May 2004 Archives

Paul Nesselroade opens his recent “Wedge Update” at ARN (here) by saying,

Recently, a few Intelligent Design (ID) critics have created some confusion over the meaning of “The Wedge.” Several statements made by ID detractors in books and blogs (web logs) have suggested “The Wedge” to be a partially concealed strategy by well-funded religious fanatics to attack science and force it to come under the thumb of a specific religious mindset. …

But is this an accurate characterization of “The Wedge,” or is this just a baseless appeal by Darwinists to impugn the motives of their adversaries? Well, as they say, when the facts aren’t on your side, argue motives.

Well, speaking of facts, here’s some information about an “Intelligent Design Conference to be held in beautiful Highlands, North Carolina this June 24-26,” sponsored by the Community Bible Church. (Information here)

The IDEA Club’s Punk Eek FAQ

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In response to postings on The Panda’s Thumb criticizing the IDEA Club’s description of punctuated equilibirum, Casey Luskin invited corrections. I have one or two suggestions. This is not exhaustive; I treat just one aspect of the FAQ.

Paul Nesselroade’s latest Wedge Update, titled “Defending the Wedge”, attempts to allay fears concerning the “wedge”. Nesselroade’s approach is two-fold: assert that the “wedge document” and the “wedge strategy” are distinct, and that the “wedge strategy” is about answering a pair of arguments made by “Darwinists”. If the “wedge strategy” is just about answering some arguments, that’s all very metaphysical and non-threatening, right?

Nesselroade is, of course, wrong. The “wedge strategy” is more than just coming up with counter-arguments to “Darwinism” or “materialism”. There is a strong practical component to the “wedge strategy” that is apparent to anyone who not only listens to what “intelligent design” advocates say, but also watches what “intelligent design” advocates do. It is in this practical component that one recognizes that the “wedge strategy” is still all about implementing the specific policies and activities that were specified in the “wedge document”. The asserted separation between “document” and “strategy” is non-existent.

I want to take up two cases of synchronicity that demonstrate just how lame these apologetics for the “wedge” really are. The first involves Nesselroade’s essay and the announcement of an “intelligent design” conference to be held June 24-26 in Highlands, NC. The second concerns an interview with Phillip Johnson back in 2001 and the Santorum amendment.

Genetic Drift

EvoMath is back from a long hiatus. In this edition I will briefly touch on genetic drift and coalescence theory. Genetic drift is the evolutionary force whereby allele frequencies fluctuate due to chance because the alleles in a generation are a random sample of the alleles in previous generation. To help understand what I am talking about, consider a heterozygous father, with genotype Aa. Under Mendelian heredity, he will pass on the A allele 50% of the time and the a allele the other 50% of the time. If he has only one child, then he clearly cannot pass on both of his alleles, and thus one of those alleles–say a–will be lost from his lineage. The remaining allele, A, will then have “drifted” to 100% or “fixation.” If he has more children, then he may pass on both of his alleles, but it is not likely to be exactly at a 50:50 ratio.

Genetic drift occurs whenever a population has a finite size, and since all populations are finite, it occurs in all populations. However, in large populations it can be very weak and thus negligible compared to other evolutionary forces.

Entropy: Common pitfalls

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Introduction

Entropy may seem to be at first a simple concept but when trying to apply these concepts correctly one invariably runs into frustrating issues and areas of confusion. In this posting I intend to explore some of these confusions and I hope to explain how one applies entropy calculations correctly.

The Scientist reports that paternal mitochondria have been found in the muscle cells of a sufferer from myopathy, by a team from the Beth Israel Deaconess Medical Center and Harvard Medical School. This means that paternal mitochondria not only find their way into the oocyte (the female egg cell), as Ankel-Simons and Cummins reported in 1996, but also can continue into the mature organism. What effect does it have on Mitochondrial Eve?

John Wilkins has written a FAQ on the probability of abiogenesis.

What Louis Pasteur and the others who denied spontaneous generation demonstrated is that life does not currently spontaneously arise in complex form from nonlife in nature; he did not demonstrate the impossibility of life arising in simple form from nonlife by way of a long and propitious series of chemical steps/selections. In particular, they did not show that life cannot arise once, and then evolve. Neither Pasteur, nor any other post-Darwin researcher in this field, denied the age of the earth or the fact of evolution.

From the early views of Aristotle, through the research by Louis Pasteur to abiogenesis research, Wilkins shows how these fascinating concepts evolved.

A worthy addition to the Probability of Abiogenesis FAQs

Read further on Talk.Origins

Bilateral symmetry in a sea anemone

anemone gastrula

There are quite a few genes that are known to be highly conserved in both sequence and function in animals. Among these are the various Hox genes, which are expressed in an ordered pattern along the length of the organism and which define positional information along the anterior-posterior axis; and another is decapentaplegic (dpp) which is one of several conserved genes that define the dorsal-ventral axis. Together, these sets of genes establish the front-back and top-bottom axes of the animal, which in turn establishes bilaterality—this specifically laid out three-dimensional organization is a hallmark of the lineage Bilateria, to which we and 99% of all the other modern animal species belong.

There are some animals that don't belong to the Bilateria, though: members of the phylum Cnidaria, the jellyfish, hydra, sea anemones, and corals, which are typically radially symmetric. A few cnidarian species exhibit bilateral symmetry, though, and Finnerty et al. (2004) ask a simple question: have those few species secondarily reinvented a mechanism for generating bilateral symmetry (so that this would be an example of convergent evolution), or do they use homologous mechanisms, that is, the combination of Hox genes for A-P patterning and dpp for D-V patterning? The answer is that this is almost certainly an example of homology—the same genes are being used.

Continue reading Bilateral symmetry in a sea anemone (on Pharyngula)

The results of the Second Panda Poll, PP2, show that the readers of this blog overwhelmingly think that the case against evolution should not be taught in the public schools. In response to the question,

The arguments against evolution are unsound and should not be taught as science in the public schools,

nearly 90 % of respondents strongly agreed or agreed. Approximately 10 % disagreed or strongly disagreed.

Shannon entropy applied

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Introduction to Shannon entropy

Motivated by what I perceive to be a deep misunderstanding of the concept of entropy I have decided to take us onto a journey into the world of entropy. Recent confusions as to how to calculate entropy for mutating genes have will be addressed in some detail.

I will start with referencing Shannon’s seminal paper on entropy and slowly expand the discussion to include the formulas relevant for calculating the entropy in the genome.

But first some warnings

Speaking of bathroom walls...check out this long thread on Creationist genetics. It's an enlightening peek into the mind of a creationist. I had originally commented on the curious tale of Jacob and Laban in the book of Genesis, in which Jacob is able to modify the coat color of sheep and goats by having them mate in front of appropriately colored sticks. I pointed out that this is nonsense—genetics doesn't work that way.

We then got many overwrought comments from a creationist, Susan Williams, defending the Bible. Confronted with a story that contradicts plain, simple, observable biology, she resorts to the Rush Limbaugh defense: it's just a joke, you aren't supposed to take it literally.

That's fine with me. I wonder, though, why creationists insist on defending as literally true other tales from the Bible that contradict the scientific evidence? As long as they are willing to give God a sense of humor and a willingness to illustrate his lessons with allegory and jokes, why not carry that to it's logical conclusion and recognize that the Bible is not a scientific document?

The Bathroom Wall

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With any tavern, one can expect that certain things that get said are out-of-place. But there is one place where almost any saying or scribble can find a home: the bathroom wall. This is where random thoughts and oddments that don’t follow the other entries at the Panda’s Thumb wind up. As with most bathroom walls, expect to sort through a lot of oyster guts before you locate any pearls of wisdom.

I ran across the following interesting website

Phylogenetic trees of taxa are often created and used for the calculation of ancestral traits of the internal nodes of these trees. However, seldom are these ancestral traits visualized in an intuitive manner.

Ancient Wings allows users to see how the ventral hindwing of 54 butterflies in the genus Bicyclus have changed over time. By clicking on each of the nodes within the evolutionary tree, the user can see how eyespots’ sizes and positions relative to the wing have evolved. The ancestral wing pattern traits were calculated using COMPARE 4.4, a program by Emilia Martins of Indiana University. The phylogenetic tree and its historical calibration are by Antonia Monteiro of SUNY at Buffalo.

Ancient Wings website

The paper, “Ancient Wings: animating the evolution of butterfly wing patterns”, and the program can be found at this website.

Since we have seen some poorly argued claims about entropy and its relevance to evolution, I will explore the concepts of entropy as they apply to genome evolution and will show that the evidence shows how simple processes like variation and selection are sufficient to explain the evolution of complexity or information/entropy in the genome.

While various ID authors (here and elsewhere) have argued that such natural processes are unable to explain the evolution of information in the genome, it should be clear that the actual evidence contradicts any such suggestions.

In the past I have argued with various people on the topic of entropy. Jerry Don Bauer a.k.a. Chronos has shown some interesting confusions as to the concept of entropy and believes that he has shown that using the laws of entropy he has shown that macro-evolution could not have happened.

Dog Genome Yields Information That May Benefit Human Health

A new genetic analysis of man’s best friend could help scientists explain why a border collie has knack for herding or why poodles sport a curly coat. In the May 21 issue of Science, researchers at Fred Hutchinson Cancer Research Center report the first extensive genetic comparison of domestic dog breeds.

The study, led by Fred Hutchinson researchers Drs. Elaine Ostrander, Leonid Krugylak and graduate student Heidi Parker, revealed distinct DNA blueprints for each of the 85 varieties of purebreds that were analyzed as well as similarities between certain breeds. The researchers expect that understanding these genetic relationships will help them uncover the genes responsible for the physical features and behaviors unique to each breed as well as the diseases to which they are commonly susceptible, such as cancer, deafness, blindness, heart disease and hip dysplasia.

The findings also have generated excitement among those who study diseases of the human animal. Because at least half of the more than 300 inherited canine disorders-including a number of cancers-resemble specific diseases of man, many scientists believe that the dog genome holds a wealth of information that will benefit human health.

There are a number of things claimed for this study, most of which confirm things that we already knew or suspected.

  • The nearest relatives of dogs are wolves.
  • Dog breeds are genetically distinct.
  • Dog breeds cluster into four large groups. One is more closely related to wolves, and includes the Alaskan Malamute and Siberian Husky. Another includes mastiff-like breeds. The third includes herding dogs. The fourth comprises hunting dogs.
  • The analysis is being used to find genetic bases for various canine diseases.

The clustering noted above is shaking up some notions of the history of certain breeds:

Noticeably absent from this ancient cluster were several breeds long regarded as the most ancient by breeders, including the Pharaoh Hound and the Ibizan Hound – depicted on Egyptian tomb walls. The researchers said their analysis indicated that the modern representatives of these breeds were recreated in more recent times from combinations of other breeds. The researchers also found genetic evidence for a recent origin of the Norwegian Elkhound, believed to be of ancient Scandinavian origin.

(PR Newswire)

I think that it is important to note that this study is based on microsatellite analysis, not whole-genome data. The claim of the headline and press release that this study “may benefit human health” appears to be a long way from turning possibility into performance. It seems certain that the canine study will be useful in helping track down genetic diseases in dogs, but to have that carry over to humans we would have to know that many of the same microsatellite markers exist in both species, and that has not yet been established as far as I can tell. (As an organismal biologist skimming bioinformatics, though, I could easily be wrong on this. I would be grateful to anyone who can point to work where this has been accomplished.) Some microsatellite studies show useful cross-species comparisons are possible, and other studies show that they don’t work so well, depending upon the particular species under consideration. By contrast, comparative genomics has already identified the genetic basis of a human disease, Bardet-Biedl Syndrome (BBS).

Archaeology and the Explanatory Filter?

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Since I seem to be on a roll, I thought I’d take a look at a claim that’s made frequently by ID proponents, namely that archaeology uses a design detection procedure akin to that allegedly formalized by Dembski’s Explanatory Filter. (Gary Hurd: Feel free to interject/comment/correct at will.)

Gene duplication versus ID

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Gene duplication is mentioned as one example in which information and complexity in the genome can increase leading to biochemical novelty and even irreducibly complex systems. Despite this ID proponents object to gene duplication as a relevant mechanism. I will explore some of the objections and show how science has and is addressing these objections. I intend to show that the objections raised by ID proponents are mostly without merit.

Behe

Behe mentions in this 2003 interview that

My current work is an attempt to model the evolution of new protein functions through gene duplication. Gene duplication is purported to be a major pathway for the Darwinian evolution of biochemical novelty. However, as in other areas, Darwinists have not closely examined whether gene duplication can realistically do all that they ascribe to it. I hope to help them out in this area by asking those questions.

It seems that Behe may not be familiar with the research on gene duplication when he states that

The hitch, as always, is that Darwinists virtually never explain in any detail how natural selection would actually get from protein A to protein B after the gene for protein A duplicated. After all, gene duplication just leaves you with a second copy of the same gene — nothing different. The problem is, as everyone agrees, that the duplicated gene is much more likely to suffer a deleterious mutation than a beneficial one. Nonetheless, Darwinists hope that the occasional beneficial mutation just might come along. However, they never look very deeply into the matter. It turns out that to acquire some new functions, such as the capacity to bind a new molecule, multiple mutations would be expected to be needed, not just a single mutation. The requirement for multiple mutations would quickly render gene duplication an untenable explanation, since a duplicated gene would be riddled with deleterious mutations before acquiring several positive ones.

Where’s the beef, Paul?

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Fifteen months ago Paul Nelson made available a “discussion paper” on Ontogenetic Depth to serve as background for an ISCID chat. In that paper he claimed that

The ontogenetic depth of a handful of extant animals (from the model systems of developmental biology) is known with precision.

That’s 15 months ago. In the chat itself Nelson cut and pasted the same claim from the background paper, and said further that

But, as I said at the beginning, the start of any scientific answer begins with correctly understanding the problem. Ontogenetic depth helps to do that. This is what any candidate theory of animal origins has to explain. it is not itself an explanation, but a description.

So somehow or other, ontogenetic depth provides a problem for biology to explain, but we’re not told what the problem is - we are not given the metric Nelson uses to describe the problem. That’s of no particular help in “correctly understanding the problem.”

The Fear of Evolution

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Last year a middle school science teacher in my local school district proposed that the Intelligent Design Network’s Objective Origins Teaching Policy be adopted by the district. After some debate and politicking it was rejected by the Board of Education, as was a watered down version offered after the rejection of the initial proposal.

After thinking about it at length and talking with people in the community and elsewhere, what I am realizing is that this is not something that has anything to do with reason and science; it is about fear.

ISCID is the International Society for Complexity, Information and Design. Over at Stranger Fruit, Jerry Don Bauer (no stranger to the ISCID boards) makes a number of statements regarding peer-review and ID:

There is a ton of peer reviewed lituraure [sic] out there-Both ARN and ISCID put out quarterly journals in this area, along with many others. You could have gotten by with that statement 2 or 3 years back, but not today. …

[ID] literature [is] being peer reviewed is it not? In fact, the very purpose for ISCID is peer review. Look at all the peer reviewed books out on the subject. Look at the papers on other sites

In what follows, I want to briefly examine these claims.

Tangled Bank #3 is online

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The Tangled Bank

Tangled Bank #3 is available at 10,000 Birds. The Tangled Bank is a biweekly roundup of science weblogging. Read and enjoy.

Remember, if you've written anything on your weblog at all relevant to biology, send a link to host@tangledbank.net so that it will be included in the next edition (scheduled for 2 June, at De Rerum Natura).

Last week I discussed the constitutionality of the Alabama Academic Freedom Act, an act that sought to empower any teacher in the state of Alabama “to present scientific information pertaining to the full range of scientific views concerning biological or physical origins in any curricula or course of learning.” Timothy Sandefur also had some choice words to say about it.

With great pleasure I am happy to report that the Alabama Academic Freedom Act did not come up for a vote on the final day of the Alabama legislative session. The house spent most of the day dealing with the General Fund budget and did not have time to consider the many bills that the religious-right had proposed but not passed.

omega

In developmental biology, and increasingly in evolutionary biology, one of the most important fields of study is deciphering the nature of regulatory networks of genes. Most people are familiar with the idea of a gene as stretch of DNA that encodes a protein in a sequence of As, Ts, Gs, and Cs, and that's still an important part of the story. Most people may also be comfortable with the idea that mutations are events that change the sequence of As, Ts, Gs, and Cs, which can lead to changes in the encoded protein, which then causes changes in the function of the protein. These are essential pieces in the story of evolution; we do accumulate variations in genes and gene products over time.

There's more to evolution than just that relatively straightforward pattern of change, however. Consider humans and chimpanzees. We're both made of mostly the same stuff: the keratin that makes up our hair and the organization of hair follicles is nearly identical, and our brains each contain the same structures. The differences are in regulation. We both have the same kinds of hair, but chimps have more of it turned on all over the place, while we've mostly down-regulated it everywhere except a few places. The differences in our brains may be mostly differences in select timing: our brains are switched on to grow for longer periods of time in development, and there are almost certainly specific regions and patterns of connectivity that are tweaked by adjusting different levels of different gene products in different places at different times.

Continue reading "Upstream plasticity and downstream robustness in evolution of molecular networks" (at Pharyngula)

Hmmm. Let's see. Intelligent Design creationists made a big push in Minnesota. They had a friendly education commissioner who stacked the deck in their favor, and when the sensible scientists, educators, and citizens who wrote the science standards came up with a darn good document, she formed a special committee of creationists to put together revisions. End result: the revisions were scrapped, and our conservative stealth creationist commissioner finds herself thrown out on her ear.

Sounds like a defeat for Intelligent Design to me.

But no! How could I be so deluded? The Discovery Institute has declared it a victory!

Minnesota has become the second state to require students to know about scientific evidence critical of Darwinian evolution in its newly adopted science standards. On May 15, the Minnesota legislature adopted new science standards that include a benchmark requiring students to be able to explain how new evidence can challenge existing scientific theories, including the theory of evolution.

The benchmark reads, "The student will be able to explain how scientific and technological innovations as well as new evidence can challenge portions of or entire accepted theories and models including "...theory of evolution. ..." The benchmark is included in the "History and Nature of Science," strand of the science standards for grades 9-12.

"This is a significant victory for the vast majority of Americans who favor teaching evolution but who want it taught fully, including scientific criticisms of the theory," said Dr. John West, Associate Director of Discovery Institute's Center for Science and Culture. Discovery Institute supports teaching students more about evolutionary theory, including introducing them to mainstream, peer-reviewed scientific debates over key aspects of modern evolutionary theory (known as neo-Darwinism).

Dr. West added that he expected some Darwin-only supporters would try to downplay or ignore the new benchmark. "Undoubtedly some Darwin-only supporters will claim that the standard doesn't really mean what it says, or that schools don't really need to follow it. Minnesotans who support the standard will need to make sure that it is actually implemented in Minnesota schools."

When these guys speak, you know they are lying. They've changed their logo and name so many times, they might as well just go straight to the most appropriate one: Ministry of Truth.

Minnesota wins

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On Pharyngula PZ Meyers reports that:

It’s nothing but good news for biology from the Minnesota legislature this week. The Intelligent Design creationists’ amendment to the state science standards went down in flames.

Read more at Pharyngula

A temporary glitch

I've noticed that a lot of people are using the badges for the Panda's Thumb (and good for you!) that I host on my site, pharyngula.org, and some of the graphics in my articles here are similarly hosted there. You may find that those graphics aren't available today: my server is offline for the next several hours while some major electrical work is done on my campus. My apologies, and we expect everything to come back online by late this afternoon or early evening, Central Time.

(Oh, and Pharyngula will also be unavailable during that time.)

Let me start this off with a quote from Charles Darwin:

I have been struck with the likeness of many of the half-favourable criticisms on sexual selection, with those which appeared at first on natural selection; such as, that it would explain some few details, but certainly was not applicable to the extent to which I have employed it. My conviction of the power of sexual selection remains unshaken; but it is probable, or almost certain, that several of my conclusions will hereafter be found erroneous; this can hardly fail to be the case in the first treatment of a subject. When naturalists have become familiar with the idea of sexual selection, it will, as I believe, be much more largely accepted; and it has already been fully and favourably received by several capable judges.

Descent of Man, preface

And now let’s look at this news story that has as its focus a “challenge” to sexual selection.

Lunch with the FT: Rainbow warrior

Simon London Wrote:

“If you have a theory that says something is wrong with so many people, then the theory is suspect,” says Joan Roughgarden, looking up from her Caribbean chicken salad. “It is counter-intuitive that nature should have done such a bad job - or, if you prefer, that God should have made so many mistakes.”

The theory in question is Charles Darwin’s theory of sexual selection; the “mistakes” are homosexuals, bisexuals, transsexuals - anyone who does not fit into the neat categories of heterosexual male and female.

By challenging the great 19th-century naturalist, Roughgarden, a professor of biological sciences and geophysics at Stanford University, is making waves in academia and beyond. The implications, not only for science but also for society, could be profound. After all, you don’t need to be versed in the Origin of Species to share Darwin’s twin assumptions that, broadly, the purpose of sex is reproduction and that females select mates on the basis of genetic characteristics or traits.

Being versed in Darwin studies would mean that one would know that instead of Origin of Species one should be looking at Descent of Man for Darwin’s full explication of his theory of sexual selection. And when one looks there, does one find that sexual selection is founded strictly upon the two “assumptions” identified above? No, one does not.

Continue reading “Darwinism in Crisis Again?” on The Austringer.

Behe published his book “Darwins Black Box” in 1996. In it he stated the principle of “irreducible complexity” and claimed that, amongst other things, the clotting system and the eubacterial flagella were irreducibly complex, and were not evolvable. Since that time, researchers have uncovered significant evidence for the evolution of both the clotting system and the eubacterial flagella, what has Behe been researching while this has been going on? Well at a recent ID conference Behe has apparently produced a calculation that shows that the evolution of new binding sites between proteins and things such as other protein, DNA and small molecules is so unlikely as to be impossible.

The process of reviewing the Kansas state science standards started this week, and already contention has arisen over the selection of members of the review committee. (See here for a news story.) Board members have nominated one (or in some cases more) people they would like to be on the committee along with those selected directly by the Department of Education. Given that at least four of the ten Board members are supporters of “revisiting” the issue of evolution, we can anticipate, I think, that Kansas may once again be a focus national interest in the evolution/creationism issue.

Furthermore, as noted in my previous post on Kansas here, Board of Education elections are this summer and fall and there is a possibility that the creationists will gain a majority. The architect of the 1999 standards, Steve Abrams, is still on the BOE, John Calvert and other IDnet members are still in Kansas, and other creationists from 1999 are still politically active in the state.

Therefore, in preparation for this, I would like to take a quick look at what has happened since the first time Kansas became infamous for its science standards, and then look at what we might expect this time around. In this post, I will summarize briefly what happened in Kansas in 1999, what has happened in other states since then, and, most importantly, what we might expect to happen in 2004. I offer this both for the benefit of those of you in Kansas who will directly involved and for those of you who should be preparing for when the anti-evolution movement comes to your neighborhood. (P.S. If you would like to get involved with Kansas Citizens for Science, please visit KCFS and send us an email.)

So now let’s look at the situation.

Well our first poll is over and the majority of the five hundred and nine votes cast say that giant pandas are not bears: 28% yes, 62% no, and 10% dunno. I hate to say it, but the majority is wrong.

Giant pandas (Ailuropoda melanoleuca) form the most basal branch of the bear family. The figure below shows the relationship of the bears to the rest of the extant order Carnivoria (Mammalia). It is the composite of two maximum parsimony phylogenies, Figures 1 and 8 of Bininda-Emonds et al. (1999), derived from data present in scientific literature. The scale of the tree is millions of years before present and was derived from data in Tables 2 and 9 of Bininda-Emonds et al. (1999).

The giant panda first appears in the fossil record about 3 million years ago during the Early Pleistocene. It had a wide distribution in the Pleistocene ranging from Myanmar to eastern China and as far north as Beijing (Schaller et al. 1985 p11 ). The giant panda lineage branched off from the other bears around 22 million years ago (Bininda-Emonds et al. 1999). It has been suggested that the giant panda is a descendent of Agriarctos, a “small, bearlike animal of the Ursavus lineage from the mid-Miocene in Europe” and the last surviving member of Ursidae subfamily, Agriotherinnae (Schaller et al. 1985 p229).

On April 26, 2004 I received an email message which is reproduced here in its entirety:

Dr. Perakh, I recently picked up a copy of your Unintelligent Design and wanted to alert you to some errors. As a brief introduction, I am a graduate student in Astronomy and have followed the intelligent design movement for several years. I find debunking such creationist claims an entertaining mental exercise and overwhelmingly approve of the purpose of your book. On pages 173-178, you discuss Hugh Ross’s treatment of thermodynamics in a cosmological setting. You correctly point out that Ross’s treatment is not overwhelming rigorous–however, his claim that the universe cools because it is expanding is correct.

Reed Cartwright is correct about how the Lemon test ought to be applied--and of course he's right about the real intent of the authors of the law in question. What I find interesting about the law is its careful, even scrupulous avoidance of the teaching of religion.

The Discovery Institute has issued a press release about the Alabama “Academic Freedom Act”. As is customary, they applaud the efforts of anti-evolution activists to corrupt American education. This bill seeks to empower any teacher in the state of Alabama “to present scientific information pertaining to the full range of scientific views concerning biological or physical origins in any curricula or course of learning.”

Before I turn to the press release, I want to address the bill itself. First off, Alabama Citizens for Science Education has both an educational analysis and a legal analysis of an earlier version of the “Academic Freedom Act.” The National Center for Science Education also has information on the legislation.

Now on the question of constitutionality of this law, the Lemon Test–from Lemon v. Kurtzman (1971) and modified in Agostini v. Felton (1997)–holds that for a law to satisfy the establishment clause of the US Constitution:

Two previous entries on this blog by John Lynch have discussed the scientific output (or lack thereof) of two intelligent design superstars, Jonathan Wells and Michael Behe. Despite claims that both of these ID supporters are actively engaged in research, Lynch documents that they have published little or no scientific research in the last six years. Now let's look at the record of another one of ID's superstars, William Dembski.

Mother Nature

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Dame Nature!

What is the "maternal instinct"? Does it even exist? There is a stereotype of the ideal mother as someone who expresses unconditional love, who sacrifices all for her children, and who is ferocious and unstinting in defense of her children. Women who compromise on this behavior, who express some reservations and perhaps some self-interest, may be labeled "bad mothers" or perhaps even worse, "feminists".

If self-sacrifice is the ideal maternal characteristic, though, then we should be asking our women to aspire to this biological pinnacle of mother love:

The prize for "extreme maternal care" goes to one of the various matriphagous (yes, it means mother-eating) spiders. After laying her eggs, an Australian social spider (Diaea ergandros) continues to store nutrients in a new batch of eggs—odd, oversized eggs, far too large to pass through her oviducts, and lacking genetic instructions. Since she breeds only once, what are they for?

These eggs are for eating, not laying. But to be eaten by whom? As the spiderlings mature and begin to mill about, the mother becomes strangely subdued. She starts to turn mushy—but in a liquefying rather than a sentimental way. As her tissue melts, her ravenous young literally suck her up, starting with her legs and eventually devouring the protein-rich eggs dissolving within her.

That story is from Sarah Blaffer Hrdy's Mother Nature, a book that discusses the meaning of motherhood and how it fits into biology and natural selection. I think we'd all agree that it is a little creepy, and perhaps too extreme—we should expect human mothers to love their children unconditionally, but carving off bits of flesh to make their sandwiches would probably be a bit much.

There are alternatives in the continuum of maternal commitment. Hrdy's book makes the point that motherhood is far, far more complex than any caricature of a blind maternal extinct can encompass. Being a mother is a difficult and pragmatic affair, and the lesson of biology is that Nature is solidly pro-choice...or that the answers are never simple and straightforward.

Continue reading "Mother Nature" (on Pharyngula)

In a recent news release, the Discovery Institute trumpets the results of two new surveys conducted by Arnold Steinberg & Associates. These surveys appear to follow along the same lines as an earlier Zogby International survey conducted for the DI.

In both Steinberg surveys and the Zogby survey, respondents were asked whether public school biology teachers should “Teach the scientific evidence for and against [Darwin’s theory of evolution]” or “Teach only the scientific evidence for it.” In all three polls, between seventy and eighty persent of those responding selected the first answer. This question is a very nice example of a question that is intelligently designed to produce the answer that the people commissioning the survey wanted to hear.

Otto: Apes don’t read philosophy.

Wanda: Yes, they do, Otto, they just don’t understand it.

“A Fish Called Wanda”

In his new book, The Design Revolution, “intelligent design” advocate William A. Dembski invokes the late philosopher Sir Karl Popper as an authority on “testability” (ch. 39, pp.281-282). Perhaps Dembski has read Popper, perhaps he hasn’t. It’s certain, though, that Dembski does not understand Popper, and has a long history of not understanding Popper. Which is surprising, because Popper was an extraordinarily accessible philosopher.

Dembski bases his chapter on “Testability” in The Design Revolution (ch.39) on an essay he posted to the Internet in 2001. Between these two, Dembski switches from the term “falsifiability” to “refutability” instead. This is an odd thing for Dembski to do. It is explainable as a response to criticism that I made of his use of “falsifiability” in 2001, as I showed then that Dembski’s use of “falsifiability” differed markedly from that of Popper, who defined its usage in science and philosophy. The new version of Dembski’s argument shows a continuing misunderstanding of Popper and overlooks the fundamental flaws in Dembski’s argument.

Guest Column, by Mark Isaak

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This is a guest column written by Mark Isaak. Mark is a long time follower and participant in the origins debate and the author of the Index of Creationist Claims.

Am I Being Censored?

by Mark Isaak

Creationists sometimes complain that they are prevented from publishing in peer-reviewed journals. I have addressed the falsehood of that claim elsewhere. But what about non-creationists getting published in creationist journals? As I recall, Glenn Morton was prevented from publishing in a creationist journal after he stopped being a young-earth creationist. Here I recount my own experiment in this area.

The National Science Foundation has just released a report on the growing, or should I say shrinking, problem getting home-grown scientists at a time when other nations are doing a better job, and retaining more scientists.

Being an American organisation, of course the NSF is focussing on the problems for that nation, but it inadvertently highlights a number of problems that are more widely being felt.

The IDEA Center is an organization that aims to support the diffusion of Intelligent Design (ID) notions by coordinating the activity of local chapters of (mostly) high school and undergraduate students (“IDEA clubs”) devoted to the study, discussion and promotion of ID. Their spiffy new web site provides a wealth of material and information for club members and other ID-interested parties. Their approach is very serious, scientific and professional. They prominently announce:

Our mission statement states that the IDEA Center aims to: 1. Promote, as a scientific theory, the idea that life was designed by an Intelligent Designer 2. Educate people about scientific problems with purely natural explanations for the origins and evolution of life 3. Challenge the philosophical assumptions of Darwinism, naturalism, and materialism From: The Science of IDEA

and assure:

This scientific approach [based on empirical observations of the natural world - AB] is the method that the IDEA Center takes when discussing intelligent design theory. From: Religious and scientific affiliations

In the spirit of scientific inquiry, the site provides a number of FAQs and Primers related to evolutionary biology subjects, ID arguments, etc. Today I am just going to focus on their recent and particularly bad “Featured FAQ” “Can irreducibly complexity be evolved via gene duplication and co-optation of parts?” (hereafter referred to as “IC, duplication and co-optation”, for short) which was brought to the attention of Panda’s Thumb members through the ID discussion board at ARN.

Another Tangled Bank

I would like to draw everyone's attention to a broad-based attempt to incite more general science-based weblogging, the Tangled Bank, and the latest entry in a biweekly series of science links, at The Invasive Species Weblog. Read it and follow the links, and just as importantly, submit your work to host@tangledbank.net.

Objective Origins: Just Say Noah!

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In a local school board election today, Darby, Montana, voters rejected candidates supporting an “objective origins” policy that borrowed from Intelligent Design Network, the Discovery Institute, and from the lousy Ohio model lesson plan. After a contentious sequence of events marked by threats of lawsuits, inappropriately closed board meetings, and the formation of an active and involved citizens group whose motto was “Objective Origins: Just say Noah!,” the vote today rejected supporters of the ID-inspired policy by a 2-1 margin. Here’s the Ravalli Republic story.

A little news about our namesake:

National Zoo officials said Sunday they do not believe there will be a pregnant panda this year at the animal park.

“It looks as though Tian Tian and Mei Xiang did not breed this year,” said assistant Curator Lisa Stevens. According to zoo officials, the pair had tried to mate several times since Friday.

“Tian Tian gets an ‘A’ for effort, but I have to say he gets an ‘F’ for technical merit,” said Stevens. “He did not make the connection we were all hoping for.”

Continue reading “No cubs, but pandas get A for effort” at CNN

We are all familiar with the spread of lies, half-truths and out of context quotes in the evolution wars. But it happens in other domains of science as well. Opponents of genetically modified foods, or stem cell research and of measured ecological research that fails to match expectations are all subject to this misrepresentation.

But it also happens when science encroaches, as opponents think, on the question of human nature. Here is a heartfelt and justifiably angry reaction by B. F. Skinner’s daughter to claims her father used her as a guinea pig.

Charles Colson's website, Breakpoint, is a good source for novel ID arguments. Their latest one involves the giant panda. The poor creature has been slowly going extinct for some time now. Their limited diet and leisurely reproductive rate, coupled with rampant habitat encroachment, do not bode well.

The connection with evolution? Well it seems that evolutionists are supposed to be stiff-upper-lip-types who don't get fazed by extinction.

GCISE has a new color pamphlet available that describes who we are. If you are in Georgia or care about Georgia, print it out and share it with other concerned citizens.

GCISE has been been leading the fight to protect science education in Georgia.

GCISE was founded in response to the placement of warning stickers on Biology textbooks in Cobb County in 2002 that state:

This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully, and critically considered.

We successfully fought to have the word “evolution” returned to the state curriculum and to restore important concepts from the AAAS benchmarks such as the age of the Earth, plate tectonics, the Big-Bang Theory, and the effect of humans on the environment.

GCISE is assisting classroom teachers to present evolution and the scientific method accurately and objectively.

Nobel Nominated?

In an ARN report on the recent ID conference at Biola University (formerly known as the Bible Institute of Los Angeles), the following caught my attention.

Featured speakers included Dr. Henry Schaefer, University of Georgia and five-time nominee for the Nobel Prize, and Dr. Michael Behe, Professor of Biochemist [sic] at Lehigh University.

The description of Dr. Henry Fritz Schaefer III as a “five-time nominee for the Novel Prize” is common amongst anti-evolutionists. In fact he often leads their lists of scientists who “challenge Darwinism.” However, there is no official record of Dr. Schaefer’s nominations because the Nobel Foundation doesn’t release nominations.

According to the Statutes of the Nobel Foundation, information about the nominations is not to be disclosed, publicly or privately, for a period of fifty years. The restriction not only concerns the nominees and nominators, but also investigations and opinions in the awarding of a prize.

From Nobel.se.

Update on Kansas

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As most readers of the Panda’s Thumb know, Kansas was the scene of a major creationist success in 1999 when the creationist majority of the state Board of Education worked with a local group of mostly young-earth creationists to pass state science standards that eliminated “macroevolution” as well as other parts of earth science and cosmology.

The resulting publicity made world-wide news for the next year and a half, and in the fall of 2000 voters in Kansas elected some new pro-science Board members who promptly reinstated the eliminated standards - and all was well.

Or so we thought. But in 2001, two pro-science Board members were defeated (one by a genuine stealth campaign,) and the Board reverted to a 5-5 split between the creationist conservatives and the pro-science moderates. Now the summer and fall of 2004 finds us facing both a new round of elections and a review of the science standards. Almost certainly the teaching of evolution will come under attack, and, pending the outcome of the election, possibly send Kansas back to world-wide infamy.

So here’s a report on the current state of affairs in Kansas.

A colleague in passing recently noted, of a committee we both endure, that "work expands to fill the amount of space allotted", and I casually remarked that it sounded a lot like a gas.

This got me thinking.

I read this article with stark disbelief. It's a pandering bit of fluff for Hovind's "Dinosaur Adventure Land"...in the freaking New York Times. There is a very brief quote from Eugenie Scott, but otherwise the whole think is one happy ad for Kent Hovind and creationism, and it even glosses over his tax evasion troubles. Don't like Disneyland because they talk about dinosaurs living millions of years ago? Take the kids to Kent Hovind's backyard instead, where they can play on the swings while fundamentalists do their best to keep them ignorant and stupid!

Just how low can the NY Times sink? Pretty low, as this article shows. I rant some more about it here, but it's well-nigh impossible to adequately express my outrage.

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