Category Archives: Evolution

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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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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