Friday, May 28, 2010

Todd Wood and the Neandertal Genome

Todd Wood has written a post on the Neandertal genome and what it means for the origins of modern humans. His post is called the Neandertal Non sequitur and the title refers to his reaction to Fuz Rana's analysis over at Reasons to Believe. But that is not subject of this post.

I should note that he is almost alone in spelling the word "Neandertal" the way the Germans have been spelling it for the last hundred years. Hats off. On to the post. He writes:
In my hominid baraminology paper, I merely cite Darwin's claim that similarities form a pattern that looks like a genealogy, thus supporting the inference of common ancestry.

I've been criticized for this stance, but I'm not going to address those criticisms today. I'll just assert that I'm correct, which I am. The fact of similarity is easy to account for. Being created by one God would be a good reason for some degree of similarity to exist. Likewise, being created to occupy the same world or to participate in the same ecosystem would also necessitate some biological similarity. These types of considerations could explain why all living things use the same basic biochemical building blocks (amino acids, nucleotides, etc.), for example.
And if that were the only thing that supported common ancestry, that would be a defensible position. But it is not. One of the principle reasons that the trees derived from genetic data hold up is that we can look at the fossil record and see corroboration of where those the branches lie. It is not just that we have a record of some Neandertal genes being present in the modern genome. We also have the observed evidence of the morphological similarities between Neandertals and modern humans. In addition, in many places in which these two hominid forms appear, their behavior is hard to distinguish. There are countless other examples.

Genetic evidence suggests a diversification between fish and tetrapods several hundred million years back. Lo and behold, we find fishapods in the Devonian—animals, to quote Sir Arthur Keith, "In the throes of transition." Put simply, the further we go back in the fossil record, the fewer branches we find. This is exactly what you would expect with universal common descent based on evolution. Similarity might be easy to account for in the creationist perspective. When the fossil record is factored in, it is not.

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Thursday, May 27, 2010

Sinn Fein has Responded to the Culture Minister

In lightning fashion, Sinn Fein, the political arm of the IRA, has responded to the letter by Nelson McCausland urging the Ulster Museum to include more creationism in their displays (see the post just below this one). In the Londonderry Sentinel, they write:
"The fact that a Culture Minister has used undue influence to seek an arms length body, namely the Ulster Museum, to include matters that are issues close to Nelson's personal beliefs, is wholly unacceptable.
"The letter which written specifies a time frame for changes to be made to current installations at the museum before summer including the issue of creationism, which is clearly a religious viewpoint, and more representation for the Orange Order."
Of course, the letter is not entirely devoid of political jabs:
"Nelson McCausland's partisan view of the world is not that of the vast majority nor is it anything to do with a truly shared future. This is a Culture Minister who speaks of a shared future yet has refused to enter a catholic church, has taken part in sectarian parades through nationalist districts in Belfast, has failed to bring forward a strategy for the development of the Irish language, and his department has previously sent out personal invites to Orange fest.
I said it last post. Politics and science don't mix.

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Why Politics and Science Don't Mix

A royal row is brewing over in Ireland where the Culture Minister, Nelson McCausland, has written a letter to the Ulster Museum encouraging them to change their exhibits to include more creationism. As Henry McDonald of the Guardian reports:
Nelson McCausland, who believes that Ulster Protestants are one of the lost tribes of Israel, has written to the museum's board of trustees urging them to reflect creationist and intelligent design theories of the universe's origins.

The Democratic Unionist minister said the inclusion of anti-Darwinian theories in the museum was "a human rights issue".

McCausland defended a letter he wrote to the trustees calling for anti-evolution exhibitions at the museum. He claimed that around one third of Northern Ireland's population believed either in intelligent design or the creationist view that the universe was created about 6,000 years ago.
Richard Dawkins responded typically but correctly:
Dawkins said it was irrelevant if a large number of people in Northern Ireland refused to believe in evolution. "Scientific evidence can't be democratically decided," Dawkins said.
This is similar to the US movement for "academic freedom" bills, although not nearly as extreme. The US is somewhat shielded from this sort of nonsense because of the establishment clause. Apparently, no such thing exists in UK law. Of course the museum could just ignore the letter but the YEC movement is quite strong in Ireland and so I am guessing this is not the last we will hear of this.

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Monday, May 24, 2010

Jerry Coyne on Religious America

Jerry Coyne wonders: Do religious Americans accept evolution? He writes:
Well, now I’ve seen it all. There are many ways that accommodationists try to show that faith and science are compatible, but never before have I seen a scientist with this aim play so fast and loose with the data. Dr. Joel Martin, the Curator of Crustacea and chief of the Division of Invertebrate Studies at the Natural History Museum of Los Angeles County, has written an astonishing article in the journal Evolution: Education and Outreach, “Compatibility of major U.S. Christian Denominations with Evolution”.
He fails to mention that this article is now behind a subscription wall. This journal was offered free for two years by Springer but now the article costs 34 dollars. Onward. Even though Coyne has it in mind to ridicule scientists who have religious convictions, he makes a valid point with his analysis of Dr. Martin's paper:
When Martin totals up the number of American Christians who belong to evolution-accepting faiths versus evolution-denying faiths, he gets 94,050,000 Americans in the former class and 45,850,000 in the latter, with 9,800,000 belonging to the “unclear” category. Voila! Nearly 63% of American Christians are of evolution-accepting faith! (This is, of course, heavily weighted with Catholics, who represent 71% of the “evolution-accepters).

The problem is obvious: the proportion of faiths that accept evolution is not the same as the proportion of believers who accept evolution.
Coyne is quite correct. Poll after poll have shown that a large percentage of all polled Americans do not accept evolution and that the correlation between lack of acceptance of evolution to religious expression is very high. In fact, recent earth creationism has taken hold in evangelical Christianity so much so that, as the Internet Monk put it a bit back:

Creationism has become a main plank in the platform of conservative Christian culture warriors. As a result, this issue has become more than a debate among Bible scholars who differ on their interpretations of Genesis. It has become a “litmus test” issue for many, identifying who is and who is not a faithful Christian.

So, unfortunately, despite the fact that Bruce Waltke’s views on these matters have been published in his writings for years, the BioLogos video was too provocative in the culture of fear that marks today’s climate in American Christianity.

As we have found out, now that we are home schooling once again, if one prowls the Home schooling resources, the YEC position is not just popular, it is the de facto position. Coyne ends by writing:
It is individuals who reject evolution, fight science textbooks, and make trouble for evolution—many of these in opposition to the “official” positions of their faiths.
I believe that he is correct.

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Sunday, May 23, 2010

Steve Matheson Fires Back

Steve has posted a response to the Discovery Institute's claim that he admitted design was the best alternative. It is here. One of the key arguments that design proponents (or "cdesignproponentsists" if you prefer) put out is that evolutionary theory does not have a good explanation for origins of life questions. Stephen Meyer, author of The Signature in the Cell, believes that this is where design comes in. Matheson responds:
It may be the case that we don't have a complete account of the origin of life, and it's certainly true that we don't have a complete account of the origin of genetic information control systems. But such an admission implies nothing about whether such an account is possible or even likely, and that's where Meyer would have to do his philosophical work in order to help his case. In other words, to assert that "we haven't explained X" is most assuredly not to assert that "we cannot explain X." Think about it: there would be no such thing as science if this were the case. Scientists are all about asserting that "we haven't explained X," then proposing a way to change that.
Origins of life questions have never been a center of evolutionary biology studies. During the formation of the synthesis, these question were largely ignored and it was not until the Miller-Urey experiments in 1953 that these question were associated with evolutionary theory. These question are, in a sense, like those governing those of the Big Bang. One can theorize back only so far until it becomes a conjecture. Evolution deals primarily with the changes in established life forms and with common descent issues. One can look at the fossil record and see that, as one moves through time, there is greater diversity of life from simpler forms to more complex forms and that transitional fossils (fishapods, frogamanders) exist at junctures that, chronologically, precede in one case, teleost fish and tetrapods and in the other case, frogs and salamanders. This is very largely corroborated by DNA studies, which reflect the similarities and differences in organisms and have given rise to divergence trees. That these trees mirror, to a very large extent, the fossil record is not exactly a smoking gun for universal common descent but it is pretty good model from which to work.

Hi experience was not entirely positive, however:
Anyway, Meyer spent a lot of time explaining why it matters that certain origin-of-life postulates are ineffective, but he never bothered to show that the current theories are in fact ineffective. What he did instead was attack a strawman (random flying-together of biological structures) at length, then erect a second one (a crude caricature of self-organization ideas) and attack it more briefly. Current thought focuses on the RNA World, and Meyer completely omitted any discussion of it. He meant to mislead the audience, and I think he was successful.
This straw man argument is not so unusual. While the Discovery Institute continually claims that evolutionary biologists put up straw men arguments about design, every single argument against evolution made by the writers there, from Phillip Johnson to William Dembski, takes the form of one. Steve's second and third posts should be up soon.

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Friday, May 21, 2010

Discovery Institute Claims Victory

The Discovery Institute is claiming victory in the recent symposium at Biola on May 14, in which Stephen Meyer faced his critics. In a post on Evolution News & Views, Rob Crowther writes:
The critics were Steve Matheson, a theistic evolutionist from Calvin College, and Arthur Hunt a Darwinist and biologist from the University of Kentucky. Both have written critically of SITC and intelligent design and were clearly not very enamored of the thesis of Meyer’s book, that the best explanation for the origins of biological information is that it comes from an intelligent source, a mind.

At least they started out seemingly unimpressed. I am certain Hunt remained so, but I’m not so sure about Matheson. He was critical to be sure, but in an amazingly candid and very revealing moment, he exposed his own presupposition that keeps him from accepting intelligent design theory.

Matheson basically conceded that ID is the best explanation currently on the table, but not one that he likes. Yes, he agreed, codes are produced by minds. Yes, there is digital code in DNA. Yes, design is a good explanation for that code. So, Meyer responded, you are admitting that the explanation I’ve offered, intelligent design, is currently best? The point wasn’t lost on the audience, or on Matheson I suspect.

Steve has not responded to this post—yet. Without the entire context, it is difficult to determine whether or not this is a fair representation of what Steve meant. It certainly puts the ball in his court.

Arthur Hunt, on the other hand, has written a somewhat technical response to the meeting here in which he suggests that Stephen Meyer conceded some very important points regarding specified information in proteins:
...if some protein functions do not require lots of specified information, then these should be quite accessible to what ID proponents would call “Darwinian mechanisms”. This concession has lots of ramifications – it renders Doug Axe’s suggestions about the isolation of functional proteins in sequence space somewhat less relevant, and it weakens the case (I suspect an important aspect of “Darwin’s Dilemma”) that a supposed requirement for new proteins during evolution (such as occurred in the Cambrian Explosion) makes such evolution improbable or impossible, at least without intelligent design. More generally, while it may be that absolute statements are not made by ID proponents, I think it important to have ID advocates backing down from claims or even hints that all (or even most) proteins have high specified information contents.
It has been a hall mark of William Dembski's research (if I am characterizing it correctly) that proteins have high levels of specified complexity and that evolutionary mechanisms cannot attain that level of complexity. Aside from the fact that in every instance, Dembski's modeling fails to duplicate real biotic environments, Hunt is correct that this is a major concession.

Thursday, May 20, 2010

Hominid Discoveries: Google Earth Helps Out

Apparently, subsequent to the recent discovery of Australopithecus sediba, Lee Berger used Google Earth to help map undiscovered caves in the vicinity of the find. As detailed on Mashable, here is a Google Video detailing the collaboration.


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Josh Rosenau Ponders on Todd Wood

Josh Rosenau has a long piece over at Thoughts from Kansas in which he examines Todd Wood's creationism and response to the new BIO-Complexity journal. Wood is hopeful about the new journal because it represents an effort, at last, of the ID establishment to put its money where its mouth is. Josh agrees, and then contrasts the ID movement with standard creationism. He writes:
The thing that's so shocking about the failure of all previous attempts at an ID journal is that the young earth creationist movement has actually done quite well at creating its own pseudoscientific infrastructure. They have several journals that imitate the peer-review of proper scientific journals. Sure, authors have to swear that their results won't contradict a fundamentalist reading of the Bible, and the actual arguments they make tend to fall apart once you start pushing on them, but many of the papers are quite sharp, and do a decent job of testing hypotheses within the straightjacket imposed on them by fundamentalist ideology.
While it is quite true that the modern-day recent earth creationist movement has a large infrastructure, their imitation of peer-review is a very poor one and is anti-scientific at its core. Rosenau is correct to call it a straightjacket but it results in a discipline that cannot even be called peer-reviewed because everyone that reviews the articles is sympathetic to them and, for the sake of the theology, doesn't dare disagree with them. This results in a skewing of the data in such a way that the results the results do not stand up to an even cursory examination. It also, as Randy Isaacs found out with the RATE project, results in intellectual dishonesty.

He continues:
In the past I've cited Wood as a reminder to anti-creationists that it's not enough to simply dismiss creationism as irrationality run amok. Wood's approach is rational, but premised on faulty assumptions. Rationality is dependent on the quality of the minds inputs and presuppositions, and some folks tend to wrongly claim that simply being rational would solve all our problems.

I also point it out in the hopes that Wood will, at some point, confront the special pleading he's using, and will realize that if he extends his arguments to their logical results, he'll have to abandon his creationism. His critiques of ID creationism and of old earth creationism are spot on, and if he'd only turn the same analytical approach toward his adherence to young earth creationism, interesting things might happen.
This is wishful thinking. Wood, at one point, addressing the nature of evidence, wrote:
As a point of application, I think modern creationists would be much better served if we stopped coddling their every doubt and fear with new "evidence for creation" and instead helped to wean them off evidence altogether. A truly close Christian walk with Jesus should render evidence irrelevant. This is where we really want to be, not buffeted about by the wind and waves but confidently walking through the storm with our eyes fixed unwaveringly on Christ.
As I have written before, I believe that this represents some sort of dualism in that the clear evidence from creation is not just rendered as secondary in importance, but ignored. The researchers of the RATE project found unequivocal evidence of over 500 million years of radioactive decay yet still managed to conclude that there was support for a young earth. Why? Because the evidence had to be subjugated to the theology. If, as Wood suggests, we should be called upon to "wean them off of evidence altogether," what does the evidence mean? Why would God create a beautiful and wondrous creation filled with majesty and awe only to have us ignore it?

One might argue that Wood means that we, as Christians, should focus entirely on our walk with God and not even bother at all with the questions of origins. For most people, this is an entirely appropriate perspective and it has always been my position that Christians should think carefully before exposing themselves to scientific areas that might affect their faith but for which there is little importance in their daily lives.

But we know from his other posts that Wood is a card-carrying recent earth creationist, who runs the Center for Origins Research at Bryan College. The focus of this research is "baraminology," which is the study of the search for the original created kinds. Their view of creationism is this:
Creationism isn't some modern, extremist anomaly. It was the dominant view of western culture and the church for nearly two millennia. From ancient commentaries on Genesis to medieval books on Noah's Ark to Renaissance monographs on Flood geology, we are seeking to recover the history of that intellectual domination.
Much is left out of this definition. For example, while creationism was the dominant view in western culture for nearly two millenia, what is not said is that once we began to acquire the tools to examine planet earth and the cosmos, beginning in the 1400s, creationism became less and less sustainable until, by the late 1800s, no practicing geologists and very few practicing clergy supported it. It was only the work of the Seventh Day Adventists in the early 1900s that led to a resurgence of this view, one that was (and is) totally without established scientific support. To recover that intellectual domination would carry scientific achievement back six hundred years and negate all of the advancements that have been acquired since then. Is this really what he wants?

It reminds me of something that Conrad Hyers once wrote, and I paraphrase: "if the Bible is found to be in accordance with science of the 20th century, it is necessarily out of accordance with the science of the 19th century and that of the 18th century and so on." Why does Wood presuppose that the science of six hundred years ago is the correct model?

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Wednesday, May 19, 2010

Mark Souder's Resignation

Congressman Mark Souder has resigned. Souder was a large supporter of abstinence education and conservative values. The problem: he was also an adulterer. Souder resigned after it came to light that he had an affair with one of his staff members. The GOP does not need this sort of publicity.

Lost amidst all of the fallout of this, though is that he was also a tireless crusader for intelligent design. As The Sensuous Curmudgeon writes:
The competition for “Biggest Idiot in Congress” is ferocious. Every galaxy-class fool in the US seems to be there, fighting for the title. But Souder easily stands out from the rest as being especially idiotic. He won our Buffoon Award for saying: “I personally believe that there is no issue more important to our society than intelligent design.” See: Buffoon Award Winner — Mark Souder, Creationist Congressman. [color in original]
It is clear from reading his writings that he knew little about evolution but felt that it dovetailed nicely with his "conservative values."This is, unfortunately, common among GOP political figures. As far as his adultery is concerned, I tend to view that sort of thing very dimly and have never found apologies by chastened public figures convincing. He knew what he was doing. Like Bill Clinton and Tiger Woods, he wasn't sorry for what he did. He was sorry he got caught. Good riddance and bad rubbish.

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New Early Reptile Identified

A find that was originally thought to be an early dinosaur has now been identified as an early reptile. A University of California Santa Barbara news release has this to say:
After scientists pieced together an entire skull of this 230-million-year-old azendohsaur –– a group known previously from just teeth and jaws –– these animals have now been aligned with a very early branch of the reptile evolutionary tree.

In a study published in the journal Palaeontology, UC Santa Barbara Earth Science professor Andre Wyss and other scientists concluded that many aspects of Azendohsaurus are far more primitive than previously assumed, which means that its plant-eating adaptations –– similar to those found in some early dinosaurs –– were developed independently.
This shows that the early reptiles diversified and adaptively radiated along side the dinosaurs. It also shows that as reptiles adapted and radiated to different niches, some adaptations were common in both dinosaurs and reptiles. This "adaptation" is common in biological organisms and shows up in the fossil record in numerous places.

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Monday, May 17, 2010

David Klinghoffer: Signature of Controvery

David Klinghoffer has taken it upon himself to defend Signature in the Cell, the book by Stephen Meyer on Intelligent Design. In a new online book Signature of Controversy, he has collected rebuttals of different individuals, including Stephen Meyer to the criticisms of the book. The Discovery Institute is providing it as a free download here. More on this later.

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Sunday, May 16, 2010

Douglas Theobald and Universal Common Ancestry

Douglas Theobald has written a technical paper on a test for universal common ancestry. The text of the paper is posted at Panda's Thumb, which also gives a short synopsis. Mike Steele and David Penny have also broken down the article here. They write:
So what is the signal in sequence data that provides the evidence for common ancestry? In essence, it is site-specific correlations in the amino acids between different species. These correlations fall off as the coalescence between lineages in a tree becomes deeper in the past, but if there are sufficient data, the correlations' cumulative significance becomes statistically strong. Conversely, if two lineages have completely separate origins, correlations between amino-acid site patterns in the corresponding two extant species vanish.
This article basically suggests, if I understand it correctly, that if species were independently created (think: *poof*), they would show smaller correlations in the coalescence results. This indicates that the further back you go, the sequence data shows common descent. As you go back in the fossil record and compare that to the genetic data of different species, certain protein sequences remain in common. Hat tip to Panda's Thumb.

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Friday, May 14, 2010

A Review of BIO-Complexity

Bounded Science reviews the new BIO-Complexity journal and its guidelines. He finds much wanting:
As long as scientists reject ID as supernaturalism, there will be none of the "scientific controversy over ID" referred to at BIO-Complexity. It seems that the forum is designed to get scientists, identified by their real names, to engage in highly restricted exchanges on ID that create the impression of genuine controversy. This could aid the Discovery Institute in its "teach the controversy" campaign, the objective of which is to get ID into the science curricula of public schools.
Barbara Forrest has identified four different tactics that are used by the intelligent design movement to further the goals of establishing the validity of intelligent design: 1. Teach the Controversy, in which it is asserted that there is disagreement within the scientific community about how effective evolutionary theory is at explaining past and present biodiversity, 2. Teach the full range of scientific views, in which it is asserted that both evolutionary theory and intelligent design are on equal footing and 3. critical analysis/thinking, in which teachers are encouraged to question the validity of evolution. As she correctly points out, we should always engage critical thinking in performing science. The goal here, though, is to poke holes in evolution while elevating ID, and 4. teach the strengths and weaknesses of evolution. This relies on usually specious arguments against evolution that have been rebutted time and again by the scientific community but which are continually promoted by ID supporters.

This new journal seeks to accomplish all of the goals at once. The ID community has long argued that since the scientific community is not willing to engage it in examining the strengths and weaknesses of evolutionary theory or to deign to debate ID as if it were on an equal footing with evolutionary theory that they have taken the moral high ground. The problem with this stance is that it relies on some patently false positions such as the claim that there is disagreement within the biological community about evolution (the dissent from Darwin list), there are no transitional fossils, that the Cambrian explosion reflects creation by divine fiat and not evolution, and that evolution lacks explanatory power. None of these have been shown to have any scientific merit and yet they are continually promoted by design supporters. As I mentioned in an earlier post, there are only two ways in which this would work and the Discovery Institute does not seem interested in pursuing either path.

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Wednesday, May 12, 2010

Updates on the John Freshwater Case

Panda's Thumb updates us on the continuing John Freshwater case in Mount Vernon, Ohio. Freshwater, if you remember, has been accused of teaching creationism and branding students' arms with crosses. There is, apparently, a revolving door of attorneys.

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X-Ray Images of Archaeopteryx Show Original Chemistry

In the "Way Cool" department, bright x-ray images of Archaeopteryx have revealed that part of the original bone chemistry still exists. In an article in ThaiIndian, this is reported:
The discovery could revolutionise the field of palaeontology says the team led by scientists at the University of Manchester and the Department of Energy’s SLAC National Accelerator Lab in the US.

By recording how ‘bright X-rays’ interacted with the fossil, the team have created maps showing chemical elements which were part of the living animal itself.

The maps show that portions of the feathers are not merely impressions of long-decomposed organic material — as was previously believed.

Instead, they include fossilised fragments of actual feathers containing phosphorous and sulphur, elements that compose modern bird feathers.

Trace amounts of copper and zinc were also found in the dinobird’s bones: like birds today, the Archaeopteryx may have required those elements to stay healthy, said a Manchester release.
Despite the fact that "SLAC National Accelerator Lab" is redundant (SLAC stands for "Stanford Linear Accelerator"), this is yet more evidence that despite having mostly dinosaurian characteristics, Archaeopteryx had some crucial derived traits that support its transitional status. As Prothero1 notes, there have been five different kinds of feathers identified in the fossil record on various dinosaurs and early birds. The next step is to see when true flight feathers evolved.

1Prothero, D. 2007. Evolution: What the fossils say and why it matters. Columbia Univ Pr.

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Tuesday, May 11, 2010

Pete Enns on the Creation Stories of Genesis

Pete Enns has an excellent series on the creation stories in Genesis over at BioLogos. The first of these is here. He has since expanded the series into three posts. The true value of these posts lies, of course, in that they show us how Genesis was written down and what is likely the proper way to interpret it. He writes:
The book of Genesis includes two very different creation stories. The first, “Genesis 1” runs from verse 1:1 to the middle of 2:4 (2:4a). The second, “Genesis 2,” runs from verse 2:4b to 2:25.

Beginning in the 18th century, European Old Testament scholars discussed this point in earnest. The next two centuries brought the discovery of numerous creation stories from ancient Mesopotamia, Egypt, and Canaan. With the discovery of these creation stories, scholars could now see clear evidence to support a nonliteral reading of the Genesis texts, since each biblical story shares characteristics of different Near Eastern stories.
Pete's analyses and those before his give us a clear understanding of the role of humans and their relationship to God. This is a spiritual relationship and the entire purpose of both creation stories is to tell us that God dwells on high but that He created humans to be among them. There is no science here and those who interpret Genesis 1 and 2 that way completely miss the point.

That these and other analyses will be ignored by the leading young earth creation sites is a given. Such analyses are, in a sense, time-inspecific. In this construct, when the earth was created is almost irrelevant, as is how it was created. How humans appeared is only important in the sense of the fact that they are created by God to relate to him. These chapters show that they are not scientific accounts of anything.

I have often thought that this kind of analysis should be central to Sunday school teaching about how we are to relate to God such that the richness of the scripture can be felt. It might also be a way of alerting people to the scriptural vacuity of young earth creationism.

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Two New Articles From Science and a Walk Through Modern Human Origins

Science Magazine is providing two new articles about the Neandertal genome to all interested parties. The articles, along with a bit of backstory can be accessed here. Here is part of the conclusion from the Green et al. article:
The analysis of the Neandertal genome shows that they are likely to have had a role in the genetic ancestry of present-day humans outside of Africa, although this role was relatively minor given that only a few percent of the genomes of present-day people outside Africa are derived from Neandertals.
I was raised in the "regional continuity" school of modern human origins and tend to view early modern human archaic retentions as reflecting Neandertal ancestry of sorts. Historically, Neandertals have been given the taxonomic status Homo sapiens neandertalensis, as opposed to Homo sapiens sapiens, which is what modern humans are. Implicit in this is that the behavior and appearance of Neandertals was not sufficiently different from us to warrant a separate species designation.

Several studies done in the late 1980s and early 1990s seemed to cast a disparaging light on this interpretation. Branching analysis by Cann (1988) and Krings et al. in 1997 on the mitochondrial DNA of modern humans indicated strongly that modern humans had originated as a speciation event in sub-Saharan Africa between 140 and 280 thousand years ago and had replaced the modern humans they came into contact with as they migrated north. This gave rise to the removal of the "sapiens" part of the taxonomic name of Neandertals.

Having their backs against the wall, the regional continuity folks had to rely on the not-inconsequential evidence from skeletal morphology and archaeology which seem to indicate a level of continuity between Neandertals and modern humans. My Ph.D. work showed that this level of archaicness in the early modern human sample was systematically underplayed by those espousing replacement of Neandertals and that several specimens routinely considered to be modern humans were only barely so.

Then David Maddison et al. showed in the early 1990s that some of the original studies done isolating modern humans from all that had come before were not run correctly. They showed, instead, that branches that called for the origins of modern humans in other parts of the Old World were equally parsimonious with the African branch. Relethford (1991), further, suggested that, while the Krings et al analysis showed a difference between modern humans and Neandertals, there was no way to really know how much of a difference constituted a separate species.

There have been three sort of competing hypotheses regarding regional continuity. Wolpoff and others (1989, 2001, 2003) have argued that modern human arose through gene flow between different areas of the Old World. Bräuer (1990) and Smith (2005) have developed independent models involving an "assimilation" of the Neandertals into the modern populations in which limited but measurable gene flow existed between the two. It now seems that one of those models is correct.

Literature Cited

Bräuer, G. and K. Rimbach (1990). "Late archaic and modern Homo sapiens from Europe, Africa, and southwest Asia: Craniometric comparisons and phylogenetic implications." Journal of Human Evolution 19(8): 789-807.

Cann, R. (1988). DNA and human origins. Annual Review of Anthropology, 17(1), 127-143.

Krings, M., Stone, A., Schmitz, R., Krainitzki, H., Stoneking, M., & Pääbo, S. (1997). Neandertal DNA sequences and the origin of modern humans. Cell, 90(1), 19-30.

Maddison, DR, Ruvolo, M and Swofford, DL (1992) Geographic Origins of Human Mitochondrial DNA: Phylogenetic Evidence from Control Region Sequences. Systematic Biology 1992 41(1):111-124; doi:10.1093/sysbio/41.1.111

Relethford, J. (2001). Ancient DNA and the origin of modern humans. Proceedings of the National Academy of Sciences 98(2): 390.

Smith, F., I. Jankovic, et al. (2005). "The assimilation model, modern human origins in Europe, and the extinction of Neandertals." Quaternary international 137(1): 7-19.

Wolpoff, M. and E. Trinkaus (1989). "The place of the Neandertals in human evolution." The Emergence of Modern Humans: Biocultural Adaptations in the Later Pleistocene: 97–141.

Wolpoff, M., J. Hawks, et al. (2000). "Multiregional, not multiple origins." American Journal of Physical Anthropology 112(1): 129.

Wolpoff, M., J. Hawks, et al. (2001). "Modern human ancestry at the peripheries: a test of the replacement theory." Science 291(5502): 293.

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New Paper at BIO-Complexity

A new paper at BIO-Complexity is up. It is called "Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness." It is heavily biochemical in nature and is going to take some time to digest. The paper is described by Jay Richards as a "take-home lesson." All of the authors are employed at the Biologic Institute.

Monday, May 10, 2010

More on the Neandertal/Modern Link

The Independent has an article on the Neandertal/modern human link, called Making Woopee with Neandertals. Steve Connor writes:
The latest study aimed at answering this question suggests the latter – when Neanderthal man met Homo sapiens woman it resulted in what scientists euphemistically call "gene flow". It seems that this interbreeding, which probably took place somewhere in the Middle East when the first modern humans migrated out of Africa, has resulted in a little bit of Neanderthal in all of us today with a non-African ancestry.
The story also shows how hard it can be do science:
This enabled them to compare the Neanderthal genome with that of five modern-day people from around the world, and, to Paabo's astonishment, Neanderthal DNA sequences were found in the genomes of the three people who lived outside Africa. Paabo freely admits that he was biased against such a finding. His earlier work on mitochondrial DNA suggested no such interbreeding between Neanderthals and modern humans, so his initial reaction was that the data had to be a statistical fluke, or erroneous.

But it is a measure of greatness in science if you can accept something that you had previously rejected, when faced with new and convincing evidence.

Comparisons between the genomes of modern humans and the Neanderthals clearly indicated that there was a small but significant amount of interbreeding early in the evolutionary history of Homo sapiens, most probably after our species had first emerged from Africa between about 80,000 and 50,000 years ago. Other scientists, such as Professor Joao Zilhao of Bristol University, who has long argued that there was close cultural and biological interaction between Neanderthals and modern humans, can rightly feel vindicated for their somewhat unfashionable stance.
This shows two things:

1. it shows how science can and should be done. New information should always be incorporated into the existing framework of a particular discipline. On one side of the fence, there is the perspective that Neandertals were replaced by early modern humans that came from North Africa. On the other side is the idea that Neandertals interbred with the incoming moderns and that the modern Europeans are a result of this hybridization. Maybe the answer lies somewhere in between. As Jan Simek once put it, maybe there was hybridization here in this valley but replacement two valleys over. It is becoming increasingly clear that the transition to modern humans was neither simple nor quick.

2. it shows how stark the contrast between conventional science and young earth creationism really is. For YECs, there are no new ideas or hypothetical constructs to be tested. Data that does not fit the model must be shoehorned, twisted or distorted to fit or else be ignored, as much data is. The ability to take a favored concept or theory and rethink it based on new ideas or new information is the hallmark of science, not creationism.

This new finding shows how science progresses and how only by adding the new information to the mix will we ever be able to understand the transition to modern humans. As such, it enriches our understanding of modern human ancestry in particular and the universe in general.

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Neandertal, Early Modern Hybridization

The Telegraph has a story about research indicating a shared history between Neandertals and early modern humans. This story appeared a few days ago in the New York Times. I did not link to this. Richard Alleyne, the Telegraph science correspondent writes:
Human-Neanderthal relations occurred as the first pioneering bands of homo sapiens ventured out of Africa, scientists believe.

When they reached the Middle East they ran into groups of Neanderthals who preceded them and it is now thought that they mated.

The discovery emerged from the first attempt to map the complete Neanderthal genetic code, or genome. It more or less settles a long-standing academic debate over interbreeding between separate branches of the human family tree.

Evidence in the past has pointed both ways, for and against modern humans and Neanderthals mixing their genes.
This is support for the contention of Erik Trinkaus that the Lagar Velho burial in Portugal reflects hybridization, as well as the findings of Dave Frayer and Fred Smith, who have long argued that the early modern humans in Europe from Mladec, Stetten, Predmosti and several other sites have traits present in their Neandertal antecedents from the area. This will certainly add fuel to the fire in the continuity/replacement debate concerning the appearance of modern humans.

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Thursday, May 06, 2010

Stephen Meyer Faces His Critics: Update 2

I received this note from the Apologetics Department at Biola University about the possibility of getting a transcript of the panel discussion on May 14. Here is what they say:
Hello James,

Thank you for your note. While we will not have a transcript of the evening available, we are recording the event and it will be available to purchase as a DVD. To place your order, please call our office at 562.906.4570. Let me know if you have any questions!

Kristen Anderson
Administrative Assistant
M.A. in Christian Apologetics
Biola University
(562) 906-4570

BIO-Complexity: A New Journal

The Discovery Institute is promoting a new peer-reviewed journal, BIO-Complexity, which is funded by the Biologic Institute, an arm of the Center for Science and Culture. Here is the mission statement:
BIO-Complexity is a peer-reviewed scientific journal with a unique goal. It aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life. Because questions having to do with the role and origin of information in living systems are at the heart of the scientific controversy over ID, these topics—viewed from all angles and perspectives—are central to the journal's scope.
Jay Richards has written a story about the new journal on the Discovery Institute's main site in which, along the way, they commit another terminological inexactitude.One of the major complaints voiced by those espousing ID is that they cannot get heard. Richards claims that the peer review process is a Catch-22 because, while an article has to face review and revision, if it has a hint of "design" it is rejected. He writes:
But surely, you might ask, there’s an open-minded editor at some journal somewhere who would give ID a fair shake? I do know of one such editor, Richard Sternberg, who several years ago sent out for review an article by some guy defending a design perspective and then, when the article passed peer-review, Sternberg published it. If there are any remaining open-minded editors willing to send out similar articles for peer-review, the Sternberg affair reminds them what will happen if they do.
This account is wholly and completely false. Here, in fact, is what happened.
  • Stephen Meyer (some guy) wrote a paper on the Cambrian Explosion called The origin of biological information and the higher taxonomic categories, which showed up in the Proceedings of the Biological Society of Washington in 2004. The paper was reviewed quite negatively in many places, Panda's Thumb being one, the Paleontological Association being another.
  • Richard Sternberg handled the entire editorial process himself. He claims that he sent the paper out to several individuals to read but has never identified who these people were.
  • A statement issued by the Council of the Biological Society of Washington, the publishers of the journal states that the paper never would have made it through the review process had it been done so correctly. It reads:
    The Council, which includes officers, elected councilors, and past presidents, and the associate editors would have deemed the paper inappropriate for the pages of the Proceedings because the subject matter represents such a significant departure from the nearly purely systematic content for which this journal has been known throughout its 122-year history.

  • The paper was withdrawn subsequent to publication when it was pointed out that the quality of the science was unacceptable.
Following the Sternberg affair, the American Association for the Advancement of Science issued a statement on Intelligent Design. All the Sternberg affair should tell prospective article writers is what happens when the proper procedures for peer review aren't followed. The whole publication of the article has the appearance of having been done "under the table." It is not encouraging that a writer for the Discovery Institute cannot get the basic facts right regarding so prominent an incident.

Beyond this, however, there is a further, perhaps deeper problem inherent in this whole endeavor. Much of Richards' post (and indeed much of the writings of most ID supporters) laments the fact that intelligent design cannot get a "fair shake" in the academic community as a whole and that, with the advent of this new journal, things will be different.

Why, then, is the editorial board composed almost entirely of Discovery Institute fellows or people that are already known to be sympathetic to the intelligent design argument? The editorial board for the journal consists of thirty individuals. This list includes Michael Behe (Darwin's Black Box, The Edge of Evolution), Scott Minnich, William Dembski (No Free Lunch), Richard Sternberg, Robert Marks, Jonathan Wells (Icons of Evolution) and Douglas Axe to name a few.

This is how the review process is set up:
Manuscripts submitted as Research Articles or Critical Reviews that fall within the stated scope and adhere to the journal's standards of originality, clarity, format, and tone are assigned to a member of the Editorial Board for peer review. Two or more reviewers will be consulted for each reviewed manuscript. Authors are encouraged to suggest suitable reviewers, though the Editor may elect to use other reviewers.
Now here's the real catch-22 situation: in order to gain much needed credibility, the BIO-Complexity editorial board must employ reviewers that are well-known in the biological community and can competently vet (or not) a given paper. Without this assurance, the scientific community will have no way of knowing how any given ID-supportive paper was reviewed and no credibility will have been gained. This is exacerbated by the fact that the Discovery Institute does not have a good track record in published literature supporting intelligent design.

To give up the identity of the reviewers, on the other hand, compromises the "anonymous reviewer" aspect of the process. Compounding this might be the reluctance of many well-respected biologists to want to be known as having reviewed an ID-supportive paper.

This was all gone about the wrong way. One way that this could have worked is if an isolated researcher without ties to the Discovery Institute decided to start a new biocomplexity journal and recruited known experts in the field. Then, and only then, could papers be submitted in an impartial way and only then would ID stand on its own merits. The way BIO-Complexity is currently set up, with a heavily pro-ID editorial board, it already looks like the fix is in.

What would they do with a paper that is sent out to an anonymous reviewer who tears it up? The only paper in recent memory other than the Meyer 2004 paper that has attempted to support intelligent design in an academic setting is the Dembski/Marks paper from a few months back which was criticized (here and here) as having little bearing on biological systems and mathematically unsound.

The only other way that this would work is if competent scholars in biological complexity were to submit papers. Then the journal would probably get a wide variety of papers, some supportive of ID (maybe) and some not. Even if some of them were not supportive, though, the board would be foolish not to publish them. If it only accepted ID friendly papers which were then reviewed by the biological community as a whole and found wanting, it would be another nail in the coffin for the scientific argument for ID.

The Discovery Institute have set themselves up a huge task here and are finally putting their cards on the table. Lets see what kind of hand they have.

Stephen Meyer to Face His Critics: Update

Somehow, I linked to the wrong description of the event that I posted about yesterday. Here is the correct announcement:
Dr. Stephen Meyer has written a book that is shaking the evolutionary establishment like “Darwin’s Black Box” and “Evolution: A Theory in Crisis” did in previous decades. Meyer has assembled a set of ideas based on the latest research on living cells that must be answered if traditional Darwinism is to survive. So we have assembled a powerful group of credentialed critics of Meyer’s “Intelligent Design” position to let him have it with both barrels. No hiding in dark libraries or murky laboratories - if Meyer has the goods, he needs to debate his toughest critics face to face! In addition, we will be screening some clips of the latest Illustra Media DVD titled “Darwin’s Dilemma” and providing free copies to each family who attends.
I have just heard from Steve Matheson, who will be on the panel. Steve is no friend of Signature in the Cell, Stephen Meyer's most recent book, so I suspect it will be a lively time.

BTW, the event description that I accidentally linked to takes place the following day and is called "The Cambrian Explosion: The Data Behind Darwin's Dilemma." It is hosted by "Paul Nelson, Rick Sternberg, Doug Axe, Stephen Meyer, John Bloom, and more."

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Wednesday, May 05, 2010

Stephen Meyer to Face His Critics

Stephen Meyer is to lead a panel discussion on "Darwin's Dilemma," that there appears to be evidence against "Darwinism" being the explanation for the Cambrian Explosion. Here is the Discovery Institute's Announcement:
The “Cambrian Explosion” is one of the most difficult and dynamic counterexamples to Darwinian evolution that the fossil record has ever revealed. We have assembled a group of experts in the field to talk in detail about this “hard evidence” that cannot be easily dismissed by proponents of Darwinism. Most of our speakers are those featured in the DVD “Darwin’s Dilemma.” So come and hear the scientists themselves expound upon the data.
The event is going to held at Biola University, in La Mirada, California, on May 14. For those of us without the bus fare, it would be nice if a transcript of the event was published, especially since Dr. Meyer rarely answers his critics in print. I will write Mr. Luskin to see if that can be done.

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Monday, May 03, 2010

Steve Matheson, Signature in the Cell and a Persistent Misunderstanding on the Part of the Discovery Institute

Steve Matheson has posted his reviews of chapters 9 and 10 of Stephen Meyer's Signature in the Cell. It does not start well. He writes:
Chapter 9 is called "Ends and Odds." Chapter 10 is "Beyond the Reach of Chance." Between them, they advance a straw man so idiotic that I wonder whether Meyer will be able to reclaim any significant intellectual integrity in the chapters that follow.
Matheson's point is that Meyer has gone to great lengths to argue that complex biological systems are too intricate to have arisen by chance. The problem is that this is exactly what Richard Dawkins argued in The Blind Watchmaker, in 1986. Dawkins wrote in that book that selection doesn't act all at once but rather in steps so that organisms become better adapted to their environments gradually. This is not random and does not happen by chance (Hence the METHINKSITISAWEASEL program). Yet, that is exactly what Meyer is arguing again.

This central failing of the book was addressed by Francisco Ayala, who wrote:
The keystone argument of Signature of the Cell is that chance, by itself, cannot account for the genetic information found in the genomes of organisms. I agree. And so does every evolutionary scientist, I presume. Why, then, spend chapter after chapter and hundreds of pages of elegant prose to argue the point? It is as if in a book about New York, the author would tell us that New York is not in Europe, and then dedicate most of the book to advancing evidence that, indeed, truly, New York is not in Europe.
What, then, is Meyer's point? Is this a misunderstanding of evolution on a phenomenally basic level? Beginning evolutionary biology students are taught that selection is not random and yet this seems to have completely escaped Meyer and the other writers at the Discovery Institute.

This sort of straw man is echoed in William Dembski's writings, in which he he equates genetic variation with a mathematical fitness function to show that evolution cannot create new forms. As I wrote about this:
Basically, he is stating that genetic variation, left to its own devices, won't turn up anything complex no matter how many iterations it goes through. In this instance, all fitness functions are averaged. Here's the problem: in no environment are fitness functions averaged. That is like saying that the earth has one climate all over and that it imposes no selection pressures.
This has been echoed by other writers and Dembski has never responded to this criticism. It is as if the concept of natural selection is completely foreign or is so repugnant as to be unacceptable and therefore, the DI writers continue to misunderstand it.

The problem that I have with this perspective is that this misunderstanding of natural selection has not gone uncorrected. Kenneth Miller, Richard Dawkins, P.Z. Myers, Jerry Coyne, Steve Matheson and Darrel Falk, just to name a few have written treatises strongly rebutting this position held by Meyer, Dembski and Michael Behe. These have been ignored. Therefore, to continue to promote this misunderstanding of natural selection and its role in evolution constitutes, as they say, a terminological inexactitude. This would not be the first time the Discovery Institute was accused of that.

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John Freshwater Case Drags On

The hearing for John Freshwater in the Mount Vernon Township in Ohio may drag on much longer than anticipated. Dean Narciso of the Columbus Dispatch writes:
Participants hope to wrap up a hearing on whether John Freshwater should keep his teaching job by sometime in June, but sessions could resume next fall, they said yesterday.
It is not clear how this case will affect other student/teacher incidents across the country, but to drag this out helps no one.