July 2004 Archives

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).

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.

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.

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.

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.

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.

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.

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.

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

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 21^st 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.

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 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.

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 15^th.

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.

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.

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.

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 21^st 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.

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.

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.)

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

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.

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 :)

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.

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 14^th most inspirational woman in the owrld (and as she wryly notes, Dolly Parton is the 9^th). 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

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.

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).

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)