July 2004 Archives

The Privileged Wedge

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Not surprisingly the Discovery Institute is getting a good mileage out of Gonzalez's thesis. Next I will explore the link between Privileged Planet, Rare Earth and the Intelligent Design movement. The book "Privileged Planet" presents a very poorly supported design argument in which the authors make claims about measurability and habitability which cannot be supported. In fact, when the authors try to link their ideas with Dembski's ideas, they only accept chance as an alternative to 'design' implicitly accepting that regularities (laws of nature) can in fact be 'designers'. Rather than strengthening the design inference, the authors have managed to undermine the design inference. The observed coincidences (can we say cherry picking) leading to a claim of correlation are not scientifically supported but do make for some interesting apologetic tools. Recently the book was reviewed in Nature: "Bright Blue Dot" by Douglas A. Vakoch in Naturel Vol 24 p 808-809

Evolution reveals biochemical networks and functional modules Christian von Mering, Evgeny M. Zdobnov, Sophia Tsoka , Francesca D. Ciccarelli , Jose B. Pereira-Leal , Christos A. Ouzounis §and Peer Bork, PNAS December 23, 2003 vol. 100 no. 26 15428-15433

The combined history of genomes provides a glimpse at past evolutionary events, revealing selective forces that acted at all levels of cellular and organismal function. Although the individual gene and its immediate regulatory elements form the primary unit of selection, evolution does not stop there (1). Instead, selection can also act on entire groups of genes, leading to joint transfers of genes between genomes (2, 3), concerted gene loss (4), gene fusion events (5), coregulation of genes through common regulatory elements (6), and the creation and maintenance of operons containing nonhomologous but cotranscribed genes (7, 8).

Scale Free Networks

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RNA networks, protein networks all seem to exhibit a scale-free structure. I intend to show that this scale free structure and other aspects of these networks not only can be expected from simple evolutionary principles but also how this scale free structure helps explain such issues as modularity, robustness, and evolvability.

Characteristics of scale-free networks

As is well known DNA sequences map to RNA or protein structures.

  • There are far more sequences than structures
  • Contains few highly-connected motifs and many less connected nodes
  • Motifs have a neutral network which extends throughout sequence space

For these frequent structures, their networks expand through sequence space, this means that gor any given fold, one can traverse through sequence space (that is change every nucleotide position) without changing the structure of the fold. In addition these structures are close in the sense that any such structure is within a small distance from any random sequence.

These findings have significant implications for our understanding of evolution.

The good folks over at the Access Research Network have this post up about some recent work published in the PNAS. The paper in question is entitled “Nitrate Assimilation in Plant Shoots Depends on Photorespiration” and is available here. A readable summary of the paper's findings can be found here.

The primary finding of the paper is that the photorespiration system in plants, which decreases the efficiency of photosynthesis, also serves an important function in allowing plants to convert nitrate into organic forms of nitrogen. Prior to this work it was commonly thought that the photorespiration was just an evolutionary vestige from a time when the atmosphere contained more carbon dioxide than it does today.

The ID's are presenting this as an indictment of evolutionary theory. The ARN summary concludes with this observation: “Evolutionary presuppositions stood in the way of scientific progress. A design model would have simply tried to determine the reason for the phenomenon. ”

To put it kindly, this is hardly the only interpretation of the facts. I have posted a complete reply to this piece of ID silliness over at EvolutionBlog. While crafting my reply, I contacted Dr. Arnold Bloom of UC Davis, the lead author of the paper. I showed him the summary of his work at ARN. He was not amused, and he gave me permission to use his reply in my posting. Check it out!

Edward B. Lewis, 1918-2004

Edward Lewis

It hasn't been a good week for biology. I've just learned that Francis Crick has died, and while I was at SDB I heard news that grieved me even more: Ed Lewis has died.

Lewis was one of the giants of Drosophila genetics. He was a student of Thomas Hunt Morgan, and one of the rare practitioners of pure genetics at the time molecular biology was swallowing up the field. He's mentioned several times in Jonathan Weiner's book, Time, Love, Memory (you've all read it, right? If not, get it—it's a wonderful view of neurobiology and genetics and molecular biology, from the perspective of Seymour Benzer). I'll quote a few passages from that book that give a taste of what Lewis was like.

Continue reading "Edward B. Lewis, 1918-2004" (on Pharyngula)

Reuters via CNN is reporting the death of Francis Crick, the co-discoverer of the structure of DNA. After the double-helix discovery and subsequent Nobel Prize, Crick continued his research at Cambridge University’s Medical Research Council, focusing on the genetics of viruses, protein synthesis and embryology. Subsequently, he moved to La Jolla, where he served as president of the Salk Institute for Biological Studies. There, he turned his attention to the study of the brain and the nature of consciousness.

Tangled Bank #8

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The Tangled Bank

Tangled Bank #8 is online right now. Follow the links and read about biology!

I am also semi-online—I just got back home after screaming across the Montana mountains and the Dakota prairies with Calgary cowboys, Canadian mounties, and a few frustrated creationists in hot pursuit. I've got a pile of great stuff from the SDB conference (including some stuff from a fun evo-devo session) to dump out of a scribbled-upon notebook onto the web, but first...sleep. Lots of sleep.

Icons of ID: Neutrality

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In this posting I will start exploring the importance of neutrality on evolution. In fact as the evidence will show, neutrality is not only a requirement for evolvability but it also can be selected for itself. In other words, evolutionary principles can lead to neutrality and evolution will tend towards areas with many neutral neighbours

Neutrality is a fascinating concept which has been shown of importance in understanding RNA and protein evolution. Additionally the vaste neutral networks may help understand ‘convergent evolution’. Perhaps the lack of sequence similarity, but strong phenotype similarity can be understood by neutral evolution and drift. In other words, due to the vasteness of neutral networks, the sequence may have drifted while the phenotype remained basically the same. Thus what may appear to be convergent evolution may very well have been divergent evolution after all. And homologies, which fail to be detected at the sequence level may still exist at the phenotype level.

Icons of ID: Another false positive?

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Thanks to Nobody on ARN I was made aware of the following story on Growing Tiny Totally Tubular Formations

Would this be another example of false positive for an ID hypothesis?

Tubular structures found on a Martian meteorite had been suggested as evidence of life, he said.

Goldstein pointed out that finding a chemical means to grow such self-organizing systems highlights the fact that living organisms are not needed to create such structures.

An Exchange on Another Blog

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It was requested that I provide a pointer here on PT to a discussion I've been having on my blog, Dispatches from the Culture Wars. The subject of that discussion was a critique I wrote of an article by Robert Meyer entitled Were We Fooled by Stephen J. Gould?, on a site called intellectualconservative.com. My original critique can be found here, and the continuing discussion from emails can be found here. Mr. Meyer's article was one of the worst examples of either ignorance or rank dishonesty from creationists that I have ever encountered. He claims, for example, that Gould was "honest enough to admit" that evolution was in "grave crisis", that he denied the existence of transitional forms, and that Punctuated Equilibrium was the same thing as Goldschmidt's hopeful monster idea. All three of those statements are so blatantly false that either Meyer is utterly ignorant of the subject upon which he is pontificating, or he is flat out lying. Anyway, check out the discussion and jump in if you feel like it.

The Tangled Bank needs you!

The Tangled Bank

Another Tangled Bank is coming up this week. Send your links to good science and medicine writing to Reagan Kelly, who will be hosting it at reagank.com. (The usual e-mail address for submissions is still messed up, so send it direct to the host, or to me).

I will explore how evolutionary processes by virtue of being Markov processes, are expected to generate nested hierarchies. In fact, I argue that evolutionary processes are the only known processes which can generate such nested hierarchies. On the ARN discussion boards we have seen much confusion as to the nature of evolutionary processes, nested hierarchies and common descent. It is trivial to show that a process of inheritance with variation (and selection) will generate a nested tree. The problem however is recovering the correct tree using only present day genetic data. That evolution is a Markov process is self evident. First inheritance depends solely on the parents and not on all the preceding ancestors, secondly transitions in DNA can be described by probabilities. This means that evolution is memory-less.

From Theobalt’s 29+ Evidences for Macroevolution FAQ

As seen from the phylogeny in Figure 1, the predicted pattern of organisms at any given point in time can be described as “groups within groups”, otherwise known as a nested hierarchy. The only known processes that specifically generate unique, nested, hierarchical patterns are branching evolutionary processes. Common descent is a genetic process in which the state of the present generation/individual is dependent only upon genetic changes that have occurred since the most recent ancestral population/individual. Therefore, gradual evolution from common ancestors must conform to the mathematics of Markov processes and Markov chains. Using Markovian mathematics, it can be rigorously proven that branching Markovian replicating systems produce nested hierarchies (Givnish and Sytsma 1997; Harris 1989; Norris 1997). For these reasons, biologists routinely use branching Markov chains to effectively model evolutionary processes, including complex genetic processes, the temporal distributions of surnames in populations (Galton and Watson 1874), and the behavior of pathogens in epidemics.

Icons of ID: Avida and Common descent

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The evidence for common descent, which is a logical prediction from Darwinian descent is quite extensive.

Douglas Theobald presents an excellent outline of the argument at 29+ Evidences for Macroevolution The Scientific Case for Common Descent

I will show how simple experiment with digital and real DNA both recapture the expected nested hierarchies and phylogenies. I hope this may resolve some of the confusions about Darwinian evolution, common descent, phylogenetic reconstruction based on DNA and nested hierarchies. So in other words, while Darwinian evolution leads inevitably to a nested hierarchy, such phylogeny may not always be recoverable using DNA.

Kennewick Man update

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For those following the Kennewick Man case, involving attempts by Native American creationists to block the study of a 10,000 year old skeleton discovered in Washington State, there's a new development. As reported by inappropriate response, the Army Corps of Engineers is still trying to interfere with study of the bones. Now, you may recall that, in April of 1998, the Corps, evidently on direct orders from the Clinton Administration*, dumped 500 tons of rocks on the discovery site, destroying any possibility of further excavation.

Unclear on the concept

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As you know, the book Why Intelligent Design Fails:A Scientific Critique of the New Creationism edited by our own Matt Young and Taner Edis http://www2.truman.edu/~edis/books/id/ has just been published. I am one of the authors, with a chapter on the evolution of bacterial flagella. So I feel particularly honoured that one of the first responses to the book is to my chapter.

Unfortunately, the response shows the author is somewhat unclear on the concepts involved.

This week's Nature includes a wonderful description of an exotic group of deuterostomes from the lower Cambrian, 520 million years ago. Deuterostomes are animals characterized by their embryology: when they gastrulate, the site of closure of the migrating tissues, the blastopore, becomes the anus of the animal. This is in contrast to the protostomes, in which the blastopore becomes the mouth. We chordates are deuterostomes, as are echinoderms, some marine worms called hemichordates, and the urochordates, or sea squirts.

Shu et al. have identified some animals called vetulocystids, and they are most closely related to modern echinoderms. Echinoderm evolution is confusing and complicated, largely because the modern forms are so highly derived and distinct from the ancestral forms, and because the echinoderm lineage has been spectacularly diverse morphologically. The authors jump from some somewhat speculative interpretations of the fossil anatomy (the specimens, as you can see below, are peculiar and the structures difficult to identify) to an idea that clarifies the organization of the deuterostome lineage.

Vetulocystis fossils

Continue reading "Spectacular echinoderms from the Lower Cambrian" (on Pharyngula)

The book is finally shipping. Here’s the publisher’s information on it…

Why Intelligent Design Fails

A Scientific Critique of the New Creationism

Edited by Matt Young and Taner Edis

http://www2.truman.edu/~edis/books/id/

Buy directly from Rutgers University Press on-line and get a 20 % discount and free shipping (see below)

“This book is a readable and devastating scientific analysis of intelligent design creationism. …unlike ID’s proponents, these authors have done the real science that deflates the claims of intelligent design. Their work deserves the respect of everyone with a say in what is taught in public school science classes.” – Barbara Forrest, co-author of Creationism’s Trojan Horse: The Wedge of Intelligent Design

“A terrific book that explores, fairly and openly, whether proponents of ID have any scientifically valid gadgets in their toolbox at all. …accessibly written throughout and an invaluable aid to teachers and scientists.” – Kevin Padian, Professor and Curator, University of California, Berkeley, and President, National Center for Science Education

“‘Intelligent-design theory’ makes extravagant claims, but refuses to come up with even a small fraction of the evidence needed to sustain them. Why Intelligent Design Fails brings together clear and devastating arguments by true scientists, which will convince perceptive and fair-minded readers that ‘intelligent design’ belongs to the history of propaganda, not to the achievements of science.” – Norman Levitt, Author of Prometheus Bedeviled: Science and the Contradictions of Contemporary Culture


The current issue of Nexus: A Journal of Opinion* features a deeply flawed student article by Crystal V. Hodgson, Coercion in The Classroom: The Inherent Tension between The Free Exercise and Establishment Clauses in The Context of Evolution. Hodgson's analysis is more honest than that of most proponents of creationism; nevertheless, her understanding of the First Amendment partakes of the confusion so common among them.

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.

The previous wall got a little cluttered, so we’ve splashed a coat of paint on it.

An urban legend says that men won’t ask for directions; I have no idea whether or not the legend is true. But, according to a book review in Natural History magazine, sociobiologists have a fanciful explanation:

…women back then [in our hunter-gatherer past] strongly preferred sexual partners who didn’t get lost in the hunt. If sons inherited the spatial abilities of their fathers, and women persisted in this preference, not getting lost would increase–until somehow, now, men prefer not to appear lost (Deborah M. Gordon, “Dad’s Not Lost,” Natural History, July/August 2004, pp. 52-55).

The book under review is Richard C. Francis, Why Men Won’t Ask for Directions: The Seductions of Sociobiology, Princeton, 2003. I have not (yet?) read the book, so I rely on Gordon’s review. Apparently, Francis finds many sociobiological explanations unconvincing and posits instead alternative physical mechanisms that can account for the observed behavior without reference to sociobiological principles. The book ought to sell well, since most of the behaviors that Francis describes are sexual.

An excellent review paper discussing the evolution of evolutionary theory is:

Ulrich Kutschera · Karl J. Niklas The modern theory of biological evolution: an expanded synthesis Naturwissenschaften (2004) 91:255-276

While the paper has some very interesting things to say, I will focus on a more narrow issue namely the success of Darwinian simulations of early plant evolution by Karl Niklas. For this we need to go back in time 400 Million years (Ma) to the early Devonian and look at the evolution of ancient vascular plants.

AccessExcellence has an outstanding Tutorial by Karl Niklas which I will use to clarify some of the issues.

I encourage the reader to first read the Tutorial and then return here.

See also the PBS Website

As a final note, I will compare Niklas’s findings with some of the claims by ID proponents, largely based on TRIZ that Darwinian evolution cannot be inventive.

The description of our site in the right sidebar says that “The Panda’s Thumb is the virtual pub of the University of Ediacara,” and the University of Ediacara (U of E) is “an online virtual University dedicated to the study of the origins of life in the cosmos.”

At the U of E site, Chris Nedin explains where the name “Ediacara” came from

The name “Ediacara” (pronounced Edi-ak-ra) comes from the Ediacara fauna, the first example of multicelled metazoans found in the fossil record. The significance of the fauna was first realized by geologists in South Australia, who found abundant fossils at the Ediacara Hills in the Flinders Ranges, about 650 km north of Adelaide. They realized that not only did the fauna contain jellyfish, soft corals and possibly worms and proto-arthropods, similar to modern forms, but that the fauna was significantly older than any other animal fossils yet found (600-540 million years old), even predating the Cambrian explosion. Whilst debate still continues as to the exact nature of the fauna, few now doubt that at least some of the forms represent examples of modern animal groups. The origin of the metazoa and thus all animal groups must now be placed even further back in time, and may never be found, since it is thought that the precursor organisms were miofaunal - tiny worm-like organisms living in the interstitial spaces between sand grains and thus having little chance of fossilizing.

“Ediacara” thus represents not only a major milestone in the history life on Earth, but also in the history of the Internet, being - as it is - the worlds first virtual university.

Apropos of this explanation, here’s a really neat story from the internet today. See here for the whole story and some neat pictures.

Italian scientists rally behind evolution

At the beginning of March, members of Italy’s scientific community were called to action. Their impetus? A decree by the ministry of education to remove evolutionary theory from middle school science curriculum.

The Rev. George Coyne, director of the Vatican Observatory, said that evolution is a scientific conclusion that does not deny the existence of God. “Whether evolution is true or not is a separate issue,” he said. “It’s true from a scientific view. God could create an evolutionary world just as He could create a static world.”

Pigliucci explained that anti-evolutionist sentiment in Italy is a part of an extreme right-wing political minority that links evolution to Marxism and is uninformed about accurate Darwinian theory. This connection, though, is weak, he said. Out of admiration, Marx wanted to dedicate the capitol to Darwin, but the naturalist refused, recognizing that any political affiliation could taint his scientific credibility.

Overwhelmed with protest –from both the scientific community and the general public – Moratti retracted the proposal within a week. In an official statement, she said: “The teaching of Darwin’s theories are ensured starting in elementary school. A commission headed by Rita Levi-Montalcini will work with me to develop a precise proposal.” The commission has not yet determined when to begin discussions.

I just want to let y’all know that the Democratic Party has released their platform for the upcoming US elections. It contains this support for science education:

At a time when all good jobs increasingly depend on advanced skills, we will strengthen technical training for those who do not attend college. Finally, we must place a special emphasis on expanding achievement in math and science. These are subjects where America has always led the world and must continue to lead in the 21st century.

It looks like the GOP is going to ride NCLB as their education horse into the election. You can read the full text of the Democrats’ education platform on De Rerum Natura.

This issue came up in comments and is something I’ve been meaning to post about. It seems that most people, both pro and con, are of the opinion that ID “theory” accepts an old Earth. Most write-ups about ID in newspapers and magazines make mention of this as being something that distinguishes ID from old-school creationism. But it’s simply not the case. Leading ID proponents argue that the age of the Earth is irrelevant to ID, and that ID advocates are free to believe in an old Earth or a young Earth as they see fit. Indeed, it would be hard to explain the involvement of people like Paul Nelson, who is openly YEC, if ID theory were committed to an old Earth. Instead, they argue that the detection of “design”, whatever that means, is the only thing that ID is concerned with. And that’s prompted many critics to point out that ID is effectively useless when it comes to understanding natural history. In other words, ID “theory” isn’t a theory at all, it’s a collection of crappy criticisms.

The person most responsible for this strategy is Phillip E. Johnson, often referred to as the father of the ID movement. Most have assumed that Johnson is an old-Earther, since he doesn’t defend a young Earth or make it a part of ID. (The strategy is to change the subject when it comes up,) But as far as I know, Johnson has never committed himself in print one way or another. But in a recent article in Touchstone magazine, Johnson does us the favor of clarifying his position on the age of the Earth. And his position is…that he has no position.

Tribes have announced that they will not ask the Supreme Court to take the Kennwick Man case (Bonnichsen, et al. v. United States). That decision, as I blogged earlier, held that a skeleton found on federal land is not automatically a "Native American" simply because it predates the arrival of Columbus.

Much more info at the Friends of America's Past website.

Polarity in the mammalian egg

immunofluorescent mouse embryo

When you get immersed in the Drosophila literature, it's easy to lose sight of an important fact: flies are weird. Honestly, every species has unique properties, so it's not that we wouldn't be saying exactly the same thing about some other species if it had become the dominant experimental model system, but it's good to constantly remind ourselves of the diversity we see in biology.

One of the most noticeable properties of early fly development is the existence of an extensive maternal contribution to the embryo's organization. Mother Fly goes to a fair amount of effort to stamp her eggs with molecular labels that say, "This End Up". Is this a common strategy? Well, yes—lots of animals give their progeny a boost in reliability of development by incorporating an asymmetric distribution of informational macromolecules. There seem to be some exceptions, though, and they happen to be of particular interest to us, because they are us: mammals. Mammalian ova lack any overt asymmetries, and their early cleavages are simple and equal, producing a clump of cells called a morula with no discernible up, down, left, right, back, or front. So how does a young mammalian zygote figure out which end is supposed to be the head and which the tail?

Continue reading "Polarity in the mammalian egg" (on Pharyngula)

Bedrock Science

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It’s and oldie, but a goodie.

Mo Rocca interviews Carl Baugh for the Daily Show

Clip Description: “There is no conflict between true science and the Bible.”

I won’t say more, or I will spoil it for you.

(Thanks to Nightshade on IIDB for the link.)

Two Reviews

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Two new reviews about books critiquing the ID movement:

The first is a short dual review of [u]Why Intelligent Design Fails[/u] and [u]The Cultures of Creationism[/u], appearing in New Scientist magazine. PT’s own Matt Young is coeditor of the first.

The second is a review of [u]Creationism’s Trojan Horse: The Wedge of Intelligent Design[/u], appearing in Science and Theology News. Our own Paul Gross is coauthor of this book.

Thanks to Glenn Branch for the heads-up.

Dynamic control of gap genes

gap genes

Here's a refinement in the story of early pattern formation in the Drosophila embryo. Just to recap a little bit, I've told you that in flies there is a molecule, bicoid, that is expressed in a gradient and that is a transcription factor that regulates the expression of other genes. In particular, there is a set of gap genes, Hunchback and Krüppel and Knirps and Giant and Tailless that read the gradient of the bicoid morphogen and are turned on in specific bands along the length of the embryo.

All of this is more or less accurate, but I have to tell you now that it is also a great simplification. Development is much, much more complicated than that. From that description, you'd think that the bulk of the work in specifying identities along the longitudinal axis is done once the bicoid gradient is set up—everything from that point could require nothing but passive obedience from the downstream genes to what bicoid tells them to do. There are also a great many interactions between different downstream genes that are important in shaping the distribution of gene expression, however, and one thing developmental biologists can't do is get trapped into simple linear thinking.

Continue reading "Dynamic control of gap genes" (on Pharyngula)

Calgary!

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SDB Calgary

Oh, boy. Next week is time for the...


Society for Developmental Biology 63rd Annual Meeting
University of Calgary, Canada
July 24 - 28, 2004


It's going to be glorious—check out the program. Expect me to come back inspired and all charged up about SCIENCE!

  • I'll be leaving next Thursday with my son as batman/factotum/chauffeur, so Pharyngula might be a bit quiet for a while. Maybe. Depends on whether they have the internet up there in Canada. (OK, they probably do. It's going to depend more on how much time I have.)
  • Are there any Calgarians or DB geeks out there who want to get together some evening and babble or drink that potent Canadian beer? Let me know.
  • I'd also be willing to temporarily loan one or a few people the keys to the Pharyngula soapbox. If you're interested in being a guest weblogger, drop me a line. (Creationists, right-wingers, and evangelical fundamentalists need not apply.)

I'll be taking lots of notes. Expect them to appear online sometime during or after the meeting.

Comparing Primate Genomes

From ScienceDaily:

Comparing primate genomes is an approach that can help scientists understand the genetic basis of the physical and biochemical traits that distinguish primate species. James Sikela and colleagues, for example, collected DNA from humans, chimpanzees, bonobos, gorillas, and orangutans to identify variations in the number of copies of individual genes among the different species. Their work is published in this month’s issue of the open-access journal, PLoS Biology.

Overall, Sikela and colleagues found more than 1,000 genes with changes in copy number in specific primate lineages. All the great ape species showed more increases than decreases in gene copy numbers, but humans showed the highest number of genes with increased copy numbers, at 134, and many of these duplicated human genes are implicated in brain structure and function.

Because some of these gene changes were unique to each of the species examined, they will likely account for some of the physiological and morphological characteristics that are unique to each species. One cluster of genes that amplified only in humans was mapped to a genomic area that appears prone to instability in human, chimp, bonobo, and gorilla. This region has undergone modifications in each of the other descendent primate species, suggesting an evolutionary role. In humans, gene mutations in this region are also associated with the inherited disorder spinal muscular atrophy. This fact, along with the observation that there are human-specific gene duplications in this region, suggests a link between genome instability, disease processes, and evolutionary adaptation.

The research paper is available at the Public Library of Science - abstract is below:

Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.

The Get Fuzzy for July 15th.

If your paper doesn’t have Get Fuzzy, you can get it delivered to you via email by signing up to Comics Basic at Comics.com.

Philosophy of biology blog

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A new blog “dedicated to the history and philosophy of biology, including Darwinism, evolutionary ethics and game theory” has been started by the philosophy department at Florida State University, Michael Ruse’s home department.

It’s early days yet, with a couple of posts about rational behavior and economic evolution. Keep an eye out - they are seeking contributors, and yours truly has offered.

“Junk DNA”

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A common comment by IDists concerns “junk DNA”: they will claim that it is only “evolutionists” who would have thought that so much of the genome was “junk,” but that an IDist would assume that what looked like junk was in fact there for a purpose. Therefore, as scientists start to learn about previously unknown functions for some of that “junk DNA,” some of the IDists are crowing “We told you so - if you just wouldn’t have been so dogmatically attached to your theory of blind, purposeless evolutionary processes, you wouldn’t have set research back by dismissing so much of the genome as “junk.” (I could go find quotes to this effect, but I will assume that those of you who keep up with the IDists know what I am talking about.)

Now in November of last year, Scientific American had an article, “The Unseen Genome: Gems Among the Junk,” in which writer W. Wayt Gibbs (not an IDist)summarized some of the new research on what has been considered the junk part of the genome, and in the process made some similar comments about how “dogmatism” has misled biologists into mislabeling and thus ignoring the “junk.”

However, in March of this year Scientific American published a letter by Harold Brown, a member of the philosophy department of Northern Illinois University, responding to this charge of dogmatism with some very pertinent points. I’d like to discuss what Brown had to say.

Tangled Bank #7

The Tangled Bank

Tangled Bank #7 is online at Rhosgobel! The next edition will be in two weeks, at reagank.com.

Former Vermont Governor Howard Dean M.D. became a household name earlier this year when he was running for president. After dropping out of the race, Dean used the network he established to start Democracy for America, “a grassroots organization that supports socially progressive and fiscally responsible political candidates.” On July 5, Dean wrote an editorial on Bush’s war on science in The Daily Camera (Boulder, CO).

The Bush administration has declared war on science. In the Orwellian world of 21st century America, two plus two no longer equals four where public policy is concerned, and science is no exception. When a right-wing theory is contradicted by an inconvenient scientific fact, the science is not refuted; it is simply discarded or ignored.

Presidential scientific commissions have long enjoyed relative immunity from politics. Presidents of both parties have depended on impartial, rational advice from such groups for decades. Yet under the Bush administration, there has been a concerted effort, led by Karl Rove and other political ideologues based in the White House, to stack these commissions with Republican loyalists, especially those who espouse fundamentalist views on scientific issues.

Will it be long before a prominent panel of fundamentalist theologians, conservative columnists and a few token scientists take up the question of whether the theory of evolution should be banned from the nation’s classrooms? Stay tuned. In George Bush’s America, ignorance is strength.

Uncommon Dissent

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William Dembski's latest offering is an anthology entitled Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing. The publisher is the Intercollegiate Studies Institute, a right-wing think-tank.

When I first noticed this book at Amazon I was vaguely optimistic. I didn't expect to agree with many of the essays, but it seemed like an attempt, rare among creationists, to produce something serious. I was hoping that the tone would be respectful, and that I would be given some plausible reason for why the evidence for evolution, so convincing to me, is not convincing to other thoughtful people.

Sadly, it seems that I was expecting too much. I have already done several entries over at EvolutionBlog addressing the book.

In this post I discuss the qualifications of the contributors to the volume and find them, for the most part, wanting.

I have also written a series of lengthy entries about the opening essay in the volume, written by philosopher Robert Koons.

Part One is available here.
Part Two is available here.
Part Three is available here.

I expect to be writing replies to the other essays in the volume as I read them. Here, let me make a few comments about William Dembski's long introduction to the volume.

Icons of ID: Circadian Rythms II

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This is the second installment in my postings on Circadian Rhythms. After having introduced the IC argument for Circadian rhythms, I intend to explain in general terms how the Circadian clock works.

Let me repeat Behe’s definition of Irreducible Complexity

“By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly… “

Michael Behe in Darwin’s Black Box

On the Application of Irreducible Complexity by Joshua A. Smart

Knockout Experiments

The best tool thus far in determining whether a gene product is indispensable has been the knockout experiment. In a knockout experiment, mutagenesis is used to produce a null mutant, a gene that exhibits no phenotype whatsoever. The use of knockout experiments in determining an irreducible core is obvious.

A common riff on the role of medical and technological advances is that they have somehow insulated humanity from evolution, or the ordinary course of evolution. This is an old canard - it goes back to the days before Darwin, and is a basic justification of eugenics programs (not just the Nazi horrors, but the more “positive” programs of encouraging the “better” kind of humans to interbreed).

It is thought that if medicine has interfered with the selective pressures we faced in the past, we will face degeneration, or be in control of our own evolution, or something, that will interfere with the “normal” course of evolution.

A [url = http://www.prospect-magazine.co.uk/[…]rticle=12713]very nice article[/url] by Gabrielle Walker in Prospect Magazine, a UK publication of The Independent, discusses this in some detail.

Expertise and the CSC

Over at stranger fruit, I discuss the expertise of the Fellows of the Center for Science and Culture and their ability to examine evolution. All welcome!

The Pulitzer Prize winning Edward J. Larson has a new book, Evolution: The Remarkable History of a Scientific Theory. He teaches both history and law at the University of Georgia. His background is in the history of science, specifically biology.

”Everyone will agree, whether you like it or not, the theory of evolution is one of the most important concepts of the last 200 years,” Larson said. ”Whether you like it or not, it influences what we think about the world, even for people who don’t accept the theory or all of the theory of evolution. It still influences society, the culture in which they operate and influences a lot of other people, and therefore it impacts our society. And yet, I couldn’t find a book that told the story of its history, full of its controversies, full of the objections, full of the implications as a story that normal people like you and I could read, rather than a technical work of science that is really dry.”

Read the rest at the Athens Banner-Herald newspaper. (Use username ‘tricky’ and password ‘marymary’ if you don’t have an account.)

Teaching Science in the Schools

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Francisco J. Ayala, Teaching Science in the Schools American Scientist, Volume 92, Number 4 July-August 2004

… It is often argued that the American tradition of fairness and “equal time” beckons that these alternative theories be taught. But these theories are not scientific and therefore have no place in the science curriculum. Not all scientific knowledge is equally certain. When there is uncertainty, alternative hypotheses should be taught in science classes, but only those grounded on naturalistic explanations subject to refutation by empirical observation and experiment. Schools should not teach astrology as an alternative to astronomy, alchemy as an alternative to the periodic table or witchcraft as an alternative to medicine.

The theory of evolution needs to be taught in the schools because nothing in biology makes sense without it. Modern biology has broken the genetic code, deciphered the human genome, opened up the fast-moving field of biotechnology and provided the knowledge to improve health care. Students need to be properly trained in science in order to improve their chances for gainful employment and to enjoy a meaningful life in a technological world.

Continue reading at American Scientist Online

Butterfly wings

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From EurekAlert:

A butterfly’s wing is a uniquely visual exhibition, not only of the aesthetics of nature, but of the machinery of evolution. Biologists have long appreciated that butterfly wing patterns dramatically exemplify the intricate interplay between genes and the environment – as the patterns evolve to give butterflies advantages in evading predators and attracting mates.

In a paper in the July 13, 2004, issue of Current Biology, biologists Robert Reed and Michael Serfas add a new piece to the evolutionary puzzle of the butterfly wing. By comparing among species the molecular machinery that controls wing development, the researchers are revealing how the regulation of two key genes has evolved in association with specific color patterns. The color patterns they studied vary among species, existing in a continuum including simple lines, teardrops and rounded spots.

Robert D. Reed and Michael S. Serfas (2004) “Butterfly Wing Pattern Evolution Is Associated with Changes in a Notch/Distal-less Temporal Pattern Formation Process” Current Biology 14(13): 1159-1166. doi:10.1016/j.cub.2004.06.046

I’ll leave it to PZ to perhaps comment on this :), but below is the abstract of the paper.

Abstract:: In butterflies there is a class of “intervein” wing patterns that have lines of symmetry halfway between wing veins. These patterns occur in a range of shapes, including eyespots, ellipses, and midlines, and were proposed to have evolved through developmental shifts along a midline-to-eyespot continuum. Here we show that Notch (N) upregulation, followed by activation of the transcription factor Distal-less (Dll), is an early event in the development of eyespot and intervein midline patterns across multiple species of butterflies. A relationship between eyespot phenotype and N and Dll expression is demonstrated in a loss-of-eyespot mutant in which N and Dll expression is reduced at missing eyespot sites. A phylogenetic comparison of expression time series from eight moth and butterfly species suggests that intervein N and Dll patterns are a derived characteristic of the butterfly lineage. Furthermore, prior to eyespot determination in eyespot-bearing butterflies, N and Dll are transiently expressed in a pattern that resembles ancestral intervein midline patterns. In this study we establish N upregulation as the earliest known event in eyespot determination, demonstrate gene expression associated with intervein midline color patterns, and provide molecular evidence that wing patterns evolved through addition to and truncation of a conserved midline-to-eyespot pattern formation sequence.

Genomics for beginners

It's in an unexpected place—O'Reilly's Macintosh developers pages— but here's a useful and brief tutorial in getting started with Bioinformatics and Comparative Genomics.

(via nodalpoint.org)

Teaching the Science of Evolution

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NSCE reports

Alberts and Labov on teaching evolution

Bruce Alberts, president of the National Academies, and Jay Labov of the Center for Education at the National Research Council have written an article on “Teaching the Science of Evolution,” which appears in the current issue of the journal Cell Biology Education.

Alberts and Labov write, “Cell and molecular biologists have provided some of the most compelling evidence to support the theory of evolution and should therefore be among those who raise their voices the loudest to support science curricula that help students understand the processes of evolution. As scientists, we also should make it our responsibility to present the evidence for biological evolution to all of our students, especially in introductory courses. Most students who enroll in our introductory courses will use them as their terminal courses in science. At least some of those students will go on to careers as teachers or as public servants who will be asked to make decisions about whether to allow nonscientific approaches to teaching evolution to appear in science curricula. It is our responsibility to equip them with the knowledge and understanding of science that they will need to confront such challenges.”

From the National Academies:

Bruce Alberts and Jay B. Labov Teaching the Science of Evolution Cell Biology Education Volume 3 Summer 2004, 75-80

More at Cell Biology Education

Yesterday Pim noted that the Discovery Institute prevented Eugenie Scott from quoting from online material, stating that the material did “not do justice to the complexity of ID”. Now - somewhat ironically - the DIs Center for Science and Culture has had a make-over and the very articles Scott was using are filed under “Scientific Research and Scholarship”. Hard to know what to say really. If the DI/CSCs “scientific research and scholarship” does “not do justice to the complexity of ID” where are we to go to get the truth about ID? Well, the Thumb, of course :)

Icons of ID: Avida

Intelligent design proponents have raised a myriad of criticisms against the Avida experiments, most of these criticisms miss the point. For instance, the claim that Avida does not accurately model biological evolution. But there are some claims that deserve a closer look. Since I am very interested in these issues, I will address a few of them.

Statistically insignificant sequence space distances are assumed between novel, more complex functions. This is an artefact of logic functions and not protein sequence.

Another example of a system that could not have evolved via Darwinian pathways is discussed at ISCID.

It is hard to imagine how such a character could have evolved by a Darwinian mechanism. Darwinism requires an environment wherein an organism gradually evolves. For organism to evolve they require some sort of selective constraint. Darwinian theory explains traits according to the best adapted in a particular environment, but a highly radioactive environment has simpley never been present on earth. This must certainly mystified Darwinists.

Luckily science is not constrained by one’s lack in imagination and has found some interesting clues as to plausible scenarios.

The Tangled Bank

Another Tangled Bank is coming up this week. Send your links to good science and medicine writing to Radagast, who will be hosting it at Rhosgobel. (The usual e-mail address for submissions is still messed up, so send it direct to the host, or to me).

Adelaide is an unusual city, a mix of parochialism and conservatism and progressive, innovative thinking. One of the examples of the latter is the Thinkers in Residence program, where world renowned thinkers are invited to Adelaide to discuss issues relevant to urban and regional development. Currently, the Thinker in Residence is Baroness Susan Greenfield, a world authority on neuroscience cognition the pharmacology of Alzheimer’s disease. Baroness Greenfield is considered to be the 14th most inspirational woman in the owrld (and as she wryly notes, Dolly Parton is the 9th). Last Friday night I went to a symposium on “Neurotransmitters in the Brain”, where I listened to here give a talk entitled “Is there more to the brain then neurotransmitters?”.

What has this got to do with evolutionary biology?

On July 5, 2004, the school board in Darby, Montana voted 3-2 not to adopt a proposed “objective origins policy” on its second reading. The policy had been tentatively approved on February 2 at its first reading, but is now rejected. The proposal sparked intense local controversy and national media attention earlier this year. The fate of the polic …

Read the full story at NCSE Web

New Book: Evolution vs. Creationism

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A new book Evolution vs. Creationism: an introduction by Eugenie C. Scott has been published. It can be ordered via Amazon.Com

Henry Gee’s column

Intelligent design?

The fact that the work seems so surprising exposes another, more dangerous conceit that scientists are prone to. Dangerous, because it leaves science wide open to the temptations of so-called ‘Intelligent Design’. Advocates of this view object to evolution by invoking what Richard Dawkins has called the ‘Argument from Incredulity’ - that is, if I don’t believe that something is possible, it cannot happen.

Read more at Nature

Thanks to Glenn Branch for pointing out this interesting article.

Icons of ID: Reliability revisited

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The more I read about Dembski’s explanatory filter and his reliability claims the more I come to the conclusion that Dembski has created a big problem for himself by suggesting on the one hand that it is reliable:

Briefly, the claim that specified complexity is a reliable marker of design means that if an item genuinely instantiates specified complexity, then it was designed. As I argue and continue to maintain, no counterexamples to this claim are known.

Dembski, ISCID No False Positives and the Lust for Certainty on November 2002

and

I argue that the explanatory filter is a reliable criterion for detecting design. Alternatively, I argue that the Explanatory Filter successfully avoids false positives. Thus whenever the Explanatory Filter attributes design, it does so correctly.

Dembski, “The Explanatory Filter: A three-part filter for understanding how to separate and identify cause from intelligent design”, Mere Creation Conference originally titled “Redesigning Science.”, 1996.

But on the other hand Dembski also accepts the risk of false positives (although he considers this, incorrectly, the inevitable nature of science).

Dembski Reviewed

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The Presbyterian Church of New Zealand recently reviewed one of Dembski’s latest books, The Design Revolution. The reviewer, Alistair McBride, is a former science teacher and current minister. He has this to say about the book.

For me the book is characterised by a great deal of polemic and special pleading which makes it difficult to tread a path through the argumentation.

His real target is something he calls Darwinism. As I read the chapter “The Only Game in Town” I found he tries to narrow the debate down to a particular understanding of what Darwin wrote. …

… From my reading, the branch of evolutionary biology has come to see that “natural selection” plays only a part in the overall scheme of the theory of evolution and to argue solely against a narrowly defined Darwinist position obfuscates the issues being discussed in the wider scientific community.

Follow this link to read the rest.

Thanks to Glenn Branch for the heads up.

Is neutral evolution non-Darwinian?

„…Variations neither useful not injurious would not be affected by natural selection, and would be left either a fluctuating element, as perhaps we see in certain polymorphic species, or would ultimately become fixed, owing to the nature of the organism and the nature of the conditions.…”

Charles Darwin, Origin of species (1859)

Are you ravenous for information? Today’s issue of Nature announces that Nature has created a central science news service, [Enable javascript to see this email address.]. Anyone with a subscription to any Nature journal (or a university subscription) can access all of the news, anyone at all can subscribe to the free daily news service, and everyone can try the whole thing out for free for two months at http://www.nature.com/news.

It’s quite handy. Just today I discovered that adaptive immune systems have evolved not once, but at least twice – once in the jawed vertebrates, and again, in an entirely different way, in their sister group, the lampreys (left). You may recall that Intelligent Design proponent Michael Behe listed the adaptive immune system as one of several “irreducibly complex” systems that supposedly scientists had no idea how to explain with evolution. This was debunked in rather excruciating detail a few years ago, but it is worth pointing out that every month brings out new discoveries filling in details on the evolution of the vertebrate immune system.

Touchstone magazine this month has an issue devoted to antievolution, running under the title, “Darwin’s Last Stand?” In a question and answer section, there is a question that William A. Dembski provides an answer for:

Touchstone: Where is the ID movement going in the next ten years? What new issues will it be exploring, and what new challenges will it be offering Darwinism?

Dembski: In the next five years, molecular Darwinism – the idea that Darwinian processes can produce complex molecular structures at the subcellular level – will be dead. When that happens, evolutionary biology will experience a crisis of confidence because evolutionary biology hinges on the evolution of the right molecules. I therefore foresee a Taliban-style collapse of Darwinism in the next ten years. Intelligent design will of course profit greatly from this. For ID to win the day, however, will require talented new researchers able to move this research program forward, showing how intelligent design provides better insights into biological systems than the dying Darwinian paradigm.

(Anonymous (Touchstone Magazine), (2004). “The Measure of Design: A conversation about the past, present & future of Darwinism and Design.” Touchstone, 17(6), pp. 60-65.)

The structure of the answer is quite interesting. Asked about the future of intelligent design, Dembski immediately responds with speculations about Darwinism.

The fact of the matter is that “intelligent design” has not, to date, offered any new challenges to any part of evolutionary biology. Every single argument made by ID advocates had its origins elsewhere, either in the biological literature or in antievolutionary sources. According to Dembski, designers are innovators, but thus far ID advocates have tallied up a big goose egg on innovative critiques of evolutionary biology.

Icons of ID: Paley’s watch

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We’re all familiar with the use of William Paley’s famous watch analogy as an indicator of design. But did you know that cyanobacteria have their own watches? In the 9/4/99 issue of Science, an article appears entitled “New Timepiece Has a Familiar Riing,” written by Marcia Barinaga. The article even has a nice picture of cyanobacteria, with a caption that some might enjoy:

Thus starts a posting titled “Finding a watch in the ocean” by an intelligent design proponent on biological clocks.

These biological clocks, also known as ‘circadian clock’ have all the attributes of ‘design’, they seem to be complex and specified (clock, feedback loop, oscillator). So what do we know about these circadian clocks?

I've been writing a fair amount about early pattern formation in animals lately, so to do penance for my zoocentric bias, I thought I'd say a little bit about homeotic genes in plants. Homeotic genes are genes that, when mutated, can transform one body part into another—probably the best known example is antennapedia in Drosophila, which turns the fly's antenna into a leg.

Plants also have homeotic genes, and here is a little review of flower anatomy to remind everyone of what 'body parts' we're going to be talking about. The problem I'll be pursuing is how four different, broadly defined regions of the flower develop, and what that tells us about their evolution.

flower anatomy

Continue reading "MADS boxes, flower development, and evolution" (on Pharyngula)

We love you, Grandma.

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A bit of new research suggests that the rise of human civilization may have been predicated on increasing lifespans. This allowed older adults to be, well, grandparents. And that allowed them to pass on their knowledge and skill well after their own reproductive lives were over. Kin selection strikes again.

Old Age Was Secret of Modern H. Sapiens’ Success.

Modern humans began to live long and prosper only about 30,000 years ago, researchers report. Results published online this week by the Proceedings of the National Academy of Sciences reveal a striking increase in human longevity during the Upper Paleolithic Period when the number of people surviving to old age increased four-fold. […]

The findings support the so-called grandmother hypothesis, which posits that older women no longer responsible for their own children help support the group by strengthening social bonds and providing greater opportunities to pass on specialized knowledge. “There has been a lot of speculation about what gave modern humans their evolutionary advantage,” Caspari remarks. “This research provides a simple explanation for which there is now concrete evidence: modern humans were older and wiser.”

Although some might say that H.L. Mencken disproved this hypothesis long ago when he remarked, “The older I grow the more I distrust the familiar doctrine that age brings wisdom.”

For a group that claim their ideas to be driven by science, rather than religious ideology, the Paleyists turn up in religious settings far more often than scientific ones. The latest issue of Touchstone magazine is largely given over to “Darwin’s last stand”, and has many essays from Paleyist stalwarts.

Of interest is the essay by Discovery Institute Fellow Jonathan Witt, “The Gods must be tidy!”. In this essay, amongst other things, he blames “Darwinism” for bad art and architecture. There are a number of errors in the essay; once again we have anti-evolutionists completely misunderstanding the basis of evolutionary biology (and the dreary old Nazis get trotted out again). I can’t deal with all the errors in one short essay, so I will concentrate on some of the more interesting ones.

In this episode of Icons of ID I will take a quick look at how the definition of information used by ID proponents is nothing more than an argument from probability. In fact when ID proponents claim that chance and regularity cannot create complex specified information (CSI) all they are saying is that such pathways, as far as we know, are improbable. If a pathway is found that is probable, the measure of information, which is confusingly linked to probability decreases. In fact, I argue, that intelligent designers similarly cannot generate specified complex information since the probability of intelligent designers designing is close to 1.

The eminent evolutionary biologist Ernst Mayr – who is a member of NCSE – celebrated his 100th birthday on July 5. Writing in the July 2 issue of Science, he reflected on his eighty years of “watching the evolutionary scenery,” from his education in Germany through the development of the Modern Synthesis to the discoveries of molecular biology. “[E]volutionary biology is an endless frontier,” he concluded, “and there is still plenty to be discovered.”

The Panda’s Thumb is pleased to join its voice to the chorus of those around the world who have wished Professor Mayr a very happy birthday.

Note: Modified from NCSE’s release.

A while back I was looking through my 1970s Funk & Wagnals’ Wildlife Encyclopedia and read the entry on River Dolphins. In it a particular passage caught my eye because it was not very parsimonious.

We usually take it for granted that because whales, porpoises and dolphins are so obviously descended from land animals, their ancestors must have returned directly to the sea. As a result, it is something of a surprise to learn there are such animals as river dolphins, and we suppose they have come up rivers from the sea. In fact, the ancestors of dolphins could just as easily have left the land fro the rivers, and later invaded the sea. This is supported by the primitive characters exhibited in the skeletons of the freshwater dolphins. In most whales, porpoises and dolphins the seven neck vertebrae are squashed together and fused, and the animals have no visible neck. In freshwater dolphins the vertebrae are separate and there is still some sign of a neck. Also, the skull of a freshwater dolphin has not undergone the same fundamental changes as the skulls of its marine relatives, and in several ways is more like the skull of the extinct dolphin Squalodon of 15 millions years ago.

The problem of this hypothesis is that it requires the river dolphins of the Amazon, Ganges, Yangtze, etc. to all be autochthonous and essentially unrelated, since those river systems are separated by good span of geography. So I went digging to see how science has progressed in 30 years, and found this gem.

Hamilton H et al. (2001) Evolution of River Dolphins. The Royal Society Proceedings: Biological Sciences, 268: 549-556.

To all Mac OS X users: a whole pile of bioinformatics tools have been made freely available to us, as announced on nodalpoint.org:

Many Life Science researchers need bioinformatics tools for the desktop. But many of the common Open Source tools are difficult to install for people without much Linux/Unix knowledge. We have created a user friendly install package for the MacOSX platform. The package installs most of the common bioinformatics packages: EMBOSS, Blast, HMM etc and also installs some biological databases. Together with the packages it is possible to configure webservices e.g. Blast. Researchers will find it very useful to be able to install a user friendly GUI in top of EMBOSS (embossRUNNER).
All packages can be downloaded at www.ebioinformatics.org. Detailed instructions and HOW-TOs have being published on the latest issues of EMBnetNews (free from www.embnet.org).

It's a 252MB gzipped file that will take up about 850MB installed. You'll also need to install X11 for Mac OS X; this is included on the Panther CDs (disc 3), but isn't installed by default. You'll need a fast connection and a bit of room on your hard disk for all this stuff! They also recommend that you get a three-button mouse, the one thing I'm lacking on my laptop.

The instructions for installation are in multiple volumes of EMBnetNews, and unfortunately they've been superceded in steps. Volume 9.1 has the original, rather convoluted instructions, but you might want to see them to get the list of stuff that is going to get plopped onto your computer. Volume 9.2 has details on Blast and GUI frontends. Volume 9.3 has more on Blast and performance information, and describes a major change in the installation procedure: it now just takes one double-click on a single installer package to put everything in one directory on your computer (in other words, ignore the instructions in 9.1). Volume 10.1 is just a short note listing some recent additions.

This probably isn't something anyone should do on a whim. It's going to require about as much horsepower and resources as, say, the latest version of Diablo, or whatever the hot new graphics-intensive video game might be. And once you've got it running, it's not going to be obvious how to do anything with it unless you've got a bit of molecular biology background.

I've put it on my machine, and it was fairly straightforward; it only took about an hour for everything, and that includes the download time (I have a fast connection). Don't ask me for help with it, though, I'm just tinkering myself and puzzling my way through all the bits and pieces.

I cross-posted my last essay on science standards and ID over at ARN, and someone there offered this:

Concerning the Ohio standards, Meyer [Stephen Meyer, of the Discovery Institute] said this:

[quote] Dr. MEYER: Well, we agree with you, Ken, and this is one of the reasons that we asked–certainly there were political supporters of design in Ohio who are getting the cart before the horse. That’s one of the reasons we took the theory off the table for the purposes of the state testing standards. We understand that this is a new theory. We think it’s unrealistic to think that teachers would be able to be informed enough to teach it well at this point, and so we said, ‘Look, the main focus,’ as you have said, ‘of biological research is evolutionary theory. Let’s look at that openly and in a critical manner.’ [endquote]

Do you agree with this?

I’d like to respond to this question here.

State science standards and ID

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A common tactic of the ID movement is to try to insert ID-influenced statements into state and local science standards, such as in Ohio and Darby, Montana recently. The argument is that science standards are biased towards philosophical naturalism and towards dogmatically teaching “evolution only”, and therefore standards should include statements that question these “biases, such as “teaching the evidence for and against evolution” or “teaching alternative theories of origins.”

Kansas is currently reviewing its science standards, and it is likely that these issues will once again arise here. As a member of the state standards review committee and as a former curriculum director, I am interested in whether these types of ID-influenced statements have a proper place in state standards.

Rather than immediately address the question of whether these kinds of statements are appropriate, I would like to first talk more generally about what standards are, what they are not, why they are important, and how they are established. Having a proper understanding of how standards relate to the overall subject of teaching science in the public schools should help put the activities of the ID movement into perspective.

In case you’ve been living in a box somewhere, the NASA/ESA spacecraft Cassini-Huygens successfully fired its rockets on July 1, slowing down enough to be captured by Saturn’s gravity and enter a highly elliptical orbit around Saturn. If the rocket burn had failed, Saturn’s gravity boost would have given Cassini enough velocity to escape the solar system, so this was a fairly important part of the 7-year mission.

Cassini threaded a gap in the rings (twice), flew within one Saturn-diameter of Saturn, and took some ultra-close snapshots of Saturn’s rings. Soon afterwards, Cassini made a moderately close Titan flyby, getting the first decent images of the surface of the solar system’s second-biggest moon.

Clicking these thumbnails will take you to the full resolution version on the NASA website.

As you can see (left), in the wavelengths of visible light (400-700 nanometers), Titan appears covered in impenetrable red haze. However, by using longer infrared wavelengths (2000, 2800, and 5000 nanometers), the Cassini cameras can peer through the haze.

Last Sunday I had the opportunity to hear Susan Epperson of Epperson v. Arkansas. Her case struck down anti-evolution laws around the country as unconstitutional. She was invited to speak at the Evolution Conference 2004 in Fort Collins, CO. The title of her talk was “‘There is a striking resemblance between you and a monkey’: The Epperson vs. Arkansas evolution ruling, Supreme Court, 1968”. Epperson, although a daughter of Arkansas, now lives and teaches in Colorado because her husband is in the Air Force and he teaches at the Air Force Academy. She currently teaches introductory chemistry at the University of Colorado at Colorado Springs.

Susan Epperson is the daughter of Dr. Thomas L. Smith who was a biology professor at the College of the Ozarks, a Presbyterian college, and a student of Thomas Hunt Morgan at Columbia. Epperson was raised in a devoutly Presbyterian family, and evolution was never a problem for her faith. She holds a bachelor’s degree from the College of the Ozarks in biology and a master’s in zoology from the University of Illinois.

The TalkOrigins Archive now has an RSS 2.0 compliant feed.

The Talk.Origins Archive is a collection of articles and essays, most of which have appeared in talk.origins at one time or another. The primary reason for this archive’s existence is to provide mainstream scientific responses to the many frequently asked questions (FAQs) that appear in the talk.origins newsgroup and the frequently rebutted assertions of those advocating intelligent design or other creationist pseudosciences.

In the last few weeks I have addressed various Icons of ID. I have come to the conclusion that the Explanatory Filter (EF) is fundamentally unreliable. In fact, I believe that the evidence shows conclusively that such concepts as Irreducible Complexity (IC), Complex Specified Information, Law of Conservation of Information are fundamentally flawed. This means that the ID hypotheses, at least those based on elimination, are fundamentally flawed.

Bembi Babelmandebski’s view from 2014 – The 450th anniversary of Galileo’s birth

By Amiel Rossow

——————————————————————————–

Foreword by the editors of Whorls magazine

We are happy to present an article by I. D. “Bembi” Babelmandebski, Ph.D, Senior Fellow, Interplanetary Society of Informational Sages (ISIS)[1]

Besides having published, by the latest count, 765 books, Dr. Babelmandebski (Bembi for his friends and colleagues) holds a world record in the number of his degrees, both earned and bestowed honoris causa, in areas ranging from stamp collection to mosquitology and from the geography (perhaps more properly named the moonography) of Jupiter’s moons, to complicated specificity of the fairy tales of his nanny. Unfortunately, the editors of that infamous outlet of the Darwinist-Galileanist orthodoxy, the Guinness Book of World Records, refused to register Dr. Babelmandebski’s record thus confirming the well known fact of the vicious conspiracy of materialists to keep hidden from public the supernatural origin of Dr. Babelmandebski’s degrees. Fortunately, today, in 2014, the complete and final victory of information over matter, so convincingly demonstrated by Dr. Babelmandebski’s article, has made explicit those despicable maneuvers by materialistic “scientists,” so that Dr. Babelmandebski now lawfully takes his long deserved place in the roster of greatest scientists and philosophers of all times, above Isaac Newton, Copernicus, Aristotle, Kant, and Hegel…

Dr. Babelmandebksi, who makes his home between the towns of Taco and Wiesel, is also famous for his barbecue which he sells to everybody including unbelievers and materialists, both methodological and ontological, for the same low price as to his colleagues in the ID movement (in a way similar to that described by another barbecue master at http://www.brazosbarbecue.com/).

Dr. Babelmandebski’s formidable intellect (officially confirmed by his Australian colleagues of the bioceramics fame) is of such a caliber that our editors could not come up with proper epithets which would do justice to this titan of all sciences and all branches of mathematics, philosophy, theology, and culinary art. We are confident our readers will enjoy this masterpiece of logic, mathematical rigor, and poetical beauty typical of Dr. Babelmandebski’s groundbreaking work, not any less than they could enjoy the incomparable taste of his affordable barbecued food.

Tangled Bank #6

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A new Homo erectus specimen

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homo erectus skulls

Carl Zimmer places the recent discovery of a new Homo erectus specimen in the broader context of human evolution—read his article on The Little Ones.

NCSE RSS Syndication

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The National Center for Science Education, a clearinghouse for information on teaching evolution and opposing non-science in science classrooms, has long had a web site with both breaking news and critical resources. Now, the NCSE web site has syndicated content using an RSS 2.0 compliant feed. Please pass the word along…

As a follow-up to my recent articles on early genes in fly development, I've also written a summary of why flies have some problems as a model system in evolution, titled "Flies, spiders, fish and the evolution of segmentation". Early pattern formation in the metazoa is a delightfully complicated bramble, but there are some emerging comparative data that may resolve the differences.

Evo-devo is leading the way and guiding research, but I assure you, Intelligent Design creationism is nowhere to be found, except perhaps in hampering the educations of the next generation of scientists.

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