I just had an idea for a movie: SQUIDNADO!

I got email this morning…and so did every member of the science & math division at the University of Minnesota, Morris. This happens every once in a while, since our official email addresses are all publicly accessible, and anyone can grab them and spam the heck out of us all. What was unusual is that this email was directly addressed to me, personally, and the sender decided that he needed to put me in my place and flaunt his erudition to every one of my colleagues.

I am unperturbed by his effort, because in every case, without exception, the loon just ends up exposing his inanity. I mean, you’ve got to realize that trying to harass an entire university division is a poor decision in the first place, right? That thinking that most of the faculty are at all interested in your disagreement with me is somewhat delusional? That you’ve immediately put the wrong foot forward by arbitrarily spamming a whole mob of disinterested people with your long-winded and ultimately pathetic excuses?

You should have known that I’d happily post your email to my blog, where people can opt-in and choose to read the whole thing voluntarily. So yes, I include every word of the thing below.

It’s from Ted Steele, who wrote that very silly article, Cause of Cambrian Explosion – Terrestrial or Cosmic?, in which he proposed that squid fell to earth in comets. I laughed at it in my article, Squids from SPAAAAAAAAACE!, and what has irritated him is that my criticisms were picked up by that prestigious newspaper, The Sun, in an article titled ARE YOU SQUIDDING? Are octopuses aliens? Bizarre new theory suggests the sea creatures’ eggs arrived on earth on a comet from outer space. So the real concern is that a bunch of working class blokes are going to be reading their paper down at the pub, looking for topless pics and anti-immigrant rants, and they’re going to stumble across this weird American egghead who thinks Ted Steele is full of crap.

I think he should be more concerned that The Sun finds his work amusing than that I think it’s garbage. But read on. He’s indignant.

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Squids from SPAAAAAAAAACE!

I was reading this article with a provocative title: Cause of Cambrian Explosion – Terrestrial or Cosmic?. It set my alarm bells ringing from the title onward.

Look at those authors! So many, yet the paper itself is so empty of data. Most I don’t know. Steele I’ve heard of — he was promoting neo-Lamarckism in the 1980s, and thinks the Cambrian explosion was caused by retroviruses squirting new complex genes into the ancestors of all animals. Brig Klyce I’ve bumped into a few times on the internet…he’s a panspermia fanatic. Milton Wainwright is the guy who used an EM to look for odd blobs and declared they are evidence of alien life. The Wallis’s were part of a time that announced that diatoms came from outer space. Oh, and Chandra Wickramasinghe…yes, we have crossed paths multiple times. He published a lot in the Journal of Cosmology, with an editor, Rhawn Joseph, who really, really doesn’t like me.

Wickramasinghe has been making bank on this nonsensical idea that genes for complex intelligent life have periodically rained down on the Earth from outer space. There is no evidence for it, and no reason to invoke this random phenomenon to explain biology — we have random phenomena enough, thank you very much, and none of them have the extreme weirdness of the space virus explanation.

I guess I have heard of quite a few of the authors! And it’s a most unsavory stew of notorious crackpots.

Let’s take a look at the abstract for this gem of a paper, shall we?

We review the salient evidence consistent with or predicted by the Hoyle-Wickramasinghe (H-W) thesis of Cometary (Cosmic) Biology. Much of this physical and biological evidence is multifactorial. One particular focus are the recent studies which date the emergence of the complex retroviruses of vertebrate lines at or just before the Cambrian Explosion of ~500 Ma. Such viruses are known to be plausibly associated with major evolutionary genomic processes. We believe this coincidence is not fortuitous but is consistent with a key prediction of H-W theory whereby major extinction-diversification evolutionary boundaries coincide with virus-bearing cometary-bolide bombardment events. A second focus is the remarkable evolution of intelligent complexity (Cephalopods) culminating in the emergence of the Octopus. A third focus concerns the micro-organism fossil evidence contained within meteorites as well as the detection in the upper atmosphere of apparent incoming life-bearing particles from space. In our view the totality of the multifactorial data and critical analyses assembled by Fred Hoyle, Chandra Wickramasinghe and their many colleagues since the 1960s leads to a very plausible conclusion — life may have been seeded here on Earth by life-bearing comets as soon as conditions on Earth allowed it to flourish (about or just before 4.1 Billion years ago); and living organisms such as space-resistant and space-hardy bacteria, viruses, more complex eukaryotic cells, fertilised ova and seeds have been continuously delivered ever since to Earth so being one important driver of further terrestrial evolution which has resulted in considerable genetic diversity and which has led to the emergence of mankind.

It’s a moderately long paper, because it’s really easy to layer on thick coats of bullshit when you don’t care about the quality of the evidence. So I’m just going to look at — can you guess? — his second focus, “the remarkable evolution of intelligent complexity (Cephalopods) culminating in the emergence of the Octopus”.

It’s garbage.

There are novelties in cephalopod evolution, and I’ve written about them before. In particular, cephalopods carry out a significant amount of gene editing, that is, they use enzymes to modify a few of the bases in RNA before it is translated into protein. This is not a shocking surprise — it’s not a universal modification of every RNA, but it has been observed in phyla all across the animal kingdom — although some gullible sources claim it is a violation of the central dogma (they’re wrong). But the key thing is that it’s not unique to cephalopods, lots of organisms have the enzymes, so you can’t use it as evidence for the claim that gene editing came from outer space.

In particular, there is no reasonable justification for this claim:

Thus the possibility that cryopreserved Squid and/or Octopus eggs, arrived in icy bolides several hundred million years ago should not be discounted (below) as that would be a parsimonious cosmic explanation for the Octopus’ sudden emergence on Earth ca. 270 million years ago. Indeed this principle applies to the sudden appearance in the fossil record of pretty well all major life forms, covered in the prescient concept of “punctuated equilibrium” by Eldridge and Gould advanced in the early 1970s (1972, 1977); and see the conceptual cartoon of Fig. 6. Therefore, similar living features like this “as if the genes were derived from some type of pre-existence” (Hoyle and Wickramasinghe, 1981) apply to many other biological ensembles when closely examined. One little known yet cogent example is the response and resistance of the eye structures of the Drosophila fruit fly to normally lethally damaging UV radiation at 2537 Å, given that this wavelength does not penetrate the ozone layer and is thus not evident as a Darwinian selective factor at the surface of the Earth (Lutz and Grisewood, 1934) and see Hoyle and Wickramasinghe (1981, p.12e13). Many of these “unearthly” properties of organisms can be plausibly explained if we admit the enlarged cosmic biosphere that is indicated by modern astronomical research e discoveries of exoplanets already discussed. The average distance between habitable planets in our galaxy now to be reckoned in light years e typically 5 light years (Wickramasinghe et al., 2012). Virion/gene exchanges thus appear to be inevitable over such short cosmic distances. The many features of biology that are not optimised to local conditions on the Earth may be readily understood in this wider perspective.

We’ve gone from a few viral genes raining down on Earth and getting incorporated into life, to frozen squid eggs drifting from Alpha Centauri to Earth in icy meteors and somehow crashing into our oceans and surviving to populate the seas. I don’t think the authors understand the word “parsimonious”. If this were true, cephalopods would represent an entirely novel lineage, and more than having a few molecular novelties, they would be completely unrelated to any other animal lineage on the planet. They would not be related to other molluscs. They would not be protostomes. They would not be eukaryotes. They would be totally alien.

The authors even seem to be superficially conscious of this problem. Here is the “conceptual cartoon of Fig. 6”.

This diagram is what you get when you pretend that lineages are made solely of apomorphies, or the derived traits that distinguish each species from other organisms, and close your eyes to the plesiomorphies, or shared similarities. A phylogenetic tree is not “forced”, it is produced by identifying shared traits. The octopus has molecular similarities to snails, and the two together have similarities to other invertebrates, and all of them have shared attributes with all animals. You don’t get to just ignore all that! This is equivalent to saying that octopuses have tentacles, therefore octopuses are from outer space, completely neglecting the fact that octopuses have homologous genes linking them to insects and sea cucumbers and people.

To back up the remarkable assertion that cephalopods fell from space, they present no evidence, other than a flurry of citations of … N. Chandra Wickramasinghe. It’s an embarrassingly masturbatory display. Wickramasinghe and his associates have been churning out these useless, garbage papers for decades, and now they use the volume of shit he has produced as evidence that his shit is valid. He occasionally sprinkles in references to other authors, which he gets wrong: Stephen J. Gould would not recognize figure 6 as an accurate representation of punctuated equilibrium. This is not how science is supposed to work. It’s simply fraudulent.

Wickramasinghe used to be associated with Cardiff University — they fired him and closed his astrobiology ‘department’, which turns out to have been a bit of a Potemkin village anyway. It was run entirely by Wickramasinghe as a part-time employee, and the entirety of the staff were “honorary”, unpaid volunteers.

“It was only costing them between £14,000 and £15,000 (about $24,000) a year to retain me as a part time director of the centre.

“All the other staff, totaling about 12, is honorary research fellows and associates who were not costing the university anything at all. They have brought a huge amount of credit to Cardiff University and so it amazed me that the university would discontinue their support for astrobiology. “What they did to me is a travesty of normal university practice and I still don’t understand the motive. I can’t believe for a moment that they are strapped for £15,000 a year to maintain a centre that has, for good or bad, a very high profile internationally. “We continue to make headlines in various things that we do. Some of our work remains controversial but it is in the nature of science to promote controversy as long as it is intelligent controversy. That’s within the rules of the game. If people agree 100 per cent what they’re doing then science becomes a bit insubstantial. “I just fail to understand why they do this. It could be ageism because, at 71, I’m over the retirement age by a couple of years, but I’ve been around for years and have published many papers. I was Sir Fred Hoyle’s longest-running collaborator from the time I was a student at Cambridge.”

Cardiff claims the closure was entirely due to budgetary reasons, but I rather suspect that, contrary to Wickramasinghe’s claim, his slack work and low standards of evidence have frequently brought discredit to the university.

Don’t cry for Chandra, though. He was snapped up by the University of Buckingham to form a “centre for astrobiology”. I think that might mean he was allowed to host a webpage on their site, because he’s never had a real research unit, and I doubt that he’s been given the funds for one now.

But yeah, if you see his name on anything, or apparently any of the names in that long list of articles, you’ve found a treasure trove of pseudoscience.

So…when creationists sneak bad papers into legit journals, does evolution collapse?

A few days ago, a paper was pointed out to me as a particularly horrible example of bad social science: it was titled “The conceptual penis as a social construct”. I glanced at. It was a murky mess and so bad that I couldn’t even get past the first paragraph, so I abandoned it as simply too much effort to criticize. As it turns out, it was a hoax: the authors were trying to pull a Sokal and expose “‘academic’ fields corrupted by postmodernism”.

We intended to test the hypothesis that flattery of the academic Left’s moral architecture in general, and of the moral orthodoxy in gender studies in particular, is the overwhelming determiner of publication in an academic journal in the field. That is, we sought to demonstrate that a desire for a certain moral view of the world to be validated could overcome the critical assessment required for legitimate scholarship. Particularly, we suspected that gender studies is crippled academically by an overriding almost-religious belief that maleness is the root of all evil.

The lead author is Peter Boghossian, whose own biases are rather obvious in that passage, and I think he overplayed his hand. He actually completely failed to demonstrate what he set out to do.

He sent the crap paper to NORMA: International Journal for Masculinity Studies, a journal with an impact factor of 0, and it was rejected. So, wait, the fake paper was punted? How does that demonstrate that “gender studies is crippled academically”?

NORMA nicely sent them off to resubmit to an even more poorly ranked journal, Cogent Social Sciences, which is so new it doesn’t even have an impact factor, and which is also a pay-to-publish journal. Boghossian then coughed up $625 to convince them to publish it.

At this point the hoax has become completely meaningless. There are bad, predatory journals out there that will take anything a hack scribbles up and publish it for a profit. This is not news. It is also not unique to gender studies or sociology. I’ve pointed out these bad papers more than a few times in journals in science fields.

So when I point out that Erik Andrulis published, in complete seriousness, a paper titled Theory of the Origin, Evolution, and Nature of Life that attempts to explain chemistry, development, and evolution as functions of spiral gyres, does that discredit those fields? When David Abel of the Department of ProtoBioCybernetics and ProtoBioSemiotics publishes a paper on the origin of life that is packed full of buzzwords and pseudoscience, does that mean that Nick Lane and Bill Martin are full of crap, too? Because the Journal of Cosmology exists, astronomy is fake science? John Bohannon created an automatic molecular biology paper generator that churned out garbage papers. They were accepted by 157 science journals. I guess we can scratch the entire field of molecular biology.

As I wrote about that last example:

I agree that there is a serious problem in science publishing. But the problem isn’t open-access: it’s an overproliferation of science journals, a too-frequent lack of rigor in review, and a science community that generates least-publishable-units by the machine-like application of routine protocols in boring experiments.

The lesson to be learned here is that Boghossian executed a poorly performed experiment that didn’t succeed in what he engineered it to do, and which was embarrassingly derivative, and then analyzed the results poorly. At least it cost the hack $625 to attempt some click-bait sensationalism.


There’s more. See Kris Wager, and Ketan Joshi lists lots of examples of hoaxes in science disciplines that didn’t indict entire broad fields of research.

When did Oklahoma start electing shaved apes to their legislature?

Oh, actually, shaved apes would be an upgrade from Josh Brecheen, who is more like a shaved and bipedal member of the subgenus Asinus. He’s a new legislator who has announced his intention to introduce creationism into Oklahoma schools (or, as perhaps I should refer to them, “skools”) for a set of reasons he laid out in a notably ignorant column in the Durant Daily Democrat.

His column is amazing. The faculty of Southeastern Oklahoma State University are covering their eyes in shame right now, since apparently this creationist-cliche-spewing plagiarist and professional goober managed to successfully graduate from their institution. My students ought to be worried, too, because now I feel like I’ve got to tighten up my standards and start flunking more students out lest they come back and haunt me from positions of power. Seriously, it’s a remarkable work he’s posted: it’s largely cribbed from the creationist Lee Strobel, but at the same time, he’s managed to make standard creationist arguments worse. Here’s his whole column, with a little helpful annotation from me.

One of the bills I will file this year may be dismissed as inferior by “intellectuals” [It’s not a promising beginning when you’re discussing a scientific topic and immediately dismiss intellectuals] so I wanted to devote particular time in discussing it’s [sic] merits. It doesn’t address state waste, economic development, workers comp reform or lawsuit reform (although I have filed bills concerning each) [I dread learning about their quality, given the dreck espoused here] but it is nonetheless worthy of consideration. It is an attempt to bring parity [a familiar refrain, in which a fringe belief is undeservedly promoted to equal time with well-established science] to subject matter taught in our public schools, paid for by the taxpayers and driven by a religious ideology [says the guy who wants to promote a religious ideology] . I’m talking about the religion of evolution [eyes roll everywhere]. Yes, it is a religion [No, it isn’t]. The religion of evolution [Seriously. It isn’t. It’s a scientific theory that explains a large body of confirmable facts, and that provides a useful framework for new research. It has no resemblance to any faith of any kind.] requires as much faith as the belief in a loving God [God: no evidence, no math, no experiments, no observations. Evolution: evidence, math, experiments, observations. Case closed.], when all the facts are considered (mainly the statistical impossibility of key factors [Here comes the bad math]). Gasp! Someone reading this just fell out of their enlightened seat!!! [Only at the sight of three exclamation points…we’re all wondering if he typed this while wearing his underpants on his head] “It’s not a religion as it’s agreed upon by the entire scientific community,” some are saying at this very moment [No, we’re not, because its status as a science rather than a religion is determined by its properties, not some kind of consensus or vote]. Are you sure? Let’s explore the facts. [As if Brecheen has any.]

As a high school and university student forced to learn about evolution [If only someone had forced him to learn about logic and grammar!] I was never told there were credible scientists who harbor significant skepticism toward Darwinian Theory [Because there aren’t any, at least not in the sense Brecheen is talking about. There are critics of aspects of the theory and differences in emphasis, but no credible, knowledgeable scientist has any doubts about the overall fact of evolution]. I easily recall a full semester at SOSU where my English 1 professor forced us to write [What we professors call “teaching”, or dumber students call “forcing”] almost every paper over the “facts” of evolution. That professor had a deep appreciation for me [Oh, really?] by semester end due to our many respectful debates [In the classroom, professors tend to avoid expressing what they really think of some of the clowns in our student body. Don’t mistake professionalism for intellectual respect] as I chose to not be blindly led [Says the creationist]. I specifically remember asking how in 4,000 years of recorded history how we have yet to see the ongoing evidence of evolution [But we do! Bacterial resistance, new species, observations of changing frequencies of alleles, etc., etc., etc.] (i.e. a monkey jumping out of a tree and putting on a business suit [Jebus. What a maroon. No, evolution does not predict that monkeys will don business suits]).

Following a 2001 PBS television series, which stressed the “fact” of evolution, approximately 100 [100 fringe cranks out of a population of about a million scientists] physicists, anthropologists, biologists, zoologists, organic chemists, geologists, astrophysicists and other scientists [Don’t forget the dentists! Relatively few on the “Dissent from Darwinism” list were actually qualified biologists, and quite a few have since been very surprised to learn that they were included] organized a rebuttal. So much disagreement arose from this one sided TV depiction that this group produced a 151 page rebuttal stating how the program, “failed to present accurately and fairly the scientific problems with the Darwinian evolution”. These weren’t narrow minded fundamentalists, backwoods professors or rabid religious radicals [Actually, yeah, they were] ; these were respected world class scientists like Nobel nominee [Anyone can be nominated, and nominations are supposed to be secret; why this is always cited as a qualification is mysterious] Henry Schafer, the third most cited chemist [chemist, no expertise in biology] in the world and Fred Figworth [This is called a plagiarized error. Lee Strobel made this typo, and now it gets echoed in creationist rants everywhere. There is no Figworth at Yale; his name is Sigworth] , professor of cellular and molecular physiology at Yale Graduate School.

Ideologues teaching evolution as undisputed fact are not teaching truth [Yes, they are. Evolution is firmly established.]. Renowned [Fact not shown] scientists now asserting that evolution is laden with errors are being ignored [Also laughed at] . That’s where we should have problems with state dollars only depicting one side of a multifaceted issue [Oklahoma: mountain state, archipelago, rain forest, or lunar mare? That’s a multifaceted issue, too. Shall we teach invented geography with equal time?]. Using your tax dollars to teach the unknown, without disclosing the entire scientific findings is incomplete and unacceptable [OK, if we’re to teach the complete story, we’ll rightfully have to invest 179.99 days in teaching the scientific evidence, which all supports evolution, and 3 minutes on creationism on the last day. Fair’s fair]. For years liberals have decried how they want to give students both sides of an argument so they can decide for themselves [Both sides doesn’t imply a body of evidence is equal to a body of myth and superstition], however when it comes to evolution vs. creation in the classroom, the rules somehow change [Wrong. We’re consistent: we want the scientific evidence taught. It’s not our fault the creationists haven’t provided any]. Their beliefs shift, may I say… evolve to suit their ideology.

We must discuss the most recognizable icons of the evolution religion. Darwin sketched for The Origin of Species a visual [This one? Wrong. It’s not in the Origin, it’s in Darwin’s notes, which I doubt that Brecheen has read. It also looks nothing like what he describes] to explain his hypothesis that all living creatures evolved from a common ancestor. The tree of life scenario, engrained upon most of our memories [What he’s about to describe isn’t the tree of life, and I don’t know where he came up with it, but plucked from his ass seems a reasonable hypothesis], depicts gue transitioning into a hunched over monkey which then turns into a business suit [What’s with all the monkeys in business suits?].

Darwin himself knew the biggest problem with his visual (cornerstone concept of his hypothesis) was the fossil record itself. He acknowledged major groups of animals, he coined “divisions” (now called phyla) appear suddenly in the fossil record [Fair enough, Darwin does propose this as an issue, saying that there should have been long periods of time prior to the Cambrian, during which life swarmed in the seas. Of course, he’s since been shown to have been right.]. The whole basis for evolution is gradual differences and changes to be confirmed by modified fossils (phyla cross-over [What? Never heard of it]). Even Christians believe in biological change from species to species (adaption) over time. The taxonomic hierarchy which includes species, genus, family, order and class must be visualized [What?] for understanding separation from phyla and species classifications. As an OSU Animal Science graduate [I’m so sorry, OSU] I readily admit the adaption of animal species from interbreeding such as Santa Gertrudis cattle, a “weenie” dog or even a fruit fly. Even the difference among lions, tigers and cougars could be attributed to species adaption and interbreeding if one so decried [sic]. Additionally, human differences seen notable in ethnicity proves that change among species is real but this is NOT evolution [No, it is evolution. You don’t just get to define away obvious examples of changes over time as non-evolution] , its [sic] adaption. Changes with the classification of species is DRAMATICALLY different then changes among Phyla [Again, I say, what? I’ve been grading a lot of papers lately. I can tell when a student is trying to BS his way through a topic he doesn’t understand, and Brecheen is showing all the signs] . Phyla changes would be if an insect, with its skeleton located on the outside of soft tissue (arthropods), transformed into a mammal, with its skeleton at the core of soft tissue (chordates) [Ah, so that’s what he’s getting at. An insect must turn into a mammal for evolution to be true. Sorry, guy, such a phenomenon would demonstrate that evolution was wrong — biologists make no such prediction]. Phyla changes must be verified for Darwin’s common ancestor hypothesis to be accurate [Nope. This nonsense about “phyla changes” or “phyla cross-over” is simply stuff Brecheen has made up out of whole cloth (or stolen from one of his creationist source). Real biologists argue that mammals and insects evolved from a common ancestor in the pre-Cambrian, which would have been a generalized worm-like creature. Organisms do not suddenly leap across lines of descent; it’s like arguing that before you’ll believe I’m descended from my grandmother, I have to give birth to my cousin].

The rapid appearance of today’s known phylum-level differences, at about 540 million years ago, debunks the tree of life (common ancestor) scenario [No, it doesn’t.]. This biological big bang of fully developed [Nonsense. Cambrian organisms were precursors to modern forms, and the full range of extant forms was not present in the Cambrian—there were no bumblebees or birds, no squirrels or snakes.] animal phyla is called the Cambrian explosion. The Cambrian explosion’s phyla fossils and the phyla of today are basically one in [sic] the same [Nope. The Cambrian chordates, for instance, were represented only by small wormlike swimmers that were spineless and jawless and brainless; modern chordates are significantly more diverse. Mr Brecheen, for instance, possesses a jaw, although he may be lacking in some of the other key characters]. These phyla fossils of that era are fully developed [What does that even mean? Of course they were functional organisms], not in a transitional form [“Transition” refers to an intermediate between two forms. They were transitional between pre-Cambrian forms and modern chordates]. In fact we don’t have a transitional form fossil [Of course we do.] crossing phyla classification [Again with this bizarre “phyla crossing” nonsense. We expect no such thing] after hundreds of years of research looking at sediment beds spawning the ages. There are certainly plenty of good sedimentary rocks from before the Cambrian era to have preserved ancestors if there are any [Again, we do! We have fossils from the Vendian/Ediacaran; we have 600 million year old embryos; we have trace fossils and the small shelly fauna. Brecheen’s ignorance is not evidence of absence] . As for pre-Cambrian fossils being too tiny or soft for secured preservation there are microfossils of bacteria in rocks dating back beyond three billion years [As I just said, we’ve got ’em. They’re worms and slugs and fans and weird quilted creatures] . Absolutely ZERO phyla evidence supporting Darwin’s hypothesis has been discovered after millions of fossil discoveries [Imagine Brecheen closing his eyes real tight right now, sticking his fingers in his ears, and going “lalalalala”. What exactly did he learn in that OSU Animal Science program? It sure wasn’t any basic biology]. Darwin’s cornerstone hypothesis where invertebrate’s transition into vertebrates is majorly lacking [No, it isn’t. The molecular evidence is robust. Brecheen just doesn’t understand it, or more likely, never saw it] and so is Darwin’s “theory”.

I will be introducing legislation this session to ensure our school children have all the facts [So, Oklahoma, you elected this idiot to office. Are you going to stand by and watch him poison your educational system with this garbage?].

Another reason to avoid visiting Answers in Genesis

Those porn sites you’ve been browsing? They’ve been slurping in more of your private data than you think. A paper has been published documenting the invasive practices of many websites. They’re doing something called history hijacking, using code that grabs your entire browsing history so they can monitor every site you’ve visited. Cute, huh? There are tools you can use to block this behavior if you’re using Firefox, at least.

Several people have written to me about this because of Table 1 on page 9 of the paper. There among the porn and gaming and commercial sites one stands out as unusual. It’s the only site with the category of “religion”.

It’s Answers in Genesis.

Yep, don’t be surprised. Answers in Genesis wants to know where you’ve been.

Even better, a reader named Ivan extracted the sleazy history hijacking code from the AiG site. Wanna see it? It’s actually rather amusing. I’ve put it below the fold.

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The Politically Incorrect Guide to Darwinism and Intelligent Design: Chapter 3: Simply incorrect embryology

This article is part of a series of critiques of Jonathan Wells’ The Politically Incorrect Guide to Darwinism and Intelligent Design that will be appearing at the Panda’s Thumb over the course of the next week or so. Previously, I’d dissected the summary of chapter 3. This is a longer criticism of the whole of the chapter, which is purportedly a critique of evo-devo.

Jonathan Wells is a titular developmental biologist, so you’d expect he’d at least get something right in his chapter on development and evolution in The Politically Incorrect Guide to Darwinism and Intelligent Design, but no: he instead uses his nominal knowledge of a complex field to muddle up the issues and misuse the data to generate a spurious impression of a science that is unaware of basic issues. He ping-pongs back and forth in a remarkably incoherent fashion, but that incoherence is central to his argument: he wants to leave the reader so baffled about the facts of embryology that they’ll throw up their hands and decide development is all wrong.

Do not be misled. The state of Jonathan Wells’ brain is in no way the state of the modern fields of molecular genetics, developmental biology, and evo-devo.

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Ann Coulter: No evidence for evolution?

I’ve now read all of the science-related (that’s applying the term “related” very generously) stuff in Ann Coulter’s awful, ghastly, ignorant book, Godless, and it’s a bit overwhelming. This far right-wing political pundit with no knowledge of science at all has written a lengthy tract that is wall-to-wall error: To cover it all would require a sentence-by-sentence dissection that would generate another book, ten times longer than Coulter’s, all merely to point out that her book is pure garbage. So I’m stumped. I’m not interested in writing such a lengthy rebuttal, and I’m sure this is exactly what Coulter is counting on—tell enough lazy lies, and no one in the world will have time enough to correct them conscientiously. She’s a shameless fraud.

What to do? Well, we can’t take apart the whole thing, but what we can do is focus on individual claims and show that Coulter is outrageously wrong—that she has written things that indicate an utter lack of knowledge of the subject. Some of us at the Panda’s Thumb are going to be doing just that—look there later for more—and what I’m going to do here is address one very broad claim that Coulter has made repeatedly, and that is also common to many creationists.

That claim is that there is no evidence for evolution. I know, to anybody who has even a passing acquaintance with biology, that sounds like a ridiculous statement, like declaring that people can live on nothing but air and sunlight, or that yeti are transdimensional UFO pilots. Yet Coulter baldly makes the absurd claim that “There’s no physical evidence for [evolution]”, and insists in chapter 8 of her new book that there is “no proof in the scientist’s laboratory or the fossil record.” This is like standing outside in a drenching rainstorm and declaring that there is no evidence that you are getting wet.

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Modules and the promise of the evo-devo research program

Since Evolgen recognizes the importance of evo-devo, I’ll return the favor: bioinformatics is going to be critical to the evo-devo research program, which to date has emphasized the “devo” part with much work on model systems, but is going to put increasing demands on comparative molecular information from genomics and bioinformatics to fulfill the promise of the “evo” part. I’m sitting on a plane flying east, and to pass the time I’ve been reading a very nice review of the concept of modularity in evo-devo by Paula Mabee (also a fish developmental biologist, and also working in a small college in a small town in the midwest…but rather deservedly better known than yours truly). In addition to summarizing the importance of the concept of modularity to evolution and development, the paper also does something I always appreciate: it summarizes the key questions that the modern evo-devo research program is working to answer.

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Here’s how you evaluate the scientific rigor of a field

Warning: it’s boring, tedious, hard work. There’s nothing flashy about it.

First step: define a clear set of tested standards. For clinical trials, there’s something called Consolidated Standards of Reporting Trials (CONSORT) which was established by an international team of statisticians, clinicians, etc., and defines how you should carry out and publish the results of trials. For example, you are supposed to publish pre-specified expected outcomes: “I am testing whether an infusion of mashed spiders will cure all cancers”. When your results are done, you should clearly state how it addresses your hypothesis: “Spider mash failed to have any effect at all on the progression of cancer.” You are also expected to fully report all of your results, including secondary outcomes: “88% of subjects abandoned the trial as soon as they found out what it involved, and 12% vomited up the spider milkshake.” And you don’t get to reframe your hypothesis to put a positive spin on your results: “We have discovered that mashed-up spiders are an excellent purgative.”

It’s all very sensible stuff. If everyone did this, it would reduce the frequency of p-hacking and poor statistical validity of trial results. The catch is that if everyone did this, it would be harder to massage your data to extract a publishable result, because journals tend not to favor papers that say, “This protocol doesn’t work”.

So Ben Goldacre and others dug into this to see how well journals which had publicly accepted the CONSORT standards were enforcing those standards. Read the methods and you’ll see this was a thankless, dreary task in which a team met to go over published papers with a fine-toothed comb, comparing pre-specified expectations with published results, re-analyzing data, going over a checklist for every paper, and composing a summary of violations of the standard. They then sent off correction letters to the journals that published papers that didn’t meet the CONSORT standard, and measured their response.

I have to mention this here because this is the kind of hard, dirty work that needs to be done to maintain rigor in an important field (these are often tests of medicines you may rely on to save your life), and it isn’t the kind of splashy stuff that will get you noticed in Quillette or Slate. It should be noticed, because the results were disappointing.

Results
Sixty-seven trials were assessed in total. Outcome reporting was poor overall and there was wide variation between journals on pre-specified primary outcomes (mean 76% correctly reported, journal range 25–96%), secondary outcomes (mean 55%, range 31–72%), and number of undeclared additional outcomes per trial (mean 5.4, range 2.9–8.3). Fifty-eight trials had discrepancies requiring a correction letter (87%, journal range 67–100%). Twenty-three letters were published (40%) with extensive variation between journals (range 0–100%). Where letters were published, there were delays (median 99 days, range 0–257 days). Twenty-nine studies had a pre-trial protocol publicly available (43%, range 0–86%). Qualitative analysis demonstrated extensive misunderstandings among journal editors about correct outcome reporting and CONSORT. Some journals did not engage positively when provided correspondence that identified misreporting; we identified possible breaches of ethics and publishing guidelines.

Conclusions
All five journals were listed as endorsing CONSORT, but all exhibited extensive breaches of this guidance, and most rejected correction letters documenting shortcomings. Readers are likely to be misled by this discrepancy. We discuss the advantages of prospective methodology research sharing all data openly and pro-actively in real time as feedback on critiqued studies. This is the first empirical study of major academic journals’ willingness to publish a cohort of comparable and objective correction letters on misreported high-impact studies. Suggested improvements include changes to correspondence processes at journals, alternatives for indexed post-publication peer review, changes to CONSORT’s mechanisms for enforcement, and novel strategies for research on methods and reporting.

People. You’ve got a clear set of standards for proper statistical analysis. You’ve got a million dollars from NIH for a trial. You should at least sit down and study the appropriate methodology for analyzing your results and make sure you follow them. This sounds like an important ethical obligation to me.

How hard is it to get your garbage paper published?

Not very. The problem is that while the majority of science journals are legit and at least try to be honest, there are some that simply rubber-stamp submissions…and then charge a fee, of course.

Experts debate how many journals falsely claim to engage in peer review. Cabells, an analytics firm in Texas, has compiled a blacklist of those which it believes are guilty. According to Kathleen Berryman, who is in charge of this list, the firm employs 65 criteria to determine whether a journal should go on it—though she is reluctant to go into details. Cabells’ list now totals around 8,700 journals, up from a bit over 4,000 a year ago. Another list, which grew to around 12,000 journals, was compiled until recently by Jeffrey Beall, a librarian at the University of Colorado. Using Mr Beall’s list, Bo-Christer Björk, an information scientist at the Hanken School of Economics, in Helsinki, estimates that the number of articles published in questionable journals has ballooned from about 53,000 a year in 2010 to more than 400,000 today. He estimates that 6% of academic papers by researchers in America appear in such journals.

If 6% of papers in shoddy journals is 400,000 papers, that implies that almost 7 million papers are published each year. No wonder I can’t keep up. But still, 6% is a fairly low percentage, and as the article says, there are tools to evaluate journals. Cabell’s blacklist seems to require payment to access — and a rather hefty payment at that — so it’s only going to be accessible if you have an institutional subscription. Anyone can browse Beall’s list of predatory journals. All of these lists have pitfalls, some of them discussed in this review of Cabell’s.

Both sides profit from these unscrupulous journals — the publishers get money, and the academics get to pad their CVs, and you’re punished if you point that out.

But one academic has been prepared to stick his neck out and investigate his own institution. Last year Derek Pyne, an economist at Thompson Rivers University’s business school, in British Columbia, published a paper in the Journal of Scholarly Publishing, itself published by the University of Toronto Press. In it, he reported that many of the business school’s administrators, and most of its economics and business faculty with research responsibilities, had published in journals on Mr Beall’s blacklist. Dr Pyne also claimed that these papers seemed to further their authors’ careers. Of the professors who had published in the blacklisted journals, 56% had subsequently won at least one research award from the school. All ten instructors promoted to full professor during the study period had published in a journal on Mr Beall’s list.

By the way, Beall of Beall’s blacklist faced all kinds of pressure to stop, and the list is now maintained by someone who demands anonymity; Pyne also got in trouble.

Subsequently, Dr Pyne told school officials that an administrator up for promotion had published widely in blacklisted journals. This earned Dr Pyne an e-mail from the university’s human-resources department on June 15th, threatening him with disciplinary action for “defamatory language and accusations”. When asked, the university declined to comment.

So, apparently, if you’ve got a goofy pile of crap you want published as peer-reviewed science, there’s somebody somewhere who will oblige you. That makes an ‘experiment’ in which someone wants to discredit an entire academic field by getting garbage papers published somewhere rather pointless and inconclusive, don’t you think? You have to wonder what kind of twit would consider such an exercise meaningful.