Posted by Timothy Sandefur on September 04, 2004 | Comments (12) | TrackBack (0)

I was delighted to see The Scientist mention the Panda's Thumb's crew's posts regarding the Stephen Meyer article.

Posted by PZ Myers on September 03, 2004 | Comments (0) | TrackBack (0)

Neurulation is a series of cell movements and shape changes, inductive interactions, and changes in gene expression that partitions tissues into a discrete neural tube. It is one of those early and significant morphogenetic events that define an important tissue, in this case the nervous system, and it's also an event that can easily go wrong, producing relatively common birth defects like holoprosencephaly and spina bifida. Neurulation has been a somewhat messy phenomenon for comparative embryology, too, because there are not only subtle differences between different vertebrate lineages in precisely how they segregate the neural tissue, but there are also differences along the rostrocaudal axis of an individual organism. A recent review by Lowery and Sive, though, tidies up the confusion and pulls disparate stories together.

Continue reading "Neurulation in zebrafish" (on Pharyngula)

Posted by PZ Myers on September 02, 2004 | Comments (4) | TrackBack (0)

Hox genes are metazoan pattern forming genes—genes that are universally associated with defining the identities of regions of the body. There are multiple Hox genes present, and one of their unusual properties is that they are clustered and expressed colinearly. That is, they are found in ordered groups on the chromosome, and that the gene on one end is typically turned on first and expressed at the head end of the embryo, the next gene in order is turned on slightly later and expressed further back, and so on in sequence. That the tidy sequential order on the chromosome is associated with an equally tidy spatial and temporal pattern of expression in the body has always been one of the more fascinating aspects of these genes, and they are one of the few cases where we see an echo of phenotypic form comprehensibly laid out in the DNA.

However, there are some exceptions to the tidy clustering, and they occur right in two animals that have been central to developmental/genetic research, Caenorhabditis elegans and Drosophila melanogaster. These animals have broken clusters. Almost everywhere else, the Hox genes are ordered in one place, but in two of the most common research organisms, they've been split apart into two groups…so what's going on? We have what looks a little bit like a universal rule in genetic organization, and then it gets violated with seemingly little consequence. How do worms and flies get away with it?

One way to find out is to look for more exceptions to Hox ordering, and here's a doozy: an animal, the tunicate Oikopleura dioica, has blown its Hox gene clusters to flinders and scattered the individual Hox genes all over its genome, with no detectable linkage between them.

Continue reading "Hox cluster disintegration" (on Pharyngula)

Posted by Timothy Sandefur on September 01, 2004 | Comments (38) | TrackBack (0)

(Trofim Denisovich Lysenko)

On my own weblog, Freespace, I've been urging readers to join me in helping the Victims of Communism Memorial Foundation. The Foundation needs another $23,000 in order to dedicate the monument in Washington D.C. this October. I thought I'd post a little here about one of the shocking atrocities that communism visited upon the world of biological science, in the person of Trofim Denisovich Lysenko.

Continue reading  “Biologists as Victims of Communism”

Posted by PvM on August 31, 2004 | Comments (4) | TrackBack (0)

In my research related to Meyer’s paper I ran across the following:

From Jay Richards [1] we read  in The Washington Post, August 21, 1999 an article on Darwinism and Design

Consider the hypothesis of universal common descent. Numerous molecular comparisons now suggest that bacteria, fungi, protozoa, plants and animals—while they share interesting commonalities—are not descended from a single organism. Fossil evidence reveals that the major groups of animals appeared relatively suddenly in the ‘Cambrian explosion,’ with no record of common ancestors.

Continue reading  “Icons of ID: No preCambrian ancestors”

Posted by PvM on August 30, 2004 | Comments (5) | TrackBack (0)

After PBS aired the very successful series ‘Evolution’, Meyer, as directory of the Discovery Institute’s Center for the Renewal of Science and Culture, wrote the following somewhat puzzling letter to the editor

Meyer is objecting to the claim by PBS that there exists a Universal Genetic Code.

Secondly, and more importantly, the existence of these variant codes is not consistent with a key prediction derived from Darwin’s theory of universal common ancestry. To see why, imagine typing on a keyboard in which the assignment between the keys and the letters that appear on your screen have been secretly changed. When you hit a specific letter such as an “n,” a different letter such as “t” appears. Or, imagine that every time you hit, say, an “o,” a period and a double space appears on your screen. Now envision submitting such a paper to a professor (without any information about the special new code that your computer used). Will your paper make sense? Will you get a good grade? I doubt it.

What is this fascination of Meyer to use linguistic strawmen arguments [1] when trying to discuss evolutionary concepts? But as others have shown, the genetic code shows, not surprisingly,  support for (neo)Darwinian theory. The variants are found as small twigs within the evolutionary tree of life. In fact, since Darwin argued for one or more common ancestors, I find Meyer’s claim not only incorrect but also exhibiting what is more commonly known as ‘a strawman’ argument.

Continue reading  “Meyer v Universal Genetic Code: Common Descent”

Posted by Richard B. Hoppe on August 30, 2004 | Comments (21) | TrackBack (1)

Here. 

It’s going to be interesting to see how this plays out over time.  (I don’t know how long that archive will last.  If it slides out of view I’ll look for a deeper archive.)

(URL courtesy of Roland98 on II)

RBH

Posted by Jim Foley on August 30, 2004 | Comments (34) | TrackBack (0)

Panda’s Thumb recently had an item about the strange case of the ISCID’s list of papers supporting Intelligent Design. Strange, because the ISCID won’t publicly release the details of the papers (i.e. “we have lots of evidence, but we can’t tell you what it is”).  Could it be that, like another such list once touted by the Discovery Institute, they don’t actually provide much evidence for intelligent design? Nah, surely not.

Anyway, I’ve just found another paper which should be added to the ISCID list - not least because it gives ID a pedigree of hundreds of years. It was published in 1710 in the world’s first scientific journal, The Philosophical Transactions of the Royal Society. I found out about this paper in Bryan Sykes’ book “Adam’s Curse” which is about the Y-chromosome responsible for gender determination in mammals - having a Y-chromosome makes you a male. The paper is:

An argument for Divine Providence, taken from the constant Regularity observed in the Births of both sexes. By Dr. John Arbuthnott, Physician in Ordinary to Her Majesty [Queen Anne], and Fellow of the College of Physicians and the Royal Society.

Continue reading  “A new (but old) Intelligent Design paper”

Posted by Reed A. Cartwright on August 29, 2004 | Comments (19) | TrackBack (0)

Biblical creationism offers two explanations for what we see in nature: “God did it” and “the Fall did it.”  Such theology often argues that God created nature perfectly and corruption entered into the world after the Fall.  Such things like blind cave fish are explained as post-Fall degeneration.  Such theology often argues that any similarities observed between “unrelated” organisms are due to common design.  This is often invoked to explain similarities between humans and other creatures, because biblical creationism holds that humans are not related to any other species.  However, these explanations are unable to account for common design flaws, which are features that are clearly biological flaws but are shared between organisms that are supposed to be unrelated.  Unary pseudogenes are an excellent example of this problem for biblical creationism.

Humans, chimps, gorillas, and other primates lack the ability to synthesize ascorbic acid (vitamin C) and must eat a diet that includes it to survive. Other animals are able to synthesize ascorbic acid because they have a complete metabolic pathway. However, humans et al. are missing a key enzyme, L-gulano-gamma-lactone oxidase, which is involved in the synthesis of ascorbic acid. However, we do have the non-functioning remains of this gene still in our DNA, as do other primates which have been studied: chimps, gorillas, orangutans, and macaques. In all five species the gene is broken in the same way (deletion of same exons) and is found in the same place in the genome.

Biology explains this shared flaw by proposing that in an ancestor of all five species, a deletion occurred in the L-gulano-gamma-lactone oxidase, rendering it non functional. This deletion was then passed to its descendents, producing the pattern that we see today. Biblical creationism is unable to explain it because either God would have to have made a flawed creation or humans would have to be related to other species. Neither are options that biblical creationism allows.

I have proposed this problem many times to biblical creationists who insist that humans do not share a common ancestor with any other species.  None of them have yet to account for this interesting fact of nature.

References

1. Nishikimi M et al. (1994) “Cloning and chromosomal mapping of the human nonfunctional gene for L-gulono-gamma-lactone oxidase, the enzyme for L-ascorbic acid biosynthesis missing in man.” Journal of Biological Chemistry 269: 13685-13688

2. Ohta Y and Nishikimi M (1999) “Random nucleotide substitutions in primate nonfunctional gene for L-gulano-gamma-lactone oxidiase, the missing enzyme in L-ascorbind acid biosynthesis.” Biochimica et Biophysica Acta 1472: 408-411

Posted by PvM on August 29, 2004 | Comments (5) | TrackBack (0)

Meyer [1] quotes a paper by Scott Gilbert (in fact this paper seems to be quite often quoted by ID-creationists).

Scott F. Gilbert, John M. Opitz, and Rudolf A. Raff, “Resynthesizing Evolutionary and Developmental Biology,” Developmental Biology 173 (1996): 357-372.

and presents their argument as follows

Gilbert et al. (1996) attempted to develop a new theory of evolutionary mechanisms to supplement classical neoDarwinism, which, they argued, could not adequately explain macroevolution.

But did they claim that classical NeoDarwinism could not adequately explain macroevolution?

The NCSE presented an analysis of the Analysis of the Discovery Institute’s “Bibliography of Supplementary Resources for Ohio Science Instruction”

Scott F. Gilbert (coauthor of [25] and [27]) wrote:

“My research on turtles and my research into evolutionary developmental biology is fully within Darwinian parameters. My gripe has been that neo-Darwinism has supposed that population genetics was the only genetics needed to explain Darwinian evolution. I claim that developmental genetics is also needed. So my research has been to include developmental genetics into the Darwinian mix.” And Douglas L. Erwin (author of [24]) told NCSE, “While the article considers the relationship between micro - and macro- evolution, the Discovery Institute is inaccurate in saying that I am challenging the standard view of evolution. The treatment of macroevolution in that paper is an extension, but by no means a challenge. Further, although more work may be needed to fully understand macroevolutionary events, there is no evidence that requires, or even suggests, a role for so-called ‘intelligent design’.”

Continue reading  “Meyer v Gilbert”

Posted by Dr.GH on August 29, 2004 | Comments (7) | TrackBack (0)

Most of the entries, and comments here at Panda’s Thumb are about the Intelligent Design strain of creationism.  I actually spend more time trying to respond to creationists of the young Earther sort  on different websites scattered in the cyberaether.  Just as the Discovery Institute is the principle abscess of IDC, the Answers in Genesis Ministries, along with the Institute for Creation Research, and Dr.Dino are the main vectors of YECism.

I recently took a fresh look at four articles I have written about various falsehoods originating, or promoted by AiG personnel.

Continue reading  “Intelligent Design isn't intelligent, but YEC is scary”