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.
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?