists to do some digging from time to time, which is why I criticized an article in the "TRUTH" issue of SEED last month [Silent Mutations and Neutral Theory].

It's complicated. I want science journalists to give us an informed opinion. I don't want them to go out of their way to present contrary opinions just for the sake of "balance" and "fairness." On the other hand, I do want them to present contrary points of view when the news they're covering is itself biased and unfair.

It's tough to be a science journalist these days. They don't get no respect from either their journalist colleagues, or their science colleagues!

[Hat Tip: Jason Spaceman on talk.origins]

More Expert Opinion on Junk DNA from Scientists

The Nature issue containing the latest ENCODE Consortium papers also has a New & Views article called "Genomics: ENCODE explained" (Ecker et al., 2012). Some of these scientist comment on junk DNA.

For exampleshere's what Joseph Ecker says,

One of the more remarkable findings described in the consortium's 'entrée' paper is that 80% of the genome contains elements linked to biochemical functions, dispatching the widely held view that the human genome is mostly 'junk DNA'. The authors report that the space between genes is filled with enhancers (regulatory DNA elements), promoters (the sites at which DNA's transcription into RNA is initiated) and numerous previously overlooked regions that encode RNA transcripts that are not translated into proteins but might have regulatory roles.

And here's what Inês Barroso, says,

The vast majority of the human genome does not code for proteins and, until now, did not seem to contain defined gene-regulatory elements. Why evolution would maintain large amounts of 'useless' DNA had remained a mystery, and seemed wasteful. It turns out, however, that there are good reasons to keep this DNA. Results from the ENCODE project show that most of these stretches of DNA harbour regions that bind proteins and RNA molecules, bringing these into positions from which they cooperate with each other to regulate the function and level of expression of protein-coding genes. In addition, it seems that widespread transcription from non-coding DNA potentially acts as a reservoir for the creation of new functional molecules, such as regulatory RNAs.

If this were an undergraduate course I would ask for a show of hands in response to the question, "How many of you thought that there did not seem to be "defined gene-regulatory elements" in noncoding DNA?"

I would also ask, "How many of you have no idea how evolution could retain "useless" DNA in our genome?" Undergraduates who don't understand evolution should not graduate in a biological science program. It's too bad we don't have similar restrictions on senor scientists who write News & Views articles for Nature.

Jonathan Pritchard and Yoav Gilad write,

One of the great challenges in evolutionary biology is to understand how differences in DNA sequence between species determine differences in their phenotypes. Evolutionary change may occur both through changes in protein-coding sequences and through sequence changes that alter gene regulation.

There is growing recognition of the importance of this regulatory evolution, on the basis of numerous specific examples as well as on theoretical grounds. It has been argued that potentially adaptive changes to protein-coding sequences may often be prevented by natural selection because, even if they are beneficial in one cell type or tissue, they may be detrimental elsewhere in the organism. By contrast, because gene-regulatory sequences are frequently associated with temporally and spatially specific gene-expression patterns, changes in these regions may modify the function of only certain cell types at specific times, making it more likely that they will confer an evolutionary advantage.

However, until now there has been little information about which genomic regions have regulatory activity. The ENCODE project has provided a first draft of a 'parts list' of these regulatory elements, in a wide range of cell types, and moves us considerably closer to one of the key goals of genomics: understanding the functional roles (if any) of every position in the human genome.

The problem here is the hype. While it's true that the ENCODE project has produced massive amounts of data on transcription binding sites etc., it's a bit of an exaggeration to say that "until now there has been little information about which genomic regions have regulatory activity." Twenty-five years ago, my lab published some pretty precise information about the parts of the genome regulating activity of a mouse hsp70 gene. There have been thousands of other papers on the the subject of gene regulatory sequences since then. I think we actually have a pretty good understanding of gene regulation in eukaryotes. It's a model that seems to work well for most genes.

The real challenge from the ENCODE Consortium is that they question that understanding. They are proposing that huge amounts of the genome are devoted to fine-tuning the expression of most genes in a vast network of binding sites and small RNAs. That's not the picture we have developed over the past four decades. If true, it would not only mean that a lot less DNA is junk but it would also mean that the regulation of gene expression is fundamentally different than it is in E. coli.

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[Image Credit: ScienceDaily: In Massive Genome Analysis ENCODE Data Suggests 'Gene' Redefinition.

Ecker, J.R., Bickmore, W.A., Barroso, I., Pritchard, J.K. (2012) Genomics: ENCODE explained. Nature 489:52-55. [doi:10.1038/489052a]
Yoav Gilad
& Eran Segal

PZ, Poutine, and the End of the World

One of the highlights of Eschaton 2012 was taking PZ Myers to the Elgin Street Grill for poutine. He had the plain, ordinary version diluted with a chicken burger. I had the chili poutine.

Other highlights included his two talks. The one on Saturday morning was about the sorry state of science education in the United States. That was depressing.

PZ's talk on Saturday evening was at the Canadian Museum of Natural History, just around the corner from the hotel. There were about 200 people in the audience. He tackled a very difficult topic, the role of chance in evolution. Naturally he covered random genetic drift but most of his talk was about coalescent theory because he wanted to explain some recent results from the sequence of the gorilla genome (Scally et al. 2012).

The authors of that paper report that, "In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other." PZ explained why this is exactly the result you would expect. (See his blog post at: A tiny bit of knowledge is a dangerous thing.)

He also pointed out that the Intelligent Design Creationists got all excited about this result, thinking that it overthrows the theory of evolution and proves the existence of God. (I exaggerate slightly, but you get the point!) What this means if that the IDiots really don't understand evolution.

While we don't expect everyone to see immediately why 30% of our genes could be more similar to gorilla genes than to chimp genes, we do expect those who criticize evolution to have a better understanding. Instead, what we see is that those "experts" who post at Evolution News & Views (sic) don't even have an introductory college level understanding of evolution. Their ignorance of evolution produces some remarkably stupid posts on that blog—the website of the Discovery Institute.

I made a similar point in my talk except that I focused on the IDiot's lack of knowledge of mutation [see Breaking News: IDiots Don't Understand Genomes or Biology].

PZ took on a challenging task but he succeeded better than I could have imagined. While the audience didn't follow all of the explanation, they could see that it was based on solid evidence and theory. Many of them learned for the first time about chance in evolution and that's a plus, in my opinion.

Now let's work on the IDiots.

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Scally, A, Dutheil, J.Y., Hillier, L.W., Jordan, G.E. et al. (2012) Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-175. [PubMed]

Did Life Arise 3.5 Billion Years Ago?

J. William Schopf is a paleontologist at the University of California, Los Angeles (USA). He became famous in the 1990s for his studies of the Apec chert—ancient rocks in the northern part of Western Australia near the town of Marble Bar. Parts of these rocks have been reliably dated to 3.465 billion years ago.

Schopf claimed to have discovered bacteria fossils in these rocks. He published his results in a highly cited Science paper back in 1993 (Schopf, 1993). The title of the paper "Microfossils of the Early Archean Apex chert: new evidence of the antiquity of life" establishes his claim.

It's worth quoting the abstract of the paper because it shows the confidence Schopf exuded. Not only did he claim that the 3.5 billion year old Apex chert contained bacterial fossils but, even more astonishingly, he identified eleven different species and clearly stated that they resembled cyanobacteria.

Eleven taxa (including eight heretofore undescribed species) of cellularly preserved filamentous microbes, among the oldest fossils known, have been discovered in a bedded chert unit of the Early Archean Apex Basalt of northwestern Western Australia. This prokaryotic assemblage establishes that trichomic cyanobacterium-like microorganisms were extant and morphologically diverse at least as early as approximately 3465 million years ago and suggests that oxygen-producing photoautotrophy may have already evolved by this early stage in biotic history.

The data were immediately challenged. There were two problems, First, many paleonotologists questioned whether the "fossils" were really fossils. They suggested that the structures could easily be inorganic in nature and not remnants of living organisms. Secondly, the presence of cyanobacteria—among the most complex bacteria—is inconsistent with molecular data. Even though the early tree of life is complicated, the available evidence indicates that cyanobacteria arose late in the evolution of bacterial taxa. It's very unlikely that the earliest forms of life could be cyanobacteria, or even photosynthetic bacteria.

The publicity associated with the presumed discovery of the earliest forms of life was too much to resist. In spite of the criticisms, the "fact" of these "fossils" made it into the textbooks within months of the discovery. The original figures have often been purged from more recent editions but the widespread claim that life originated 3.5 billion years ago persists.

Schopf defended and promoted his work in a trade book—The Cradle of Life— published in 1999. In that book he appeared to address most of his critics. He insisted that his "fossils" met all the rigorous tests of science.

The Fossils Aren't Fossils

Over the years, the challengers became more and more emboldened. In 2002 Martin Brasier published a re-analysis of Schopf's original fossils and noticed that the published images were not as complete as they could be. In the figure shown here, Brasier et al. (2002) compare Schopf's original images ("b" and "c") with a larger view of the same material.

The "fossils" look much more like inorganic inclusions that just happen to resemble strings of bacteria, according to Brasier. A debate between Martin Brasier and Bill Schopf took place in April 2002 and it was widely perceived to have resulted in victory for Brasier. The "fossils" aren't fossils.

A report in Nature presented the bottom line (Dalton, 2002).

The textbooks say that oxygen-producing microorganisms evolved some 3.5 billion years ago. But as that claim and its author come under attack, the history of life on Earth may have to be rewritten...

Supporters and critics of Schopf alike describe him as a driven and tenacious character — nicknamed 'Bull' Schopf by some — whose energy and enthusiasm has done much to raise the profile of micropalaeontology, and to draw funding into the field. "He has a driving ambition to be in the limelight, and he doesn't like to admit he's wrong," says one former colleague. But these traits have led Schopf into conflict with his collaborators on at least one previous occasion.

A similar piece in Science helps drive the point home (Kerr, 2002).

The search for fossils in rocks formed before the Cambrian explosion of life 540 million years ago "has been plagued by misinterpretation and questionable results," leading paleontologist William Schopf of the University of California, Los Angeles (UCLA), once noted. Now Schopf's own claim for the oldest known fossils--fossils that have entered textbooks as the oldest ever found--is under attack as a misinterpretation of intriguingly shaped but purely lifeless minerals.

A paper in this week's issue of Nature argues that the microscopic squiggles in a 3.5-billion-year-old Australian chert are not fossilized bacteria, as Schopf claimed in a 1993 Science paper (30 April 1993, p. 640), but the curiously formed dregs of ancient hot-spring chemistry. "There's a continuum [of putative microfossils] from the almost plausible to the completely ridiculous," says lead author Martin Brasier, a micropaleontologist at the University of Oxford, U.K. "Our explanation is that they are all abiogenic artifacts."

If true, the analysis calls into question the fossil record of life's first billion years. It would also raise doubts about the judgment of Schopf, the man chosen by NASA to set the standard for distinguishing signs of life from nonlife at the press conference unveiling martian meteorite ALH84001 (Science, 16 August 1996, p. 864). But Schopf says that such speculation is unwarranted. "I would beg to differ" with Brasier's interpretation, he says. "They're certainly good fossils."

The latest paper by Pinti et al. (2009) extends earlier observations of the Apex chert that re-interpret it as a hydrothermal vent. Temperatures reached 250° during formation of the vent and the alternation between molten and cooler forms of material was not conducive to life. Furthermore, deposits of iron oxides and clay minerals could be mistaken for microfossils .

Organic Traces of Early Life?

One of the early signatures of life is trace organic matter. In theory, it is possible to distinguish between organic molecules that form by chemical processes and organic molecule that are synthesized by living organisms. The key is the ratio of the two isotopes of carbon; ¹²C and ¹³C. The common isotope is ¹²C and living organisms preferentially incorporate ¹²C when they synthesize carbohydrates, lipids, and other molecules of life.

The result is that organic molecules made in cells have a smaller percentage of the heavy isotope, ¹³C. The presence of "lighter" organic molecules is evidence of life—or so the story goes.

Even this evidence of early life is being challenged. For example, a review of the evidence for life in the 3.7 billion year old rocks of western Greenland points out two potential problems (Fedo et al., 2006). First, the material has probably been misidentified—it is not what it was claimed to be. Recent evidence suggests that the rocks are igneous, not sedimentary. Secondly, the isotope ratios may not be accurate and/or they can be explained by non-biological processes. Isotope ratios are not an unambiguous indication of life.

These problems, and others, with the Akilia rocks of western Greenland have been known for many years. They were discussed in a hard-hitting Nature News and Views article by Stephen Moorbath in 2005. You may not understand the technical details (I don't) but there's no mistaking the tone when Moorbath says ...

This persuasive discovery seems an almost inevitable, yet highly problematic, consequence to the increasing scientific doubts about the original claim. We may well ask what exactly was the material originally analysed and reported? What was the apatite grain with supposed graphite inclusions that figured on the covers of learned and popular journals soon after the discovery? These questions must surely be answered and, if necessary, lessons learned for the more effective checking and duplication of spectacular scientific claims from the outset.

To my regret, the ancient Greenland rocks have not yet produced any compelling evidence for the existence of life by 3.8 billion years ago. The reader is reminded that another debate on early life is currently in progress on 3.5-billion-year-old rocks in Western Australia, where chains of cell-like structures, long identified as genuine fossils10, have recently been downgraded by some workers11 to the status of artefacts produced by entirely non-biological processes. To have a chance of success, it seems that the search for remnants of earliest life must be carried out on sedimentary rocks that are as old, unmetamorphosed, unmetasomatized and undeformed as possible. That remains easier said than done. For the time being, the many claims for life in the first 2.0–2.5 billion years of Earth's history are once again being vigorously debated: true consensus for life's existence seems to be reached only with the bacterial fossils of the 1.9-billion-year-old Gunflint Formation of Ontario12.

There's another, potentially more serious, problem with using isotope ratios as evidence of early life. Gérard et al. (2009) have recently documented the presence of modern bacteria in drillcore samples of rocks that are 2.7 billion years old. They detected trace amounts of ribosomal RNA that were sufficient to identify more that ten diverse species of bacteria living in these subsurface formations.

If modern bacteria can invade and colonize ancient rocks then it's highly likely that more ancient bacteria can also live in ancient rocks. Over the course of millions of years, these colonizers can leave traces of organic molecules. But those molecules do not show that life existed in those places at the time when the rocks were formed. In other words, just because you have "light" organic molecules in rocks that are billions of years old does not mean that the cells that created those molecules lived billions of years ago.

The conclusion of the Gérard et al. (2009) paper is worth quoting,

Our results strongly suggest that contemporary bacteria inhabit what are generally considered exceptionally well-preserved subsurface Archaean fossil stromatolites of the Hamersley Basin, Western Australia. They are possibly in very low numbers, their distribution confined to microfractures where water may circulate (perhaps only intermittently), and their metabolic activities might be extremely low. However, upon geological timescales spanning 2.7 Gy, even such low cell numbers must have contributed significantly to the pool of biogenic signatures associated to these rocks, including microfossils, biological isotopic fractionation and lipid biomarkers. Although our results do not necessarily invalidate previous analyses, they cautiously question the interpretation of ancient biomarkers or other life traces associated to old rocks, even pristine, as syngenetic biogenic remains when bulk analyses are carried out.

What does all this tell us about early life? It tells us that the evidence for life before 3 billion years ago is being challenged in the scientific literature. You can no longer assume that life existed that early in the history of Earth. It may have, but it would be irresponsible to put such a claim in the textbooks without a note of caution.

What else does this story tell us? It tells us something about how science is communicated to the general public. The claims of early life were widely reported in the media. Every new discovery of trace fossils and trace molecules was breathlessly reported in countless newspapers and magazines. Nobody hears about the follow-up studies that casts doubt on those claims. Nobody hears about the scientists who were heroes in the past but seem less-than-heroic today.

That's a shame because that's how science really works. That's why science is so much fun.

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Brasier, M.D., Green, O.R., Jephcoat, A.P., Kleppe, A.K., Van Kranendonk, M.J., Lindsay, J.F., Steele, A., and Grassineau, N.V. (2002) Questioning the evidence for Earth's oldest fossils. Nature 416::76-81. [PubMed]

Dalton, R. (2002) Microfossils: Squaring up over ancient life. Nature 417:782-784. [doi:10.1038/417782a]

Fedo, C.M., Whitehouse, M.J. and Kamber, B.S. (2006) Geological constraints on detecting the earliest life on Earth: a perspective from the Early Archaean (older than 3.7 Gyr) of southwest Greenland. Phil. Trans. R. Soc. B 361:851-867. [doi: 10.1098/rstb.2006.1836]

Gérard, E., Moreira, D., Philippot, P., Van Kranendonk, M.J., and López-García, P. (2009) Modern Subsurface Bacteria in Pristine 2.7 Ga-Old Fossil Stromatolite Drillcore Samples from the Fortescue Group, Western Australia. PLoS ONE 4: e5298. [doi:10.1371/journal.pone.0005298]

Pinti, F.L., Mineau, R., and Clement, V. (2009) Hydrothermal alteration and microfossil artefacts of the 3,465-million-year-old Apex chert. Nature Geoscience 2:640-643. [doi: 10.1038/ngeo601]

Schopf, J.W. (1993) Microfossils of the Early Archean Apex chert: new evidence of the antiquity of life. Science 260:640-646. [PubMed]

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Gérard, E., Moreira, D., Philippot, P., Van Kranendonk, M., & López-García, P. (2009). Modern Subsurface Bacteria in Pristine 2.7 Ga-Old Fossil Stromatolite Drillcore Samples from the Fortescue Group, Western Australia PLoS ONE, 4 (4) DOI: 10.1371/journal.pone.0005298

Pinti, D., Mineau, R., & Clement, V. (2009). Hydrothermal alteration and microfossil artefacts of the 3,465-million-year-old Apex chert Nature Geoscience, 2 (9), 640-643 DOI: 10.1038/ngeo601