Students vs Icons of Evolution

 
I teach in a second year course on "Scientific Misconceptions and Controversies." In my part of the course we discuss creationism and evolution. The object is to learn to think rationally about the controversy.

Students have to read Icons of Evolution and write an essay analyzing the arguments in one of the chapters (their choice). They have no problem recognizing the flaws in the logic and the outright mistruths in that book. For typical university students with a rudimentary understanding of evolution it's like shooting fish in a barrel.

The Discovery Institute sees it differently but they must live on another planet.


Here's how David Klinghoffer describes Jonathan Wells in a recent posting on Evolution News & Views [Celebrating Ten Years of Icons of Evolution].

A Berkeley PhD in molecular and cell biology, Wells is among the most lucid and accessible scientist-writers devoted to the modern project of critiquing Darwin. When I say the book is sweetly reasoned, I don't only mean that it's well reasoned but that there's an appealing geniality, a sweetness, to the man's writing that stands out in contrast to the donkey-like braying of a Darwinian biologist Jerry Coyne, the sinister coilings of a Richard Dawkins, the ugly "humor" of a P.Z. Myers. Yes, you can get a sense of a person's character, and perhaps too his credibility, from the words he uses.

And here's an example of "sweet geniality" from page 234 of Icons.

What about scientists who knowingly make false utterances or misleading omissions but believe the overall effect is not misleading because they are teaching "a deeper truth"? Does the commitment to a supposed deeper truth excuse conscious misrepresentations? Such an excuse probably wouldn't help a stock promoter. Under federal law, a stock promoter is not justified in mistating the facts just because he or she deeply believes that a company is destined to prosper. The stock promoter commits fraud by misrepresenting the truth, regardless of his or her underlying beliefs. Shouldn't scientists be held to the same standard?

Fraud is a dirty word, and it should not be used lightly. In the cases described in this book, dogmatic promoters of Darwinism did not see themselves as deceivers. Yet they seriously distorted the evidence—often knowingly. If this is fraud when a stock promoter does it, what is it when a scientist does it?

...

If dogmatic promoters of Darwinian evolution were merely distorting the truth, that would be bad enough. But they haven't stopped there. They now dominate the biological sciences in the English-speaking world, and they use their position of dominance to censor dissenting viewpoints.

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Darwinism and Junk DNA

 
Robert Crowther has posted a criticism of Francis Collins on Evolution News & Views (sic): Francis Collins, Evolution and "Darwin of the Gaps".

Much of Collins’s case for Darwinian evolution is based on so-called “junk DNA.” This is the part of the genome that does not appear to code for the production of proteins. In mammals, the vast majority of DNA has been dismissed as “junk.”

Junk DNA, according to Darwinists like Collins, gives evidence of common descent—the idea that all life, including human life, branches off from a common evolutionary tree. As life evolved, according to this view, garbled, useless genetic information accumulated and has remained fixed—like dirt swept under a carpet—even as mammals, for example, diversified from a common ancestor.

But the argument from junk DNA—also called “ancient repetitive elements” (AREs)— depends on the premise that no function will ever be discovered for AREs. Collins’s faith in Darwinian theory would be severely hamstrung if the premise were shown to be wrong. It is a faith based on gaps in scientific knowledge. Hence, “Darwin of the gaps.”

I don't want to defend Francis Collins. I want to emphasize something else; namely that the concept of junk DNA is about as far removed from "Darwinism" as you can possibly be and still be an evolutionary biologist. If it has any meaning at all, "Darwinism" has to be a synonym for the belief in natural selection as the most potent mechanism of evolution. Junk DNA is completely non-Darwinian and there's no way you could describe it as compatible with "Darwinian theory."

Why do creationists have so much trouble understanding this? It's not that hard.

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Michael Egnor Answers the Questions

 
I treid to answer Michael Egnor's questions as best I could [A Quiz for Atheists from a Creationist]. Now Egnor has answered his own questions at: What I Really Believe.¹

Some Sandwalk readers will be delighted to discover that Egnor refers to Aristotle in support of his beliefs, proving that Aristotle is good for something!

Most Sandwalk readers will be interested in this ...

That's what I believe. Note that these beliefs are entirely compatible with modern science; in fact, classical philosophy and classical theism is the source for modern science, which only originated in civilizations that embraced this classical view of the world. Some enlightenment philosophers moved away from some aspects of classical philosophy (e.g. final causes), but classical philosopohy and classical theism remain the foundation of Western Civilization and of modern science.

Many of you are modern scientists. How many think that classical theism is important in your work? How about classical philosophy?

Really? No one thinks that? Where do the IDiots come up with these ideas?

More and more scientists, philosophers, and theists are recognizing that science and theism are incompatible. That sort of makes it hard to claim that classical theism remains the foundation of modern science, doesn't it?

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1. Comments aren't allowed on Evolution News & Views so you can leave comments for Michael here.

The Casey Luskin Lesson Plan on Teaching the Controversy

 
I often criticize the Intelligent Design Creationists for not coming up with anything other than criticism of evolution. That criticism is perfectly justified as we can see in Casey Luskin's latest posting on Evolution News & Views: Back to School Lesson Plans That Actually Help Students Understand Evolution. He's even gone as far as proposing a lesson plan on evolution for grades 4-7. One of the important parts of that lesson plan is the challenges to evolution.

It's Monday, and it's Thanksgiving Day in Canada, so I'm taking a bit of a break. Let's have some fun with Luskin's lesson plan. I'll quote each of his points with a brief response.

Step 3: Learn About the Case against Evolution (1.5 hours). Now students will learn about some of the science that challenges evolution. Watch the DVD Icons of Evolution.
- Ask students to explain the difference between microevolution and macroevolution.

This is far too complicated for public school students. The simple answer is that microevolution describes changes occurring within populations and macroevolution describes the history of life. Macroevolution includes things such as speciation that are not part of microevolution and it also includes things like asteroid impacts, ice ages, and drifting continents in order to explain the history of life. There's an important part of evolutionary theory called "Hierarchical Theory" where proponents argue for higher-level mechanisms of evolution such as species selection. They aren't part of microevolutionary explanations. Thus, microevolution is necessary but not sufficient to explain macroevolution [Macroevolution].

-The video mentions the Galápagos finches. Do the finches represent an example of microevolution or macroevolution?

It's on the border between microevolution and macroevolution. The value of the work on the Galapogos finches is that the results suggest how new species are formed. They formed from a combination of physical isolation events (different islands) plus microevoutionary events involving natural selection, and random genetic drift. Such speciation events occurred repeatedly in the history of life and these studies show how they can be explained by purely natural causes.

-The video mentions mutations in fruit flies which gave fruit flies an extra pair of wings. Were these fruit flies able to fly better and survive with the extra wings?

No.

-Are mutations helpful or harmful? Ask for examples of harmful mutations? How about helpful ones?

A harmful mutation is one that decreases fitness. There are hundreds of examples of genetic diseases in humans. A beneficial mutation is one that increases fitness. Antibiotic resistance in bacteria is a classic example but so is HIV resistance in humans. Dozens of field studies have shown that beneficial mutations can arise fairly quickly in populations that are challenged by environmental change. Molecular data documents thousand of beneficial changes to genes and enzymes over time.

-What was the Cambrian explosion?

The Cambrian Explosion was a period in the history of life where we see the appearance of new types of animals. The dates are approximately 500 million years ago and the time frame for the visible appearance of these groups ranges from 10-50 million years. It's important to note that the fossils of the Cambrian don't look like any species that are alive today and they don't contain any examples of land life. It's also important to note that the Cambrian explosion doesn't apply to plants, fungus, protozoa, and bacteria.

What caused the appearance of primitive animal groups 500 million yeas ago, over a period of tens of millions of years? Scientists don't really know but there are lots of ideas on the table. One thing that's very clear from molecular evolution is that the origin of the various lineages (phyla) goes back several hundred million years.

-Does the fossil evidence show that species have evolved by small gradual changes, or large sudden changes? Do fossils support Darwin’s theory? Why or why not?

The are many examples of slow gradual changes over millions of year but there are also examples of patterns called Punctuated Equilibria. In these examples you see very small changes—such as the speciation events in the Galapagos finches—happening at the time of speciation. In other words, the fossil record mimics the sort of thing you see in the Galapagos islands where the small changes occurring at speciation are quickly fixed in the population within ten or twenty thousand years. There's hardly any fossil record of the intermediates showing the transition between these closely related species.

There's nothing in the fossil record suggesting that large sudden changes can occur rapidly. That's a lie propagated by creationists who don't understand evolution and who have a religious agenda that interferes with their ability to do science.

-The video also mentions the origin of life. Does the evidence support the claim that the building blocks of life were present on the early earth? Why or why not?

The origin of life is an interesting scientific problem that hasn't been solved. Although it has nothing to do with evolution, it's clearly related. Some scientists think that life arose in a primordial soup containing abundant supplies of all the necessary building blocks we see today. There is plenty of scientific evidence that some of these building blocks—such as simple sugars and amino acids—can arise spontaneously. In fact, many of them have been detected in outer space. Other scientists prefer scenarios where life began much more simply with very small, highly abundant, chemicals that are still around today in the oceans. It will be interesting to watch for new discoveries as you grow up because science is poised to make significant advances in these areas.

You should keep an open mind on this question and watch for new discoveries from religious leaders that will help you understand the origin of life. It's possible—alghough not very likely—that religious organizations such as The Discovery Institute will come up with a scientific explanation of how, and when, God created life on Earth.

-Compared to humans, was the first life simple or complex? How about compared to a calculator, computer, or cell phone? Are living organisms more or less complicated than human technology? What do students think?

All available scientific evidence points to a common ancestor that was much more simple than humans, or most other species that are living today. Those primitive ancestors are much less complex than a modern computer because, in addition to having only a few hundred genes (at most), the internal cell biology and biochemistry was undoubtedly sloppy and inefficient. No modern machine is anything like that.

We are at the stage in technology development where it is possible to build better life forms than those that evolved naturally and you should look forward to learning about these new artificial forms of life in the next few years. You might even want to think about a future career in science so you can learn this technology.

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Stephen Meyer Explains the Origin of Information

 
Intelligent Design Creationism is struggling to maintain scientific credibility. The movement claims to be scientific, not religious, and it's strongest defense is that it offers credible scientific explanations of biological phenomena.

Most of us don't see it that way. All we see is a bunch of people who attack science in general and evolution in particular. They publish lots and lots of stuff that raises questions about standard scientific explanations—some of the criticisms are valid but most are nothing more than wishful thinking. What we never, ever, see is a true explanation of how intelligent design creationism actually works.

This video was published on the Evolution News & Views (sic) blog [Stephen Meyer on Intelligent Design: What is the origin of the digital information found in DNA?]. Watch it to see if Meyer¹ explains the origin of information according to the Intelligent Design Creationism Model. Wait right 'till the end to make sure you don't miss the explanation of how an intelligent creator put information into DNA. Learn who the creators(s) is/are and why they did it. Find out when she did it. Wait to see how this accounts for life as we know it today.

Folks, this is the best they have to offer. It's why we call them IDiots. There's nothing there but obtuse rhetoric about the origin of life and information. They have nothing to offer but criticism of evolution.

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1. Stephen Meyer is one of the founders of the Discovery Institute in Seattle. He has a Ph.D. in the History and Philosophy of Science from Cambridge University (UK).

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.

The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion

This is the second in a series of postings by a guest blogger, Arlin Stoltzfus. You can read the first part at: Introduction to "The Curious Disconnect". Arlin is challenging the status quo in modern evolutionary theory. He's not alone in this challenge but it's important to distinguish between kooks who don't know what they're talking about and serious thinkers who have something to say. Arlin is going to explain to you why everything you thought you knew about mutationism is wrong. I'm happy to give him a chance to post on Sandwalk.

This will be on the exam.

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The Curious Disconnect

The Curious Disconnect is the blog of evolutionary biologist Arlin Stoltzfus, available at www.molevol.org/cdblog. An updated version of the post below will be maintained at www.molevol.org/cdblog/mutationism_myth1 (Arlin Stoltzfus, ©2010)

The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion

The mutationism myth tells the story of how, just over a century ago, the scientific community responded to the discovery of Mendelian genetics by discarding Darwinism, and how Darwinism subsequently was restored.Our journey to explore The Curious Disconnect-- the gap between how we think about evolution and how we might think if we were freed from historical baggage-- begins with the Mutationism Myth. In this, the first of four parts, we are not going to confront any tough scientific or conceptual issues. Instead, we are just going to review an odd story about our intellectual history.

The Mutationism Story

While "myth" has the connotation of falsehood, the story that a myth tells isn't necessarily a false one. The mutationism myth, at least, is anchored in historical events.¹

The mutationism myth tells the story of how, just over a century ago, the scientific community responded to the discovery of Mendelian genetics by discarding Darwinism, and how Darwinism subsequently was restored. The villains of the story are the influential early geneticists or "Mendelians" who saw genetics as a refutation of Darwinism; the heroes are first, the founders of population genetics, theoreticians who sorted everything out in favor of Darwinism by about 1930, and second, the architects of the Modern Synthesis, activists who popularized and institutionalized what we're calling "Darwinism 2.0".

This story has been re-told in secondary sources for nearly 50 years, though I sense that the frequency is decreasing as this episode passes into ancient history. To find examples, try looking up "mutationism" (sometimes "Mendelism" or even "saltationism") in the index of a book about evolution.

I encourage you to consult whatever sources you have and to share the stories that you find. Note that you won't always be successful. A quick survey of several dozen contemporary books on my shelf reveals that most don't address this episode specifically (a notable absence, in some cases ²); some tell the mutationism myth with varying degrees of panache; and a few provide a historical account rather than a myth. The few historical accounts that I found were in Gould's 2002 The Structure of Evolutionary Theory, Strickberger's 1990 textbook Evolution, and the Wikipedia entry on "Mutationism".

Sample stories

Lets look at a few examples of the mutationism story. Readers who want to check out a freely available online source from the scholarly literature may refer to Ayala and Fitch, 1997 (http://www.ncbi.nlm.nih.gov/pubmed/9223250?dopt=Citation). One example that really caught my eye is not from scientific literature, but from the 2005 obituary for Ernst Mayr in The Economist:

It was not that biologists had given up on evolution by the 1940s-quite the contrary. But they had got very confused about its mechanism. . . . The geneticists of the early 20th century did not help. They rediscovered the laws of inheritance first developed 40 years earlier by Gregor Mendel, an unsung Moravian monk. They also discovered the idea of genetic mutation. But instead of linking these things to natural selection, they came up with the idea of "saltation"-in other words, sudden mutational shifts from one well-adapted species to another. Nor, the geneticists complained, had there been enough time for natural selection to do its work, given what they had discovered about the rate at which mutations occur, and the fact that most mutations are deleterious. It was all a bit of a mess. . .Mr Mayr's advantage over the laboratory-bound biologists who had hijacked and diluted Darwin's legacy was that, like Darwin, he was a naturalist-and a good one. (anonymous, 2005)

Of course, this is a magazine article, written by anonymous staff writers-- typically one doesn't see such florid language in the scholarly literature. But did the staff writers of the Economist (representing elite opinion) really originate this story, based on their own personal recollections of the 1930's? Of course not. Mayr himself popularized the image of geneticists as laboratory-bound geeks lacking the organic insight of "naturalists". This disdain for the geneticists who "hijacked" Darwin's legacy is readily apparent when evolutionary writers depict geneticists as fools holding "beliefs" that have "obvious inadequacies", unable to understand or "grasp" their own scientific findings:

"It is hard for us to comprehend but, in the early years of this century when the phenomenon of mutation was first named, it was regarded not as a necessary part of Darwinian theory but as an alternative theory of evolution! There was a school of geneticists called the mutationists, which included such famous names as Hugo de Vries and William Bateson among the early rediscoverers of Mendel's principles of heredity, Wilhelm Johannsen the inventor of the word gene, and Thomas Hunt Morgan the father of the chromosome theory of heredity. . . Mendelian genetics was thought of, not as the central plank of Darwinism that it is today, but as antithetical to Darwinism. . . It is extremely hard for the modern mind to respond to this idea with anything but mirth" (Dawkins, 1987, p. 305)

"According to mutationism, random changes in the hereditary material are sufficient for adaptation without much, or any, selection at all. Mutations just somehow happen to be adaptive, the right changes simply manage to occur. The inadequacies of this view are obvious" (Cronin, 1991, p. 47).

"Darwin knew nothing of this [i.e., genetics] but as it turned out, his ignorance was sublimely irrelevant to the problem he was really interested in tackling: evolution. This point was not fully grasped by biologists. Many early geneticists at the dawn of the 20th century, thought their discoveries of the fundamental principles of genetics somehow cast doubt [on], or rendered obsolete, the concept of natural selection. It took several decades of experimentation and theoretical (including mathematical) analysis to show not only that there was no conflict inherent between the emerging results of genetics and the older Darwinian notion of natural selection, but that the two operate in different domains." (Eldredge, 2001, p. 67)

"Mendelian particulate inheritance (today, we call the "particles" genes) was originally identified with De Vries's "mutation theory", according to which new variations or species originated in large jumps, or macromutations, and evolution was exclusively explained by mutation pressure. Darwinian naturalists, believing that Mendelism was synonymous with mutation theory, held on to theories of soft inheritance, while they considered selection a weak force at best. They did not know of the new findings in genetics that would have supported Darwinism. (SegerstrŒle, 2002)

Notice how, in every version of the story above, the position taken by early geneticists just doesn't make sense. This isn't a story of theory versus theory, its a story of confusion ultimately yielding to reason.

If de Vries and the other geneticists are playing the role of the pied piper in this story, the "naturalists" are like the children lured away from their Darwinian home. Ultimately the innocents are returned, and order restored, by (oddly enough) mathematicians:

"Between 1918 and 1932 Fisher, Haldane, and Wright showed that Mendelian genetics is consistent with natural selection. Only then, more than 60 years after the publication of The Origin of Species, was the genetic objection to natural selection finally removed. Modern molecular and developmental genetics have confirmed in exquisite chemical detail the key aspects of genetics necessary for Darwin's ideas to work: that the genetic material is DNA, that DNA has a sequence, . . . mutates . . . contains information . . " (p. 16 of Stearns and Hoekstra, 2005)

Anatomy of a Myth

In a subsequent post, we will look at original sources to see what the "mutationists" actually believed, and why. And eventually we will integrate this into the bigger picture of how evolutionary theory developed. But for now, lets just summarize the pattern that is apparent in the literature.

First, the mutationism story is clearly a story or myth, and not an ordinary scientific truth claim. We can see this because the story-tellers are not using ordinary scientific conventions to convince us that the story is true. If you or I were making an ordinary scientific argument (for instance) for an effect of "translational selection" on codon usage, we would mention a correlation between codon frequencies and the abundance of corresponding tRNAs, citing the classic work of Ikemura (1981), and we might even repeat a figure showing this correlation, to impress this point upon the minds of readers (e.g., just as in Ch. 7 of Freeman & Herron, 1998).

When I see instances of the mutationism story, typically I don't find quotations illustrating what the mutationists believed, nor facts & figures to refute their views, but only vague attributions and generalized claims. Apropos, the following quotation from Ernst Mayr never fails to make me laugh:

The genetic work of the last four decades has refuted mutationism (saltationism) so thoroughly that it is not necessary to repeat once more all the genetic evidence against it. (Mayr, 1960)

And the puissant Dr. Mayr proceeds on, not boring the reader with any tiresome "genetic evidence", nor citing sources that might allow the reader to evaluate the truth of his statement. Its a story, after all.

By contrast, the 3 sources that I mentioned above as providing scientific history, rather than myth, all make reference to specific experimental and theoretical results, and reveal knowledge of specific historically important scientific works. For instance, Strickberger's reference list includes Johannsen, 1903, as well as the 1902 paper by Yule that reconciled Mendelian genetics with quantitative variation (in neo-Darwinian mythology, credit for Yule's work is given to little Ronny Fisher, who was 11 at the time).

Second, every story has a plot or "action", and the main action of the mutationism story is a turn of fate in which power is temporarily in the hands of the wrong people or ideas. In archetypal terms, its a story of usurpation and restoration: the throne is usurped, and the kingdom falls into darkness and confusion until the throne is restored to the king's rightful heirs. The mutationism episode didn't have to be told that way: it might have been presented as a period of reform (in which old ideas were abandoned) or discovery (when new territory was mapped out). Instead, its presented as a mistake, an interlude of confusion, a collective delusion.

Indeed, another way to look at the mythic action is that the Mendelians are wizards or false prophets who place the kingdom under a spell, leading folks astray and causing them to believe things that they just shouldn't have believed.

What delusional spell did the Mendelians cast? In the story by Eldredge, or by Stearns & Hoekstra above, the spell is that Mendelian genetics is inconsistent with "the concept of natural selection" (Eldredge). In the story told by SegerstrŒle, Cronin, Mayr and The Economist, the delusional spell is a bit different: the principle of selection is irrelevant because mutational jumps alone explain evolution.

Third, the key to restoring Darwin's kingdom was to add the missing piece of genetics. Ultimately, after the period of darkness ended, the discovery of genetics "provided the missing link in Darwin's theory" (SegerstrŒle, 2002), or "The missing link in Darwin's argument was provided by Mendelian genetics" (Ayala & Fitch, 1997). Darwinism was restored, not by taking away the power of genetics, but by redirecting it to support Darwinism. Clearly, genetics is the key to ruling the kingdom, like the One Ring that Rules them All in Tolkien's world. The ones who have the ring have the power.

The story is made more fascinating by the fact that the key to power is literally a code of rules developed by a monk that remained lost for nearly half a century. The usurpers who discover The Monk's Code misinterpret it, and use it to overthrow the true king, establishing a reign of error. But when The Founders decipher the true meaning of the Monk's Code, The Architects campaign throughout the kingdom, spreading the news: the Monk's Code proves that Darwin is the true king. Darwin's rule is re-established, all opposition ceases, and the kingdom is unified.

Homework

If you would like to contribute a mutationism story, I would be happy to start a collection if you make it easy for me by providing a complete and well formed text item. Be sure to provide a quoted passage with a source, citing exact page numbers. If we get enough stories, lets try to recruit a sociologist or historian to study this further.

Summary

To summarize, the mutationism story is a myth that is retold in secondary sources. The basic story is simple: the discoverers of genetics misinterpreted their discovery, thinking it incompatible with Darwinism; Darwinism went into disfavor; population geneticists came along and showed that genetics was the missing key to Darwinism; Darwinism was restored and once again reigned supreme.

Next time on the The Curious Disconnect, we'll start pulling on some of the loose threads of this story.

For now, note how the writers quoted above are genuinely baffled by our scientific history. It just doesn't make sense to them. A century ago, most of an entire generation of scientists thought of genetics as a contradiction of Darwinism. This is a historical fact, and presumably it has an explanation that rational folks can understand by examining what scientists of the time wrote. But this historical fact mystifies Dawkins, Eldredge, Cronin, and others.

References

Anonymous. 2005. Ernst Mayr, evolutionary biologist, died on February 3rd, aged 100. The Economist, February.

Ayala, F. J., and W. M. Fitch. 1997. Genetics and the origin of species: an introduction. Proc Natl Acad Sci U S A 94:7691-7697.

Cronin, H. 1991. The Ant and the Peacock. Cambridge University Presss, Cambridge.

Dawkins, R. 1987. The Blind Watchmaker. W.W. Norton and Company, New York.

Eldredge, N. 2001. The Triumph of Evolution and the Failure of Creationism. W H Freeman & Co.

Freeman, S., and J. C. Herron. 1998. Evolutionary Analysis. Prentice-Hall, Upper Saddle River, New Jersey.

Gould, S. J. 2002. The Structure of Evolutionary Theory. Harvard University Press, Cambridge, Massachusetts.

Ikemura, T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol 151:389-409.

Mayr, E. 1960. The Emergence of Evolutionary Novelties. Pp. 349-380 in S. Tax, and C. Callender, eds. Evolution After Darwin: The University of Chicago Centennial. University of Chicago Press, Chicago.

SegerstrŒle, U. 2002. Neo-Darwinism. Pp. 807-810 inM. Pagel, ed. Encyclopedia of Evolution. Oxford University Press, New York.

Stearns, S. C., and R. F. Hoekstra. 2005. Evolution: an introduction. Oxford University Press, New York.

Strickberger, M.W. 1990. Evolution (1st edition).

Notes
¹ The defining characteristic of a myth is not that it isn't literally true, but that it isn't told for reason of being literally true, but for reason of being meaningful or poignant: a myth is a story with a cultural value, not necessarily a literal-truth value. The connection between myths and untruths, then, has to do with discoverability: when we find a pattern P = { X people are repeating story Y }, where X is a large number, this pattern by itself does not prove that Y is a myth because X people might have all discovered or verified Y independently; but if Y has diverse elements that are untrue (or unverifiable), then we can conclude that its repetition does not signify independent verification, suggesting that its a myth.



²The Oxford Encyclopedia of Evolution does not have an article on mutationism; the article on Morgan says nothing of his views on evolution; there is no article on Bateson; mutationism is only addressed peripherally in Hull's article on the history of evolutionary theory; it is mainly addressed in SegerstrŒle's article on neo-Darwinism.

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Predictions of Intelligent Design Creationism

I love it when they make predictions. Here's what Casey Luskin just posted over on Evoluton News & Views (sic) [A Response to Questions from a Biology Teacher: How Do We Test Intelligent Design?]

Regarding testability, ID makes the following testable predictions:

(1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).

Such natural structures exist. They are perfectly compatible with evolution. This prediction does not distinguish between Intelligent Design Creationism and real science.

(2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.

The vast majority of of species with novel information have arisen gradually with plenty of transitional fossils to document their evolution. In a small number of cases (e.g. Cambrian Explosion) the evidence for evolution from known precursors is too sophisticated for creationists to follow. This prediction is not supported; therefore, Intelligent Design Creationism is falsified for all species where we have lots of data.

(3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.

Convergence is perfectly consistent with evolution. This prediction is meaningless.

(4) Much so-called “junk DNA” will turn out to perform valuable functions.

Most of our genome is junk. The evidence for this is overwhelming. Intelligent Design Creationism has been falsified.

That was easy.

In this regard, ID is falsifiable. When we test these predictions, ID passes those tests.

No it doesn't. Two of the "tests" are consistent with evolution so the "test" is meaningless. Intelligent Design Creationism fails the other two tests.

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Do Graduate Students Understand Evolution?

 
The other day I was discussing how to teach evolution with one of my colleagues and the discussion turned to the presumed distinction between students who were really interested in science and everyone else. My colleague claimed that students who were science oriented probably managed to acquire a good understanding of evolution in spite of the fact that some undergraduate courses weren't doing a very good job of teaching the subject.

I pointed out that my impression was different. I suggested that most Professors in our department don't have a firm grasp of one of the most fundamental concepts in biology (evolution), and neither do our graduate students. I reminded my colleague of the times when we cringe at graduate student presentations when the topic of evolution comes up.

Ryan Gregory must have felt the same way since he was prompted to do a survey of graduate students in science departments at Guelph University. The result is published in BioScience. You can read about it on Ryan's blog: How well do grad students grasp evolution?.
Here's the press release...

Science Students Could Brush Up On Darwin, U of G Study Finds

October 01, 2009 - News Release

Even students pursuing advanced degrees in science could brush up on their knowledge of evolution, according to a new study by University of Guelph researchers.

The finding reveals that there is room for improvement in how evolution is taught from elementary school up, said Ryan Gregory, a professor in Guelph’s Department of Integrative Biology, who conducted the research with former student Cameron Ellis.

The study was published today in BioScience. It’s particularly timely, given that this year is the bicentennial of Charles Darwin’s birth and the 150th anniversary of publication of On the Origin of Species, which underpins understanding of the diversity of Earth’s organisms and their interrelations.

“Misconceptions about natural selection may still exist, even at the most advanced level,” Gregory said.

“We’re looking at a subset of people who have spent at least four years, sometimes even six or seven years, in science and still don’t necessarily have a full working understanding of basic evolutionary principles or scientific terms like ‘theories.’”

Many previous studies have assessed how evolution is understood and accepted by elementary, high school and undergraduate students, as well as by teachers and the general public, Gregory said. But this was the first to focus solely on students seeking graduate science degrees.

The study involved nearly 200 graduate students at a mid-sized Canadian university who were studying biological, physical, agricultural or animal sciences. About half of the students had never taken an evolutionary biology course, which is often not a prerequisite.

The researchers found that the vast majority of the students recognized the importance of evolution as a central part of biology. Overall, they also had a better understanding of evolutionary concepts than most people.

“That was encouraging, especially because it was across several colleges — it wasn’t just the biology students,” Gregory said.

But when the students were asked to apply basic evolutionary principles, only 20 to 30 per cent could do so correctly, and many didn’t even try to answer such questions. Of particular interest to Gregory is the finding that many students seem less than clear about the nature of scientific theories.

“This is telling us that traditional instruction methods, while leading to some basic understanding of evolution, are not producing a strong working knowledge that can be easily applied to real biological phenomena.”

Gregory has studied evolution-related topics for years and recently co-organized a workshop designed to improve how the subject is taught in public schools. He is also associate editor of Evolution: Education and Outreach, a journal written for science teachers, students and scientists. He recently created Evolver Zone, a free online resource for anyone interested in evolutionary biology.
He is also helping bring an evolution-inspired art exhibit to U of G this month. “This View of Life: Evolutionary Art in the Year of Darwin, 2009” highlights diverse artists’ views of Darwin’s ideas and evolution in general. It runs Oct. 9 to 30 in the science complex atrium.

Some of us know what the problem is. What are we going to do about it? How are we going to convince professors that evolution education has to change when most of them don't even recognize there's a problem because their own views of evolution are flawed?

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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

The Biologic Institute Expands

 
Posted yesterday on Evolution News & Views: European scientists working in conjunction with Biologic Institute.

The anti-ID crowd has an old canard about there being no serious scientists who doubt Darwin, let alone any that support intelligent design. And they like to say that there is no science being done by ID scientists. Both ideas are not just false, but absurdly so. Note this announcement of new scientific arrivals at Biologic Institute. Professor Matti Leisola, the Dean of Chemistry and Materials Science at Helsinki University of Technology in Finland; Colin Reeves, Professor of Operational Research in the School of Mathematical and Information Sciences at Coventry University; and Professor Stuart Burgess, Head of the Department of Mechanical Engineering at the University of Bristol.

Three "serious scientists", eh? And not a biologist in the bunch. That's what we've come to expect in an institute that's supposed to be studying evolution creationism.

John Pieret has the scoop on these dudes. All three of them are creationists with strong ties to the Young Earth Creationist movement [The "Pros" from Dover]. John had the idea of comparing these guys to the Three Stooges. I thought it was appropriate so I "borrowed" it.¹

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1. I steal a lot of John's ideas but let's not tell him, OK? It gives him a swelled head.

Who Knew?

 
The misreporting of the evolution issue is one key reason for this site. Unfortunately, much of the news coverage has been sloppy, inaccurate, and in some cases, overtly biased. Evolution News & Views presents analysis of that coverage, as well as original reporting that accurately delivers information about the current state of the debate over Darwinian evolution.

Evolution News & ViewsJonathan Wells has a Ph.D. He can explain why "Darwinism" is false in only two paragraphs [Persisting in Spite of the Evidence: Why Darwinism Is False].

Darwin called The Origin of Species “one long argument” for his theory, but Jerry Coyne has given us one long bluff. Why Evolution Is True tries to defend Darwinian evolution by rearranging the fossil record; by misrepresenting the development of vertebrate embryos; by ignoring evidence for the functionality of allegedly vestigial organs and non-coding DNA, then propping up Darwinism with theological arguments about “bad design;” by attributing some biogeographical patterns to convergence due to the supposedly “well-known” processes of natural selection and speciation; and then exaggerating the evidence for selection and speciation to make it seem as though they could accomplish what Darwinism requires of them.

The actual evidence shows that major features of the fossil record are an embarrassment to Darwinian evolution; that early development in vertebrate embryos is more consistent with separate origins than with common ancestry; that non-coding DNA is fully functional, contrary to neo-Darwinian predictions;¹ and that natural selection can accomplish nothing more than artificial selection — which is to say, minor changes within existing species.

Amazing.

When it comes to evaluating Creationist arguments, we are often faced with a difficult decision. Is the Creationist just ignorant or is he lying? I think it's much easier to answer that question in Wells' case. He has a Ph.D. in biology from a reputable university. It's not possible for him to be that ingnorant about the basic facts of biology.

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1. It's a lie that non-coding DNA is fully functional and it's a lie that "neo-Darwinism" predicts the presence of large amounts of junk DNA in some species.

Facts Supporting Intelligent Design Creationism?

 
We all know that the Intelligent Design Creationist movement consists almost exclusively of attacks on science. The idea seems to be that if you can cast doubt on evolution then this is evidence in favor of God.

Some unnamed Professor has challenged students to come up with facts that support Intelligent Design Creationism. The only criterion is; "fact can be any observation in biology that is substantiated by publication in a scientific journal,"

Casey Luskin attempts to meet the challenge over on the Discovery Institute propaganda site, Evolution News & Views: Helping Students Answer a Professor's Challenge to "Find a Fact" That Supports Intelligent Design (Part 2).

Here's a list of "scientific" publications submitted by Luskin. I haven't read all of them but, of the ones I've read, there isn't a single one containing a fact that supports the existence of God, let alone evidence that he/she designed anything at all. Furthermore, many of them aren't from a scientific journal. It looks like Casey Luskin has goofed, once again.

Let me know if any of these publications contain evidence of Intelligent Design Creationism. Is this the best they can do? (I've put asterisks in front of the ones I've read.)

*Douglas D. Axe, "Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors," Journal of Molecular Biology, Vol. 301:585-595 (2000)

*Douglas D. Axe, "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds," Journal of Molecular Biology, 1-21 (2004)

*Michael Behe, Darwin's Black Box: The Biochemical Challenge to Evolution (Free Press, 1996)

*Michael J. Behe & David W. Snoke, "Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues," Protein Science, Vol 13:2651-2664 (2004)

Geoff Brumfiel, “Outrageous Fortune,” Nature, Vol. 439: 10-12 (Jan. 5, 2006)

Bract, "Inventions, Algorithms, and Biological Design," in Progress in Complexity, Information, and Design (Vol. 1.1, 2002)

*William A. Dembski, The Design Inference: Eliminating Chance Through Small Probabilities (Cambridge University Press, 1998)

a. William A. Dembski and Robert J. Marks II, “Conservation of Information in Search: Measuring the Cost of Success” (In publication, 2009)

b. William A. Dembski and Robert J. Marks II, “The Search for a Search: Measuring the Information Cost of Higher Level Search” (In publication, 2009)

*William Dembski and Jonathan Wells, The Design of Life: Discovering Signs of Intelligence in Living Systems, (FTE, 2008) (see www.thedesignoflife.net)

*Wayt T. Gibbs, “The Unseen Genome: Gems among the Junk,” Scientific American (November, 2003)

Guillermo Gonzalez and Jay Wesley Richards, The Privileged Planet: How our Place in the Cosmos is Designed for Discovery, (Regnery, 2004)

*Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009)

Hiroaki Kitano, ”Systems Biology: A Brief Overview,” Science, Vol. 295: 1662-1664 (March 1, 2002)

Wolf-Ekkehard Lönnig, "Dynamic genomes, morphological stasis, and the origin of irreducible complexity," in Dynamical Genetics pp. 101-119 (Valerio Parisi, Valeria De Fonzo, and Filippo Aluffi-Pentini eds., 2004)

Casey Luskin, “Human Origins and Intelligent Design,” Progress in Complexity and Design, (Vol 4.1, November, 2005)

Casey Luskin, "Intelligent Design Has Scientific Merit in Paleontology," part of the "Does Intelligent Design Have Merit?" debate at OpposingViews.com (September, 2008)

*Wojciech Makalowski, “Not Junk After All,” Science, Vol. 300(5623) (May 23, 2003)

Stephen C. Meyer, Marcus Ross, Paul Nelson & Paul Chien, "The Cambrian Explosion: Biology's Big Bang," in Darwinism, Design, and Public Education (John A. Campbell and Stephen C. Meyer eds., Michigan State University Press, 2003)

*a. Stephen C. Meyer, “The Cambrian Information Explosion,” in Debating Design (edited by Michael Ruse and William Dembski; Cambridge University Press 2004)

b. Stephen C. Meyer, “The origin of biological information and the higher taxonomic categories,” Proceedings of the Biological Society of Washington, Vol. 117(2):213-239 (2004)

Scott A. Minnich & Stephen C. Meyer, “Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria,” in Proceedings of the Second International Conference on Design & Nature, Rhodes Greece (M.W. Collins & C.A. Brebbia eds., 2004)

Paul Nelson and Jonathan Wells, “Homology in Biology,” in Darwinism, Design, and Public Education, (Michigan State University Press, 2003)

*Richard v. Sternberg, "On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic– Epigenetic System," Annals of the New York Academy of Sciences, Vol. 981: 154–188 (2002)

J.T. Trevors and D.L. Abel, "Chance and necessity do not explain the origin of life," Cell Biology International, Vol. 28: 729-739 (2004)

D. L. Abel & J. T. Trevors, “Self-organization vs. self-ordering events in life-origin models," Physics of Life Reviews, Vol. 3: 211–228 (2006)

Øyvind Albert Voie, "Biological function and the genetic code are interdependent," Chaos, Solitons and Fractals, Vol. 28:1000–1004 (2006)

Jonathan Wells, "Using Intelligent Design Theory to Guide Scientific Research" Progress in Complexity, Information, and Design (Vol. 3.1.2, November 2004)

Jonathan Wells, "Do Centrioles Generate a Polar Ejection Force?," Rivista di Biologia / Biology Forum, Vol. 98:71-96 (2005)

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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.

The University of Vermont Does the Right Thing

 
My impression of the University of Vermont has just gone way up. According to WCAX News in Vermont, the University has decided that Ben Stein is not an appropriate commencement speaker [Stein Withdraws as UVM Speaker].

Burlington, Vermont - February 2, 2009

Ben Stein won't be bidding UVM graduates goodbye after all.

Just last week, the university announced that Stein, who is highly acclaimed as an actor, author, and economist, would be delivering this year's commencement address. But Monday, the school announced that he has now withdrawn as speaker.

Stein has made headlines recently for his views regarding Darwin's theory of evolution, intelligent design and the role of science in the Holocaust. Several people from the academic community-- both locally and beyond the UVM campus-- quickly expressed concern over his selection and once notified of that, Stein withdrew from the ceremony.

"This is not, to my mind, an issue about academic freedom or the openness of the campus to all points of view. Ben Stein spoke here last spring to great acclaim," UVM President Dan Fogel said. "It's an issue about the appropriateness of awarding an honorary degree to someone whose views in many ways ignore or affront the fundamental values of scientific inquiry and I greatly regret that I was not attuned to those issues."

Fogel said the school's honorary degree committee has a list of potential candidates and he will consult others before extending an invitation to another potential commencement speaker.

Good for President Fogel. He's right. It is not appropriate to award an honorary degree to "someone whose views in many ways ignore or affront the fundamental values of scientific inquiry."

I wonder if Dan Fogel realizes that he has just earned himself a prominent place in "Expelled II"?

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Evolution News & Views

 
From time to time I mention the Disco site called Evolution News & Views. It has a lofty purpose that's prominently displayed on every posting.

The misreporting of the evolution issue is one key reason for this site. Unfortunately, much of the news coverage has been sloppy, inaccurate, and in some cases, overtly biased. Evolution News & Views presents analysis of that coverage, as well as original reporting that accurately delivers information about the current state of the debate over Darwinian evolution.

Here's a posting from Robert Crowther dated yesterday afternoon.

So, Darwinists are admitting that up until Friday, Jan. 16 2009 @ 4:10PM, evolution was “mostly theory.” Interesting. I am now certain that dogs adapt to their environment, too. Last night my dog kept barking and I shook my finger and spoke very firmly to her and made her sit on her bed. She stopped barking. So, at 7:10 pm I had a perfect example of evolution. Or was it adaptation? Or was it bad parenting? Whatever, we now see that dogs evolve, which previously had been believed to be “mostly theory.” My peers, who were there reviewing the moment, are skeptical because they think my dog is asexual. Regardless, this is all speculation — except for poor Kali. She still lacks an opposable thumb.

We may need a better word than IDiot to describe these people.

Is there an atheist bus campaign in Seattle? I'd like to donate.

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The Meat-Robots Are Stirring

 
The mind-body problem is one of the more serious problems in philosophy. At the risk of over-simplifying, the two main camps can be described as dualism and monism. A dualist thinks that there's more to the mind than just neurons—the word that comes up most often is consciousness. The monist rejects the idea that there is some vitalist component to the mind. It can all be explained by the structure of the brain and the laws of physics and chemistry.

Monists are materialists, for the most part. Dualists often believe in supernatural beings.

Michael Egnor writes articles on Intelligent Design Creationism for the Evolution News & Views website at the Discovery Institute. He thinks the materialists have been winning but it's time for the zombies meat-robots to strike back.

As a general anti-science strategy, it's easy to see why the mind-body problem is resurfacing. The IDiots have lost the battle over evolution so they have to look around for something else to attack. We (scientists) don't understand exactly how the mind works. That's a perfect gap to shove God into, for now.

The materialist project to explain the mind reads less like a compendium of scientific and philosophical investigation than like a psychiatrist’s case log. Succinctly, the materialist project is batsh*t. The mind is a catastrophe for materialism. Materialism doesn’t explain the mind, and it probably can’t explain the mind. Materialism flounders on the hard problem of consciousness — the problem of understanding how it is that we are subjects and not just objects. Now a number of scientists and other academics are challenging this repellent materialist nonsense. There’s no scientific or even logical justification for the inference that the mind is merely the brain, without remainder, and the philosophical and sociological implications of the materialist view of the mind are abhorrent. Now there’s a reality-based push-back to materialist superstition, and the materialists have an insurrection on their hands.

The meat-robots are stirring.

I wonder if the meat-robots have something substantial to contribute to the discussion or whether they'll just be complaining about science, as they always do?

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Dealing With the Controversy

 
Here's an exercise for those of you who are truly interested in teaching accurate science. Go to the recent posting by Casey Luskin on Evolution: News & Views and figure out how to respond to his challenge. He's claiming that a great deal of evolution is "random" but that's not what the "Darwinists" are saying ["Random" Samples of Media and Textbook Descriptions of Darwinian Evolution].

Is he right?¹ What should we teach in school?

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1. Yes, and no. As usual Casey Luskin has only a superficial understanding of evolution and a very weak grasp of reality. However, from time to time he accidentally stumbles onto an important point. Let's set aside the fact that he has no idea what he's talking about and address how we should respond to such criticisms. My view is here: [Evolution by Accident].

Good Science Writers: Stephen Jay Gould

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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