Discovery Institute: So much for Academic Freedom!
(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
Teve Tory · 18 December 2015
"Itâs conceivable they arenât up on the latest in phylogenetic methods and their applications."
Heh.
Jeffrey Shallit · 18 December 2015
Just when you think John West and the Discovery Institute couldn't stoop any lower, they surprise you by going even lower.
JimboK · 18 December 2015
"Read the article?!? We don't need to read no stinking article!"
DS · 18 December 2015
"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. :)
Bob O'Hara · 18 December 2015
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.
Nick Matzke · 18 December 2015
I focused on the methods point but PZ makes several other points also worth making: http://scienceblogs.com/pharyngula/2015/12/18/taking-a-phylogenetic-approach-to-the-law/
Arthur Hunt · 18 December 2015
Two words come to mind: "Broader Impacts"
https://me.yahoo.com/a/JxVN0eQFqtmgoY7wC1cZM44ET_iAanxHQmLgYgX_Zhn8#57cad · 18 December 2015
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
DS · 18 December 2015
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.
Michael Fugate · 18 December 2015
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?
Matt G · 18 December 2015
Dr GS Hurd · 18 December 2015
Bravo Nick!
DS · 18 December 2015
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?
harold · 18 December 2015
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.
Mike Elzinga · 18 December 2015
prongs · 18 December 2015
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.
Robert Byers · 18 December 2015
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???
phhht · 18 December 2015
Yardbird · 18 December 2015
James Downard · 18 December 2015
Nick Matzke · 19 December 2015
Yardbird · 19 December 2015
Rolf · 19 December 2015
Mike Elzinga · 19 December 2015
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.
harold · 19 December 2015
Daniel · 19 December 2015
Robert Byers · 19 December 2015
phhht · 19 December 2015
prongs · 19 December 2015
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.
bbob · 19 December 2015
I notice that the Discovery Institute has no method of commenting on the 'diatribes' that they offer as intellectual discourse.
Rolf · 20 December 2015
MiddleStMan · 20 December 2015
Rolf · 20 December 2015
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
John · 20 December 2015
John · 20 December 2015
Henry J · 20 December 2015
Beware the dark side of the farce?
John · 20 December 2015
Nick Matzke · 21 December 2015
I'm Kylo Ren, except, unlike Kylo Ren, I'm angry for a reason. :-)