Discovery Institute: So much for Academic Freedom!

| 38 Comments

(Update: paper preprint and bonus material available free here)

It appears that John West and the Discovery Institute skipped past reading the Science paper and went straight to accusing the author of misconduct. So much for “Academic Freedom”! I don’t even think they read the Supplemental Material, and I’m pretty sure they wouldn’t understand if if they did. It’s conceivable they aren’t up on the latest in phylogenetic methods and their applications.

In any event, though, I welcome any opportunity to explain why my research is in the public interest and how this work connects to my other work scientifically. It’s very late here in Australia, so I will give the short version.

Short version

Evolutionary biologists do research not just on evolutionary questions, but also research to develop and test the methods and computational tools that are used to answer evolutionary methods. One huge category of such methods is phylogenetics (something like 1% of all published research in all fields involves phylogenetics, according to David Hillis), within that there is Bayesian phylogenetics, within that there is dated Bayesian phylogenetics (where dates are estimated along with the phylogeny), and within that there is “tip-dated” Bayesian phylogenetics, where fossils from different time points are included directly in the analysis. And, within that there is tip-dated Bayesian phylogenetics with the possibility of sampling direct ancestors, a technique which has only become available in the last year or so.

Well, the Science paper did a Bayesian tip-dating sampled-ancestors analysis in the phylogenetics program Beast2, with the Beast2 analysis (which is quite complex to get right) set up using R code that I wrote and called “BEASTmasteR” (http://phylo.wikidot.com/beastmaster). (Yes, ha, BEASTmasteR - but it’s late.) BEASTmasteR is being used for various analyses at the moment – dinosaurs, fossil dogs, etc. I developed BEASTmasteR for Beast2 at NIMBioS, and it was built on R code I wrote for Beast1 while in grad school on a previous grant when tip-dating was in its earliest days (tip-dating is how you put fossils in a dated Bayesian phylogeny, one of the goals of the bivalves project). It is customary to gratefully cite grants that supported your work, including software (and this is the first publication I’ve gotten out using BEASTmasteR - although I believe papers have already been published by others using it!).

What good is tip-dating? What good are sampled ancestors analyses? The short answer is that they allow us to include more information in phylogenetic analyses than we could before, and to estimate things that we couldn’t estimate before (like probability of direct ancestry – this is something that *should* be of great interest to the creationists at the Discovery Institute, except that they never learned enough about phylogenetics to understand why this is new.) I am convinced this is “the way of the future” for phylogenetics involving fossils, but a great deal of the methods’ effectiveness depends on the details of the datasets (the short version is: fossil dogs=lots of characters=easy case; fossil clams=few characters=hard case. And, it turns out, antievolution bills=lots of characters=pretty easy case.)

At the very least, paleontologists and evolutionary biologists are interested in trying out the new methods and seeing what they can do, if the interest in talks and symposia on the topic is any guide (I have participated in such at the Society for Vertebrate Paleontology Annual Meetings in 2014 and 2015).

What’s the broader societal relevance? I happen to think that better understanding the history of life is in the public interest, as is tracking antievolution legislation. But even if you don’t buy that, consider this: phylogenetic methods for sampling lineages serially through time are also used for disease phylogenies – tracking the evolution and spread of things like HIV and Ebola year-by-year, and even month-by-month.

What software is used in these analyses? Why, Beast1 and Beast2! One particularly prominent example was this paper tracking the timing and geographic origins of the 2014 Ebola outbreak. This was published in Science even while the outbreak was still going on. This is deadly serious stuff, quite literally: note that five of the coauthors of this Beast dating study died after contracting Ebola in the field in West Africa.

Short-short version

So, here’s the short-short version: Bayesian phylogenetic dating methods are important for studying the history of life, from fossils to ongoing disease outbreaks. By pushing the methods with novel datasets and applications, we learn more about the capabilities of the methods. This was part of the point of my phylogenetic study of antievolution bills. Another point: antievolution bills seem to evolve rather like pathogens - when one strategy is shut down, more stealthy strategies begin to propagate. It’s a shame that, in a world where phylogenetic methods have life-and-death relevance, the Discovery Institute continues to promote legislation with the purpose of convincing students that all this evolution stuff is just made up.

38 Comments

“It’s conceivable they aren’t up on the latest in phylogenetic methods and their applications.”

Heh.

Just when you think John West and the Discovery Institute couldn’t stoop any lower, they surprise you by going even lower.

“Read the article?!? We don’t need to read no stinking article!”

“It appears that John West and the Discovery Institute skipped past reading the Science paper and went straight to accusing the author of misconduct.”

Maybe their subscription to Science ran out. :)

For the benefit of Ms O’Leary, I hope Nick appends an ethics statements to subsequent papers stating that no books were burnt in the production of the work.

I focused on the methods point but PZ makes several other points also worth making: http://scienceblogs.com/pharyngula/[…]-to-the-law/

Two words come to mind: “Broader Impacts”

Aha, Nick just detected directed evolution, or Intelligent Design. It takes thought to make a deception, especially one as clever as ID (don’t snicker).

So they win, after all, by having their methods exposed, because biologic change has analogies in derivation, never mind the many differences.

And you thought West was bothered? He’s just trying to act like he is.

Glen Davidson

How dare he publish a paper in the most respected scientific journal in the country! Man is he wasting grant money. Obviously they don’t use grant money to do any such thing and they are scandalized when someone else does. News flash for you DI, publishing a paper in a scientific journal is NOT wasting grant money. You should try it some time.

Look, before you post some nonsense about someone misusing grant money, you should at least have some evidence that they have in fact done that, otherwise you might open yourself up to a lawsuit. First you should be able to prove what the money was for. Then you would have to prove how much money was used for things that it was not supposed to be used for. Then you would have to determine if the stated goal of the grant was not being met. Until you can prove these three things, you’ve got nothing, which is exactly what they’ve got.

They were caught dirty, again. They didn’t like it, again. They tried to accuse someone else of something without any evidence, again. It isn’t going to work, again. Spending so much time denying the obvious is the real waste of grant money. So it’s just another case of projection.

Or you could get you friend and fellow traveller who just happens to edit a non-ID journal to bypass the normal peer review process and publish your paper that doesn’t match the journal’s mission. I wonder who do something like that?

DS said:

Maybe their subscription to Science ran out. :)

NOT FUNNY! My subscription is on “hold” (for the second or third time, I might add), and they give you no instructions on how to rectify the situation. That said, I love it when the DI’s “principles” come back to bite them on the buttocks. They are intellectual opportunists - they embrace whatever principle gives them the desired result.

Let’s be clear. there is absolutely nothing wrong with the DI sponsoring legislation in order to further their religious agenda, that is their right as they correctly point out. There isn’t anything wrong with that legislation being particularly worded so as to mislead and deny its obvious intent, that would only be a problem for anyone stupid enough to actually pass the legislation. There isn’t even anything wrong with changing the wording every round of submission so that failed bills will have a better chance in the future, that’s just smart.

There is however something seriously wrong with changing weasel words in order to specifically avoid legal problems without ever actually changing the intent or effect of the legislation. That is simply evidence of fundamental dishonesty.

And of course that’s the only reason to get your panties in a bunch when someone has the audacity to point out your duplicity. Then the name calling and accusations start to fly in a desperate attempt to draw attention away form the fact that you were once again caught dirty, just like at Dover.

Or does anyone think that such tactics would be necessary for good legislation that was actually meant to improve science education in this country?

Weird that they’re upset. All Nick Matzke has done has illustrated that the language of one local anti-evolution bill has strongly influenced other anti-evolution bills. Almost no other group would be upset by that. Usually activists would be perfectly fine with the idea that an original local effort they favor is being adopted elsewhere.

However, the explanation is probably giant, bloated, yet hypersensitive and fragile egos, combined with lack of a sense of humor.

harold said:

Weird that they’re upset. All Nick Matzke has done has illustrated that the language of one local anti-evolution bill has strongly influenced other anti-evolution bills. Almost no other group would be upset by that. Usually activists would be perfectly fine with the idea that an original local effort they favor is being adopted elsewhere.

However, the explanation is probably giant, bloated, yet hypersensitive and fragile egos, combined with lack of a sense of humor.

I think I have seen enough of these characters over the last 50 years to be able to recognize this whining as one of the clearest indications of “science envy” among ID/creationists.

ID/creationists, ever since Morris and Gish, have always sought the limelight; and their method of seeking it has been to ride on the backs of real scientists in a public debates.

I suspect that one of the major personality characteristics of an ID/creationist is extreme jealousy over the fact that somebody else might have their name on a publication in a scientific journal and they don’t.

The entire life course of an ID/creationist wannabe leader is to be a respected and feared authority figure within their subculture; and one of the ways they try to do that is to pretend that they are peers in the scientific process of vetting research data. So they will feign the ability to discuss science at “a high level.”

Nearly all pseudoscientists exhibit this characteristic of clawing their way up the social ladder in order to get to the top; and ID/creationists get this from the norms of their sectarian religion in which priests and preachers are at the pinacle of their subculture. However, those ID/creationists who go to college and graduate school to get those letters after their names are seeking to become even greater rock stars within their subculture and to be constantly talked about in the secular social media as well. It is never about buckling down and learning the real science; its those letters and the ooohs and aaahs that come with them.

What all these scientist wannabes miss in clawing their way up the social ladder is the fact that real scientists are expected to actually know the science; not pretend to know it. And if you pay attention, you will notice that ID/creationists never really comprehend any scientific discussions that are taking place in the scientific community; they are simply babbling and grousing on the sidelines and pretending to be knowledgeable critics.

The ID/creationist’s understanding of the basics of science is so poor that they can’t even recoginze what it means to understand. They can’t recognize people who actually know things because they themselves have never had such experiences. ID/creationists are incapable of formulating a research program; they simply don’t have a clue about what is involved.

ID/creationism is all about jealous social striving and constantly worrying and kvetching over who is at the top getting the goodies that they think they deserve even more.

ID/creationists love to proclaim their authoritative knowledge about every new hominid fossil, as if they have handled it, and written scientific papers in respected, legitimate journals, about it. But they have done neither. As you point out, they have neither the knowledge nor skill nor credentials to critique any hominid fossil. Yet they pretend to be authorities.

If they are such great authorities, why don’t they go dig some hominid fossils of their own? Because no respectable government would allow them to, that’s why.

Amen. A better understanding of the history of life IS in the public interest. Thats why creationist must be allowed equal time in schools etc. They are not anti-evolution bills but rather pro creationist bills. Its anti creationism in poltics and law that is the greater activist in these matters.

Why do evolutionists say these trees are accurate when they are based on fossils? The only organization of the fossils in the trees is based on deposition of the dead creatures and the comparative looks of them. The trees are not evidence for evolution but instead evolutionary conclusions are the origin for the tree constructions. In short biology relationships, trees, are not from evidence of evolutionary process or descent/ascent of one species etc to another BUT instead they, the trees, are based on presumptions not evidenced by the fossils. which came first? the concept of the evolution tree and then the fossils matched or the fossils matched and thus a tree. It seems all based on fossils as data points and not processes. The process is not fossilized, or descent/assent, but only a dead creature in a moment in time. Why shouldn’t creationists attack the tree concept???

Robert Byers said:

Amen. A better understanding of the history of life IS in the public interest. Thats why creationist must be allowed equal time in schools etc. They are not anti-evolution bills but rather pro creationist bills. Its anti creationism in poltics and law that is the greater activist in these matters.

Why do evolutionists say these trees are accurate when they are based on fossils? The only organization of the fossils in the trees is based on deposition of the dead creatures and the comparative looks of them. The trees are not evidence for evolution but instead evolutionary conclusions are the origin for the tree constructions. In short biology relationships, trees, are not from evidence of evolutionary process or descent/ascent of one species etc to another BUT instead they, the trees, are based on presumptions not evidenced by the fossils. which came first? the concept of the evolution tree and then the fossils matched or the fossils matched and thus a tree. It seems all based on fossils as data points and not processes. The process is not fossilized, or descent/assent, but only a dead creature in a moment in time. Why shouldn’t creationists attack the tree concept???

Gods you’re dumb, Byers.

Robert Byers said:

Amen. A better understanding of the history of life IS in the public interest. Thats why creationist must be allowed equal time in schools etc. They are not anti-evolution bills but rather pro creationist bills. Its anti creationism in poltics and law that is the greater activist in these matters.

Why do evolutionists say these trees are accurate when they are based on fossils? The only organization of the fossils in the trees is based on deposition of the dead creatures and the comparative looks of them. The trees are not evidence for evolution but instead evolutionary conclusions are the origin for the tree constructions. In short biology relationships, trees, are not from evidence of evolutionary process or descent/ascent of one species etc to another BUT instead they, the trees, are based on presumptions not evidenced by the fossils. which came first? the concept of the evolution tree and then the fossils matched or the fossils matched and thus a tree. It seems all based on fossils as data points and not processes. The process is not fossilized, or descent/assent, but only a dead creature in a moment in time. Why shouldn’t creationists attack the tree concept???

You’ve said this before and you are no clearer making your point this time. People have explained this to you, and discussed it with you more than once. You’re repeating yourself and just taking up space. It’s time for your posts to go to the BW.

Yardbird said:

Robert Byers said:

Amen. A better understanding of the history of life IS in the public interest. Thats why creationist must be allowed equal time in schools etc. They are not anti-evolution bills but rather pro creationist bills. Its anti creationism in poltics and law that is the greater activist in these matters.

Why do evolutionists say these trees are accurate when they are based on fossils? The only organization of the fossils in the trees is based on deposition of the dead creatures and the comparative looks of them. The trees are not evidence for evolution but instead evolutionary conclusions are the origin for the tree constructions. In short biology relationships, trees, are not from evidence of evolutionary process or descent/ascent of one species etc to another BUT instead they, the trees, are based on presumptions not evidenced by the fossils. which came first? the concept of the evolution tree and then the fossils matched or the fossils matched and thus a tree. It seems all based on fossils as data points and not processes. The process is not fossilized, or descent/assent, but only a dead creature in a moment in time. Why shouldn’t creationists attack the tree concept???

You’ve said this before and you are no clearer making your point this time. People have explained this to you, and discussed it with you more than once. You’re repeating yourself and just taking up space. It’s time for your posts to go to the BW.

Repetitive blather is rather Robert’s forte, and it is interesting see him weigh in on this thread, back to form. He seemed less resilient bumping into me over at #TIP www.tortucan.wordpress.com where he declined to actually explain or document his assorted claims beyond merely repeating them.

Robert Byers said:

Amen. A better understanding of the history of life IS in the public interest. Thats why creationist must be allowed equal time in schools etc. They are not anti-evolution bills but rather pro creationist bills.

Its anti creationism in poltics and law that is the greater activist in these matters.

This may be the first time Robert Byers said something I agree with. It feels…weird.

Nick Matzke said:

Robert Byers said:

Amen. A better understanding of the history of life IS in the public interest. Thats why creationist must be allowed equal time in schools etc. They are not anti-evolution bills but rather pro creationist bills.

Its anti creationism in poltics and law that is the greater activist in these matters.

This may be the first time Robert Byers said something I agree with. It feels…weird.

Breathe slowly and deeply. It probably won’t happen again.

Robert Byers said:

Why shouldn’t creationists attack the tree concept???

So you think what the LDS are doing with genealogy is wrong? You have no family tree? IIRC, you earlier have denied the existence of genetic relationships?

West’s response to Nick’s work, along with the DI’s ten part series attempting to rewrite history on the aniversery of Judge Jones’ decision on Kitzmiller, should be a reminder kind of people we are dealing with when science and the law uncover the continuous duplicity of ID/creationists.

Recall that Judge Jones and his family were under the protection of the US Marshall Service because the judge received death threats after his decision.

These people are not really very nice; they reject reality and play dirty to get their way.

This may be the first time Robert Byers said something I agree with. It feels…weird.

Something like one percent of what Robert Byers says is accurate and insightful.

Robert Byers said: Amen. A better understanding of the history of life IS in the public interest. Thats why creationist must be allowed a fair treatment in the scientific arena. They are not anti-evolution bills but rather pro creationist bills. Its anti creationism in poltics and law that is the greater activist in these matters.

Fixed that part. And yes, creationists are as free as anyone to conduct scientic research… they just haven’t done that. They most certainly do not deserve equal time in schools, as what is taught there should be well established science, which of course the Theory of Evolution is.

Why do evolutionists say these trees are accurate when they are based on fossils? The only organization of the fossils in the trees is based on deposition of the dead creatures and the comparative looks of them. The trees are not evidence for evolution but instead evolutionary conclusions are the origin for the tree constructions. In short biology relationships, trees, are not from evidence of evolutionary process or descent/ascent of one species etc to another BUT instead they, the trees, are based on presumptions not evidenced by the fossils. which came first? the concept of the evolution tree and then the fossils matched or the fossils matched and thus a tree. It seems all based on fossils as data points and not processes. The process is not fossilized, or descent/assent, but only a dead creature in a moment in time. Why shouldn’t creationists attack the tree concept???

I am sure that you already know that there are trees built not on fossils, but also based on ERV’s, based on genetic mutations, based on genes, based on mithocondrial DNA, based on genetic defects like the L-GULO gene, etc. And they all agree almost perfectly with each other, including the ones based on fossils.

Daniel said:

Robert Byers said: Amen. A better understanding of the history of life IS in the public interest. Thats why creationist must be allowed a fair treatment in the scientific arena. They are not anti-evolution bills but rather pro creationist bills. Its anti creationism in poltics and law that is the greater activist in these matters.

Fixed that part. And yes, creationists are as free as anyone to conduct scientic research… they just haven’t done that. They most certainly do not deserve equal time in schools, as what is taught there should be well established science, which of course the Theory of Evolution is.

Why do evolutionists say these trees are accurate when they are based on fossils? The only organization of the fossils in the trees is based on deposition of the dead creatures and the comparative looks of them. The trees are not evidence for evolution but instead evolutionary conclusions are the origin for the tree constructions. In short biology relationships, trees, are not from evidence of evolutionary process or descent/ascent of one species etc to another BUT instead they, the trees, are based on presumptions not evidenced by the fossils. which came first? the concept of the evolution tree and then the fossils matched or the fossils matched and thus a tree. It seems all based on fossils as data points and not processes. The process is not fossilized, or descent/assent, but only a dead creature in a moment in time. Why shouldn’t creationists attack the tree concept???

I am sure that you already know that there are trees built not on fossils, but also based on ERV’s, based on genetic mutations, based on genes, based on mithocondrial DNA, based on genetic defects like the L-GULO gene, etc. And they all agree almost perfectly with each other, including the ones based on fossils.

Yes I’m aware however fossils was emphasized in the thread. are you running away from making these trees on fossils? i would say the same criticism equation for fossils works for comparative genetics. Its still a great presumption that the relationships already are proven. The trees follow that. Anyways Its all about comparing living things. Creationism can do the same thing. There is no actual evidence for relationship. They see it as a reasonable analysis. Also not imagining other options.

Robert Byers said:

Daniel said:

Robert Byers said: Amen. A better understanding of the history of life IS in the public interest. Thats why creationist must be allowed a fair treatment in the scientific arena. They are not anti-evolution bills but rather pro creationist bills. Its anti creationism in poltics and law that is the greater activist in these matters.

Fixed that part. And yes, creationists are as free as anyone to conduct scientic research… they just haven’t done that. They most certainly do not deserve equal time in schools, as what is taught there should be well established science, which of course the Theory of Evolution is.

Why do evolutionists say these trees are accurate when they are based on fossils? The only organization of the fossils in the trees is based on deposition of the dead creatures and the comparative looks of them. The trees are not evidence for evolution but instead evolutionary conclusions are the origin for the tree constructions. In short biology relationships, trees, are not from evidence of evolutionary process or descent/ascent of one species etc to another BUT instead they, the trees, are based on presumptions not evidenced by the fossils. which came first? the concept of the evolution tree and then the fossils matched or the fossils matched and thus a tree. It seems all based on fossils as data points and not processes. The process is not fossilized, or descent/assent, but only a dead creature in a moment in time. Why shouldn’t creationists attack the tree concept???

I am sure that you already know that there are trees built not on fossils, but also based on ERV’s, based on genetic mutations, based on genes, based on mithocondrial DNA, based on genetic defects like the L-GULO gene, etc. And they all agree almost perfectly with each other, including the ones based on fossils.

Yes I’m aware however fossils was emphasized in the thread. are you running away from making these trees on fossils? i would say the same criticism equation for fossils works for comparative genetics. Its still a great presumption that the relationships already are proven. The trees follow that. Anyways Its all about comparing living things. Creationism can do the same thing. There is no actual evidence for relationship. They see it as a reasonable analysis. Also not imagining other options.

You’re a halfwit, Byers. You know nothing about science. You know nothing about fossils or paleontology. You literally don’t know what you’re talking about. Hell, you can’t even say what you mean in decent English. You come here and make a fool of yourself over and over again, and most of us just give a rueful headshake and move on. Certainly no one takes you seriously.

His thinking is one-dimensional. Actually, it’s zero-dimensional. He perceives fossils as a single, zero-dimensional data point. He cannot comprehend the three spatial dimensions, and one temporal dimension, of the fossil record. The fossil record does indeed show a succession of life forms from older eras to newer eras, and laterally across continents. He cannot conceive of such a thing.

The honest attempts of some to enlighten him are like trying to teach a blind man what color is.

I notice that the Discovery Institute has no method of commenting on the ‘diatribes’ that they offer as intellectual discourse.

Robet Byers said:

Its still a great presumption that the relationships already are proven.

Meaning you don’t see any proof of relationships even within your own family? DNA relationships are accidental only, not evidence of relationship? You ought to have your brain scanned, there must be something funny going on in there.

Heh, that would be about the only place in the world we might detect a connection between ‘fun’ and ‘creationist’.

Robert, lack of humour is one of the best indicators of stupidity. Did you ever see humour, puns etcetera on a cretionist website? I haven’t. What we see at creationis sites are nonsense and banning of opponents, they can’t tolerate opposition. That is because of their bias and lack of openmindedness.

And Robert himself is disconnected from the world of realities.

John G. West has anti-Darwin fever, as usual. :(

“antievolution bills seem to evolve rather like pathogens”

Well, ‘antievolution bills’ are not organisms; they are not mechanisms either. So, to say they ‘evolve’ phylogenetically is an obvious mis-analogy. The ‘decision tree’ of antievolution bills involves human creativity, planning and intention, not mere BVSR. It does not appear that Nick did a “phylogenetic study of antievolution bills”, rather that he made a diagram that looks like the diagrams one makes in phylogenetics.

Let’s not let biology become confused with sociology, yes?

Noting this of course does not support West’s argument that Nick’s research funding was misused. The DEVELOPMENT of antievolution bills is a cultural matter (not reducible to the dead-in-the-water ‘field’ of memetics) for social scientists potentially to explore. Yet exaggerating the proper uses of ‘evolve’ is unhelpful, while the diagramming helps to see the linkages between antievolution bills.

Robert, people like you make mad! Science is all we have between a world of unpredictable events and our own future. I have collected a few links where we can see how hard science is working in the best interest of mankind, and here comes people like you making ridicule of science with the most braindead nonsense ever put on print.

STFU and don’t say anything more before you have learned and understood,(lack of understandig is your problem, you’d need help) at least some rudimental facts of science. You mighet even discover that another of the things you are clueless about, mathematics, are an important tool in the study of matters of great importance to mankind and its future and shame on you.

I have collected four links for you. Read for comprehension if you can and don’t come back unless you honestly can say that today you have learned something you were clueless about before.

Link one

Link two

Link three

Link four

harold said:

Weird that they’re upset. All Nick Matzke has done has illustrated that the language of one local anti-evolution bill has strongly influenced other anti-evolution bills. Almost no other group would be upset by that. Usually activists would be perfectly fine with the idea that an original local effort they favor is being adopted elsewhere.

No, it’s simply SOP (standard operating procedure with them).

Nick Matzke said:

Robert Byers said:

Amen. A better understanding of the history of life IS in the public interest. Thats why creationist must be allowed equal time in schools etc. They are not anti-evolution bills but rather pro creationist bills.

Its anti creationism in poltics and law that is the greater activist in these matters.

This may be the first time Robert Byers said something I agree with. It feels…weird.

You’ve succumbed to the Dark Side. YOU ARE KYLO REN!!!!!

Beware the dark side of the farce?

Henry J said:

Beware the dark side of the farce?

Well over at my FB page, we were discussing Jonny West’s latest screed. Someone asked what the DI really thought of Nick. I opined that he’s an “unhinged mix” of Darth Vader and Kylo Ren, and then Nick jumped in, saying that he IS Kylo Ren.

I’m Kylo Ren, except, unlike Kylo Ren, I’m angry for a reason. :-)

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This page contains a single entry by Nick Matzke published on December 18, 2015 9:07 AM.

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