Category Archives: Evolution

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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Pastor Hates Jesus after Reading Coyne’s Book

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Bruce Gerencser was a pastor for 27 years until he started reading books with non-Christian viewpoints. One of the 5 most influential books in his conversion to atheism was Jerry Coyne’s book, Why Evolution is True. Bruce’s kids are no longer evangelicals and left the faith that he once taught them. He openly says he hates Jesus now.

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Intelligent Design is NOT Anti-Evolution

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Intelligent Design is NOT Anti-Evolution

In order to have a discussion about whether or not Intelligent Design is anti-evolution or not we must first define “evolution”. Fortunately there are resources available that do just that.

Defining “evolution”:

Finally, during the evolutionary synthesis, a consensus emerged: “Evolution is the change in properties of populations of organisms over time”- Ernst Mayr page 8 of “What Evolution Is”

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On Darwin’s and modern evolutionists challenge to deny small steps created all biology.

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Darwin in a well known challenge in his book defied anyone showing that anything in biology could not be explained as to its origin by small steps from start to finish. Modern evolutionists also insist , however complex, that all biological entities at any point can be seen as coming from small changes in populations and from there in lineages from start to finish for anything.

It always bothered me that this line of reasoning was so important to darwins claim.

It was up to creationists to prove why accumulating small changes could not turn fish could not become fishermen or bugs into buffaloes . WHY NOT ? Darwin asked and ever since. however extreme the claim mat seem to so many.

I say lets turn the argument around on them. The line of reasoning works against them as follows.

I will use two improbable, impossible9did I say impossible) lineages of a finale creatures evolutionary origin.

ONE. to start you have a fish, then a fish breathing on land with crab legs, then it has horse legs, then its got a t-rex head, then its a ground bird with flippers, then a primate monkey, then a rabbit type creature with horns and crab legs, then a bird again, then a mouse. All this happening in about 200 million years of evolution.

TWO. you start with a fish, then a duck like creature, then a fish with flippers, then a land breathing reptile creature with a trunk, then a cat like creature with long giraffe legsm then a primate, then a shrew, then a primate again and finally a bird. 200 million years start to finish.

This is impossible by any common sense, intelligence, of any human being. never mind the intermediates. this sequence of these two creatures evolving this way from start to finish is self evident nonsense.

For evolutionists THEN explain why not BY small steps could these lineages not happen?? Why not, if small populations could be selected on to account for our real biology glory, could not my examples  easily, equally, be accounted for bu evolutions mechanism.

if evolution can explain anything we have then why not anything we can imagine??

iF you say no. then the absurdity of bugs becoming buffaloes and fish becoming fishermen makes the creationist point solid and Darwins reply worthless.

 

Lawyers and Scientists

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There’s been a skirmish between Larry Moran and Barry Arrington about whether Barry understands the Theory of Evolution, and the latest salvo is a piece at UD, entitled, Can a Lowly Lawyer Make a Useful Contribution? Maybe.

Well, in a sense, Barry makes a useful contribution in that post, as he gives a very nice illustration of a common misunderstanding about the process of hypothesis testing, in this case, basic model-fitting and null hypothesis testing, the workhorse (with all its faults) of scientific research.  Barry writes:

[Philip]Johnson is saying that attorneys are trained to detect baloney.  And that training is very helpful in the evolution debate, because that debate is chock-full of faulty logic (especially circular reasoning), abuse of language (especially equivocations), assumptions masquerading as facts, unexamined premises, etc. etc.

Consider, to take one example of many, cladistics.  It does not take a genius to know that cladistic techniques do not establish common descent; rather they assume it.  But I bet if one asked, 9 out of 10 materialist evolutionists, even the trained scientists among them, would tell you that cladistics is powerful evidence for common descent.  As Johnson argues, a lawyer’s training may help him understand when faulty arguments are being made, sometimes even better than those with a far superior grasp of the technical aspects of the field.  This is not to say that common descent is necessarily false; only cladistics does not establish the matter one way or the other.

In summary, I am trained to evaluate arguments by stripping them down to examine the meaning of the terms used, exposing the underlying assumptions, and following the logic (or, as is often the case, exposing the lack of logic).  And I think I do a pretty fair job of that, both in my legal practice and here at UD.

Barry has made two common errors here.  First he has confused the assumption of common descent with the conclusion of common descent, and thus detected circular reasoning where there is none.  Secondly he has confused the process of fitting a model with the broader concept of a hypothesised model.

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The Law of Conservation of Information is defunct

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About a year ago, Joe Felsenstein critiqued a seminar presentation by William Dembski, “Conservation of Information in Evolutionary Search.” He subsequently discussed Dembski’s primary source with me, and devised a brilliant response, unlike any that I had considered. This led to an article, due mostly to Felsenstein, though I contributed, at The Panda’s Thumb. Nine days after it appeared, Dembski was asked in a radio interview whether anyone was paying attention to his technical work. Surely a recipient of

qualifies as a someone. But Dembski changed the topic. And when the question came around again, he again changed the topic. Mind you, this isn’t how I know that Felsenstein blasted conservation of “information,” which is not information, in evolutionary “search,” which does not search. It’s how I know that Dembski knows.

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The Enigma of Lamarckism

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Lamarckism (or Lamarckian inheritance) is the idea that an organism can pass on characteristics that it acquired during its lifetime to its offspring (also known as heritability of acquired characteristics or soft inheritance).

– Wikipedia

Many of us have probably been taught that Lamarkian inheritance is anathema. Heresy. But why would that be the case? Is it for theoretical reasons or simply because of a lack of empirical evidence?

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Code Denialism Pt. 2 – Nirenberg

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The Nirenberg and Matthaei experiment was a scientific experiment performed on May 15, 1961, by Marshall W. Nirenberg and his post doctoral fellow, Heinrich J. Matthaei. The experiment cracked the genetic code by using nucleic acid homopolymers to translate specific amino acids.

Nirenberg and Matthaei experiment – Wikipedia

The Nirenberg and Leder experiment was a scientific experiment performed in 1964 by Marshall W. Nirenberg and Philip Leder. The experiment elucidated the triplet nature of the genetic code and allowed the remaining ambiguous codons in the genetic code to be deciphered.

Nirenberg and Leder experiment – Wikipedia

The Marshall W. Nirenberg Papers Public Reactions to the Genetic Code, 1961-1968

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Coyne hoodwinked and duped

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Jerry Coyne represents himself as the epitome of science, reason and critical thinking. But “Dr. Reason” or shall we say “Dr. EvolutionIsTrue” often ends up as the butt of jokes and sarcasm in the ID community.

He got hoodwinked recently. He was pranked into believing a particular internet account was real and then started quoting from it to support his arguments. Turned out his evidence was from a faked source. Finally someone intervened to stop Coyne from making anymore a joke of himself. Coyne was forced to make a retraction:

https://whyevolutionistrue.wordpress.com/2015/09/06/more-twier-hilarity/
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What is obvious to Granville Sewell

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Granville Sewell, who needs no introduction here, is at it again. In a post at Uncommon Descent he imagines a case where a mathematician finds that looking at his problem from a different angle shows that his theorem must be wrong. Then he imagines talking to a biologist who thinks that an Intelligent Design argument is wrong. He then says to the biologist:

“So you believe that four fundamental, unintelligent forces of physics alone can rearrange the fundamental particles of physics into Apple iPhones and nuclear power plants?” I asked. “Well, I guess so, what’s your point?” he replied. “When you look at things from that point of view, it’s pretty obvious there must be an error somewhere in your theory, don’t you think?” I said.

As he usually does, Sewell seems to have forgotten to turn comments on for his post at UD. Is it “obvious” that life cannot originate? That it cannot evolve descendants, some of which are intelligent? That these descendants cannot then build Apple iPhones and nuclear power plants?

As long as we’re talking about whether some things are self-evident, we can also discuss whether this is “pretty obvious”. Discuss it here, if not at UD. Sewell is of course welcome to join in.

Random Genetic Drift: a controversy?

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Over my time as a dilettante observer of the science blogging community, I have noticed a certain frisson of controversy over the idea of random genetic drift. Sewall Wright, who with Ronald Fisher and J. B. S. Haldane (Bill Bryson’s observations on Haldane’s research into diving and decompression are entertaining) established the science of population genetics, is credited with coining the phrase in 1929. Thanks to Professor Joe Felsenstein for pointing out his seminal paper. Continue reading →

Evolving complex features

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The Lenski et al 2003 paper, The evolutionary origin of complex features, is really worth reading.  Here’s the abstract:

A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features. We examined this issue using digital organisms—computer programs that self-replicate, mutate, compete and evolve. Populations of digital organisms often evolved the ability to perform complex logic functions requiring the coordinated execution of many genomic instructions. Complex functions evolved by building on simpler functions that had evolved earlier, provided that these were also selectively favoured. However, no particular intermediate stage was essential for evolving complex functions. The first genotypes able to perform complex functions differed from their non-performing parents by only one or two mutations, but differed from the ancestor by many mutations that were also crucial to the new functions. In some cases, mutations that were deleterious when they appeared served as stepping-stones in the evolution of complex features. These findings show how complex functions can originate by random mutation and natural selection.

The thing about a computer instantiation of evolution like AVIDA is that you can check back every lineage and examine the fitness of all precursors.  Not only that, but you can choose your own environment, and how much selecting it does.  There are some really key findings:

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Natural Selection and Adaptation

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Cornelius Hunter seems very confused.

 …This brings us back to the UC Berkeley “Understanding Evolution” website. It abuses science in its utterly unfounded claim that “natural selection can produce amazing adaptations.”

In fact natural selection, even at its best, does not “produce” anything. Natural selection does not and cannot influence the construction of any adaptations, amazing or not. If a mutation occurs which improves differential reproduction, then it propagates into future generations. Natural selection is simply the name given to that process. It selects for survival that which already exists. Natural selection has no role in the mutation event. It does not induce mutations, helpful or otherwise, to occur. According to evolutionary theory every single mutation, leading to every single species, is a random event with respect to need.

He has forgotten what “adaptation” means.  Of course he is correct that “Natural selection is simply the name given to [differential reproduction]”.  And that (as far as we know), “every single mutation …is a random event with respect to need”.

And “adaptation” is the name we give to variants that are preferentially reproduced. So while he would be correct to say that “natural selection” is NOT the name we give to “mutation” (duh); it IS the name we give to the very process that SELECTS those mutations that promote reproduction.  i.e. the process that produces adaptation.

Cornelius should spend more time at the Understanding Evolution website.

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