Posted by Jason Rosenhouse on April 07, 2005 | Comments (27) | TrackBack (0)

While the ID folks continue to blather about the impossibility of complex systems evolving naturalistically, real scientists are busy unravelling the steps by which such evolution actually occurred.

The March 18 issue of Science contains this research report and accompanying technical article (only available by subscription, apparently), about recent work on the evolution of swim bladders in fish. Meanwhile, Bryan Fry of the University of Melbourne in Australia has published this article in which he unravles some of the mysteries of snake venom evolution. This work is described in layman's terms by Carl Zimmer in this article from The New York Times.

Continue reading  “Swim Bladders and Snake Venom”

Posted by perakh on February 23, 2005 | Comments (89) | TrackBack (0)

Michael Behe’s book Darwin’s Black Box is one of the most popular and extensively reviewed books promoting intelligent design “theory.” The concept of “irreducible complexity” propagandized in that book has been touted by Behe and other intelligent design advocates as a great discovery and used as one of the main tools in their efforts to “destroy Darwinism” (the goal openly announced by such “leading lights” of intelligent design as Phillip Johnson [1991] and Jonathan Wells [2002]).

Irreducible complexity, according to “design theorists,” implies intelligent design of biological system. In fact, such a conclusion lacks a logical foundation. Irreducible complexity can even more reasonably be construed as an argument against intelligent design.

Continue reading  “Beyond Suboptimality: Logical Fallacy of Behe's "IC means ID" Notion”

Posted by Tara Smith on February 22, 2005 | Comments (158) | TrackBack (1)

Every now and then, I check in over at The Institute for Genomic Research (TIGR) to see what new projects they’re up to, as well as to see if they’ve released a particular genome sequence I’m waiting on.  Yesterday I noticed this project:

Innovative Metagenomics Strategy Used To Study Oral Microbes

Rockville, MD - The mouth is awash in microbes, but scientists so far have merely scratched the surface in identifying and studying the hundreds of bacteria that live in biofilm communities that stick to the teeth and gums.

In an innovative new project that could help improve the detection and treatment of oral diseases, scientists are now using a metagenomics strategy to analyze the complex and difficult-to-study community of microbes in the oral cavity.

***

In recent years, molecular methods have indicated that there are well over 400 species of bacteria in the oral cavity. But, so far, only about 150 of those species have been cultured in laboratories and given scientific names. Using a metagenomics sequencing strategy, TIGR scientists will be able to identify bits and pieces of the DNA of many of those oral microbes that so far have not been grown in labs and studied.

Now, I know that there are an insane amount of microbes in the mouth, but 400 species? Holy cow.

Continue reading  “Plaque--evidence for Design!”

Posted by Pim van Meurs on February 05, 2005 | Comments (152) | TrackBack (1)

Our congratulations go out to Carl Zimmer. Discover magazine published one of Carl Zimmer’s articles as a cover article. The article was titled “Testing Darwin” (Published in Discover Magazine Feb 2005)

Zimmer explores the relevance of work on Avida to evolution

One thing the digital organisms do particularly well is evolve.” Avida is not a simulation of evolution; it is an instance of it,” Pennock says. “All the core parts of the Darwinian process are there. These things replicate, they mutate, they are competing with one another. The very process of natural selection is happening there. If that’s central to the definition of life, then these things count.”

The work based on Avida is not well received by creationists who argue that Darwinian theory cannot explain the complexity of life. Although others have already shown that complexity and information in the genome can increase under the processes of variation and selection., Avida has recently been used to address the concept of irreducible complexity. (Note: Mark Perakh has addressed some the ever changing definitions of irreducible complexity in ID’s irreducible inconsistency revisited)

Continue reading  “Avida in Discover Magazine”

Posted by Steve on January 27, 2005 | Comments (11) | TrackBack (0)

No, this is not another post about the sexual habits of female apes.  This is about enzymes, and their ability to catalyze different reactions with different substrates, even those that aren’t found in nature.  It’s a property known as “promiscuity”, one that’s being increasingly recognized as important in enzymology and enzyme evolution. 

The usefulness of enzymes derives in part from their specificity, in that they don’t just catalyze any old reaction with any old substrate.  It would be hard for cells to maintain homeostasis if enzymes were highly nonspecific; helpful reactions would be coupled with harmful side reactions, regulation would be impossible, and things would get messy real quick.  So it’s useful for enzymes to specialize in certain functions so that they can be applied for specific tasks at specific times.  But because nature is a bit sloppy, enzymes are often able to catalyze many reactions weakly in addition to the “native” functions that they specialize in.  These additional weak activities are referred to as promiscuous activities, and they’re potentially very important in enzyme evolution.  Now a recent study (subscription required) published in Nature Genetics by Amir Aharoni and coworkers sheds some light on why enzymes are promiscuous, and what it means for their evolvability.  (There is some good non-technical commentary on the paper here and here.)  It also badly knocks down some bold claims made by leading ID proponents.

Continue reading  “Promiscuity in Evolution”

Posted by Nick Matzke on January 01, 2005 | Comments (48) | TrackBack (18)

Discovery Institute Fellow Jonathan Witt has a post over on his blog (“Darwinism and Demarcation: Ducking the Debate”, see also his comments on that post and his subsequent post, Comments on Ducking the Debate).

Witt is quite confident that modern biology is totally wrong, but it’s clear that he doesn’t even understand the basics. 

“Micajah,” a commenter on Witt’s blog, cites this press release about the cover story of this week’s issue of Cell.  The Cell article, “Accelerated Evolution of Nervous System Genes in the Origin of Homo sapiens, gives new insight into how the human brain evolved. 

Unfortunately, the comments by Witt in reply to “Micajah” and other posters indicate almost total unfamiliarity with the relevant science.  It is, I think, an example of “this is your brain on ID/creationism.”

Continue reading  “Brain evolution: Keeping your Witts about you”

Posted by Nick Matzke on December 31, 2004 | Comments (26) | TrackBack (1)

The new PNAS article “The descent of the antibody-based immune system by gradual evolution,” blogged by Carl Zimmer (“The Whale and the Antibody”) and Reed Cartwright at PT, brings to mind a famous old declaration by Michael Behe in his 1996 book Darwin’s Black Box:

“We can look high or we can look low, in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system.”

(Darwin's Black Box, p. 138)

This wasn’t true in 1996, as was documented when PT contributor Matt Inlay reviewed Behe’s immune system argument in 2002 (see “Evolving Immunity” at TalkDesign.org and the hilarious response of ID advocates when challenged).  It is even less true now, due to the new PNAS article and other evolutionary immunology research published in 2004 and before.  In fact, the ID movement is in total denial about this body of literature, yet ID advocates continue to parade around as if they have some shred of scientific credibility behind their rhetoric.  They even have the gall to claim that the scientific mainstream is dogmatically oppressing them — it’s rather like a geocentrist arguing for a stationary earth without considering Foucault’s Pendulum.

I’ll take the liberty of making some predictions for 2005:

Continue reading  “Happy New Year, ID movement! (ID and Evol. Immunology)”

Posted by Pim van Meurs on July 30, 2004 | Comments (0) | TrackBack (0)

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).

Posted by Pim van Meurs on July 29, 2004 | Comments (33) | TrackBack (0)

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.

Continue reading  “Scale Free Networks”

Posted by Pim van Meurs on July 20, 2004 | Comments (5) | TrackBack (0)

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.

Continue reading  “Simulating the early evolution of plants”

Posted by Pim van Meurs on July 11, 2004 | Comments (0) | TrackBack (0)

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.

Continue reading  “Icons of ID: Avida”

Posted by Ian Musgrave on July 10, 2004 | Comments (11) | TrackBack (0)

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?

Continue reading  “I shared a lift with Baroness Greenfield”

Posted by Pim van Meurs on July 08, 2004 | Comments (14) | TrackBack (0)

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)

Continue reading  “Complexity: Darwin and neutral evolution”

Posted by John Wilkins on June 28, 2004 | Comments (12) | TrackBack (0)

One long-standing question in understanding the origin of life is the so-called “chirality problem”. While this is an unresolved question in our understanding of the origin of life, it is used by anti-evolutionists to beat evolutionary theory over the head. As we never tire of telling folk, the origin and subsequent evolution if life are two distinct issues.

What is the “chirality problem”? Let’s start by briefly discussing what chirality is. Biological molecules of some complexity often come in two forms that while chemically identical, have different three dimensional shapes; a “left-handed” one, and it’s mirror image, a “right-handed” one (see alanine graphic). Of particular importance for living systems are amino acids (levo- or left-handed) and sugars (dextro- or right-handed). Handedness is due to the carbon atom’s bonding capacities. This property of some molecules was discovered in 1847 by none other than Louis Pasteur (the molecule was a form of tartrate) in the dregs of some wine.

[img][*]http://www.pandasthumb.org/pt-archives/L-alanine.jpg…[*]http://www.pandasthumb.org/pt-archives/D-alanine.jpg…[/img]
Chiral forms (enantiomers) of the amino acid alanine. White balls are hydrogen atoms, grey balls are carbon atoms and the red ball is an oxygen atom, The left handed form is not superimposable on the right handed form).

How, it is asked, could this have occurred at the beginning of life? Surely ordinary physical processes should have given us a mix of both left and right handed forms (known as a racemic mixture)?

Well, firstly it turns out that ordinary physical processes do produce an excess of left over right forms. Recently, though, it was discovered that life itself can generate a particular enantiomer or chiral form of a particular molecule.

Continue reading  “The Left Hand of Darwin”

Posted by RBH on June 19, 2004 | Comments (12) | TrackBack (0)

Having recently (finally!) acquired a digital camera with pretty good zoom capabilities (10x optical, 3x electronic), I’ve been lurking around the place taking pics of little things, pushing the zoom to the max.  This is my favorite so far, what I think is a Celastrina of some variety/subspecies, though the notched wing is a teaser.  (Is there a lepidopterist in the house?)  I’m particularly taken with the pattern of alternating black and white on the antennae.  Click here for a larger image (27K), and here for a still larger image (47K).

Posted by Pim van Meurs on June 11, 2004 | Comments (0) | TrackBack (0)

As I explained before, entropy may appear to be a simple concept but is easily confused. A good example is the claim made by Jerry Bauer who claims to be using Feynman’s equation to calculate the entropy of mutations.

Let’s see what Jerry claims and then compare this to what he should have said. I pointed out to Jerry that Feynman presented a hint to Jerry as to how to calculate entropy correctly:

Continue reading  “Entropy continued”

Posted by Pim van Meurs on May 29, 2004 | Comments (6) | TrackBack (0)

Introduction

Entropy may seem to be at first a simple concept but when trying to apply these concepts correctly one invariably runs into frustrating issues and areas of confusion. In this posting I intend to explore some of these confusions and I hope to explain how one applies entropy calculations correctly.

Continue reading  “Entropy: Common pitfalls”

Posted by Pim van Meurs on May 29, 2004 | Comments (0) | TrackBack (0)

John Wilkins has written a FAQ on the probability of abiogenesis.

What Louis Pasteur and the others who denied spontaneous generation demonstrated is that life does not currently spontaneously arise in complex form from nonlife in nature; he did not demonstrate the impossibility of life arising in simple form from nonlife by way of a long and propitious series of chemical steps/selections. In particular, they did not show that life cannot arise once, and then evolve. Neither Pasteur, nor any other post-Darwin researcher in this field, denied the age of the earth or the fact of evolution.

From the early views of Aristotle, through the research by Louis Pasteur to abiogenesis research, Wilkins shows how these fascinating concepts evolved.

A worthy addition to the Probability of Abiogenesis FAQs

Read further on Talk.Origins

Posted by Pim van Meurs on May 27, 2004 | Comments (7) | TrackBack (0)

Introduction to Shannon entropy

Motivated by what I perceive to be a deep misunderstanding of the concept of entropy I have decided to take us onto a journey into the world of entropy. Recent confusions as to how to calculate entropy for mutating genes have will be addressed in some detail.

I will start with referencing Shannon’s seminal paper on entropy and slowly  expand the discussion to include the formulas relevant for calculating the  entropy in the genome.

But first some warnings

• Information Is Not Entropy, Information Is Not Uncertainty!

• Pitfalls in information theory

Continue reading  “Shannon entropy applied”

Posted by jml on April 29, 2004 | Comments (4) | TrackBack (0)

As part of an essay review I am completing, last night I finished reading Larry Witham’s By Design, which “recounts the history of the intelligent design movement [and] … shows how ideas and personalities mix to challenge deep scientific presumptions.” I don’t have time at the moment to go into it, but Witham’s work is deeply flawed as an historical study and clearly demonstrates his support for the design faction (not surprising giving his Unification Church background and friendship with Jonathan Wells). That aside (and it is something I will return to eventually), Witham makes much of Behe’s scientific credentials along with his “conversion” to ID being for evidential (rather than religious) grounds.  In Chapter 8 he states:

Although critics call his design idea a “science stopper” (arguing that if a designer is presumed, many questions about origins are settled by fiat), Behe keeps up his research. (p. 132)

Tom Woodward also makes much of Behe’s standing as a research scientist in his Doubts About Darwin (Baker House, 2003), another flawed and partisan history of design.

Let’s examine Behe’s publication record over the past ten years, concentrating on peer-review scientific articles (i.e. ignoring letters, op-ed pieces, etc).

Continue Reading Behe as Research Scientist (at Stranger Fruit)

Posted by RBH on March 31, 2004 | Comments (0) | TrackBack (0)

Royal Truman, an organic chemist and ID proponent, continues his critique of the Lenski, et al., demonstration that irreducibly complex systems can evolve. Rather than cross-posting, my reply is here. From that reply:

Irreducible complexity is at the core of of the Intelligent Design movement’s claims about the unevolvability of certain kinds of systems, and is interpreted by ID proponents to be a signature of design by an Intelligent Agency. But if systems meeting the definition of irreducible complexity can evolve in a context that instantiates the general properties of evolutionary systems, then that claim is weakened, and indeed, is falsified with respect to the claim about evolutionary processes in general. And that’s what the Lenski, et al., paper does: it demonstrates that systems meeting the definition of IC can evolve in a context that instantiates the general properties and processes of evolutionary systems.

Read the whole posting on ISCID

Posted by John Wilkins on March 28, 2004 | Comments (10) | TrackBack (0)

It is, wrote the Roman poet Horace, fit and proper to die for one's homeland. The word he used for homeland was "patria" (dulce et decorum est pro patria mori), and the word has entered into biology as the suffix for exactly that. Unlike Horace's slogan, though, it applies more to living than dying. It would be nice if we humans could attempt to live for our homelands rather than die for them, but that's another rant for another time.

There are a cluster of terms used by biologists to describe where organisms live or grow, and they are: sympatric, allopatric, parapatric, peripatric, stasipatric, and dichopatric. This flock of technical terms is confusing to the newcomer (and to some biologists), but there is a kind of logic - as much as in the evolution of any technical jargon - that will make it clearer, and at the same time allow us to set up the alternative views on the fundamental evolutionary process of common descent: speciation.

Continue reading  “Living Words: Pro patria - species and homeland security”

Posted by RBH on March 28, 2004 | Comments (7) | TrackBack (1)

As I noted in an earlier posting, research using computational models of evolution are a thorn in the side of Intelligent Design proponents. That thorn is becoming sharper and more penetrating as computer models of evolution become powerful and versatile enough to begin addressing biologically interesting questions. An example from last year is Lenski, et al.’s The evolutionary origin of complex features, published in Nature.

Brief (!) Intro to the AVIDA artificial life platform

Continue reading  “Evolving Complex Stuff: "Darwinian" Evolution and Irreducible Complexity”

Posted by John Wilkins on March 27, 2004 | Comments (1) | TrackBack (0)

The phrase "complex specified information" is a core concept in the lexicon of the World's Greatest Information Theorist William Dembski, but it was not invented by him. In fact, it comes from a book published in 1973, by Leslie Orgel, entitled The Origins of Life: Molecules and Natural Selection. It is odd to think that this notion, which is supposed by Dembski to demonstrate that life, or LIFE as he like to refer to it in his The Design Inference of 1998, cannot be the result of natural selection, was coined in the context of a discussion how it actually could.

What does Orgel actually say about complex specified information, then? He didn't actually use the complete phrase "complex specified information", but the ideas are there. Perhaps in reading him, we may get a hint of how Dembski developed his reaction to Darwinian evolution, and more to the point, perhaps we'll be able to make sense of some wider, and more important, ideas in evolution.

Continue reading  “CSI, the original series...”

Posted by pz on March 26, 2004 | Comments (71) | TrackBack (2)

One of the serious shortcomings of Intelligent Design is that it does nothing to provide any new or productive insights into the workings of biology. ID proponents seem to be at least vaguely aware of this failure, in that they do frequently claim to be thinking about working on a preliminary, tentative approach towards the beginnings of a potential research program (my paraphrase), but most of the effort has been directed towards political and legal enforcement of their ideas, rather than actually testing those ideas. One advantage of pursuing only legalisms is that they don't give scientists anything to grapple. Invariably, when ID proponents do dip their toes in the scientific waters, they end up getting eaten by the sharks that lurk there.

One example: Paul Nelson, of the Discovery Institute, has been peddling a peculiar idea he calls "ontogenetic depth" as a scientific concept that emerges from Intelligent Design. To his credit, he has been presenting this idea in legitimate science venues, at the Geological Society of America and Society for Developmental Biology meetings. Note that getting on the program at these meetings is not subject to peer-review, so it is not automatically a recognition of merit that this work has been presented publicly. It is a good sign that Nelson is willing to expose his work to criticism, though.

I'm going to give it some criticism here. "Ontogenetic depth" is a developmental idea, and I'm a developmental biologist. Today I also get to play shark.

Continue reading  “Ontogenetic depth”

Posted by Nick Matzke on March 24, 2004 | Comments (3) | TrackBack (0)

Orchid flowers are amazing. Science journalist and top blogger Carl Zimmer recently wrote a blog on orchids, "Orchid Hacks," commenting on a paper by Florian Schistl in the Journal of Evolutionary Biology that showed how orchids "hack" into the mate-recognition systems of male wasps. However, there is more than one way to "hack" a bug.

Continue reading  “The Beauty and The Beast”