So much wrong

Say what you want about the Discovery Institute; they are prolific! Evolution News & Views alone publishes several articles a day. I’m lucky if I can crank out three a week, and I try to limit the proportion that are about cdesign proponentsists being wrong. It’s a continual temptation, because those posts are easier to write than, say, digging into a peer-reviewed article. PZ promises me that blogging on FtB will eventually earn me enough to buy a cup of coffee, but I have a job. All of this means that I have to let a lot of big, juicy targets sail by. So, quickly:

DentonLeaves

Thank you, Michael Denton; no evolutionary biologist ever considered the possibility that not everything is adaptive. To answer your question, some aspects of leaf shape are adaptive, some are not. Next.

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Intelligent design’s double standard

Double Tourbillon 30° mechanism by Greubel Forsey. Creative Commons image from Wikimedia.

Double Tourbillon 30° mechanism by Greubel Forsey. Creative Commons image from Wikimedia.

Despite protests to the contrary, intelligent design is a god of the gaps argument. Take a look at Discovery Institute blogs, and a large portion of the posts are essentially arguing that some aspect of biology or biochemistry is really, really complicated (for example, Howard Glicksman’s posts at Evolution News & Views). As if there are bunches of evolutionary biologists running around saying life is simple. So most intelligent design arguments boil down to “there’s no plausible evolutionary explanation for this aspect of biology, therefore it must have been designed.” And cdesign proponentsists insist on a high standard of evidence to consider an evolutionary explanation plausible. For example, here’s Michael Behe’s standard for believing that “…complex biochemical systems could arise by a random mutation and natural selection…”:

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Intelligent design’s relationship with common descent? It’s complicated.

Noah's Ark by Edward Hicks, 1845. Public domain image from Wikimedia Commons.

Noah’s Ark by Edward Hicks, 1845. Public domain image from Wikimedia Commons.

Cdesign proponentsists frequently claim that intelligent design is not creationism. For example, David Klinghoffer says:

…intelligent design is not the same thing as creationism.

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Bacterial flagellum? Never heard of it.

When I wrote about Michael Behe’s shock that any sane person would associate the bacterial flagellum with intelligent design (Michael Behe’s “Secret Obsessions“), I failed to notice something that was staring me right in the face. The masthead for intelligent design blog Uncommon Descent:

UncommonDescentMasthead

Remember, if you meet someone who thinks intelligent design advocates

…think they [bacterial flagella] are examples of “intelligent design”

or that bacterial flagella have

…been at the center of the thinly veiled creationism movement called intelligent design,

you should

back away slowly, smiling, wishing him a nice day…

Michael Behe’s “secret obsessions”

In his latest post at Evolution News and Views, Michael Behe calls the authors of posts at New Scientist and Genetic Engineering & Biotechnology News ‘crazy’ and ‘clueless’ for associating arguments about the bacterial flagellum with intelligent design (“New Paper on Flagellum Reveals Secret Obsessions“):

Suppose in the course of a pleasant conversation with a colleague you mentioned your vacation last year in Las Vegas. All of a sudden he starts ranting about Area 51 — Vegas is only a few hours away, right? Did you see any lights in the sky? Any military vehicles heading north? You should stay at the Little A’Le’Inn motel like he has six times. You’ll see some funny stuff there.

You’d probably back away slowly, smiling, wishing him a nice day…

[much later] …One crazy person is a coincidence. Two are a trend…What’s more, if you go by what they write, these folks are utterly clueless about what modern ID proponents actually argue. [my emphasis]

The evidence that these authors are crazy and clueless? The New Scientist‘s assertion that the bacterial flagellum is

Loved by creationists, who falsely think they are examples of “intelligent design”

and that of Genetic Engineering & Biotechnology News that

[T]he bacterial flagellum has been at the center of the thinly veiled creationism movement called intelligent design. Subscribers to this belief system have erroneously postulated that the flagellar motor system is “irreducibly complex” and could not have come about through Darwinian evolutionary mechanisms….It is doubtful these findings will sway the opinion of its detractors, yet they do make it extremely more difficult for them to make their case.

Seriously, that is the sum total of the evidence that these authors are ‘crazy’ and ‘clueless’ on the order of UFO true believers. A bit hyperbolic, I think. But where did these clueless authors get their crazy idea to associate the bacterial flagellum with intelligent design?

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The flip side of the Galileo Gambit: Denyse O’Leary on multicellularity

Figure 7 from Anderson et al. 2016. Evolution of GKPID’s new function by unveiling a latent protein-binding site. (A) The binding surface for Pins in GKPIDs is derived from the GMP-binding surface of gk enzymes. Homology models of Anc-gkdup (left) and Anc-GK1PID (right) are shown as white surface, with all side chains that contact either GMP or Pins as yellow sticks. Pink sticks show GMP; green ribbon shows Pins backbone, with the side chains of all Pins residues that contact the GK protein shown as sticks. The phosphate group on GMP and on Pins residue 436 are shown as orange and red sticks. Black dotted lines, protein-ligand hydrogen bonds. In the AncGK1PID structure , substitutions at sites in the binding interface are shaded red, including key substitution s36P. The binding modes of extant gk enzymes and GKPIDs are similar and support the same conclusions (see Figure 7—figure supplement 1). (B) The structure of the hinge and GMP/Pins-binding lobes is conserved between the Pins-bound GKPID (blue, rat Dlg, 3UAT), the apo-gk enzyme (brown, S. cerevisiae guanylate kinase 1EX6), and the apo-gk-s36P mutant (gray, 4F4J), all in the open conformation.

Figure 7 from Anderson et al. 2016. Evolution of GKPID’s new function by unveiling a latent protein-binding site. (A) The binding surface for Pins in GKPIDs is derived from the GMP-binding surface of gk enzymes. Homology models of Anc-gkdup (left) and Anc-GK1PID (right) are shown as white surface, with all side chains that contact either GMP or Pins as yellow sticks. In the AncGK1PID structure , substitutions at sites in the binding interface are shaded red, including key substitution s36P. (B) The structure of the hinge and GMP/Pins-binding lobes is conserved between the Pins-bound GKPID (blue, rat Dlg, 3UAT), the apo-gk enzyme (brown, S. cerevisiae guanylate kinase 1EX6), and the apo-gk-s36P mutant (gray, 4F4J), all in the open conformation.

Cdesign proponentsists really don’t seem to like research on the evolution of multicellularity. Pretty much any time real scientists learn something new about the origins of multicellularity, writers on intelligent design blogs Evolution News & Views and Uncommon Descent feel compelled to tell us why it’s wrong (for example, here, here, here, here, here, here, here, here, here, here, here, here, and here).

So I shouldn’t be surprised that Denyse O’Leary has weighed in on the latest work out of Ken Prehoda’s lab, in which Prehoda and colleagues identified a mutation crucial for forming and maintaining tissues in animals. Worse, from O’Leary’s point of view, the article describes the evolution of a new protein function, which is anathema to intelligent design thinkers. To say this post is badly argued is overly generous; it’s absolutely devoid of any substantive argument.

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The Discovery Institute still doesn’t understand free speech

The Discovery Institute has a persecution complex. They have a hard time distinguishing between rejection and mockery of their silly ideas and violation of their right to free speech. They’ve created a ‘Censor of the Year’ award to protest their treatment. The previous winners are noted free speech opponents Jerry Coyne and Neil deGrasse Tyson.

For the past month, they Institute has been in an absolute tizzy over the decision of the United Methodist Church’s decision to exclude (‘ban‘) them from its General Conference coming up in May. Because they don’t understand that free speech doesn’t obligate others to provide a platform, they think this decision amounts to ‘intolerance‘ and ‘censorship‘.

Censorship

Persecution complex? Image from an Evolution News & Views post on UMC.

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Doctor knows best, at least when he agrees with me

The Designed Body

Image from evolutionnews.org.

 

Wesley J. Smith’s latest post on Evolution News and Views complains of “The Arrogance of ‘Doctor Knows Best’” when it comes to end-of-life care. I find complaints about the arrogance of doctors ironic in light of the fact that each of Howard Glicksman’s posts on the same website begin with the following editor’s note:

Physicians have a special place among the thinkers who have elaborated the argument for intelligent design. Perhaps that’s because, more than evolutionary biologists, they are familiar with the challenges of maintaining a functioning complex system, the human body.

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Evolution is evidence against evolution (?)

Intelligent Design blog Uncommon Descent thinks Betül Kacar’s microbial evolution experiments somehow support their agenda (“E coli hybrid copes with 700 mya engineered gene“). The post quotes extensively from a recent article in Quanta Magazine, which in turn reports on Dr. Kacar’s presentation at AbSciCon (which I briefly covered here).

I’m really not sure what the logic is here. The blog post quotes extensively from the Quanta article (really the post just is quotes from the article, with two short comments added), including sections that make clear that Dr. Kacar observed evolution in action in these experiments:

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Ann Gauger teaches us about Volvox, part 2

Last time, I criticized Ann Gauger’s Evolution News and Views article “A Simple Transition to Multicellularity — Not!” for asserting that the requirement for kinesins in Volvox inversion implied a requirement for novel genes in the evolution of multicellularity. In a similar vein, Dr. Gauger presents programmed cell death and sex as problems for this transition:
The somatic cells commit suicide by a process known as apoptosis — programmed cell death — that I wrote about here. This process involves a minimum of several novel genes as well.
Where does this assertion that programmed cell death in Volvox “involves a minimum of several novel genes” come from? Programmed cell death (PCD) occurs in many unicellular eukaryotes, including Chlamydomonas reinhardtii. Furthermore, two types of metacaspases, genes involved in PCD in many algae and plants, are found in both Chlamydomonas and Volvox.
Metacaspases

Partial alignment of representative type I and type II metacaspase predicted sequences from red algae (Porphyra yezoensis; Py), green algae (Chlamydomonas reinhardtii, Cr; Volvox carteri, Vc), vascular plants (Arabidopsis thaliana; At), excavates (Trypanosoma cruzi, Tc; Leishmania braziliensis, Lb), diatoms (Thalassiosira pseudonana, Tp; Phaeodactylum tricornutum, Pt), haptophytes (Emiliania huxleyi; Eh), pelagophytes (Auroecoccus anaphagefferens; Aa), yeasts (Schizosaccharomyces pombe, Sp; Saccharomyces cerevisiae, Sc) showing the conservation of the cysteine-histidine dyad and the insertion characteristic of plant type II metacaspases. From Nedelcu, A.M. 2009. Comparative genomics of phylogenetically diverse unicellular eukaryotes provide new insights into the genetic basis for the evolution of the programmed cell death machinery. J. Mol. Evol., 68: 256–268. doi 10.1007/s00239-009-9201-1.

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