In the Darwinist community there’s a general acceptance, however uneasy, of the necessity of speaking in design-related metaphors to describe features of organisms. Such language may be regrettable since it attracts the attention of the bogeyman, “creationism,” but really it’s kind of unavoidable. In Darwin and Design, Michael Ruse sought to offer solace to fellow Darwinians. He asked,

We still talk in terms appropriate to conscious intention….In biology, we still use forward-looking language of a kind that would not be deemed appropriate in physics or chemistry. Why is this?

His answer:

Organisms, produced by natural selection, have adaptations, and these give the appearance of being designed.…If organisms did not seem to be designed, they would not work and hence would not survive and reproduce. But organisms do work, they do seem to be designed, and hence the design metaphor, with all the values and forward-looking, causal perspective it entails, seems appropriate.

So it’s precisely because organisms are not really designed, but rather built up by natural selection, that they seem designed. Well, comfort must be taken where it’s available.

Unfortunately for the Darwin faithful, the discomfort level keeps getting kicked up notch by notch as the design metaphor proves itself increasingly useful to bioengineers -- as a model to be instantiated in very practical, not merely literary, ways. If you were to imagine that life really does reflect an intelligent purpose, then that purpose would probably be reflected somehow in the genetic material, coded in DNA. So it’s of interest that a couple of new projects seek to be in relationship to DNA what your local auto parts store or catalogue is to the cars we drive. Keep in mind that cars and their parts are designed products. The Scientist has an item noting the launch of a “DNA factory.”

Need a gene promoter? You may soon be able to order one from a catalog. California synthetic biologists are launching a production facility that will provide free, standardized DNA parts for scientists around the world.

The project, called BIOFAB: International Open Facility Advancing Biotechnology -- or just BIOFAB for short -- aims to boost the ease of bioengineering with "biological parts" that are shared resources, standardized and reliable enough that they can be switched in and out of a genome like electronic parts in a radio. If BIOFAB's vision is realized, researchers will be able access an online registry and simply order what they need.

Meanwhile a not-for-profit foundation, BioBricks, seeks to make standard DNA parts available:

Using BioBrick™ standard biological parts, a synthetic biologist or biological engineer can already, to some extent, program living organisms in the same way a computer scientist can program a computer. The DNA sequence information and other characteristics of BioBrick™ standard biological parts are made available to the public free of charge currently via MIT's Registry of Standard Biological Parts.

Normally, with language, it’s the way of metaphors to develop from things in the real world that in turn lend themselves, through a certain limited similarity, to describing other things. So you start with a real chicken or a real fox, which in turn lend their names to a cowardly person or an attractive one. Here, what’s happened appears to be just the reverse: first comes the metaphor -- which is only a metaphor, remember -- and only then the instantiation into objects in the real world. Can you think of another instance of a mere metaphor behaving so strangely? I can’t.

We’ll resist the temptation to draw the obvious conclusion that speaking of the DNA sequence., a metaphor -- at all. Sorry, I guess we didn’t resist that temptation after all.

Posted by David Klinghoffer at 12:23 AM | Permalink | TrackBacks (0)

Download the full "Truth or Dare with Dr. Ken Miller" Lecture Guide Permission Granted to Copy and Distribute for Educational Use.

Ken Miller has been making the same objections about irreducible complexity and the bacterial flagellum for a long time. In his Dover testimony, his book Only a Theory, and in other writings he argues that irreducible complexity for the flagellum is refuted because about 10 flagellar proteins can also be used to construct a toxin-injection machine (called the Type-III Secretory System, or T3SS) that some predatory bacteria use to kill other cells. Miller may even boast that Judge Jones ruled that the T3SS explained how the bacterial flagellum could evolve: “[W]ith regard to the bacterial flagellum, Dr. Miller pointed to peer-reviewed studies that identified a possible precursor to the bacterial flagellum, a subsystem that was fully functional, namely the Type-III Secretory System.”³³

However, there are strong reasons to doubt these hypotheses.

First, leading biologists argue that phylogenetic data implies the T3SS could not have been a precursor to the flagellum.³⁴ As New Scientist reported:

One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. "The most parsimonious explanation is that the T3SS arose later," says biochemist Howard Ochman at the University of Arizona in Tucson.³⁵

Second, the T3SS is composed of only about ¼ of the proteins in the flagellum, and does not help one account for how the fundamental function of the flagellum—its propulsion system—evolved. The unresolved challenge that the irreducible complexity of the flagellum continues to pose for Darwinian evolution is starkly summarized by William Dembski: “At best the T[3]SS represents one possible step in the indirect Darwinian evolution of the bacterial flagellum. But that still wouldn’t constitute a solution to the evolution of the bacterial flagellum. What’s needed is a complete evolutionary path and not merely a possible oasis along the way. To claim otherwise is like saying we can travel by foot from Los Angeles to Tokyo because we’ve discovered the Hawaiian Islands. Evolutionary biology needs to do better than that.”³⁶

Dembski’s critique is apt because it recognizes that Miller wrongly characterizes irreducible complexity as focusing on the non-functionality of sub-parts. In contrast, Behe properly tests irreducible complexity by assessing the plausibility of the entire functional system to assemble in a step-wise fashion, even if sub-parts can have functions outside of the final system. The “leap” required by going from one functional sub-part to the entire functional system is indicative of the degree of irreducible complexity in a system. Contrary to Miller’s assertions, Behe never argued that irreducible complexity mandates that sub-parts can have no function outside of the final system.

Miller misconstrued the proper way of testing irreducible complexity, and his argument amounts to this: if my laptop’s power cord could also be used to power my toaster, then my laptop is no longer irreducibly complex. Because a laptop requires a number of parts necessary for function, this is preposterous. So is Dr. Miller’s straw method of testing irreducible complexity, as illustrated in the following 2 diagrams:

Figure A: Consider an irreducibly complex functional arch, divided up into many pieces, including s and t: Figure B: Take away the keystone of the arch, t, and the arch falls down. But piece s may be left standing: Does the fact that part of the arch, s, remains standing imply that the rest of the arch is not irreducibly complex? Of course not. In the same way, the fact that a fraction of the flagellum helps form a T3SS does not imply that the flagellum itself is not irreducibly complex. To refute irreducible complexity, Dr. Miller would have to show how a fully functional flagellum could form in a step-by-step fashion. He hasn’t shown anything close to that.

In contrast, pro-ID microbiologist Scott Minnich has properly tested for irreducible complexity through genetic knock-out experiments he performed in his own laboratory at the University of Idaho. He presented this evidence during the Dover trial, which showed that the bacterial flagellum is irreducibly complex with respect to its complement of thirty-five genes. As Minnich testified: “One mutation, one part knock out, it can't swim. Put that single gene back in we restore motility. Same thing over here. We put, knock out one part, put a good copy of the gene back in, and they can swim. By definition the system is irreducibly complex. We've done that with all 35 components of the flagellum, and we get the same effect.”³⁷

Moreover, Scott Minnich explained that even if Miller’s speculative scenario turned out to be true, it would not be sufficient to prove a Darwinian explanation for the origin of the flagellum because there is still a huge leap in complexity from a T3SS to a flagellum. Unfortunately, Judge Jones ignored Scott Minnich’s research and testimony supporting irreducible complexity of the flagellum, and instead ruled that Miller refuted the irreducible complexity of the flagellum. Ironically, a review article in Nature Reviews Microbiology the following year admitted that “the flagellar research community has scarcely begun to consider how these systems have evolved.”³⁸ Did Miller actually demonstrate the flagellum could have evolved by Darwinian evolution?

G. Truth or Dare: Why does Dr. Miller promote an improper way of testing for irreducible complexity and misconstrue Behe’s theories as prohibiting the use of sub-parts in other systems? Has Dr. Miller actually provided anything close to a complete evolutionary pathway for the origin of the flagellum? Has anyone done this? How does Miller’s evidence refute Scott Minnich’s genetic knockout experiments which show the flagellum is irreducibly complex with respect to its complement of about 35 genes?

[Editor's Note: Ken Miller speaks regularly on intelligent design (ID), and for years has repeatedly promoted the same misrepresentations of ID when speaking on the topic. This is Part 5 of a series of 7 posts that comprise a lecture guide for those listening to lectures by Dr. Miller against ID. When this series is complete, the entire lecture guide will be released as a single document.]

References Cited:
[33.] Kitzmiller v. Dover ruling, p. 76

[34.] See Milton H. Saier, Jr., "Evolution of Bacterial Type III Protein Secretion Systems," Trends in Microbiology 113:12 (2004).

[35.] Dan Jones, "Uncovering the evolution of the bacterial flagellum," New Scientist (Feb 16, 2008).

[36.] Dembski, Rebuttal to Reports by Opposing Expert Witnesses, p. 52

[37.] Day 20 PM Testimony, pp. 107-108.

[38.] Pallen & Matzke, “From The Origin of Species to the Origin of Bacterial Flagella,” Nat. Revs. Microbiology, Vol. 4:788 (2006).

Posted by Casey Luskin at 11:31 AM | Permalink | TrackBacks (0)

In Segraves v. California, a California state court found it legal for a public school to teach evolution. Now, if only California’s anti-dogmatism policy would likewise protect teachers who inform students about scientific dissent from neo-Darwinian evolution.

Update: For those who protest me discussing this case, I want to note that I would not have even known of this case were it not for the fact that the NCSE has been touting it and citing it for years on its Ten Major Court Cases about Evolution and Creationism page.

1. Summary

Plaintiff Kelly Segraves, a parent of children in California public schools, challenged the California State Board of Education's Science Framework that mandated the teaching of evolution.⁸⁴ Segraves alleged that the mandatory teaching of evolution prevented both himself and his family from freely exercising their religion.⁸⁵ Although the California Superior Court accepted that evolution was incompatible with the Segraves' religious beliefs, the Court held that California's anti-dogmatism policy provided sufficient accommodation for their views.⁸⁶ This policy stated that discussions about origins were intended to emphasize that scientific explanations are more about the processes of nature rather than ultimate causes.⁸⁷ The court stressed that scientific discussions should be focused on how life began and evolved and not on the ultimate cause of life's origin.⁸⁸

2. Importance and Commentary

Similar to Wright and Crowley, the Segraves decision holds that learning about evolution in public schools does not infringe upon the free exercise of religion.⁸⁹ Segraves also recognized that evolution can violate the religious beliefs of students and other members of the community, and the court emphasized the importance of embracing tolerance when dealing with such controversial subjects.⁹⁰ Under this reasoning, it is presumable that California’s “anti-dogmatism policy” would protect the teaching of any scientific theory, even if it offended the views of some citizens. This opinion is of minimal value as precedent, as it comes from a lower state court and was never officially published as a legal opinion.⁹¹ Nonetheless, it implies that evolution education policies may avoid establishing religion when they are based upon the legitimate secular purpose of avoiding dogmatism in the classroom.

[Editor’s Note: This survey of Segraves v. California is an excerpt from the article “Does Challenging Darwin Create Constitutional Jeopardy? A Comprehensive Survey of Case Law Regarding the Teaching of Biological Origins,” Hamline University Law Review, Vol. 32(1):1-64 (Winter, 2009), published by Hamline University School of Law. This excerpt covers the case Segraves v. California; the full article can be read here.]

References Cited
[84.] Segraves v. California, No. 278978 (Super. Ct. Sacramento County 1981)
[85.] Id.
[86.] Id.
[87.] Id.
[88.] Id.
[89.] Athens/1618/Segraves_vs._California.html.”>Segraves v. California, No. 278978
[90.] Id.
[91.] Id.

Posted by Casey Luskin at 8:04 AM | Permalink | TrackBacks (0)

The silence is only eerie if you try to listen too hard. Efforts to confirm that there is intelligence elsewhere in the universe have, to put it mildly, fizzled. Each new theory about why we can’t find intelligent life anywhere else in the universe ends up like a damp firecracker: there’s a bunch of crackling in the blogosphere, but there’s never any bang.

So. It seems that Paul Davies has published the equivalent of a benign stick of TNT reiterating all the failed attempts, and then coming up with a few new zany ideas. Instead, he might consider reading in Signature in the Cell about the evidence for intelligent design that booms out of DNA right here on this planet.

The Eerie Silence: Renewing Our Search for Alien Intelligence Paul Davies. Houghton Mifflin Harcourt, $27 (288p) ISBN 978-0-547-13324-9 In what has become known as Fermi's Paradox, the great nuclear physicist Enrico Fermi once asked, if there are aliens out there, where is everybody? After 50 years of looking, the SETI (Search for Extraterrestrial Intelligence) project has likewise failed to find anybody. Cosmologist Davies (The Mind of God), winner of the 1995 Templeton Prize, believes that SETI's search for narrow-band radio signals from planets around other stars needs to be broadened to look for other possible signs of life. Aliens may be using far more advanced technology than radio to signal the cosmos, such as manipulating pulsars to act as beacons or even neutrino signaling. Davies also puts forth the possibility that alien probes may be silently trolling the solar system. The author surveys popular topics in science fiction such as Dyson spheres, time travel, and wormholes, and decides that they're not feasible under physics as we understand it. He concludes with a far-ranging look at what might happen here on Earth when we make first contact. Highly recommended for both science fiction and astronomy buffs. Illus. (Apr. 13)

Posted by Robert Crowther at 11:14 AM | Permalink | TrackBacks (0)

What would be evidence against evolution, and very strong evidence at that, would be the discovery of even a single fossil in the wrong geological stratum….But not a single solitary fossil has ever been found before it could have evolved.

Richard Dawkins (2009, pp. 146-7)

Professor Dawkins is right: you can’t be older than your own grandfather, all country-western songs notwithstanding.

But he is wrong about out-of-order fossils. As the recent excitement about the tetrapod trackways in Poland illustrates, the relationship between stratigraphic position -- i.e., where in the geological column a fossil group occurs -- and phylogenetic position -- i.e., where cladistic analysis predicts the group should occur -- is anything but straightforward. Indeed, the concept of a “ghost lineage” (see below) was introduced nearly 20 years ago by paleontologist Mark Norell, to accommodate the frequent lack of congruence between fossils and cladograms. Grandpa and grandma fossil are often too young, and grandchildren too old. (Actually these are mixed-up sister group, not ancestor-descendant, relationships, but I really wanted to use that Ray Stevens song link, and “I’m my own sister group” isn’t quite idiomatic.)

The puzzle is what to make of this lack of congruence, when it occurs. One might naively read Dawkins’s “evidence against evolution” statement as a genuine prediction, and then be mystified, or heartbroken, or driven crazy, when the theory of common descent motors right around anomalous data, such as the tetrapod trackways. Kinda does have the flavor of a country-western song: "You said you'd be testable and true / but you ran off when those fossils came through / oh evolution why'd I ever listen to you..."

Deeper insights await, however. Here is the moral, so you’ll know where the story is going:

Most evolutionary theorists -- both those who study only living organisms, and those who study extinct (fossil) groups -- understand that the theory of common descent must rule out certain states of affairs, to remain empirically testable. Hence, the hypothetical "Cambrian rabbit" that would explode common descent, if such a fossil were ever actually found in Cambrian strata.

Problem is, as systematist Gareth Nelson realized in 1978, "Cambrian rabbits" are found all the time (see Part 2 of this blog series). But these paleontological discoveries are not seen as challenging common descent, because that theory is tied up in a complex bundle with assumptions about -- for instance -- the completeness of the fossil record.

Thus, when fossils occur “out of evolutionary sequence,” what is ordinarily held as falsified, or tested, is not common descent at all, but something else entirely. Common descent doesn’t take the hit because the rest of the theoretical bundle absorbs the fossil anomalies.

If you think this means that common descent is not easily tested by paleontological data -- well, you’d be right.

So, on to part 1 of the story. We should start with the concept of “ghost lineages.”

Why common descent needs ghosts in the bushes

Let’s begin with a basic logical point. Dawkins says that evolution -- meaning the theory of common descent -- would be tested, and falsified, if fossils were found out of evolutionary sequence, or “before they could have evolved,” as he puts it. This would be the case, however, only if we could predict evolutionary sequence independently of where fossils actually turn up in the geological record.

Enter cladistics. Using the anatomical characters of extant and fossil groups (and molecular data as well for extant groups), and assuming that the groups are related by common descent (remember that assumption, because we'll come back to it later), we can generate a cladogram (a phylogenetic tree) specifying which groups should have branched first -- i.e., as most primitive -- and which later -- i.e., as more, or most, derived. With that cladogram in hand, we can then turn to the fossil record to see if its sequence of first appearances fits with our cladistic prediction about the evolutionary relatedness of the groups in question.

Well, sometimes the fossil record cooperates: the branching order predicted by the cladogram matches the pattern of fossil first appearances (i.e., of representatives of the groups in question).

Often, however, the fossil record doesn’t fit the cladogram, a difficulty well known to paleontologists and systematists. In fact, the cladistic revolution in the 1970s and 80s was motivated in large measure by evolutionary theorists setting aside stratigraphy -- the fossil record -- as determining phylogeny: that is, in deciding who is related to whom, by what historical sequence. Writing in 1972, American Museum of Natural History paleontologists Bobb Schaeffer, Max Hecht, and Niles Eldredge bluntly expressed their skepticism about the relevance of the fossil record to phylogeny:

…the fossil record for most groups of organisms is too incomplete to allow the assumption that relative stratigraphic position is necessarily indicative of morphocline polarity. (1972, 37)

In simpler language: where a fossil occurs in the geological column may have nothing to do with its position in the evolutionary tree. Contra Dawkins, “derived” groups may be found too early, and “primitive” groups too late. The difficulty arises, as Schaeffer et al. continue (1972, 43), from

the frequent discovery that a morphologically “primitive” taxon may occur quite high in the stratigraphic range of a group for which it is supposed to be ancestral. This problem has vexed most paleontologists at one time or another, particularly in relation to groups with a poor fossil record.

To see the problem, consider a pair of diagrams from vertebrate paleontologist Mark Norell, taken from the 1992 paper where he formally introduced the concept of “ghost lineages.” Figure 1 shows a cladogram for groups ABCD, with their predicted branching order: first A, then B, then C and D last. This figure is also “calibrated,” by which Norell means that it predicts the stratigraphic (fossil) branching order as well: A and B should be present in the fossil record at time 9, whereas sister groups C and D should be jointly present at time 6.

Figure 2, by contrast, shows the fossil (stratigraphic) distributions of groups ABCD. Note that A, the most primitive group, is found too late (“high in the range”), relative to its predicted branching order, whereas B is too early. Moreover, C and D fail to appear at the same time.

Now here we should pause, for a brief visit with logic. Read straightforwardly, the fossil record (in Norell’s toy example) has falsified the cladogram for groups ABCD. If the fossil record gives a reliable signal, groups ABCD simply could not be related in the order predicted by the cladogram: full stop. If you belong to group B, you can’t be older than group A, which supposedly branched earlier. Likewise, C and D could not be sister groups.

But hang on a minute. As noted above, the theory of common descent comes bundled with auxiliary theories and assumptions, among them assumptions about the completeness of the fossil record.

So -- time to bring in the ghosts.

The role of ghost lineages in preserving hypotheses of common descent

Maybe group A just missed being preserved as fossils, but the group was actually present, albeit hidden, at time 9. Given the vagaries of fossilization, that’s a possibility. See Figure 3, then, where “ghost lineages” come to the rescue of the phylogeny ABCD.

The red circles are branching points, and the dotted red lines, ghost lineages.

As Norell (1992, 105) writes,

These additional entities are taxa [groups] that are predicted to occur by the internal branching structure of phylogenetic trees….I refer to these as ghost lineages because they are invisible to the fossil record.

Ghost lineages -- well, they just aren’t there, in any normal sense of “observable.” As Norell (1992, 105) notes, “ghost lineages are the unobservable predictions of the phylogenetic branching of the group ABCD” in the cladogram (Figure 1). It’s the cladogram, based on our assumption of common descent, which tells us the ghosts were there, and that groups A-D are related by common ancestry.

The fossils themselves don’t say that, however.

But, but -- okay, slow down

At this point, haven’t we wandered a long way from Dawkins’s claim about the fossil record, cited at the top of this post? Isn’t common descent, rather than being tested by fossils, really providing instead the whole interpretative framework for the evidence -- as an unquestioned first principle?

Yes -- and that will be the theme of Part 2.

References

Dawkins, Richard. 2009. The Greatest Show on Earth: The Evidence for Evolution (New York: The Free Press).

Norell, Mark A. 1992. Taxic Origin and Temporal Diversity: The Effect of Phylogeny. In M.J. Novacek and Q.D. Wheeler, eds., Extinction and Phylogeny (New York: Columbia University Press), pp. 89-118.

Schaeffer, Bobb, Hecht, Max and Niles Eldredge. 1972. Phylogeny and Paleontology. Evolutionary Biology 6:31-46.

Posted by Paul Nelson at 10:00 AM | Permalink | TrackBacks (1)

Peloza v. Capistrano Independent Unified School District is a well-known case from the 9th Circuit in 1994 where a federal court of appeals found that it is legal to teach evolution even if a teacher feels it conflicts with his religious beliefs. While the court was correct to hold that it is perfectly legal to require that evolution be part of the curriculum, unfortunately they expressed no sympathy whatsoever for the millions of Americans who feel that teaching evolution is not religiously neutral.

1. Summary

In Peloza v. Capistrano, the Ninth Circuit Court of Appeals held that a teacher can be ordered to teach evolution, even if the theory conflicts with his or her religious beliefs.⁹³ John Peloza, a high school biology teacher, brought an action against the Capistrano Unified School District challenging its requirement that he must teach evolution.⁹⁴ According to Peloza, “Evolutionism is an historical, philosophical and religious belief system, but not a valid scientific theory . . . evolutionism is based on the assumption that life and the universe evolved randomly and by chance and with no Creator involved in the process.”⁹⁵ He claimed that the school district was forcing him to "proselytize his students to a belief in evolutionism ‘under the guise of [its being] a valid scientific theory.'"⁹⁶ The court rejected this argument, stating that "[evolution] has nothing to do with how the universe was created; it has nothing to do with whether or not there is a divine Creator."⁹⁷

2. Importance and Commentary

According to Peloza, a teacher can be forced to teach evolution even if it conflicts with his or her religious beliefs.⁹⁸ Like other cases, Peloza cites to the 1987 U.S. Supreme Court ruling in Edwards v. Aguillard to justify its claim that teaching creationism is unconstitutional.⁹⁹ Yet Peloza also represents another case that rejects the claim that evolution is a religious belief system, as it implies that pro-evolution-only policies do not raise establishment concerns because it defines evolution, as “simply . . . that higher life forms evolved from lower ones.”¹⁰⁰ Under such logic, teaching scientific evidence that holds that higher life forms did not evolve from lower ones should be similarly permissible, as it constitutes mere scientific critique of a scientific viewpoint.

While the Peloza court was correct to state that evolution is based upon a scientific methodology, it dismissively swept aside Mr. Peloza’s claims that the propositions of evolution conflict with his religious beliefs. The Peloza court thus failed to heed Justice Black’s warning that constitutional analysis should not ignore the “troublesome” religious implications that evolution may have for many Americans.¹⁰¹ In Justice Black’s words, the Peloza court “write[s] off as pure nonsense the views of those who consider evolution an anti-religious doctrine.”¹⁰² Given that at least one prominent mainstream biology textbook has said that “Darwin knew that accepting his theory required believing in philosophical materialism, the conviction that matter is the stuff of all existence and that all mental and spiritual phenomena are its by-products,”¹⁰³ courts should be sensitive to the religious views of citizens regarding evolution. By failing to recognize the anti-religious implications evolution has for many Americans, courts such as the Peloza court continue to inflame community division and strife over the teaching of evolution. Nonetheless, Peloza represents another case standing for the proposition that evolution may be taught even when it purportedly conflicts with the religious beliefs of educators.

[Editor’s Note: This survey of Peloza v. Capistrano Unified Sch. Dist. is an excerpt from the article “Does Challenging Darwin Create Constitutional Jeopardy? A Comprehensive Survey of Case Law Regarding the Teaching of Biological Origins,” Hamline University Law Review, Vol. 32(1):1-64 (Winter, 2009), published by Hamline University School of Law. This excerpt covers the case Peloza v. Capistrano Unified Sch. Dist.; the full article can be read here.]

Refrences Cited
[93.] Peloza v. Capistrano Unified Sch. Dist., 37 F.3d 517 (9th Cir. 1994), cert. denied, 515 U.S. 1173 (1995).d. at 522-23.
[94.] Id. at 519.
[95.] Id.
[96.] Id. (alteration in original).
[97.] Id. at 521 (emphasis omitted).
[98.] Peloza, 37 F.3d at 522-23.
[99.] Id.. at 521 (“The Supreme Court has held unequivocally that while the belief in a divine creator of the universe is a religious belief, the scientific theory that higher forms of life evolved from lower forms is not.”).
[100.] Id. at 520.
[101.] Epperson v. Arkansas, 393 U.S. 97, 113 (Black, J., concurring).
[102.] Id.
[103.] Joseph S. Levine & Kenneth R. Miller, Biology: Discovering Life 161 (2d ed. 1994).

Posted by Casey Luskin at 10:30 AM | Permalink | TrackBacks (0)

UPDATED: Today, Premier Radio UK is airing a debate recorded earlier this week between Signature in the Cell author Stephen Meyer and noted Oxford University chemist and “new atheist” Peter Atkins. The debate is part of the kick off of promotion for Expelled: No Intelligence Allowed, which arrives in the UK on DVD this month.

Both Atkins and Meyer are accomplished scholars with very different viewpoints. The at times testy back and forth between them is as entertaining as it is enlightening.

Click here to listen to the debate, which is about an hour long.

Dr. Atkins, is a noted critic of intelligent design and author who appeared in Expelled, stating: “Religion, it’s just fantasy … and is evil as well.” According to a 1992 article by Atkins in New Scientist, “Darwin effectively swept purpose aside in the living world,” and “[a]ll reimpositions of purpose are artifices of the religious to feed their faith.” He holds little back on religion, claiming that it only offers only “empty gulping and the verbal flatulence that passes for theistic exposition.” In Atkins’ view, “Humanity should accept that science has eliminated the justification for believing in cosmic purpose.” In his 1993 book Creation Revisited, Atkins contends that the reason for the existence of the universe is because “By chance there was a fluctuation” in the “void.” (p. 149)

Dr. Meyer is the recent author of Signature in the Cell, one of the bestselling science books on Amazon.com for 2009, also named one of the “Books of the Year” by the Times Literary Supplement (TLS) in London.

Posted by Anika Smith at 11:00 AM | Permalink | TrackBacks (0)

To the Editor
The Times Literary Supplement

The RNA World

Sir:

Having with indignation rejected the assumption that the creation of life required an intelligent design, Mr Fletcher has persuaded himself that it has proceeded instead by means of various chemical scenarios.

These scenarios all require intelligent intervention. In his animadversions, Mr Fletcher suggests nothing so much as a man disposed to denounce alcohol while sipping sherry.

The RNA world to which Mr Fletcher has pledged his allegiance was introduced by Carl Woese, Leslie Orgel and Francis Crick in 1967. Mystified by the appearance in the contemporary cell of a chicken in the form of the nucleic acids, and an egg in the form of the proteins, Woese, Orgel and Crick argued that at some time in the past, the chicken was the egg.

This triumph of poultry management received support in 1981, when both Thomas Cech and Sidney Altman discovered the first of the ribonucleic enzymes. Their discoveries moved Walter Gilbert to declare the existence of an RNA world in 1986. When Harry Noeller discovered that protein synthesis within the contemporary ribosome is catalyzed by ribosomal RNA, the existence of an ancient RNA world appeared "almost certain" to Leslie Orgel.

And to Mr Fletcher, I imagine.

If experiments conducted in the here and now are to shed light on the there and then, they must meet two conditions: They must demonstrate in the first place the existence of a detailed chemical pathway between RNA precursors and a form of self-replicating RNA; and they must provide in the second place a demonstration that the spontaneous appearance of this pathway is plausible under pre-biotic conditions.

The constituents of RNA are its nitrogenous bases, sugar, and phosphate. Until quite recently, no completely satisfactory synthesis of the pyrimidine nucleotides has been available.

The existence of a synthetic pathway has now been established. (Matthew W. Powner et al, “The Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions," Nature 459, 239–242, 2009).

Questions of pre-biotic plausibility remain. Can the results of Powner et al be reproduced without Powner et al?

It is a question that Powner raises himself: "My ultimate goal," he has remarked, "is to get a living system (RNA) emerging from a one-pot experiment."

Let us by all means have that pot, and then we shall see further.

If the steps leading to the appearance of the pyridimines in a pre-biotic environment are not yet plausible, then neither is the appearance of a self-replicating form of RNA. Experiments conducted by Tracey Lincoln and Gerald Joyce at the Scripps Institute have demonstrated the existence of self-replicating RNA by a process of in vitro evolution. They began with what they needed and purified what they got until they got what they wanted.

Although an invigorating piece of chemistry, what is missing from their demonstration is what is missing from Powner's and that is any clear indication of pre-biotic plausibility.

I should not wish to leave this discussion without extending the hand of friendship to every party.

Mr Nagel is correct in remarking that Mr Fletcher is insufferable. Mr Walton is correct in observing that the RNA world is imaginary. And Mr Fletcher is correct in finding the hypothesis of intelligent design unacceptable.

He should give it up himself and see what happens.

Posted by David Berlinski at 10:53 AM | Permalink | TrackBacks (0)

It's always easier to refute your opponent's position by replacing it with an outlandish straw man. The most recent issue of the Journal of Eukaryotic Microbiology contains a paper by Guillermo Paz-y-Miño of University of Massachusetts Dartmouth and Avelina Espinosa of Roger Williams University, titled "Integrating Horizontal Gene Transfer and Common Descent to Depict Evolution and Contrast It with 'Common Design'" that takes this approach to attacking intelligent design (ID). As suggested by the title, the article attempts to critique the argument that similar features in diverse organisms can be explained by common design. It cites to both a 1996 paper by Paul Nelson in Biology and Philosophy and a response to Francis Collins published by myself and Logan Gage in Intelligent Design 101 as sources arguing for "common design." Paz-y-Miño and Espinosa purport to discuss the evidence for the Darwinian evolution of the enzyme alcohol dehydrogenase 2 (EhADH2) in the protozoan Entamoeba histolytica, but there’s one problem: no evidence for Darwinian evolution or refutation of ID, one way or the other, is presented in the paper.

Their argument seems to be as follows:

1. Set up a straw man. Claim that ID proponents argue that that Darwinism says all 2160 amino acids in EhADH2 must be created at random, all at once. Since this is highly improbable, they acknowledge it can't happen through Darwinian processes. Then try to show that EhADH2 arose by natural selection.
2. This leads into an interesting but ultimately trivial exercise in showing that the incidence of various amino acids in EhADH2 is "non-random" since they appear more (or less) often than would be predicted by the relative number of codons that code for that particular residue.
3. Do the same for nucleotides, showing that the incidence of various nucleotides in EhADH2 is highly "non-random" (90% are AT but only 10% are GC but a random sequence would predict a 50/50 spread).
4. Having unequivocally refuted a purely random origin of EhADH2 at both the nucleotide and amino acid levels, you come to this conclusion: "Natural selection has tinkered molecular improvements in ancestors of EhADH2 by favoring and retaining an adaptive peptide sequence that promotes optimal function, a classical trajectory from simple evolutionary pathways to complex proteins (Lynch 2005). Mutation rate coupled with natural selection and HGT coupled with common descent suffice to explain the origin and diversification of EhADH2 in the Entamoeba lineage."

That's basically where the purported evidence for Darwinism ends in this paper. There was a leap of logic: Where was the evidence for Darwinian evolution?

So EhADH2 has a non-random sequence. Great. Of course Darwinism doesn't assert genes have entirely random sequences (the straw man they refute in step 1). But last time I checked, ID also predicts that genes won't have random sequences. And while Darwinian selection predicts non-random gene sequences, not all types of non-random complexity can be produced by natural selection.

Neo-Darwinism contends that mutations are random, and that selection only selects for current--not future--functions. In that regard, if random mutations cannot blindly lead a gene along a step-by-step pathway wherein it is functional at each step and successive mutations confer some advantage, then Darwinian evolution gets stuck on adaptive peaks. (Michael Behe notes that occasionally a neutral or slightly deleterious mutation might be tolerated, but features that require more than two simultaneous mutations appear beyond the reach of neo-Darwinism in most population sizes.) But Paz-y-Miño and Espinosa never establish that the step-by-step Darwinian evolution of this gene is possible. Only one highly complicated step is mentioned (though not justified as plausible):

According to the paper, EhADH2 allegedly arose by a fusion of aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH) into a bifunctonal protein, EhADH2. If functional ALDH and ADH genes existed in some ancestor, what are the odds of fusing those two genes together to produce a bifunctional chimeric gene that performs both functions? Is it probabilistically likely to occur? They don't even attempt the calculation. Instead, they cite to a 2001 paper by Espinosa in the Journal of Biological Chemistry which took the ADH part of EhADH2 and found that it could be individually expressed to function. Then they took the ADH portion of EhADH2 and found that it too could be expressed to function, although it depended on some residues in the ADH-half of EhADH2. Thus, they feel this is sufficient to conclude that EhADH2 resulted from the fusion of ALDH and ADH. Perhaps, but what are the odds of a mutation fusing these two genes in the right fashion so both parts could remain functional? And is there a Darwinian pathway to fixing the other residues necessary for the ALDH half to properly function? They don't say.

The least the authors could do is validate the one "fusion" step they assert took place. But they don't. Nor do they validate any other step in the Darwinian evolution of this gene: No step-by-step account of the evolution of this gene is given or attempted.

Even if such a fusion mutation is possible, does that really explain the Darwinian origin of EhADH2? Not really; one would still also need to show that the original separate ALDH and ADH genes could evolve separately via a Darwinian pathway. Paz-y-Miño and Espinosa's paper basically asserts that if particular amino acids and particular nucleotides appear in the gene in a non-random fashion, then descent with modification via natural selection is the correct explanation for the origin of the gene (with some horizontal gene transfer sprinkled in whenever necessary).

But non-random proportions of amino acids or nucleotides says nothing about whether natural selection or intelligent design produced the sequence. As regards the debate over Darwinism and ID, this paper pursues irrelevant exercises. Natural selection is asserted, not demonstrated. This is the epitome of taking neo-Darwinism for granted. Perhaps they should have read the warnings of evolutionary biologist Austin Hughes, who is tired of being embarrassed by bad arguments:

A major hindrance to progress has been confusion regarding the role of positive (Darwinian) selection, i.e., natural selection favoring adaptive mutations. In particular, problems have arisen from the widespread use of certain poorly conceived statistical methods to test for positive selection. Thousands of papers are published every year claiming evidence of adaptive evolution on the basis of computational analyses alone, with no evidence whatsoever regarding the phenotypic effects of allegedly adaptive mutations. ... Contrary to a widespread impression, natural selection does not leave any unambiguous "signature" on the genome, certainly not one that is still detectable after tens or hundreds of millions of years. To biologists schooled in Neo-Darwinian thought processes, it is virtually axiomatic that any adaptive change must have been fixed as a result of natural selection. But it is important to remember that reality can be more complicated than simplistic textbook scenarios. ... In recent years the literature of evolutionary biology has been glutted with extravagant claims of positive selection on the basis of computational analyses alone ... This vast outpouring of pseudo-Darwinian hype has been genuinely harmful to the credibility of evolutionary biology as a science.

(Austin L. Hughes, "The origin of adaptive phenotypes," Proceedings of the National Academy of Sciences USA, Vol. 105(36):13193-13194 (Sept. 9, 2008) (internal citations removed).)

In the final analysis, Paz-y-Miño and Espinosa's article in no way refutes "common design" because ID predicts that non-random features will be reused in different organisms. Since that's exactly what we find, how is common design, in their words "unfounded" or "improbable"? Since they haven't demonstrated their Darwinian story is mathematically plausible by any stretch of the imagination, their short-curt argument makes premature conclusions.

It never ceases to amaze what passes as an argument for Darwinism. Apparently a non-random distribution of amino acids or nucleotides now refutes ID. Yep, because that's what ID proponents -- especially biochemists like Michael Behe or theorists like William Dembski -- have been saying all along: ID predicts we'll find a random distribution of amino acids and nucleotides. And when we don't find it, descent with modification by natural selection is definitely the answer. Not.

Posted by Casey Luskin at 7:25 AM | Permalink | TrackBacks (0)

Signature in the Cell continues to stir up debate and attract attention as Thomas Nagel's selection of SITC as one of the Books of the Year brought on an interesting series of letters, where Nagel was attacked (he responded, and he was attacked again) by a Darwinist who told people forgo reading SITC and instead just read Wikipedia.

This week, author Stephen Meyer himself responds in a letter, with a shortened version published yesterday. (Nagel himself responded with a letter that is published on the same page by TLS.) Below is Meyer'e letter in its entirety.

To the Editor

The Times Literary Supplement

Natural Selection and the Origin of Biological Information

I’ve been honored by the recent attention my book Signature in the Cell has received in your letters section following Thomas Nagel’s selection of it as one of your books of the year for 2009.

Unfortunately, the letters from Stephen Fletcher criticizing Professor Nagel for his choice give no evidence of Dr. Fletcher having read the book or any evidence of his comprehending the severity of the central problem facing chemical evolutionary theories of life’s origin.

In Signature in the Cell, I show that, in the era of modern molecular genetics, explaining the origin of the first life requires—first and foremost—explaining the origin of the information or digital code present in DNA and RNA. I also show that various theories of undirected chemical evolution—including theories of pre-biological natural selection—fail to explain the origin of the information necessary to produce the first self-replicating organism.

Yet, in his letters to the TLS (2 and 16 December), Stephen Fletcher rebukes Nagel (and by implication my book) for failing to acknowledge that “natural selection is a chemical as well as a biological process.” Fletcher further asserts that this process accounts for the origin of DNA and (presumably) the genetic information it contains.

Not only does my book address this very proposal at length, but it also demonstrates why theories of pre-biotic natural selection involving self-replicating RNA catalysts—the version of the idea that Fletcher affirms—fail to account for the origin of genetic information.

Indeed, either Dr. Fletcher is bluffing or he is himself ignorant of the many problems that this proposal faces.

First, “ribozyme engineering” experiments have failed to produce RNA replicators capable of copying more than about 10% of their nucleotide base sequences. (Wendy K. Johnston, et. al, “RNA-Catalyzed RNA Polymerization,” Science 292 (2001): 1319-25.) Yet, for natural selection to operate in an RNA World (in the strictly chemical rather than biological environment that Fletcher envisions) RNA molecules capable of fully replicating themselves must exist.

Second, everything we know about RNA catalysts, including those with partial self-copying capacity, shows that the function of these molecules depends upon the precise arrangement of their information-carrying constituents (i.e., their nucleotide bases). Functional RNA catalysts arise only once RNA bases are specifically-arranged into information-rich sequences—that is, function arises after, not before, the information problem has been solved.

For this reason, invoking pre-biotic natural selection in an RNA World does not solve the problem of the origin of genetic information; it merely presupposes a solution to the problem in the form of a hypothetical but necessarily information-rich RNA molecule capable of copying itself. As Nobel laureate Christian de Duve has noted, postulations of pre-biotic natural selection typically fail because they “need information which implies they have to presuppose what is to be explained in the first place.”

Third, the capacity for even partial replication of genetic information in RNA molecules results from the activity of chemists, that is, from the intelligence of the “ribozyme engineers” who design and select the features of these (partial) RNA replicators. These experiments not only demonstrate that even highly limited forms of RNA self-replication depend upon information-rich RNA molecules, they inadvertently lend additional support to the hypothesis that intelligent design is the only known cause by which functional information arises.

STEPHEN C. MEYER, Ph.D. Cantab
Author, Signature in the Cell
Senior Research Fellow, Discovery Institute
Seattle, Washington, U.S.A.

Posted by Anika Smith at 7:57 AM | Permalink | TrackBacks (0)

SACRAMENTO--California Senate Minority Leader Dennis Hollingsworth has sent a letter to the California Science Center (CSC) requesting documents related to the Center’s cancellation of a screening last October of the pro-intelligent design documentary “Darwin’s Dilemma.” The screening was sponsored by the American Freedom Alliance (AFA), a private group that had rented the Center’s IMAX theater.

Senator Hollingsworth’s letter follows two lawsuits filed against the state government-operated Science Center charging that it violated both the First Amendment and California’s open records law in its effort to stop the screening and then cover up the real story behind the cancellation.

“The constitutional implications of [the Science Center’s] actions are concerning” wrote Senator Hollingsworth in the letter, citing various court decisions protecting private parties against viewpoint discrimination. “It is fundamental that when a governmental entity or sub-unit (such as CSC) opens its facilities as a public forum, it is not constitutionally permissible to censor speech based on viewpoint or content.”

“The California Science Center’s assault on free speech should alarm everyone,” said Casey Luskin, Program Officer in Public Policy and Legal Affairs for the Discovery Institute. “If the government can ban a private group from renting a public auditorium to show a film favoring intelligent design, it can ban private groups from showing films in support of Darwin’s theory. Where does it stop?”

“Senator Hollingsworth is to be commended for launching this inquiry,” added Dr. John West, Vice President for Public Policy and Legal affairs at the Institute. “Free speech is the foundation of a free society. Government agencies have no right to discriminate against citizens because of their legally-protected viewpoints.”

Hollingsworth’s letter is directed to Dr. Joel Strom, Chair of the California Science Center Board of Directors, requesting that he instruct the museum’s management to provide copies of documents pertaining to the cancellation of the event, including e-mail communications from Science Center staff, employees, and board members which discuss the event and the topic of intelligent design versus Darwinism.

Posted by John West at 11:16 AM | Permalink | TrackBacks (0)

Each year the Access Research Network (ARN) provides an excellent service to the intelligent design (ID) debate by publishing its Top ID Stories of the year. They recently released their “Key Darwin and Design Science News Stories of the Year” for 2009, but before I review some of them I want to make a preliminary note about ARN.

ARN is one of the most important ID organizations in large part because their online “media resources” bookstore has a huge collection of ID resources, ranging from books to videos to audio products, and even YouTube clips. There are conspiracy theorists at Wikipedia who claim that ARN “acts as a de facto auxiliary website to the Discovery Institute's Center for Science and Culture.” This statement reflects a common theme on Wikipedia articles about ID that Discovery Institute is the wizard pulling the strings of some nefarious (though non-existent) ID conspiracy. Of course such "point of view" assertions are supposedly disallowed on Wikipedia, but double-standards abound when it comes to ID and Wikipedia editors insert anti-ID "points of view" all the time. I'm also not even sure exactly what the "de facto auxiliary website" statement even means--if it means anything--but in any case, it's a falsehood: ARN is a fully autonomous organization that has its own bloggers that generate their own unique content on a daily basis. But I have no problem reporting that it’s great content, and that readers of ENV might also enjoy following ARN’s blogs, such as the ID Update, ID Report, ID News, and the stellar ID Literature blog. In fact, ARN’s involvement with the ID movement predates Discovery Institute’s. So while Wikipedia is dead wrong to claim that ARN is some puppet of Discovery Institute, ARN has great people, and if you’re looking for something produced by the ID movement, there’s a good bet you can find it at ARN’s online store. Now on to review some of ARN’s top Intelligent Design stories for 2009:

”The Modern Synthesis is Gone”
Citing to a post by David Tyler at ARN’s ID Literature blog, they reviewed a groundbreaking 2009 paper by Eugene Koonin of the National Institutes of Health explaining why “[t]he edifice of the modern synthesis has crumbled, apparently, beyond repair”:

In February 2009 Eugene Koonin published a masterly analysis of the impact of genomics on evolutionary thinking (“Darwinian evolution in the light of genomics”, Nucleic Acids Research, 2009, 37(4), 1011-1034). Koonin notes that the 1959 Origins centennial was “marked by the consolidation of the modern synthesis” but subsequent years have witnessed great changes which have undermined its credibility. The modern synthesis was formulated in the 1930’s and 1940’s to draw together seemingly conflicting evidence from natural selection, population genetics, cytology, systematics, botany, morphology, ecology and paleontology into one modern theory of neo-Darwinian evolution. Three distinct revolutions have occurred over the past half-century to bring down the modern synthesis theory: the molecular, the microbiological, and the genomic revolutions. Koonin tentatively identifies two candidates to fill the vacuum left by the discarded modern synthesis. The first appears to emphasize the role of chance; the second appears to emphasize the role of law. While many in the scientific community will continue to cling to the modern synthesis for years to come, it is significant that articles are now appearing in the peer-reviewed scientific literature declaring the theory needs to be abandoned because it no longer fits the molecular, microbiological and genomic data.

The Demise of Icons and Missing Links
ARN also wrote about the demise of various missing links, including "The Ida Hype and Bust," noting that even an August 2009 issue of Science published an article on Ida titled “Much Hype and Many Errors.” But Ida wasn’t the only overhyped fossil in 2009. ARN also noted the “The Ardi Hype and Bust” noting that:

The first fossils of the species, Ardipithecus ramidus (“Ardi”), were unearthed in 1994 and were first described in a series of papers in the journal Science in October 2009. The very poor condition of the ancient bones is one reason it took researchers 15 years to excavate and analyze them. The Science editors declared Ardi to be the "central character in the story of human evolution" and named the fossil the science breakthrough of 2009. Evidently the Science editors have not been reading any of the other published opinions on Ardi. These articles reveal that Ardi is an “Irish stew” fossil that has undergone extensive reconstruction in order to become part of a PR campaign to make bold claims of ancestral status to the human line, even though at base its qualities are very similar to previously known fossils.

ARN reported that fossils weren’t the only Darwinian icons to lose force in 2009. ARN discussed how the "Peppered Moths Oscillates Back to Gray," meaning that this alleged example of natural selection “is now becoming at best a case of oscillating selection, much like what has been observed in the oscillating sizes of beaks of the Galapagos finches, which grow slightly larger during a drought but revert back to their original size when the drought is over.” Darwin’s tree of life also faced challenges in 2009, as ARN reported that the “Cambrian Explosion Continues to Challenge Materialistic Theories,” stating “A paper in the July 2009 issue of BioEssays admits the lack of a ‘materialistic basis’–that is, a plausible materialistic explanation–of the Cambrian explosion.”

Debating the Origin of Biochemical Evolution
ARN highlighted debates between Michael Behe and University of Oregon biologist Joseph Thornton regarding Thorton’s 2009 paper, “An epistatic ratchet constrains the direction of glucocorticoid receptor evolution.” ARN commented, “Although the work is interpreted by its authors within a standard Darwinian framework, it also confirms the primary thesis of Michael Behe’s recent book, The Edge of Evolution: The Search for the Limits of Darwinism, demonstrating the looming brick wall which confronts unguided evolution in at least one system. It points strongly to the conclusion that such walls are common throughout all of biology.”

In a section titled, “Failed Assault on Irreducible Complexity,” ARN discussed the stir caused by a 2009 paper in Proceedings of the U.S. National Academy of Sciences titled "The reducible complexity of a mitochondrial molecular machine." ARN reported that “The Darwinian guardians appear anxious to debunk irreducible complexity, one of the key scientific concepts for intelligent design. This was evidenced by the editor’s refusal to print a letter to the editor by Michael Behe exposing the basic problems with the article.” It also cited to my “detailed response documenting how the claims made in the paper far surpassed the data, and how distinctions between such basic ideas as ‘reducible’ versus ‘irreducible’ and ‘Darwinian’ versus ‘non-Darwinian’ were essentially ignored.”

Other potential biochemical challenges to Darwinism may come from an interesting story ARN found in ScienceDaily, which stated, “Even within cells, the left hand knows what the right hand is doing” since “molecular motors operate in an amazingly coordinated manner.” ARN reports that the story says “The new U.Va. study provides strong evidence that the motors are indeed working in coordination, all pulling in one direction, as if under command, or in the opposite direction – again, as if under strict instruction.” Similar coordinated complexity is found in ARN’s story on “Walking White Blood Cells,” where white blood cells find sites of infection or injury by “crawl[ing] swiftly along the lining of the blood vessel–gripping it tightly to avoid being swept away in the blood flow–all the while searching for temporary ‘road signs’ made of special adhesion molecules that let them know where to cross the blood vessel barrier so they can get to the damaged tissue.” ARN also reported that cells use “Cloud Computing,” as an article in Science Daily stated: “Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology” because “each system keeps working despite the failure of individual components, whether they are master genes or computer processors.” Finally, ARN highlighted some great articles by its blogger David Tyler on the topic of biomimetics

ARN’s conclusion to its top 2009 news stories is striking:

An ID skeptic might be able to dismiss any of the individual news stories above as simply aberrations to the forward marching drum of scientific materialism. However, reflecting back over these scientific developments in 2009 as a whole, a rather grim picture emerges for Darwin’s theory. In a year in which Darwin’s disciples were celebrating the 200th anniversary of his birth that the 150th anniversary of the publication of On the Origin of Species, mainstream scientific journals published articles declaring: 1) the modern synthesis was dead, 2) Darwin’s tree of life should be abandoned, 3) new “missing links” were a bust, 4) limits to Darwinism were demonstrated in the lab, 5) evolutionary icons like the peppered moths reverted back to their old colors, 6) the Cambrian Explosion lacks any plausible materialist explanation, and 7) an interdisciplinary revolution is occurring in biology that rejects the reductionist paradigm of Darwinian evolution. Meanwhile the evidence for design continues to mount with 1) peer-reviewed articles and books by ID theorists, 2) the information content in DNA demanding a non-materialistic source, 3) scientists continuing to “reverse engineer” amazing designs from biological systems, and 4) the irreducible complexity in living systems continuing to be discovered and documented. Wow, what a year!

Check ARN’s Top Stories Page or stay tuned for more updates as ARN will release its top public policy stories and top resources for 2009 in the near future.

Posted by Casey Luskin at 10:23 AM | Permalink | TrackBacks (0)

If you're wondering what a major one-night event with some of the leading voices challenging Darwinian evolution sounds like, here's your chance to find out. If you're interested in attending this year's conference, featuring Michael Medved again, along with Dr. Stephen Meyer and Dr. David Berlinski, be warned: Last year's conference sold out, and over 200 were turned away. Click here to secure your place with a ticket in advance.

From our friends at the C. S. Lewis Society:

Last year's conference, "Darwin's Legacy: The Hidden Story," was held by the C. S. Lewis Society at the University of South Florida and featured Michael Medved and Professor Steve Fuller of the University of Warwick, along with CSLS director Tom Woodward. Highlights of this event will be rebroadcast several times in the coming weeks.

Program Schedule for the rebroadcast of last year's program, "Darwin's Legacy: The Hidden Story"

WTBN 570 & 910 AM
Sat. Jan. 9th at 11 AM
Thur. Jan. 21st at 8 PM

WGUL 860 AM
Sat. Jan. 9th at 4 PM
Sat. Jan. 23rd at 4 PM

WLSS 930 AM
Sat. Jan. 9th at 11 AM
Sat. Jan. 23rd at 11 AM

Posted by Anika Smith at 2:19 PM | Permalink | TrackBacks (0)

Over at Scott McKnight's blog at Beliefnet, an anonymous blogger has started a review thread on Steve Meyer's book. Signature in the Cell. While the blogger ("RJS") says he ultimately disagrees with Meyer's argument, it's clear that he takes Meyer's argument seriously and is trying to do his best to present the argument accurately. This is much more than can be said for the many hysterical and misinformed "critiques" of Meyer's argument that are now floating around the Internet. Anyone who's actually read the book will know that most of these critiques are cliches that Meyer addresses in detail in the book, suggesting that the critics don't even know the argument they are criticizing.

A civil review like this is welcomed, and I look forward to reading the installments.

In his first installment, RJS suggests that there's a promising "third way" that Meyer doesn't address in the book:

It seems to me that there is a middle ground between the insistence that chance, happenstance, and law (the laws of physics) suffice to explain all and the suggestion that biology - life - can only be explained with reference to a creative mind. Alister McGrath (A Fine-Tuned Universe) and Simon Conway Morris (Life's Solution) provide some insight into this middle ground. The fabric of the Universe makes life possible and inevitable - not a highly contingent accident. Thinking scientifically we look for the causally connected series of events that resulted in the present reality - as part of God's method in creation.

I'm familiar with McGrath and Conway Morris's views, and think they have some merit; but I don't think they offer an alternative that Meyer fails to address. Smoothing for inconsistencies in their proposals, their idea is basically that God hard-wired or "front-loaded" everything "in the beginning" as it were to give rise to complex life somewhere, while allowing for a lot of "freedom" and variation within the cosmos. (So they're not hard determinists.)

First, taken seriously, this is quite obviously a theistic form of design that simply tries to locate all the designing activity at the beginning--in the cosmic fine-tuning and initial conditions. The design does real work, and there's no reason that the effects of that design would not be empirically detectable (as long as we have an open-minded, nonpositivist view of science). As a simple analogy, think of front-loading this way. If I shoot a gun at a target and hit it, I've intentionally aimed the bullet at the beginning, even though the bullet's trajectory follows the rules of gravity, momentum, etc. In God's case, of course, he would also establish the law-like rules and superintend them. All I can do when I shoot a gun is take them into account.
Second, some front-loading and fine-tuning is not only compatible with but necessary for Steve's argument. But I think the argument that everything can be explained this way doesn't capture the details of Steve's argument about information at the origin of life. The front-loading scenario tries to turn necessary conditions for life into sufficient conditions. Though Steve doesn't say this, if he's right, it's not at all obvious that this front-loading scenario is so much as possible. The only thing God would have to hardwire information at the beginning would be initial conditions, some proto-matter and the repetitive, law-like forces that govern the matter. But we can see the effects of both those initial conditions and the law-like regularities playing out in the material world now. They constitute the background to the information in biological systems--that is, the necessary but nowhere nearly sufficient background--the contrast medium for the information. What would it mean to tweak the expressions of gravity and electromagnetism so that they would give rise to the information-processing in cells and body plans of vertebrates? I think this explanation has plausibility only in proportion to the haziness of one's conception of specified information.

Third, even if it's possible for God to frontload things in this way, it hardly follows that this is a better explanation than the one Steve proposes, which is (at least implicitly) (1) that matter shows degrees of freedom inconsistent with such complete front-loading and (2) that intelligence plays an active and detectable role within cosmic history, and probably is not limited in the way proposed (or suggested) by Conway Morris and others. What we're interested in is the best explanation for life's features in the real world, one that takes account of the known causal powers of world as we see it.

Posted by Jay Richards at 8:54 AM | Permalink | TrackBacks (0)

I was recently asked by an e-mailer to comment on a new study about evolution of prions based via a process like Darwinian selection.

Prions are misfolded proteins (or misfolded protein complexes). They aren’t alive. They can’t replicate on their own. They require their host’s cellular machinery for producing new proteins they can "misfold" in order to propagate.

Prions can be dangerous because they propagate themselves by misfolding other properly folded proteins produced in the cell. The misfolded proteins don’t always function property, and this can disrupt activity in the cell. As the BBC article states, "Prions are associated with 20 different brain diseases in humans and animals." The new research just shows that prions don’t always make perfect copies of themselves when misfolding other proteins. This leads to variation. Naturally, those prions that are better able to infect their hosts tend to do so, and thus they tend to "evolve" towards more "virulent" forms.

Whenever you have replication, variation, and some selection pressure (such as scarce resources), Darwinian evolution is probably going to occur. Does this mean that prions help us explain how biological organisms evolve?

In this study, the evolution of prions means their original function has been disrupted and they have become less useful in their hosts. This type of evolution shows the destruction of original biological function, not the improvement of it.

Natural selection can only preserve traits that exist -- we must account for the origin of a trait before Darwinian selection can preserve it. Thus, as evolutionary biologist Rudolf Raff has observed, neo-Darwinism might model "the survival of the fittest, but not the arrival of the fittest." And the arrival of the fittest can be problem for neo-Darwinism. Although he denies that such a structure exists, Jerry Coyne admits, "It is indeed true that natural selection cannot build any feature in which intermediate steps do not confer a net benefit on the organism." Since these prions do not benefit their host, this research doesn't do much to show how living organisms evolve.

Most biological systems are significantly more complex than prions. Prions have a complexity is significantly less than that of even viruses (which also aren’t alive). The observation that proteins can get increasingly screwed up via Darwinian evolution isn't going to do much to explain how functional proteins evolved in the first place.

Posted by Casey Luskin at 6:30 AM | Permalink | TrackBacks (0)

Precisely thirty years ago this month the late Stephen Jay Gould published an article in volume 89 of Natural History purporting to demonstrate Alfred Russel Wallace’s “fatal flaw.” Wallace, who co-discovered natural selection in his now-famous Ternate Letter of 1858, first startled Charles Darwin and then prompted him after years of ponderous delay to finally complete his Origin of Species and rush it to press. By November of the following year his magnum opus was in the hands of the English public. But Wallace would break with Darwin over the source of the human intellect. While Darwin thought man and animal different in degree not kind, Wallace felt that the special attributes of the human mind, its facility for abstract reasoning, mathematics, music, even wit and humor was inexplicable by Darwin’s own principle of utility, namely, the idea that no attribute in any species would arise and be maintained unless it afforded it a functional advantage in its struggle for survival. Admitting that none of these most human of traits promoted survival, Wallace instead suggested that these qualities were explicable only through some “Overruling Intelligence.” Darwin and his disciples have been horrified ever since. Pointing to Wallace’s insistence that natural selection can only “fashion a feature for immediate use,” Gould issued his indictment: Wallace’s so-called “fatal flaw” was his “hyperselectionism.” But does this charge hold up?

Gould’s claim of hyperselectionism is odd. Gould notes that Darwin did not adhere to natural selection as the sole engine of evolution. True, it was the primary one, but pangenesis and sexual selection increasingly became subsidiary mechanisms in response to the limitations of natural selection. Wallace rejected both these ancillary notions, and he has subsequently been vindicated in his assessment as pangenesis has been replaced by modern genetics and sexual selection has come under devastating criticism in the current peer-reviewed literature. So, Wallace’s strict adherence to the principle of utility as the cornerstone of natural selection (the alleged source of his “hyperselectionism”) turns out, in fact, to have been a prudent position.

More importantly, Gould’s claim is inaccurate and misleading. It is clear that there is really no hyper in Wallace’s selectionism because he strictly limited the operations of natural selection. While it explained a lot, it did not, for Wallace, explain the origin of life, sentience in animals, or the intellect of humankind. The only reason Gould labels it “hyper” is that those limitations don’t count for Gould. Instead he tries to explain them away.

Gould argues that Wallace failed to understand Darwin’s “subtler view” and “misunderstands the nature of organic form and function.” Natural selection can, according to Gould, create organs for specified functions the very complexity of which can “perform many other tasks as well.” His example is a factory that implements a computer to process pay checks. Gould points out that “such a machine can also analyze the election returns or whip anyone (or at least perpetually tie them) in tick-tack-toe. Our large brains may have originated for some set of necessary skills in gathering food, socializing, or whatever,” he adds, “but these skills do not exhaust the limits of what such a complex machine can do.”

Gould’s reasoning is flawed on several levels. First, his example of the computer actually makes Wallace’s case. The computer possesses versatility precisely because some “overruling intelligence” (in this case a computer programmer) gives it the instructions to perform these different tasks. In order for Gould’s example to fit appropriately to his point, the computer would have to randomly or by some process of necessity within itself just spontaneously attain the capacity to generate pay checks, analyze election returns, or play games. Thus his point falls wide of its mark. Furthermore, Gould’s hand-waving about how our “large brains” might have started out (food gathering, socializing, or “whatever”) is the essential question at hand! Species of wide ranging levels of intelligence are perfectly capable of acquiring food for survival, and sociability is not unique to Homo sapiens. Bonobos and meerkats, for example, are very different animals who both live in highly complex social groups. If sociability spawned our intellectual complexity, why did this not occur with other species? Gould’s explanation winds up being only a series of unsubstantiated speculations.

So the charge of hyperselectionism is simply wrong. In fact, if anything it was Darwin who was the hyperselectionist. After all, in the face of growing anomalies with his own mechanism of natural selection it was he, not Wallace, who called upon another type of selectionism, sexual selection, to fill in the gaps.

The consequences of Gould’s allegation have been unfortunate, a mischief greatly facilitated by Michael Shermer’s In Darwin’s Shadow (2002). Shermer takes Gould’s notion of hyperselectionism and uses it to create a biographical portrait of Wallace that distorts him beyond recognition. Shermer turns Wallace’s imputed hyperselectionism into scientism, which, in a sad dismissal of 44 years labor, actually negates most of the naturalist’s work after his break with Darwin in 1869.

One is reminded of Orwell’s newspeak where words are created to ratify and promote the ruling ideology. Here Wallace’s check on natural selection through design and intelligence is called hyperselectionism, while Darwin’s genuine hyperselectionism is dubbed the “subtler view.” In perfect Orwellian fashion, evolutionary biologists and their minions not only manage to “create a medium of expression for the worldview and mental habits proper to the devotees of Ingsoc [i.e., Darwinism], but to make all other modes of thought impossible.” In this instance Wallace’s teleology is quickly disposed of in a word, hyperselectionism.

What they do not want you to know is that Gould’s charge is a product of poor logic, buttressed by analogies that make precisely the opposite point, filled in with stories that fail to rise to the level of anecdote. This typifies the Darwinian narrative and remains even in death Gould’s fatal flaw.

Posted by Michael Flannery at 8:12 AM | Permalink | TrackBacks (1)

When Tiktaalik was reported in 2006, the media went Darwin-happy over the discovery of an alleged transitional fossil. BBC News announced, "Fossil animals found in Arctic Canada provide a snapshot of fish evolving into land animals." At MSNBC, Tiktaalik co-discoverer Ted Daeschler was quoted boasting that, "If one considers adaptation as a process of collecting tools to live in a new environment, the new finding offers 'a snapshot of the toolkit at this particular point in this evolutionary transition.” The article even postured Tiktaalik as an actual ancestor of tetrapods, stating: "Scientists have caught a fossil fish in the act of adapting toward a life on land, a discovery that sheds new light on one of the greatest transformations in the history of animals." But this week Tiktaalik’s status as an actual transitional fossil between fish and tetrapods has been called into question by the discovery of unambiguous footprints (with digits) of a full-tetrapod that were made about 20 million years before Tiktaalik. An article in Nature explains the havoc wreaked by these footprints:

The fish–tetrapod transition was thus seemingly quite well documented. There was a consensus that the divergence between some elpistostegalians (such as Tiktaalik or Panderichthys) and tetrapods might have occurred during the Givetian, 391–385 Myr ago. Coeval with the earliest fossil tetrapods, trackways dating to the Late Devonian were evidence for their ability to walk or crawl on shores.

Now, however, Niedźwiedzki et al. lob a grenade into that picture. They report the stunning discovery of tetrapod trackways with distinct digit imprints from Zachemie, Poland, that are unambiguously dated to the lowermost Eifelian (397 Myr ago). This site (an old quarry) has yielded a dozen trackways made by several individuals that ranged from about 0.5 to 2.5 metres in total length, and numerous isolated footprints found on fragments of scree. The tracks predate the oldest tetrapod skeletal remains by 18 Myr and, more surprisingly, the earliest elpistostegalian fishes by about 10 Myr.

(Philippe Janvier & Gaël Clément, "Muddy tetrapod origins," Nature Vol. 463:40-41 (January 7, 2010).)

The fossil tetrapod footprints indicate Tiktaalik came over 10 million years after the existence of the first known true tetrapod. Tiktaalik, of course, is not a tetrapod but a fish, and these footprints make it very difficult to presently argue that Tiktaalik is a transitional link between fish and tetrapods. It’s not a “snapshot of fish evolving into land animals,” because if this transition ever took place it seems to have occurred millions of years before Tiktaalik.

Tiktaalik's Place in the Fossil Record: A Confirmed Failed Prediction of Evolution
Some, such as Tiktaalik co-discoverer Neil Shubin, have turned Tiktaalik's place in the fossil record into an argument neo-Darwinism. As Shubin said in PBS's Judgment Day: Intelligent Design on Trial:

What evolution enables us to do is to make specific predictions about what we should find in the fossil record. The prediction in this case is clear-cut. That is, if we go to rocks of the right age, and the rocks of the right type, we should find transitions between two great forms of life, between fish and amphibian. ...What we see when we look at the fossil record, at rocks of just the right age, is a creature like Tiktaalik.

The New York Times presaged Shubin's argument, first reporting on Tiktaalik that "the scientists concluded that Tiktaalik was an intermediate between the fishes Eusthenopteron and Panderichthys, which lived 385 million years ago, and early tetrapods. The known early tetrapods are Acanthostega and Ichthyostega, about 365 million years ago." But would neo-Darwinism have predicted true tetrapods from 397 million years ago? Definitely not: Janvier and Clément said it best: these tracks are "anachronistic." Tetrapod paleontologist Jenny Clack said the track discovery " blows the whole story out of the water." Or as a Nature news story put it, these tetrapod tracks are "more than 18 million years before tetrapods were thought to have evolved."

So where are the fish that turned into tetrapods? According to Nature, they must exist in the "'ghost range' — that is, a period of time during which members of the groups should have been present but for which no body fossils have yet been found." Shubin's arguments that these fossils confirm a "specific prediction" of evolution appear to have been wrong. (But don't expect a correction from PBS anytime soon.)

Lessons to be Learned
In 2007, Stan Guthrie discussed in Christianity Today about whether media hype on transitional forms should be believed. Saying he’s always “secretly identified with the apostle Thomas,” Guthrie wrote:

Last year, however, came word of Tiktaalik roseae, which looks discomfitingly like those offensive "Darwin fishes" on the cars of smug college professors. Giddy evolutionists immediately hailed the 375-million-year-old fossil as a "missing link" between fish and land animals. "It's a really amazing, remarkable intermediate fossil," scientist Neil H. Shubin told The New York Times. "It's like, holy cow."

So what's a Doubting Thomas to do? First, we need to remember that scientists have hailed "missing links" before, only to be embarrassed when further evidence came out. The Discovery Institute, which supports Intelligent Design, noted that enthusiasm over this latest find is a backhanded admission by paleontologists that the fossil record has not been kind to Darwin's theory.

These are good words; unfortunately, Guthrie then goes on to quote and endorse theistic evolutionists such as Francis Collins who basically fully capitulate to the claims of neo-Darwinists without much sign of a willingness to doubt. Guthrie quotes Collins saying, "The evidence mounts every day to support the concept that we and all other organisms on this planet are descended from a common ancestor," and that "the theory of evolution is really no longer a theory in the sense of being untested. It is a theory in the sense of gravity. It is a fact." But yet we see the "facts" of neo-Darwinism constantly being revised. Last year alone:

Archaeopteryx was challenged as an intermediate between dinosaurs and birds

Theropod dinosaurs were challenged as the ancestors of birds

Ardi was hyped as human ancestor based upon questionable evidence

Ida was the "link" that went bust

2010 is only a few days old and already one of the newest icons of neo-Darwinism — Tiktaalik — is coming under heavy fire. Perhaps when it comes to neo-Darwinism, Collins and those who follow him would do better to insist on taking the approach of Doubting Thomas after all.

Posted by Casey Luskin at 2:50 PM | Permalink | TrackBacks (0)

The debate between Darwin and design is coming to Tampa, Florida with a major one-night event featuring some of the leading voices challenging Darwinian evolution.

Click here to register for this event

Discovery Institute senior fellow and national radio personality Michael Medved will lead a two-hour discussion about the evidence for intelligent design and the challenges it proposes to modern evolutionary theory. Joining him will be Signature in the Cell author, Stephen C. Meyer, leading Darwin skeptic and author of The Deniable Darwin David Berlinski, and scientist, scholar and writer, Thomas Woodward author of Darwin Strikes Back.

The event will take place at The A La Carte Pavilion, Tampa, FL, Thursday, January 28th at 7pm and is hosted by the C. S. Lewis Society. Discovery Institute is one of the co-sponsors.

The cost of admission is $6 for Students and $12 for Adults. For more information and advanced ticket sales, call (727) 376-6911 x 336. Or you can simply purchase tickets to the event online.

Posted by Robert Crowther at 2:35 PM | Permalink | TrackBacks (1)

A recent article in ScienceDaily titled “ Introns Nonsense DNA May Be More Important to Evolution of Genomes Than Thought,” actually demonstrates nothing like Darwinian evolution. Introns are stretches of DNA within genes in Eukaryotes that do not code for proteins. But they aren’t functionless and can play important roles in splicing together proteins. According to the ScienceDaily article:

“The scientists also found what appear to be "hot spots" for intron insertion -- areas of the genome where repeated insertions are more likely to occur.

This implies the occurrence of convergent genetic evolution of introns at specific locations, or as the article repeatedly puts it, “parallel intron gains.” The study’s principal investigator, Michael Lynch, was clear about the implications:

Michael Lynch, the project's principal investigator, agreed that the discovery of parallelism will surprise his colleagues.

"Remarkably, we have found many cases of parallel intron gains at essentially the same sites in independent genotypes," Lynch said. "This strongly argues against the common assumption that when two species share introns at the same site, it is always due to inheritance from a common ancestor."

So there’s an admission that genetic similarity, i.e. the presence or absence of an intron at a particular locus within a gene, no longer necessarily implies inheritance from a common ancestor. This challenges a key component of the methodology commonly used to infer common descent.

But the implications of this sort of data go even deeper: According to the ScienceDaily article, “surprisingly, the vast majority of intron DNA sequences the scientists examined were of unknown origin.” That means they couldn’t find homology for those intronic DNA sequences with any other known stretch of DNA. So what possible mechanism could spontaneously produce functional genetic strings de novo inserted into identical locations in parallel lineages? Consider this comment:

“The thinking has been that these insertion events are very rare because they always have bad effects,” said postdoctoral fellow Abraham Tucker, a lead author of the Science paper.

The reason they believed such events would be rare is simple: randomly inserting a bunch of novel DNA into a gene is highly likely to destroy the gene. Hence the argument has always been—so long as we’re operating under Darwinian assumptions—that most intronic insertions will be junk. After all, what natural mechanism could blindly insert a bunch of nucleotides into a gene without destroying it?

But what if Darwinian assumptions are wrong? There is a mechanism that can produce non-deleterious functional genetic information—but it isn’t random mutation. What they call “hotspot mutations” may just be another word for “non-random insertion of DNA.”

What is the natural mechanism for creating functional, non-random DNA de novo? “Hotspot mutation” is a word for an observed effect—the presence of genetic modules in identical locations in parallel lineages where the common ancestor did not have that DNA—not an explanatory cause.

This sort of convergent genetic evolution not only pulls the rug out from the under part of the methodology used to infer common descent, but it strains the credulity of the Darwinian mechanism to insert functional genetic modules into the same location independently in separate lineages. It begs for an explanatory cause that can produce functional information. The only known cause which produces new functional genetic information (intelligent design), for now, must go unspoken.

Posted by Casey Luskin at 8:29 AM | Permalink | TrackBacks (0)

Incomparably more influential than any science textbook, Wikipedia with its seen-as-if-through-a-funhouse-mirror rendering of intelligent design passes along with its distortions directly into the bloodstream of popular consciousness. If you’re ever looking for a way to kill time, counting errors per sentence in any Wikipedia article that touches on ID will soak up plenty. This of course is a way to really kill time — not to use it effectively by somehow correcting the errors. No class of people on the planet has more time on their hands than the guys who edit Wikipedia articles. As part of what seems to be a 24/7 unpaid job, they stand ready at a moment’s notice to change any attempted correction back to its original erroneous version.

Along with other falsehoods, the ranks of Wikipedia errors include a group of myths, comprising a Darwinian Mythos of superstitious, credulous, fallacious and legendary beliefs about intelligent design. Among these, the myth as to falsifiability or testability ranks high on the Wikipedia Scale. The latter is a rough measure of how important a particular mythic theme is to the overarching conception of Darwinism as unquestionable “fact,” gauged by how insistent the Wikipedia editors are in emphasizing it.

Regarding the mythic idea that intelligent design can’t be tested or falsified and is therefore unscientific, the Wikipedia editors quote the U.S. National Academy of Sciences. They cite the distinguished scientist and philosopher Judge John E. Jones. They cite blogger PZ Myers on “Rule 702 of the Federal Rules of Evidence.” They quote philosopher Elliott Sober: “Defenders of ID always have a way out. This is not the hallmark of a falsifiable theory.”

Yet isn’t it funny that the Darwinist faithful are often perfectly happy to launch attempts to clobber intelligent design on factual and scientific grounds — just as if ID were genuine science — only to retreat immediately behind the barricade of the Falsifiability Myth? If they had confidence either in the myth or in the attack, presumably they would choose one and stick with it.

By way of illustration, the new year starts off with a series of articles based on a symposium back in June of the 1st International Society of Protistologists (North American Section), now published in a primary research journal, The Journal of Eukaryotic Microbiology. The January/February issue collects essays on how “Horizontal Gene Transfer and Phylogenetic Evolution Debunk Intelligent Design.” Biologists from Roger Williams University, the University of Georgia, the New York State Department of Health, the University at Albany (SUNY), and the University of Massachusetts contributed attempts to “Uncover Faulty Logic in Intelligent Design” or “Dispel the Myths of Intelligent Design,” as two article titles put it.

Dispel? Uncover? Debunk? That sounds very much like falsifying. Whether the dispelling, uncovering and debunking succeed is a different question but there can be no doubt that at least when they were composing their presentations, treatments of no little empirical depth and detail, the authors took it for granted that intelligent design can be tested, that ID advocates cannot simply slip out of any refutation. Otherwise, what in the world could be the purpose of the symposium? One assumes the participating biologists do not enjoy endless free time to spin their wheels. They are not unemployed obsessive compulsives, like the Wikipedia editors. Or maybe I’m naïve about academic life.

It reminds me of the old Peanuts cartoon series, where Lucy had a stand dispensing “PSYCHIATRIC HELP 5¢.” Underneath the window where she sat was the additional hand-printed information, “THE DOCTOR IS” and then a little placard that could be turned up or down, “IN” or “OUT.”

Sometimes the doctor was “IN.” Sometimes “OUT.” Sometimes intelligent design IS testable or falsifiable. Sometimes it IS NOT. If the question seemed to depend on which doctor, or which Wikipedia editor, is IN or OUT, you could ascribe the confusion to a candid difference of opinion among evolutionists. But that seems not to be the case. I’m not aware of an established opinion among them that consistently, honestly concedes that intelligent design is science but that it is science that has been tested and found to be false. In the Darwin debate, if either party really “always has a way out,” it’s not the defenders of ID but those of Darwinism.

Posted by David Klinghoffer at 12:00 AM | Permalink | TrackBacks (1)

For many years, Jerry Fodor has been an outspoken critic of Darwinian reasoning in cognitive science and the philosophy of mind / language. As a graduate student, I saw him present a colloquium on these topics, in front of a semi-hostile audience, and admired his bravado in refusing to kneel before the Altar of Darwin. Sorry if that language seems over the top, but after the end of the Darwin Year, the steady worshipful attitude towards old Charles has finally got to me.

Now, in the wake of his controversial and much discussed London Review article, Fodor — along with cognitive scientist Massimo Piattelli-Palmarini — has made his arguments fully general in What Darwin Got Wrong.

It's interesting to read the publisher's advertising copy (i.e., book description), which reveals the very strong cultural stigma, at least among the likely academic audience for Fodor's book, still attached to dissent from Darwinism:

This is not a book about God, or about intelligent design. Rather, here is a remarkable book, one that dares to challenge natural selection—not in the name of religion but in the name of good science. Most scientists are so terrified of religious attacks on the theory of evolution that it is never examined critically.

But there are major scientific and philosophical problems with the theory of natural selection.

Well, yes — and it's possible to discuss those problems only if one is not intimidated by the C word: "What are you, some kind of creationist? No? Well, you're giving aid and comfort to them!" The abuse heaped by Brian Leiter on Thomas Nagel, for the latter's recommendation of Signature in the Cell, is an example of what Fodor can expect in 2010.

But, from my firsthand experience of Fodor's courage in high-pressure academic settings, he's more than up to the challenge.

Posted by Paul Nelson at 12:18 AM | Permalink | TrackBacks (0)

Ganon was taken to the Auschwitz-Birkenau hospital, where Josef Mengele, the so-called "Angel of Death," conducted grisly experiments on Jewish prisoners.

Ganon had to lie down on a table and was tied down. Without any anesthetics, Mengele cut him open and removed his kidney. "I saw the kidney pulsing in his hand and cried like a crazy man," Ganon says. "I screamed the 'Shema Yisrael.' I begged for death, to stop the suffering."

After the "operation," he had to work in the Auschwitz sewing room without painkillers. Among other things, he had to clean bloody medical instruments. Once, he had to spend the whole night in a bath of ice-cold water because Mengele wanted to "test" his lung function. Altogether, Ganon spent six and a half months in the concentration camp's hospital.

Precisely what corrupted Mengele's eager young mind is hard to pin down. Probably it was a combination of the political climate and that his real interest in genetics and evolution happened to coincide with the developing concept that some human beings afflicted by disorders were unfit to reproduce, even to live. Perhaps the real catalyst in this lethal brew was that Mengele, first at Munich and later at Frankfurt, studied under the leading exponents of this "unworthy life" theory. His consummate ambition was to succeed in this fashionable new field of evolutionary research.

Medicine at German universities was in any case more complementary to Mengele's real interest in evolution, since it was taught in accordance with the guidelines of the social Darwinist theory that Hitler and a growing number of German academics found so attractive.

One of the earliest influence on the student doctor was Dr. Ernst Rudin, whose lectures Mengele regularly attended....Rudin was a leading proponent of the theory that doctors should destroy "life devoid of value." Rudin himself was one of the architects of Hitler's compulsory sterilization laws, which were enacted in July 1933.

...the reduced adaptation, as Darwin expressed it, does not lead to eradication, but rather the effect of natural selection has been transformed through civilization into its opposite and thus to contraselection.

The messianic quality of social Darwinism seems to have appealed to the young Mengele. His writings suggest that he was especially struck by their use of the phrase "the fate of mankind." From his youthful encounter with their distorted ideals, to his old age, a weary and broken exile, Mengele would continue to feel a personal allegiance to the social Darwinists. At the university, the question of the "biological quality of mankind" may have been esoteric to most of Mengele's classmates. But for him, it was apparently a clarion call.

Indeed, the ideas Mengele was so anxiously absorbing in his studies were precisely the ones that would propel him down the road to Auschwitz.

Posted by David Klinghoffer at 5:18 PM | Permalink | TrackBacks (0)

There are two big stories arising from the California Science Center’s censorship last October of the pro-intelligent design film Darwin’s Dilemma. The first big story, which was the primary focus of a Los Angeles Times article last week, is the act of censorship itself. As an agency of state government in California, the Science Center is required to abide by the First Amendment’s guarantee of free speech. The Science Center didn’t have to rent its facilities to the public, but once it did so, as a government agency, it was legally obliged by the First Amendment to treat all citizens equally.

But there is another big story tied to the Science Center that hasn’t received sufficient attention yet: The Center’s illegal cover-up.

The California Science Center has flagrantly violated California’s open records law in an apparent effort to hide the real story behind its censorship of Darwin’s Dilemma. The Center’s evasion of the law is the reason for the open records lawsuit recently brought by Discovery Institute against the Center. In October, the Institute filed a comprehensive open records request demanding that the Science Center turn over all documents relating to its abrupt decision to cancel the privately-sponsored screening of Darwin’s Dilemma. In early November, the Science Center released 44-pages of documents in response to the records request. At that time, the Center assured Discovery Institute that it had turned over "all documents" and that "no documents have been withheld," apart from a few e-mail addresses that were redacted. The Science Center did not tell the truth. Discovery Institute independently obtained incriminating emails involving Center officials that should have been turned over by the Center but weren’t.

Most importantly, the Institute obtained a smoking-gun e-mail confirming that the censorship of Darwin’s Dilemma was connected to the Science Center’s relationship with the Smithsonian Institution. In an Oct. 6 email to the American Freedom Alliance, Science Center Vice President Christine Sion specifically cited alleged damage to the Center’s “relationship with the Smithsonian” as the reason for canceling the Darwin’s Dilemma screening. In its open records request, Discovery Institute had asked for all documents relating to the screening cancellation that referenced the Smithsonian. The Christine Sion e-mail was clearly covered by that request and therefore should have been produced. It wasn’t. Another email from a Smithsonian official to the Science Center complaining about the screening was likewise suppressed.

These missing emails may be the tip of the proverbial iceberg. There is a huge unexplained gap in the documents produced by the Center thus far, raising suspicions that the Center may have suppressed many more incriminating documents. Notably, the Science Center failed to disclose even a single email or document relating to the Darwin’s Dilemma screening written by any decisionmaker at the Center who actually made the determination to cancel the screening. In other words, the Science Center would have the public believe that although there was lively email traffic about the screening by others at the Center, no one involved in making the cancellation decision composed even one email or other document mentioning the screening.

It is certainly beginning to look like someone at the Science Center scrubbed the record in order to hide any incriminating documents from the public in violation of the law. And that’s outrageous.

Even those who don’t care one whit about the debate over Darwinism and intelligent design ought to be concerned when a state agency flagrantly violates an open records law and then lies about it. Let’s hope that the judicial system in California is prepared to defend the public interest and to force the Science Center to comply with the law.

Posted by John West at 12:30 AM | Permalink | TrackBacks (0)

Die-hard defenders of Darwin claim that there are no valid criticisms of their viewpoint and cannot publicly admit that there is any credible dissent from neo-Darwinism. At times, the NCSE has even been forced to argue that it is "possible to discredit" the Scientific Dissent from Darwinism list by referring people to a YouTube video titled, "Evaluating an antievolution petition," created by some would-be internet critic. That's right — in their desperation to attack the Dissent from Darwinism list, the NCSE cites to some random YouTube video.

That video has some major misunderstandings about the Dissent from Darwinism list. Its creator seems to be following what Michael Behe has called the “principle of malicious reading,” which “ignores (or doesn’t comprehend) context, ignores (or doesn’t comprehend) the distinctions an author makes, and construes the argument in the worst way possible.”

The video’s false claims and outright misrepresentations about the list that are too numerous to catalogue, not the least of which is the fact that the version of the list attacked in the video is a long-outdated version that was first created back in 2001, when the list first started and had only about 100 signatories. Today the list has over 800 signatories. For the latest public version of the list, please see A Scientific Dissent from Darwinism.

Just some of the outlandish and false claims about the list in the video include:

The critic pulls a bait-and-switch by redefining evolution in a way that is clearly not intended by the list, and then claims that some list-members don’t belong under the definition that the list never intended to use. To be more specific, the critic defines evolution as "common descent," and then claims that some list-members don’t "doubt evolution," so defined and thus "shouldn’t be on the list." But the list has always been called "A Scientific Dissent from Darwinism"—using a neo-Darwinian definition of evolution as the claim that "random mutation and natural selection [can] account for the complexity of life" (from the list’s statement). The list is plainly not about skepticism of common descent; it’s about skepticism of the sufficiency of the neo-Darwinian mechanism. The fact that the critic finds list-members who accept common descent but doubt neo-Darwinism should not be surprising. The critic has given no good reason to explain why those list-members should be off the list. As evidence of the baselessness of the critic’s claims, he argues that Michael Behe, leading scientific critic of neo-Darwinism, shouldn’t be on the list simply because Behe accepts common descent. The critic must be trying hard to not understand the list.

Keep in mind that the video attacks a version of the list from back in 2001 when the list only had about 100 people. The critic then touts a bogus survey by claiming the list is discredited because he contacted people on the list who didn’t want to be on it. But this critic only contacted biologists, and of those biologists, only 16 replied. Of those 16, he only gives 1 examples of a person who claimed that they didn’t want to be on the list—and that person has been removed from the list for years! Given the list’s current total of 800+ signers, this means that the critic had contact with less than 2% of the total signers on the list. That makes for a pretty meaningless analysis of the list, as far as survey statistics go.

In what can only be understood as a purposeful attempt to misunderstand the list, this critic makes a false criticism by claiming the list "dishonestly" misrepresents the credentials of list-members by listing either their current institution or the institution where they earned their Ph.D. There is no dishonesty here: the list clearly states at the top of the first page that list-members can be listed by EITHER current institution OR location of Ph.D., as it reads: "Scientists listed by doctoral degree or current position." (emphasis in original) It’s obvious which scientists are listed by current institution and which are listed by Ph.D. institution: those listed by "Ph.D." say, simply, "Ph.D." The critic really goes overboard with these false attacks, stating “it didn't matter if you had gone to University of Florida for your freshman year in undergrad and then the rest of your time spent at an unaccredited university, Florida State is where you were shown to be a scientist at." He then lists as “a perfect example of this” one list-member who is listed as "Ph.D. Neuroscience-Case Western Reserve" and the critic incorrectly charges that the list says that he "worked" at Case Western. In fact, the list clearly says this biologist is listed by his "Ph.D." The claim that this scientist went to Case Western for his “freshman year in undergrad” and then transferred to an “unaccredited university” is preposterous and false. Perhaps it is ironic that the video itself flashed the word "Lie" at this point—because in fact the scientist in question did get his Ph.D. from Case Western Reserve (his undergrad was completed at Michigan State University). Contrary to the critic’s false claims, there are no misrepresentations about the credentials of list-members in this regard.

The critic claims that some people asked to be removed from the list but never were. Again, his criticisms are misplaced because he uses a long out-dated version of the list. For example, he claims Fred Sigworth was not removed from the list, but in fact Sigworth has not been on the list for years. The critic again asserts that there were people who wanted to be removed from the list "7 years ago," but he never gives any examples to back up his charges and accusations. Had the critic used the current version of the list, he would have found that scientists like Sigworth were removed long ago. Scientists are only added to the list at their express request. Over the years, only a few scientists have asked to be removed from the list, most because of persecution and intimidation they suffered for making their views public. There are many more scientists who have declined to sign the list because of the threat of persecution.

The critic claims that biologists such as Ralph Seelke and Michael Behe are not true skeptics of "evolution" and don’t belong on the list. This is incredible. The critic appears so desperate to discredit the list that he cites Behe, one of the leading critics of neo-Darwinism, in an attempt to boast about scientific support for evolution. Similarly, in 2007 Seelke co-authored a textbook, Explore Evolution: The Arguments For and Against Neo-Darwinism, that provides many potent criticisms of neo-Darwinism. Such scientists who the critic claims are "pro-evolution" actually have huge doubts about the core claims of neo-Darwinian theory. Due to the fact that the critic claims that leading Darwin-skeptics like Ralph Seelke and Michael Behe don’t qualify as dissenters from Darwinism, it’s clear to me that this critic has very little understanding of the list, and his objections are neither credible nor compelling.

This video also makes a variety of false scientific claims. For example, the critic claims that molecular-based phylogenetic trees agree with phylogenetic trees based upon the fossil record "seamlessly." Trisha Gura wrote an entire review article in Nature entitled "Bones, Molecules or Both?" devoted to examining the difficulties encountered by evolutionary scientists when trying to reconcile molecule-based phylogenetic trees with phylogenetic trees based upon bones. According to the article, “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology,” leading to "evolution wars" among evolutionary scientists over whether they should use "bones," "molecules," or "both" when constructing phylogenies. As Gura observes, there are "disparities between molecular and morphological trees." ¹ Similarly, a review article by Colin Patterson dimly concluded, "As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology." ² Another science article likewise wrote, "That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent." ³ Finally, Matthew Wills studied whether fossil data has helped improve the congruence of phylogenetic trees and concluded, "Despite increasing methodological sophistication, phylogenies derived from morphology, and those inferred from different molecules, are not always converging on a consensus." ⁴ Regarding the congruence of different molecular-based trees, a 2009 article from New Scientist stated, “More fundamentally, recent research suggests that the evolution of animals and plants isn't exactly tree-like either,” and then discussed tree conflicts among higher branches of the tree of life (where horizontal gene transfer isn’t thought to be an issue). It's in this context of the higher branches that a scientist states: “The problem was that different genes told contradictory evolutionary stories. … ‘We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely.’”⁵ In contrast to the claims of the video critic, morphological, fossil, and molecular data do not fit together "seamlessly" when used to construct phylogenetic trees.

The critic also claims that endogenous retroviruses (ERVs) provide unequivocal evidence for common descent, even though biologists are beginning to suspect ERVs have function and are not merely functionless genetic "junk." ⁶

Towards the end of the video, the critic performs a meaningless calculation which allegedly gives the list "every mathematical concession possible" and claims that only 0.00275% of scientists reject "evolution" (which he defines as "common descent"). But the calculation makes no reasonable "mathematical concessions" to the list since his statistic makes the pretty outlandishly false assumptions that (1) all 3,661,320 scientists that he claims exist have been contacted to sign the list and therefore that number can be placed in the denominator to determine the total percentage of scientists who doubt Darwinism, and (2) that even among those scientists who were contacted, that all who doubted neo-Darwinism chose to sign the list. Assumption (1) is false because of course only a fraction of all scientists are probably even aware of this list. Assumption (2) is false because I personally know a significant number of Ph.D. scientists—particularly professional biologists—who doubt neo-Darwinism and would like to sign the list, but are afraid to do so because they fear what might happen to their careers if the sign it. So the statistic at the end of the video is meaningless. The critic attacks one list-member for making an “enormous statistical fallacy,” but the critic doesn’t seem to know how to recognize an “enormous statistical fallacy”—his own—when he sees one.

As a final point, it should be observed that the video constantly flashes irrelevant graphics referring to young earth creationist groups and personalities that have nothing to do with the narration. An earlier version of the video calls the U.S. the "United States of Jesus." Some people may find this kind of thing really funny, but the video is clearly not a serious or credible attempt to rebut the list. Given that NCSE’s executive director Eugenie Scott has admitted that "most ID proponents do not embrace a Young Earth, Flood Geology, and sudden creation tenets associated with YEC," ⁷ the video’s free association arguments appear to be false. Apparently the NCSE and others are so desperate to deny the existence of scientific dissent from neo-Darwinism that they are resorting to relying upon this non-credible, inaccurate, and factually bankrupt YouTube video.

References Cited:

[1.] Trisha Gura, "Bones, Molecules or Both?," Nature, Vol. 406:230-233 (July 20, 2000).

[2.] Colin Patterson et al., "Congruence between Molecular and Morphological Phylogenies", Annual Review of Ecology and Systematics, Vol 24:179 (1993).

[3.] Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, "Novel Phylogeny of Whales Supported by Total Molecular Evidence," Journal of Molecular Evolution, Vol. 44, pgs. S117-S120 (Supplement 1, 1997).

[4.] Matthew A. Wills, "The tree of life and the rock of ages: are we getting better at estimating phylogeny," BioEssays, Vol. 24:203-207 (2002).

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

[6.] See Andrew B. Conley, Jittima Piriyapongsa and I. King Jordan, "Retroviral promoters in the human genome," Bioinformatics, Vol. 24(14):1563–1567 (2008); Daisuke Kigami, Naojiro Minami, Hanae Takayama, and Hiroshi Imai, "MuERV-L Is One of the Earliest Transcribed Genes in Mouse One-Cell Embryos," Biology of Reproduction, Vol. 68:651-654 (2003).

[7.] Eugenie C. Scott, Evolution vs. Creationism: An Introduction, pg. 128 (Greenwood Press, 2004).

Posted by Casey Luskin at 12:00 AM | Permalink | TrackBacks (0)