Category Archives: Evolution

Wright, Fisher, and the Weasel

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Richard Dawkins’s computer simulation algorithm explores how long it takes a 28-letter-long phrase to evolve to become the phrase “Methinks it is like a weasel”. The Weasel program has a single example of the phrase which produces a number of offspring, with each letter subject to mutation, where there are 27 possible letters, the 26 letters A-Z and a space. The offspring that is closest to that target replaces the single parent. The purpose of the program is to show that creationist orators who argue that evolutionary biology explains adaptations by “chance” are misleading their audiences. Pure random mutation without any selection would lead to a random sequence of 28-letter phrases. There are 27^{28} possible 28-letter phrases, so it should take about 10^{40} different phrases before we found the target. That is without arranging that the phrase that replaces the parent is the one closest to the target. Once that highly nonrandom condition is imposed, the number of generations to success drops dramatically, from 10^{40} to mere thousands.

Although Dawkins’s Weasel algorithm is a dramatic success at making clear the difference between pure “chance” and selection, it differs from standard evolutionary models. It has only one haploid adult in each generation, and since the offspring that is most fit is always chosen, the strength of selection is in effect infinite. How does this compare to the standard Wright-Fisher model of theoretical population genetics? Continue reading →

Hopelessly frustrated – most likely confused regarding latest on Xenoturbella

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I would be grateful if somebody could help me out here as Bioinformatics is not my strong card.

Regarding the recent Nature publication

New deep-sea species of Xenoturbella and the position of Xenacoelomorpha

I query the authors’ explanation; to wit…

The sister group relationship between Nephrozoa and

Xenacoelomorpha supported by our phylogenomic analyses implies that the last common ancestor of bilaterians was probably a benthic, ciliated acoelomate worm with a single opening into an epithelial gut, and that excretory organs, coelomic cavities, and nerve cords evolved after xenacoelomorphs separated from the stem lineage of Nephrozoa.

 

My problem arises with their placement of Ctenophora on their own phylogenetic tree as the “more primitive out-group” (for lack of better words on the spur of a rushed moment).  Myself, I always considered Ctenophora as bilateral – in this case more primitively bilateral which IMHO should root the bilateran tree… which of course begs more than one question upon rereading their analysis.

Forget Ctenophores – what about Cnidarians!?  Some taxonomists argue that Cnidarians are descendents of ancient bilateral coelomates and not the other way around. Biologists have known since the 1920s that Cnideria had a directive axis which gave them right and left-hand sides.  Volker Schmidt goes on to argue that non-radially organized hydrozoan larvae have an anterior concentration of sensory and ganglionic nerve elements, suggesting that a fundamental genetic toolkit for the establishment of bilateral and polarized anatomies was already present before the Cnidaria-Bilateria divergence.  Volker Schmidt goes so far as to suggest that diploblastic status of adult Cniderians is derived and that true mesoderm can be even be detected during Cniderian embryogenesis.  OK – I concede that last argument is particularly contentious… but you get my drift.

I am partial to the notion the UrBilateran that subsequently gave rise to “Protostomes” & Deuterostomes and was itself coelomate with possessed a dorsal nerve chord.  Any subsequent acoelomy and pseudocoelomy was derived… ditto ventral nerve chords.  But hey…  now I am being really contentious!

 

 

 

 

The Great Chain of Being: Anthropocentrism

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I am reading a book in which the authors set forth the evils of belief in “The Great Chain of Being.”

The Great Chain of Being is, in fact, firmly ingrained in our culture and spirits. It leads to certain grave errors that are commonly acknowledged but difficult for teachers to correct.

The first of these is Anthropocentrism, “the view that man is the measure of all things.”

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Structuralist Quackery

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Throughout the history of evolutionary biology, as well as many other sciences, there has been a conflict between two styles of thinking. One is conventionally called functionalism, although in evolutionary biology the term “adaptationism” is more frequently used today because a trait’s “functional fit for it’s office” is produced through adaptation by natural selection (i.e., function is explained by adaptation through natural selection). The functionalist stance is one that explains organismal traits through their functional and adaptive values.

The alternative style of thinking does not have a generic name in biology, although in other areas of study it is called “structuralist.”

Michael Denton in Evolution: Still A Theory In Crisis or Gunter P. Wagner in The Intellectual Challenge of Morphological Evolution: A Case for Variational Structuralism?

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Chargaff Parity Rule 2, Biased/Non-Random Mutations

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There is an approximate 8% excess of Adenine and Thymine above random in the DNA of humans. This suggests mutational bias and/or non-random mutation. If 3 billion coins were found to be 58% heads vs. 42% tails, then the chance hypothesis of a random unbiased coin flip would be easily rejected. The odds of such an event happening are astronomical according to the binomial distribution.

But such an imbalance is reflected in the human genome where:
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Genetic Algorithms: When Drift Overcomes Selection

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I often encounter posters here at TSZ who claim that Genetic Algorithms (GAs) either model or simulate evolution. They are never quite clear which it is, nor do they say what it means to model or simulate evolution (what would be required) and how GAs qualify as either one or the other. My position is that GAs neither model nor simulate evolution. In addition to other reasons I’ve given in the past I’d like to present the following argument.

GAs are often used to demonstrate “the power of cumulative selection.” Given small population sizes drift ought to dominate yet in GAs drift does not dominate. Why not?

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The Discontinuity of Nature

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Typology is perfectly consonant therefore with descent with modification. Each cladogram is witness to descent with modification and the existence of distinct Types. The modifications are novel taxa-defining homologs, acquired during the process of descent along a phylogenetic lineage, each of which defines a new Type.

– Denton, Michael. Evolution: Still a Theory in Crisis

I repeat, Michael Denton accepts common descent is is not a Creationist. My original thread has been inundated with scoffing and mocking and young earth creationism, all of which are far removed from the subject matter of Denton’s latest book. Trying again.

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Still a Theory in Crisis

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Michael Denton’s new book is out, Evolution: Still A Theory In Crisis.

Denton’s stance is for structuralism and against functionalism, especially as functionalism appears in it’s current form as the modern synthesis or neo-Darwinism (the cumulative selection of small adaptive changes).

Denton argues for the reality of the types, that “there are unique taxon-defining novelties not led up to gradually from some antecedent form” and that the lack of intermediates undermines the Darwinian account of evolution. He also argues that a great deal of organic order appears to be non-adaptive, including “a great number of the taxa-defining Bauplans,” and that this also undermines the Darwinian account of evolution. Evo-devo is also showing us that “Darwinian selection is not the only or even the main factor that determined the shape and main branches of the great tree of life.”

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How and Why: questions for scientists and philosophers?

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The late John Davison often remarked that science could only answer “how” questions, not “why”. It seems to me philosophers, perhaps I’m really thinking of philosophers of religion rather than in general, attempt to find answers to “why” questions without always having a firm grasp on how reality works. Perhaps this is why there is so much talking past each other when the explanatory power of science vs other ways of knowing enters a discussion. Continue reading →

Conservation and function of long noncoding RNAs

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How about some cool science as we head toward the weekend?

Let’s talk about long noncoding RNAs (lncRNA) – they are (somewhat arbitrarily) defined as stretches of DNA that are at least 200 base pairs in length that are transcribed into mRNA but have little potential to code for proteins. Determining the function (if one exists) of a particular lncRNA can often be difficult.  In part, this may be due to the fact that lncRNA evolve much more quickly than protein-coding genes do and therefore exhibit a much smaller degree of sequence conservation, which can make identifying orthologs in other related organisms more difficult.  Nevertheless, if a particular lncRNA is functionally important, we would usually expect to see copies of it in related organisms, so finding these homologs can be an important indicator of function.

A new paper in Genes and Development by Quinn et al. is a useful demonstration of this.  The authors find evidence of 47 homologs of roX, an lncRNA involved in X chromosome dosage compensation,  across 35 fruit fly species.  The researchers identity roX homologs based on a combination of short regions of sequence conservation (“microhomology”), RNA secondary structure and synteny (i.e., similarity in location along a chromosome)  Here is the abstract (I believe the paper itself is open access): Continue reading →

The Reasonableness of Atheism and Black Swans

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As an ID proponent and creationist, the irony is that at the time in my life where I have the greatest level of faith in ID and creation, it is also the time in my life at some level I wish it were not true. I have concluded if the Christian God is the Intelligent Designer then he also makes the world a miserable place by design, that He has cursed this world because of Adam’s sin. See Malicious Intelligent Design.
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It is a sampling error to use marine mammal vestigial parts as evidence for evolution.

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I note many public evolutionists, Prothero  and Shermer and many others  always stress the cases of vestigial parts in marine mammals as evidence for evolutionary biology.

Yet in reality this is a sampling error that in fact makes the opposite case against evolution.

I agree marine mamnmals once were land lovers and only later gained features to surbvve in the water. Not the impossible steps said by evolutionists, as Berlinski demonstrates, but some other mechanism.

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Is Darwinian Evolution Teleonomic?

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While many ID proposals are based on introducing teleonomy into evolution, I wanted to ask the question as to whether or not evolution, even by a Darwinian definition (i.e., natural selection and materialism) was already teleonomic.

The reason I ask this is because all sorts of things that Darwinian evolution has trouble explaining gets thrown into the basket of “sexual selection”.  Basically, the reason why an organism evolved feature X was because that feature was selected by mating.  In other words, the other organisms appreciated feature X, and therefore copulated and reproduced more with organisms showing more and more of feature X.

I find this interesting, because, especially if taken materialistically, this gives a teleonomic direction to selection, something that Mayr attempted to rule out.

Think of it this way.  If one is a materialist, then what is determining the desires of the organism?  It is the organism’s genetics!  If the organism is desiring a mate, that’s because its genetics is telling it to do so.  If an organism sees mates with feature X as being more desirable, that means its genetics are telling it to do so.  Therefore, the organism’s genes are, in a very direct way, directing the selection process themselves.

Mate selection, under materialism, seems to me to definitely fall under the umbrella of teleonomy.  And, since it governs a large component of the evolutionary process, it seems that one must then say that to a large extent the evolutionary process is teleonomic, even under Darwinian terms.

I’m curious to your thoughts on this.  I am not aware of this idea being discussed in the literature, but if someone has papers or links to other discussions of this, I would love to see them.

Beating a dead horse (Darwin’s Doubt)

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First off I must apologize for doing another post on a subject that’s been done to death around here, but I’ve been meaning to make a post about this for a while but other stuff kept coming up. Anyway, things have quietened down at work where I now only have to maintain some cell cultures, so I have a bit of time duing the christmas holiday.

My post, which is a repost of something I also brought up in a thread on Larry Moran’s sandwalk blog, is about a chapter in Stephen Meyer’s book Darwin’s Doubt and what I can, if I’m being generous, only attribute to extremely shoddy scholarship.
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Tiny sponge fossil predates the Cambrian explosion

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New tools could allow scientists to discover other fossils that significantly predate the start of the Cambrian explosion, according to David Bottjer, a professor at the USC Dornsife College of Letters, Arts and Sciences and co-author of a study announcing the finding of the sponge in the Proceedings of the National Academy of Sciences.

…

“Fundamental traits in sponges were not suddenly appearing in the Cambrian Period, which is when many think these traits were evolving, but many million years earlier,” Bottjer said. “To reveal these types of findings, you have to use pretty high-tech approaches and work with the best people around the world.”

https://news.usc.edu/83632/tiny-sponge-fossil-predates-the-cambrian-explosion/

Merry Kitzmas!

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December 20th, 2015 is the tenth anniversary of the decision in Tammy Kitzmiller, et al. v. Dover Area School District, et al. 

Judge Jones (a Bush-appointed Republican) wrote a 139-page legal opinion which can be summarized thus: 

Teaching intelligent design in public school biology classes violates the Establishment Clause of the First Amendment to the Constitution of the United States (and Article I, Section 3, of the Pennsylvania State Constitution) because intelligent design is not science and “cannot uncouple itself from its creationist, and thus religious, antecedents.”

— wikipedia article, side bar 

Despite the precedent set by Kitzmiller/Dover, creationist and Intelligent Design advocates continue to battle to remove teaching of evolution from public schools and to protect teachers who insert biblical creationist or ID speculations into science classes.

I found this interesting essay in response to our current “friend” John West from 2007, when JW applauded passage of Louisiana creationism law.

All sorts of laws advance secular purposes—that’s what laws are supposed to do, and the Constitution assumes as much—but no law may advance a merely religious purpose under the Constitution. Thus those who lobby for law to advance a religious purpose are indeed under a disadvantage, one traceable to the Constitution itself,which purposely erects a roadblock in the path of those who would want to use the government to propagate a religion. It does not erect a similar roadblock to those who would use the government for secular purposes[see essay for footnote], whether it be to set up a fire department, or run the U.S. Army, or the Post Office, or whether it be to teach students about biological science. It is therefore perfectly valid for a secularist to attack the religious motivations of her political opponents, while simultaneously rallying her own political supporters to secularism.

— Timothy Sandefur

I think it’s particularly interesting that Sandefur identifies the non-symmetry between trying to advance religious purposes and trying to advance secular ones, which I know many religious people mistake.

Happy anniversary, y’all

The Discovery Institute versus Nick Matzke

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Earlier this week, Nick Matzke published an article at Science that uses modern phylogenetics techniques to analyze how creationist (or antievolution, if you prefer) legislation has evolved in the post-Dover era (note: I have not read the paper yet).  This seems to have struck a pretty sensitive nerve over at the Discovery Institute.  On the Evolution News and Views blog, the DI’s John West published an article that all but accuses Matzke of misappropriation of taxpayer funding because he acknowledges funding support from an NSF grant that doesn’t appear to be obviously connected to the content of this particular piece of research.

Needless to say, that accusation is as silly as it is groundless, which Matzke explains here.  Regardless of the merits (or obvious lack thereof) of the allegation, I’m rather curious regarding West’s motivations for making such a claim.  It seems ugly,  intemperate and ill-advised even by the DI’s standards.  Are they upset that creationists are once again getting a black eye in a prominent and respected scientific journal?  Is the fact that the article was written by somebody who was instrumental in the ID movement’s failure during the Dover trial what’s driving this response?  Something else entirely?

Whatever the reason, I view this accusation by West as a particularly egregious example of bad behavior on the part of the DI, and I wanted to bring it up for discussion here.

 

Absolute Fitness in Theoretical Evolutionary Genetics

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Joe Felsenstein, like other population geneticists, holds a special place in the Creation/Evolution controversy because his works are regarded highly by many creationists who are familiar with genetics. This is a thread for all of us (myself included) to try to learn and understand one of the key concepts in his book Theoretical Evolutionary Genetics, namely absolute fitness. He has generously made his book available on his website (a book of this calibre could sell for hundreds of dollars).
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Those Weasely IDCists!

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A couple recent comments here at TSZ by Patrick caught my eye.

First was the claim that arguments for the existence of God had been refuted.

I don’t agree that heaping a bunch of poor and refuted arguments together results in a strong argument.

here

Second was the claim that IDCists do not understand cumulative selection and Dawkins’ Weasel program.

The first time I think I was expecting more confusion on Ewert’s part about the power of cumulative selection (most IDCists still don’t understand Dawkin’s Weasel).

here

In this OP I’d like to concentrate on the second of these claims.

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