July 18, 2004 - July 24, 2004 Archives

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.

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.

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