The Panda's Thumb
The Panda's Thumb is the virtual pub of the University of Ediacara. The patrons gather to discuss evolutionary theory, critique the claims of the antievolution movement, defend the integrity of both science and science education, and share good conversation.
- Last build:
- Wed, 10 Oct 2007 06:14:21 -0600
- Language:
- en
- Feed URL:
- http://www.pandasthumb.org/index.xml
RSS FEED IDEMS: The Panda's Thumb
- Send Me Your Links: A Message From Your Links Curator
I have been appointed “links curator” for The Panda’s Thumb. My job will be to scour the web for the best websites and blogs related to the mission of The Panda’s Thumb. To that end I have already added some links to the new links page. I will be adding more as time permits, but in the meantime I though I would throw the question open to the readers. What websites and blogs should be included? To get an idea of the type of websites I am looking for you can consult the links page. Finally, a number of scientists have made pdf’s of their papers freely available on the web here, for example. I assume they have the necessary permission to do so, but since I don’t want to get anyone in trouble for copyright issues I am somewhat reluctant to link to them. What do you think?
Comments may be left at Afarensis: Anthropology, Evolution, and Science.
Wed, 10 Oct 2007 06:14:21 -0600 - You have to spend money to make money
In biology, genetics, biochemistry, and molecular biology classes, one of the things that we used to learn that distinguishes prokaryotes from eukaryotes is the “fact” that eukaryotes have polyadenylated mRNAs, while prokaryotes do not. This morphed rather easily into a distinction – eukaryotes do polyadenylation, prokaryotes do not. For years, this was standard fare in class. However, even as generations of students (beginning with the discovery of polyadenylate tracts in hnRNA in eukaryotes) were learning of this distinction, we knew that all was not right with this. Among the lurking pieces of conflicting data was that the first biochemical entity that was shown to add poly(A) tracts to RNAs in vitro was a bacterial one, isolated and purified from E. coli (1).
Tue, 09 Oct 2007 22:34:21 -0600 - Eugenie Scott Lecture (and the DI Panic)
The controversy between evolution and intelligent design does not come down to whether a person is religious, but is a matter of sound scientific evidence, said a speaker who was on campus last night as part of Ohio University’s scientific lecture series.
“Evolution is the only scientific game in town,” said Dr. Eugenie C. Scott, executive director of the National Center for Science Education, a nonprofit organization based in Oakland, Calif., that promotes teaching evolution in public schools.
Seems that the successes of NCSE and its supporters has become a thorn in the eye of the Discovery Institute.
Tue, 09 Oct 2007 21:56:08 -0600 - Encoding Issues Fixed
I think that I’ve fixed most of the encoding issues that I am aware of. I had to edit a few lines of MT code and add some new logic to my MT-Dispatcher.
Parts of the database are still “corrupted” because of the bug. I can fix most of it, but I won’t do it right away.
Tue, 09 Oct 2007 17:40:41 -0600 - Retrospectacle for Blogging Scholarship
Shelley Batts, a PhD student at the University of Michigan, is up for a $10,000 scholarship based on the amazing quality of her blogging at Retrospectacle.
You may remember her as the student who took on abusive publishers (and won) and who let Prof. Steve Steve get kidnapped.
Go vote for her; she wins the scholarship if she gets more votes than any of the other 20 finalists.
Tue, 09 Oct 2007 12:14:09 -0600 - Scientists: Surgeons not out of a Job Anytime Soon---Or Why that Appendicitis Still Hurts.
By Douglas L. Theobald, Assistant Professor of Biochemistry, Brandeis University
”Its major importance would appear to be financial support of the surgical profession.”
—Alfred Sherwood Romer and Thomas S. Parsons, The Vertebrate Body (1986), p. 389.A recent science news article from the Associated Press reports on a novel hypothesis (Bollinger et al. 2007 JTB in press) concerning the possible function of the human vermiform appendix. Given how much creationists dislike all things vestigial, the Bollinger paper will undoubtedly be paraded on anti-evolution websites with grandiose claims about how “researchers are declaring that they have found a purpose for the human appendix”—and the paper itself unfortunately provides several tasty quote-mines ready to be plucked.
The new hypothesis, to be published in the Journal of Theoretical Biology, was proposed by a group of immunologists and surgeons from Duke University Medical Center. Bollinger et al. suggest that the structure and location of the human appendix has been specifically modified for an adaptive function, namely for housing and preserving beneficial gut bacteria during certain pathogenic infections that otherwise would clear the bowel of all enteric bacteria. Evidently, individuals who had an appendix would have a selective advantage over those individuals who had either no appendix or who had a larger appendix with a larger opening. Presumably after, say, an epidemic of amoebic dysentery, individuals with such an optimally sized appendix would be better able to repopulate the gut with good bacteria and to recover (this is an adaptationist paraphrase; the authors don’t use explicit evolutionary terms). The authors were led to this hypothesis after they noticed that human appendixes (yes, that’s the proper plural for the anatomical structure) contained significant bacterial biofilms, which are notorious for allowing bacteria to withstand all manner of malign assaults, including vigorous mechanical cleaning and chlorine bleaching.
Tue, 09 Oct 2007 09:20:50 -0600 - Unacknowledged Errors in "Unacknowledged Costs"
Back over the summer, William Dembski was talking up “Baylor’s Evolutionary Informatics Laboratory”, and one of the features there was a PDF of an essay critiquing the “ev” evolutionary computation program by Tom Schneider. Titled “Unacknowledged Information Costs in Evolutionary Computing”, the essay by Robert J. Marks and William A. Dembski made some pretty stunning claims about the “ev” program. Among them, it claimed that blind search was a more effective strategy than evolutionary computation for the problem at hand, and that the search structure in place was responsible for most of the information resulting from the program. The essay was pitched as being “in review”, publication unspecified. Dembski also made much of the fact that Tom Schneider had not, at some point, posted a response to the essay.
There are some things that Marks and Dembski did right, and others that were botched. Where they got it right was in posting the scripts that they used to come up with data for their conclusions, and in removing the paper from the “evolutionaryinformatics.org” site on notification of the errors. The posting of scripts allowed others to figure out where they got it wrong. What is surprising is just how trivial the error was, and how poor the scrutiny must have been to let things get to this point.
Now what remains to be seen is whether in any future iteration of their paper they bother to do the scholarly thing and acknowledge both the errors and those who brought the errors to their attention. Dembski at least has an exceedingly poor track record on this score, writing that critics can be used to improve materials released online. While Dembski has occasionally taken a clue from a critic, it is rather rarer that one sees Dembski acknowledge his debt to a critic.
In the current case, Marks and Dembski owe a debt to Tom Schneider, “After the Bar Closes” regular “2ndclass”, and “Good Math, Bad Math” commenter David vun Kannon. Schneider worked from properties of the “ev” simulation itself to demonstrate that the numbers in the Marks and Dembski critique cannot possibly be correct. “2ndclass” made a project out of examining the Matlab script provided with the Marks and Dembski paper to find the source of the bogus data used to form the conclusions of Marks and Dembski. vun Kannon suggested an easy way to use the Java version of “ev” to quickly check the claims by Marks and Dembski.
(Also posted at the Austringer)
Tue, 09 Oct 2007 04:26:02 -0600 - Multiple codes in DNA
In an earlier posting, I promised to provide an overview of alternative codes in DNA. Such examples include alternative splicing and alternative reading frames (ARFs) which I will discuss here
The classical view of DNA was straightforward, DNA gets transcribed into RNA, introns get removed and the resulting exons form a protein. Exons are coding sequences in genes, introns are pieces of DNA/RNA that interrupt exons. The first step involves RNA synthesis (transcription) where the DNA is transcribed into RNA and exons and introns are still present, the next step is RNA splicing where introns are being removed. Alternative splicing causes different exons to be combined into messenger RNA (mRNA). These mRNA are translated into proteins in a step called protein synthesis.
Mon, 08 Oct 2007 12:15:06 -0600 - "Intelligent Delivery"
From “This Modern World,” a brilliant cartoon on Intelligent Design (hat tip: Noodle Food):
Mon, 08 Oct 2007 09:01:40 -0600 - Comments on Dembski-Marks's "active information."
This is a guest appearance of Erik Tellgren.
I (Mark Perakh) have not contributed anything to this essay and am posting it as a courtesy to Erik.
Here starts Erik’s text:
William Dembski has been one of the most influential contributors to the Intelligent Design (ID) movement. Among other things, his work has added the terms specified information, specified complexity, and complex specified information to the basic vocabulary of the ID movement. These terms are all directly related to the logarithms of special types of probabilities, e.g. the probability of a pattern of interest given that it was produced in some way that excludes the foresight and guidance of an intelligent agent.
In a recent draft manuscript, Dembski and his coauthor Marks extend the vocabulary with three new terms [1]: endogenous information, exogenous information, and active information. They consider as given a search space and a fixed subset, called a target, that makes up some fraction ps of the search space. An issue of interest to them is how to measure how well a search algorithm [2] exploits the structure of the search problem. Two possible candidates are the probability p that a search algorithm is successful and the ratio p/ps. Readers of Dembski’s previous writings will not be surprised to discover that Marks and Dembski prefer to log-transform their probabilities and rename them ‘information’. In equations, their definitions are
endogenous information = -log2(ps),
exogenous information = -log2(p),
active information = -log2(ps/p).
Continue reading Comments on Active Information at Talk Reason
Sun, 07 Oct 2007 14:31:32 -0600 - Häggström: Uniform distribution is a model assumption
On a few occasions Dembski lamented that his critics are usually not mathematicians and hence are not really qualified to debate his mathematical exercise. Recently two professional mathematicians - Olle Häggström and Peter Olofsson, both highly qualified experts in math statistics and related fields, published essays showing serious faults in Dembski’s mathematical output. Dembski and Marks responded with an article where they attempted to refute Olle’s arguments. While some replies to Dembski and Marks have already been posted, a reply from Olle himself was expected. I am glad to inform PT visitors that Olle’s reply to Dembski and Marks has appeared here. I think Olle succeeded admirably to reveal the emptiness of Dembski-Marks’s arguments.
Sun, 07 Oct 2007 13:47:15 -0600 - Intelligent Design: A Position Statement of National Council for the Social Studies
Compare the following article in the Christian Post and the Discovery Institute ‘spin’ with the actual statement by the National Council for the Social Studies on Intelligent Design
In the Christian Post article, Crowther is quoted suggesting that the NCSE and other supporters of evolution education have flip-flopped on the topic of whether or not Intelligent Design should be allowed to be taught as a scientific alternative to evolution in social science classes.
Crowther cited several examples from previous articles in which the NCSE and other supporters of evolution education proposed social studies as an appropriate forum for discussing non-Darwinian thoughts such as Creationism and Intelligent Design. Furthermore, Crowther suggested that critics of Intelligent Design have strategically misrepresented the scientific claim as synonymous to Creationism to exclude it from being taught in science classes.
While Crowther is still misrepresenting Intelligent Design as presenting scientific claims, it is clear that for all practical purposes Intelligent Design has been found to be lacking in scientific content (Kitzmiller) and that given its historical foundations, Intelligent Design is linked with Creationism
Judge Jones Wrote:In making this determination, we have addressed the seminal question of whether ID is science. We have concluded that it is not, and moreover that ID cannot uncouple itself from its creationist, and thus religious, antecedents.
Having corrected this minor confusion amongst ID proponents, I will now explore if the NCSE has flip flopped on the topic of teaching Intelligent Design in social science classes.
Sun, 07 Oct 2007 13:30:22 -0600 - Evo-devo of mammalian molars
I've written a long introduction to the work I'm about to describe, but here's the short summary: the parts of organisms are interlinked by what has historically been called laws of correlation, which are basically sets of rules that define the relationship between different characters. An individual attribute is not independent of all others: vary one feature, and as Darwin said, "other modifications, often of the most unexpected nature, will ensue".
Now here's a beautiful example: the regulation of the growth of mammalian molars. Teeth have long been a useful tool in systematics—especially in mammals, they are diverse, they have important functional roles, and they preserve well. They also show distinct morphological patterns, with incisors, canines, premolars, and molars arranged along the jaw, and species-specific variations within each of those tooth types. Here, for example, is the lower jaw of a fox. Look at the different kinds of teeth, and in particular, look at the differences within just the molars.
This example — the lower teeth of a grey fox — shows the three-molar dental phenotype typical of placentals.Note that in this animal, there are three molars (the usual number for most mammals, although there are exceptions), and that the frontmost molar, M1, is the largest, M2 is the second largest, and M3, the backmost molar, is the smallest. This won't always be the case! Some mammals have a larger M3, and others may have three molars of roughly equal size. What rules regulate the relative size of the various molars, and are there any consistent rules that operate across different species?
To answer those questions, we need to look at how the molars develop, which is exactly what Kavanagh et al. have done.
Contine reading "Evo-devo of mammalian molars" (on Pharyngula)
Sun, 07 Oct 2007 08:29:32 -0600 - Council of Europe resolution sure to spark interest in intelligent designDenyse O'Leary Wrote:
I have ordered a copy of Harun Yahya’s Atlas of Creation, which (some say) has got the Council’s shirts in a knot, and will tell you what I think after I have read it.
Seems that Denyse is quite forthcoming about Intelligent Design being nothing more than Creationism. Seems that the Council was right after all.
Sat, 06 Oct 2007 17:27:15 -0600 - The Guardian: Experts call for creationism in the classroom
The ‘controversy’ about teaching Intelligent Design Creationism in schools may have an unexpected side-effect, namely that schools will more strongly emphasize the teaching of the scientific theory of evolution while also pointing out how Intelligent Design and other forms of creationism are not scientific and in many cases even anti-scientific and misleading.
Growing numbers of pupils believe in creationism, and science teachers should be prepared to cover the topic in their classes, education experts said today.
Sat, 06 Oct 2007 14:22:34 -0600
