Politics on your mind?

Posted by Pim van Meurs on September 11, 2007 | Comments (166) | TrackBack (0)

The Seattle Times has an interesting article on the link between political views and the brain

In a study likely to raise the hackles of some conservatives, scientists at New York University and the University of California, Los Angeles, found that a specific region of the brain’s cortex is more sensitive in people who consider themselves liberals than in self-declared conservatives.

Based on the findings we can make some predictions

Based on the results, Sulloway said, liberals could be expected to more readily accept new social, scientific or religious ideas.

Or alternatively, conservatives will be less ready to accept new scientific ideas.

Imagine that

Well now we understand

Analyzing the data, Sulloway said liberals were 4.9 times more likely than conservatives to show activity in the brain circuits that deal with conflicts and were 2.2 times more likely to score in the top half of the distribution for accuracy.

Continue reading  “Politics on your mind?”

Altruism: Even Plants Can Do It

Posted by Pim van Meurs on June 15, 2007 | Comments (22) | TrackBack (0)

A recent paper (free access) by Associate Professor Susan Dudley, published in the Royal Society journal Biology Letters argues that some plants recognize their kin.

Kin recognition is important in animal social systems. However, though plants often compete with kin, there has been as yet no direct evidence that plants recognize kin in competitive interactions. Here we show in the annual plant Cakile edentula, allocation to roots increased when groups of strangers shared a common pot, but not when groups of siblings shared a pot. Our results demonstrate that plants can discriminate kin in competitive interactions and indicate that the root interactions may provide the cue for kin recognition. Because greater root allocation is argued to increase below-ground competitive ability, the results are consistent with kin selection.

Although it were gardeners who knew this all along:

Continue reading  “Altruism: Even Plants Can Do It”

On the evolution of Irreducible Complexity

Posted by ArthurHunt on May 1, 2007 | Comments (66) | TrackBack (1)

There has been a spate of interest in the blogosphere recently in the matter of protein evolution, and in particular the proposition that new protein function can evolve. Nick Matzke summarized a review (reference 1) on the subject here. Briefly, the various mechanisms discussed in the review include exon shuffling, gene duplication, retroposition, recruitment of mobile element sequences, lateral gene transfer, gene fusion, and de novo origination. Of all of these, the mechanism that received the least attention was the last – the de novo appearance of new protein-coding genes basically “from scratch”. A few examples are mentioned (such as antifreeze proteins, or AFGPs), and long-time followers of ev/cre discussions will recognize the players. However, what I would argue is the most impressive of such examples is not mentioned by Long et al. (1). Below the fold, I will describe an example of de novo appearance of a new protein-coding gene that should open one’s eyes as to the reach of evolutionary processes. To get readers to actually read below the fold, I’ll summarize – what we will learn of is a protein that is not merely a “simple” binding protein, or one with some novel physicochemical properties (like the AFGPs), but rather a gated ion channel. Specifically, a multimeric complex that: 1. permits passage of ions through membranes; 2. and binds a “trigger” that causes the gate to open (from what is otherwise a “closed” state). Recalling that Behe, in Darwin’s Black Box, explicitly calls gated ion channels IC systems, what the following amounts to is an example of the de novo appearance of a multifunctional, IC system.

Continue reading  “On the evolution of Irreducible Complexity”

Axe (2004) and the evolution of enzyme function

Posted by ArthurHunt on January 14, 2007 | Comments (26) | TrackBack (0)

Douglas Axe recently (well, sort of) published an article in the Journal of Molecular Biology entitled “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” (Axe, J Mol Biol 341, 1295-1315, 2004). In his discussion of the experimental observations, Dr. Axe mentions some numbers that are likely to generate much discussion amongst Intelligent Design advocates and critics. For example, Stephen Meyer (2004) cites Axe at a key point in the argument in his recent article advocating Intelligent Design, “The Origin of Biological Information and the Higher Taxonomic Categories,” much discussed in previous Panda’s Thumb threads (here).

“Axe (2004) has performed site directed mutagenesis experiments on a 150-residue protein-folding domain within a B-lactamase enzyme. His experimental method improves upon earlier mutagenesis techniques and corrects for several sources of possible estimation error inherent in them. On the basis of these experiments, Axe has estimated the ratio of (a) proteins of typical size (150 residues) that perform a specified function via any folded structure to (b) the whole set of possible amino acids sequences of that size. Based on his experiments, Axe has estimated his ratio to be 1 to 10^77. Thus, the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 10^77.”

More recently, Dembski cited Axe in his Expert Witness Report for the Dover trial (see this).

“Recent research by Douglas Axe (see Appendix 3) provides such evidence in the form of a rigorous experimental assessment of the rarity of function-bearing protein sequences. By addressing this problem at the level of single protein molecules, this work provides an empirical basis for deeming functional proteins and systems of functional proteins to be unequivocally beyond Darwinian explanation.”

Given that this subject is often raised by ID proponents (such as this), and that the Biologic Institute (where Axe works) has made some news accounts, it seems appropriate to review Axe’s work. The purpose of this PT blog entry is to try and lay out the study cited above (Axe DD, J Mol Biol 341, 1295-1315, 2004) in a form that is accessible to most interested parties, and to discuss a larger context into which this work might be placed. Needless to say, the grand pronouncements being made by the ID camp are not warranted.

Continue reading  “Axe (2004) and the evolution of enzyme function”

PNAS: Evolution of complexity in signaling pathways

Posted by Pim van Meurs on October 31, 2006 | Comments (9)

PNAS has published an article by Soyer and BonHoeffer titled Evolution of complexity in signaling pathways

Abstract: It is not clear how biological pathways evolve to mediate a certain physiological response and why they show a level of complexity that is generally above the minimum required to achieve such a response. One possibility is that pathway complexity increases due to the nature of evolutionary mechanisms. Here, we analyze this possibility by using mathematical models of biological pathways and evolutionary simulations. Starting with a population of small pathways of three proteins, we let the population evolve with mutations that affect pathway structure through duplication or deletion of existing proteins, deletion or creation of interactions among them, or addition of new proteins. Our simulations show that such mutational events, coupled with a selective pressure, leads to growth of pathways. These results indicate that pathways could be driven toward complexity via simple evolutionary mechanisms and that complexity can arise without any specific selective pressure for it. Furthermore, we find that the level of complexity that pathways evolve toward depends on the selection criteria. In general, we find that final pathway size tends to be lower when pathways evolve under stringent selection criteria. This leads to the counterintuitive conclusion that simple response requirements on a pathway would facilitate its evolution toward higher complexity.

Read on for some of my thoughts.

Continue reading  “PNAS: Evolution of complexity in signaling pathways”

A working list of species "concepts"

Posted by John Wilkins on October 2, 2006 | Comments (1)

Students are often overwhelmed by the number of species concepts cited in the literature. Here is a working list of species concepts presently in play. I quote “Concepts” above because, for philosophical reasons, I think there is only one concept - “species”, and all the rest are conceptions, or definitions, of that concept. I have christened this the Synapormorphic Concept of Species in (Wilkins 2003).

Read the rest on Evolving Thoughts.

Alert! Alack! I have been quote mined!

Posted by Nick Matzke on September 17, 2006 | Comments (469)

Anyone who has been a “creationism watcher” for any length of time is familiar with the venerable creationist tactic of “quote mining.” Since creationists, essentially universally, can’t (or don’t want to) deal with actual scientific data pertaining to evolution, they attempt maintain a facade of respectibility by quoting statements from biological authorities. This can take many forms; for example, for the 1987 Supreme Court Edwards v. Aguillard case, the creationist lawyer Wendell Bird, apparently with the help of Paul Nelson, assembled a massive 500-page brief that consisted almost entirely of thousands of quotes from authorities on every topic bearing on “creation science”, from astrophysics to biology to philosophy to religion. This failed to convince the Supremes, but Bird turned his brief into a large two-volume book, The Origin of Species Revisited. Other elaborations on creationist quote-mining include various “Quote Books”, including The Quote Book (1984 booklet, inserted in Creation magazine I believe) and The Revised Quote Book (1990) from Answers in Genesis, the Handy Dandy Evolution Refuter (now online), and Henry Morris’ That Their Words may be used against Them (comes with CD!). Then we have endless collections of quotes on creationist websites, 50 of which were recently surveyed and ranked against the Talk.Origins Quote-Mine Project. Sometimes these quotes evolve and mutate over time (here is an example from Of Pandas and People), and sometimes they even spontaneously generate from thin air, as with this imaginary quote from Clarence Darrow.

You may be saying, “Surely this is a problem, but only famous authorities get quote mined. It would never happen to me!” Think again. On September 5, 2006, an article I coauthored in Nature Reviews Microbiology on flagellum evolution was published on the NRM website as an Advanced Online Publication. Before the ink was even dry – heck, before the ink was even wet, the October issue hasn’t come out yet – Casey Luskin at the Discovery Institute is quote mining it! The mining occured in Luskin’s insta-response to the revised edition Chris Mooney‘s book The Republican War on Science. Check this out:

Continue reading  “Alert! Alack! I have been quote mined!”

Friday flagellum blogging -- spirochete flagella

Posted by Nick Matzke on August 4, 2006 | Comments (33)

Treponema flagellum baseA paper that just came out in Advance Online Publication section of Nature, Murphy et al. 2006, reports the first in situ structure of a flagellar motor in a spirochete, Treponema primitia. Such things have been done before, for the bacterial lab rat Salmonella, but spirochetes are a whole different bacterial phylum, and they have weird flagella. First, instead of the flagella sticking outside of the cell and doing what any self-respecting flagellum would do, the flagella of spirochetes rotate entirely within the periplasm (the space between the inner and outer membrane, which includes the cell wall). You might think that there would be no room for the flagellum to rotate in such a restricted space, or that it would tear apart the membranes – but intuitions are very unreliable at the sub-microscopic scale. The intracellular rotation of the flagella evidently cause the whole cell to gyrate, moving it through liquid in a corkscrew-like fashion.

Continue reading  “Friday flagellum blogging -- spirochete flagella”

Target? TARGET? We don't need no stinkin' Target!

Posted by Dave Thomas on July 5, 2006 | Comments (125)

Genetic Algorithms are simplified simulations of evolution that often produce surprising and useful answers in their own right. Creationists and Intelligent Design proponents often criticize such algorithms for not generating true novelty, and claim that these mathematical recipes always sneak the “answer” into the program via the algorithm’s fitness testing functions.

4steiner.gif

There’s a little problem with this claim, however. While some Genetic Algorithms, such as Richard Dawkin’s “Weasel” simulation, or the “Hello World” genetic algorithm discussed a few days ago on the Thumb, indeed include a precise description of the intended “Target” during “fitness testing” on of the numerical organisms being bred by the programmer, such precise specifications are normally only used for tutorial demonstrations rather than generation of true novelty.

In this post, I will present my research on a Genetic Algorithm I developed a few years ago, for the specific purpose of addressing the question Can Genetic Algorithms Succeed Without Precise “Targets”? For this investigation, I picked a math problem for which there is a single, specific answer, yet one for which several interesting “quasi-answers” - multiple “targets” - also exist.

PT readers, you are about to enter the Strange and Curious world of “The MacGyvers.” Buckle up your seat belts, folks - our ride through Fitness Landscapes could get a little bumpy.

Continue reading  “Target? TARGET? We don't need no stinkin' Target!”

Getting it wrong

Posted by Tara Smith on May 19, 2006 | Comments (1)

So, archaea are apparently the topic of the week. While I wrote here about the pathogenic potential of some species of these organisms, a new essay in Nature and a new review in Science focus more on their evolution (and the evolution of the other two domains of life) than any health application.

In the essay mentioned, Norman Pace discusses the eukaryote/prokaryote dichotomy. Currently the archaea are classified as prokaryotes since they, like bacteria, lack a true nucleus. However, molecular sequence analysis has shown that the archaea and eukaryotes are actually more closely related to each other than either group is to bacteria (see figure, from Pace’s Nature essay). As such, nomenclature that places the bacteria and archaea together into a group is misleading.

(Continued at Aetiology)

The Evolution of Cooperation: Hawks, Doves, Ravens and Starlings

Posted by RBH on May 4, 2006 | Comments (47)

The evolution of cooperation has long been a vexing problem in biology. In the 1960s and later, a number of proposals to account for various forms of cooperation were offered, including group selection, kin selection, and reciprocal altruism. Both kin selection and reciprocal altruism have some biological data to which to appeal. In The Selfish Gene Dawkins argued that cooperative behavior could emerge as ‘selfish’ genes evolved in the context of other genes (indeed, he’s said that the book could have been title The Cooperative Gene with no change in content) and to the extent that cooperation is an effective strategy for gene vehicles (organisms) to increase reproductive success, but that was largely a formal argument rather than an empirical one. And group selection (which Dawkins emphatically rejects), in my view at least is still on shaky empirical grounds. (Apologies to Steve Rissing, a friend and Project Steve Steve with whom I argue about that.)

A difficulty of doing research on cooperation is the same difficulty that plagues much research on other complex evolutionary phenomena, namely time: interesting multi-celled animals have (relatively) long lifetimes and following a population for many generations is impossible for a single researcher.

Enter computer models. I will not here rehearse the history of computer modeling of evolutionary processes, since I’ve previously touched on it here, here and here on PT.

Of present interest is a study of the evolution of cooperation in a computer model of evolution. Prior work has shown that there are conditions in which several kinds of ‘strategies’ for interactions among artificial agents can evolve. Robert Axelrod, for example, has done a slew of work on that topic. Game theory informs much of that research, and has been useful in predicting the occurrence of certain kinds of strategies in multi-agent contexts.

A new study by Mikhail Burtsev & Peter Turchin (Nature, 440:1041-1044, April 2006) provides a good deal more insight into how cooperative strategies can evolve.

More below the fold.

Continue reading  “The Evolution of Cooperation: Hawks, Doves, Ravens and Starlings”

IBM Discovery Could Shed New Light on Workings of the Human Genome

Posted by Pim van Meurs on April 29, 2006 | Comments (31)

IBM researchers have shown how science explores new and innovative approaches to discover DNA patterns which are shared by areas of the human genome that were considered to have little or no influence on its function and areas which do have function.

From the IBM Press Release

As reported today in the Proceedings of the National Academy of Sciences (PNAS), regions of the human genome that were assumed to largely contain evolutionary leftovers (called “junk DNA”) may actually hold significant clues that can add to scientists’ understanding of cellular processes. IBM researchers have discovered that these regions contain numerous, short DNA “motifs,” or repeating sequence fragments, which also are present in the parts of the genome that give rise to proteins.

Continue reading  “IBM Discovery Could Shed New Light on Workings of the Human Genome”

Purpose, specification and function

Posted by Pim van Meurs on February 10, 2006 | Comments (6)

Two threads combine in this posting. First my comments on the Beckwith thread where I show how Dembski and Behe use the term specification or purpose to refer to “function”, and secondly a thread on strings in which the concept of purpose arose again.

First let’s revisit Dembski’s and Behe’s position on function which shows that their use of the term specification or purpose clearly refers to function.

van Till wrote:

However, when it comes time for Dembski to support his conviction that the bacterial flagellum is specified, the procedure becomes considerably more casual, almost facile. Speaking on the specification of biological systems in general, Dembski simply asserts that, “Biological specification always refers to function. An organism is a functional system comprising many functional subsystems. In virtue of their function, these systems embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the sense required by the complexity-specification criterion.”NFL, p. 148.In these four brief sentences the foundation of Dembski’s entire strategy for certifying the specification of biotic systems is laid.

Or in Behe’s terms “a purposeful arrangement of parts” where purpose and function are interchangeable.

Behe wrote:

Q The whole positive argument for intelligent design as you ve described it, Professor Behe, is look at this system, look at these parts, they appear designed correct?

A Well, I think I filled that out a little bit more. I said that intelligent design is perceived as the purposeful arrangement of parts, yes. So when we not only see different parts, but we also see that they are ordered to perform some function, yes, that is how we perceived design.

Page 44 of Behe’s cross examination on Day 11 of the Kitzmiller trial. See also Analysis of Behe’s Testimony, Part 1: Purpose and Function at “Dispatches from the Culture Wars”

Continue reading  “Purpose, specification and function”

Coopting cooption

Posted by Nick Matzke on November 28, 2005 | Comments (35)

2,4-dinitrotoluene (or 2,4-DNT, a chemical relative of the explosive TNT)Dembski has posted a contest on his blog, seeking the best case of gradual evolution by cooption (hmm, sounds like something evolutionary biologists have been talking about for decades) in the case of human-designed technology.

I’m talking about an actual history of invention in which an initial technology does A, and then a small change allows it to do B, after which a further small change allows it to do C, after which co-opting an existing system (without extensive modification) allows it to do D, etc. The evolution of a motorcycle from a motor and a bicycle is not a good example in this regard because the motor and bicycle require extensive design-work to adapt them to each other.

I hereby nominate the gradual evolution of “intelligent design” during the descent with modification of the manuscripts of Of Pandas and People, reviewed in this series of posts.

I expect my $100 by week’s end. Seriously, though, speaking of cooption: Dembski’s last-ditch, backup-backup argument against cooption as an explanation of irreducible complexity – that we had no well-documented examples of natural cooption – was destroyed by Scott Minnich during the Kitzmiller v. Dover trial.

Continue reading  “Coopting cooption”

The Cambrian Revisited

Posted by Pim van Meurs on October 12, 2005 | Comments (26)

Although I hate to give credibility to statements which are so anti-science, I also believe that educating those who are willing to hear the “rest of the story” is important.

Point in case:

In a recent blog posting, Denyse O’Leary stated the following on the Cambrian explosion. Since her comments may be of direct interest to this group, I would like to repeat them here and discuss why they are flawed.

Continue reading  “The Cambrian Revisited”

Shannon Information and Biological Fitness

Posted by Pim van Meurs on August 29, 2005 | Comments (32)

For Neurode…

Bergstrom (Department of Zoology University of Washington Seattle, WA, USA) and Lachmann (Max Planck Institute for Mathematics in the Sciences Leipzig, Germany) have published a paper titled “Shannon Information and Biological Fitness”.

They conclude that

In this paper we have shown that two measures of information, Shannon entropy and the decision-theory value of information, are united into one single information measure when one looks at the strategies that natural selection will favor, namely those that maximize the long term growth rate of biological organisms. Furthermore, we have shown that in evolving biological systems, the fitness value of information is bounded above by the Shannon entropy. These results suggest a close relationship between biological concepts of Darwinian fitness and information-theoretic measures such as Shannon entropy or mutual information.

Continue reading  “Shannon Information and Biological Fitness”

Carl Zimmer: Tangling the tree

Posted by Pim van Meurs on July 11, 2005 | Comments (4)

Carl Zimmer on “The Loom” describes recent work on the phylogenetic tree. Researchers have looked at vertical and horizontal transmission of genetic information in various bacteria.

I would like to focus on a particular aspect of the findings, namely the scale free nature of the horizontal gene transfer networks. People may remember the scale free networks in RNA for instance and how such networks have some very important properties. Scale free networks can be explained through the simple process of duplication and preferential attachment. In this case, the researchers showed that the horizontal ‘vines’ of the tree form scale free networks.

So what?

Continue reading  “Carl Zimmer: Tangling the tree”

To explain ID, *don't* look up the homologies

Posted by Nick Matzke on June 12, 2005 | Comments (128)

http://www.arn.org/docs/mm/flag_dithani.gifWilliam Dembski has just blogged about a short comment I made this morning on The Thumb answering someone’s question about whether or not a detailed evolutionary model for the bacterial flagellum would deserve a Nobel Prize.  In that comment, I pointed to this long web article I wrote on the evolution of the bacterial flagellum (which is already badly in need of an update), but I said that, no, such a model would clearly not deserve a Nobel, because it would be entirely routine and conventional — simply the application of the current paradigm (modern evolutionary theory) to fill in one more little gap in our knowledge of evolutionary history.  Although creationists don’t realize it, discoveries showing how complex system evolved come out all the time in the scientific literature.  (A number of examples are linked from my comment here.)

Dembski’s post in reply is entitled “To Explain the Flagellum � Just Look Up All the Homologies.”  There are numerous dubious assertions in Dembski’s short post that would take all day to write up, but I just want to focus on one limited point for the moment.  Will the ID advocates admit that they made a mistake in asserting that, except for the 10 proteins of the Type III secretion system, they other 30-40 parts of the flagellum were “unique”?

Continue reading  “To explain ID, *don't* look up the homologies”

The Revenge of Calvin and Hobbes

Posted by Andrea on May 30, 2005 | Comments (63)

In “Darwin”s Black Box” (DBB), ID”s arch-biochemist Behe glibly labeled evolutionary hypotheses for the origin of “irreducibly complex” systems as “hops into the box of Calvin and Hobbes” (for those who don”t know what the heck this refers to, go here to learn about Calvin and Hobbes, and here for info on their box, or even better go spend some time here, and come back tomorrow).  This overconfidence has come back to haunt him as more and more evidence accumulated in support of the evolutionary origin of his various IC systems, from the flagellum to the complement and clotting cascades. 

The topic where the idea of unevolvability of IC systems has probably taken the most beating is the vertebrate adaptive immune system, where not only evidence for evolution has accumulated at a steady pace, but even more embarrassingly for Behe, it has developed exactly along the lines predicted by those “Calvin and Hobbes jumps” he originally dismissed.  A recent paper in the journal PLoS Biology [1] is the latest turn in the death spiral of irreducible complexity of the immune system, and I think provides a good opportunity to take a look at how science works, as opposed to ID navel-gazing.

Continue reading  “The Revenge of Calvin and Hobbes”

Swim Bladders and Snake Venom

Posted by Jason Rosenhouse on April 7, 2005 | Comments (27)

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”

Beyond Suboptimality: Logical Fallacy of Behe's "IC means ID" Notion

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

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”

Plaque--evidence for Design!

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

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!”

Avida in Discover Magazine

Posted by Pim van Meurs on February 5, 2005 | Comments (152)

http://www.discover.com/images/issues/feb-05/feb05-cover-main.jpgOur 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”

Promiscuity in Evolution

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

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”

Brain evolution: Keeping your Witts about you

Posted by Nick Matzke on January 1, 2005 | Comments (48)

http://www.cell.com/webfiles/images/covers/cell/cell.119.7.lrg.gifDiscovery 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”

Happy New Year, ID movement! (ID and Evol. Immunology)

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

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)”

Evolution reveals biochemical networks and functional modules

Posted by Pim van Meurs on July 30, 2004

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

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

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”

Simulating the early evolution of plants

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

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”

Icons of ID: Avida

Posted by Pim van Meurs on July 11, 2004

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”

I shared a lift with Baroness Greenfield

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

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”

Complexity: Darwin and neutral evolution

Posted by Pim van Meurs on July 8, 2004 | Comments (14)

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”

The Left Hand of Darwin

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

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”

Small Treasures

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

http://my.sota-oh.com/~rbh/pics/sazure1.jpgHaving 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).

Entropy continued

Posted by Pim van Meurs on June 11, 2004

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”

Entropy: Common pitfalls

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

http://www.sci.osaka-cu.ac.jp/biol/cbiol/Updated.gif

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”

Spontaneous Generation and the Origin of Life

Posted by Pim van Meurs on May 29, 2004

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

Shannon entropy applied

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

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

Continue reading  “Shannon entropy applied”

Behe as Research Scientist

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

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)

Evolution of Irreducible Complexity, continued

Posted by RBH on March 31, 2004

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

Living Words: Pro patria - species and homeland security

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

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 m