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.
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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:
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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?
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.
Veteran TSZers may recall an entertaining thread in which a bunch of us tried to explain the cardinality of infinite sets to Joe G:
A lesson in cardinality for Joe G
At UD, commenters daveS and kairosfocus are now engaged in a long discussion of the transfinite, spanning three threads:
An infinite past can’t save Darwin?
An infinite past?
Durston and Craig on an infinite temporal past…
The sticking point, which keeps arising in different forms, is that KF cannot wrap his head around this simple fact: There are infinitely many integers, but each of them is finite.
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.”
In a recent OP at Uncommon Descent, Vincent Torley (vjtorley) defends a version of libertarian free will based on the notion of top-down causation. The dominant view among physicists (which I share) is that top-down causation does not exist, so Torley cites an essay by cosmologist George Ellis in defense of the concept.
Vincent is commenting here at TSZ, so I thought this would be a good opportunity to engage him in a discussion of top-down causation, with Ellis’s essay as a starting point. Here’s a key quote from Ellis’s essay to stimulate discussion:
However hardware is only causally effective because of the software which animates it: by itself hardware can do nothing. Both hardware and software are hierarchically structured, with the higher level logic driving the lower level events.
I think that’s wrong, but I’ll save my argument for the comment thread.