This is just an effort to help keep Joe’s thread focused and to help keep it from being derailed. People can use it or not. I hope they will.
CharlieM: Can someone explain to me, why is all of this not just a model of directed evolution? Surely it is set up to be directed towards a target?
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 
possible 28-letter phrases, so it should take about 
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 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
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!
Michael Behe is best known for coining the phrase Irreducible Complexity, but I think his likening of biological systems to Rube Goldberg machines is a better way to frame the problem of evolving the black boxes and the other extravagances of the biological world.
Continue reading
In his endless pursuit of that wascally Weasel, Mung made the following silly claim:
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.
That is clearly false, but for the benefit of Mung (and his cousin Elmer) I have modified my Weasel program to incorporate both drift and selection. They can now see for themselves that small population sizes are insufficient to guarantee that drift dominates selection.
The code is here. Compile it under Linux using “gcc -std=gnu99 -lm weasel.c -o weasel”.
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.”
My favorite subject-specific journal is Molecular Biology and Evolution (MBE). This journal publishes on topics primarily related to molecular evolution and evolutionary genomics, which are among my favorite subjects in biology. I’m happy to report that the latest issue of MBE is out today, and there are lots of great articles that I think will be of interest to folks here, many of which are open-access.
I sadly don’t have time to write up any of these articles, but I thought it might be useful to “sample” a few in case any any of you would like to read and discuss them. Here are a handful that seem particularly interesting:
Cross-posted from UD: The Alternatives to Methodological Naturalism conference is doing a design contest with a cash prize.
Among Christianity’s many odd doctrines is the notion of original sin. The details vary from denomination to denomination, but a common view is that all humans are born into a state of sin because Adam succumbed to temptation in the Garden of Eden, and that this state of sin makes us worthy of God’s eternal condemnation. Only Christ’s sacrifice can redeem us.
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?
Paul Nelson, Evolution, or design ? I transcribed it for who is too lazy to see the video, but its worth to watch, a great speech:
Thanks to another reader, I have gotten a copy of McDonald’s actual paper. Reading it, I wonder how many of the Discovery Institute authors have actually read it. How many have just taken what one of their fellows said previously and done what most 10th grade students do for research papers (i.e. change a few words in an attempt to avoid plagiarism).
By adding their own interpretation of the prior authors work (using secondary sources instead of primary sources), quite a bit of error has crept in. I’m sure it’s just a bit of error, we all know that no creationist would say something that wasn’t true, especially if he is quoting an actual scientist’s paper.
No, I can’t do it, that level of sarcasm is too much for me. These people are liars. Either they are directly lying in order to make someone appear to say something that they actually didn’t or they are the worst researchers ever and shouldn’t be allowed to write non-fiction. Which is it creationists?
A century later we know that the overwhelming obstacle facing spontaneous generation is probability, or rather improbability, resulting from life’s enormously complex phenotypes. If even a single protein, a single specific sequence of amino acids, could not have emerged spontaneously, how much less so could a bacterium like E. coli with millions of proteins and other complex molecules? Modern biochemistry allows us to estimate the odds, and they demolish the spontaneous creation of complex organisms.
Looks like IDists aren’t the only ones to appeal to probability arguments. How does Wagner know what the probabilities are, or that spontaneous generation is even within the realm of what is possible?
It was not merely Judge John E. Jones who ruled against teaching “intelligent design” (ID), a thinly veiled surrogate for “creation science,” in public schools. The citizens of Dover, Pennsylvania, exercised the power of the ballot to ensure that their city did not appeal Kitzmiller. If the case had reached the Supreme Court of the United States, the justices possibly would have split 5-4 in favor of allowing public schools to teach ID.
Today ID lost its prospect of winning in the Supreme Court: Justice Antonin Scalia, Known For Biting Dissents, Dies At 79. As noted in the Wikipedia article on Edwards v. Aguillard (1987), in which the court nailed shut the coffin of creation science,
Justice Antonin Scalia, joined by Chief Justice William Rehnquist, dissented, accepting the Act’s stated purpose of “protecting academic freedom” as a sincere and legitimate secular purpose. They construed the term “academic freedom” to refer to “students’ freedom from indoctrination”, in this case their freedom “to decide for themselves how life began, based upon a fair and balanced presentation of the scientific evidence”.
Has quite a familiar ring, doesn’t it? The rhetoric of the ID movement was designed by a law professor, Phillip Johnson, to suit a creationism-friendly judge of the Law of the Land. This is indeed a sad day for ID, which already had acquired a moribund pallor.
There exists in nature biological forms not explicable by Darwinian theory.
A new video has been posted on youtube.
Do non-adaptive and beyond-adaptive order pose an existential challenge to Darwinism?
Denton says yes.
Even on his birthday, don’t say Darwin unless you mean it
How Darwin’s name is taken in vain, with mini-reviews of some of the worst offenders
Don’t say Darwin unless you mean it. Above all, don’t say “Darwin” when you mean “evolution”. It’s like saying “Dalton” when you mean atoms. Our understanding of atoms has moved on enormously since Dalton’s time, and our understanding of evolution has moved on similarly since Darwin’s. Neither of them knew, or could have known, the first thing regarding what they were talking about, and both would be delighted at how thoroughly their own work has been superseded. (Dalton of course deserves further discussion in his own right, which I will be providing in a few weeks time.)
From John Dalton’s A New System of Chemical Philosophy (1808)
Imagine if a lot of people decided that atomic theory was against their religion. We would see a parallel world of sacred science, in which molecules were “intelligently constructed”, and real chemistry would be referred to as Daltonism, or possibly, these days, neo-Daltonism. The scientific dissidents from Daltonism would invoke Dalton’s name on every possible occasion, and draw attention to the many inadequacies of atomic theory as he presented it in 1808.
The big numbers game: Fine Tuning
Creationist fine tuning claims are incomprehensible. I know certain physicists argue for cosmological fine tuning (I’m not sold, for reasons I may discuss later). I believe the claims we’ve seen lately are far removed from any serious claim of fine tuning, and reflect a lack of comprehension of physics or basic math by those that use them.
Here’s a typical claim: “The force of gravity is determined by the gravitational constant. If this constant varied by just one in 10^60 parts, none of us would exist.” (1). You will find this claim repeated in the UD comments section, and even their own glossary of definitions (2-5). Creationists love it, because the big numbers, to them, mean impossible, therefore God. Right?
But wait. Humans have only measured the gravitational constant “big G” to parts per million accuracy (with variations between measurement methods at hundreds of parts per million (6)). So, using Chem 101 terminology, the statement above says that we know a constant to about 6 significant figures, but if the value was different at the digit 54 decimal past the frontier of human understanding, we’d be hosed. Where did this precise value come from? What math-a-magics creates precision from fine air?
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:
Continue reading
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?
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.
