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Fortune magazine CLAIMS that Barack Obama is the first president to publish a scientific article. Obama_2016.png They are referring to:
Obama, Barack (2016). "United States Health Care Reform: Progress to Date and Next Steps." The Journal of the American Medical Association. Published online July 11, 2016.
See also JAMA's Twitter feed:

(edited to add a point on Aegirocassis and Parapeytoia)

This week, the Discovery Institute Press put out another book called Debating Darwin’s Doubt. I took one for the team and bought it, in part because a a decent chunk of the book is responding to me. I’m pretty sure I’ve never been mentioned so much in a book!

Sadly, though, looking through it, almost all of it is material re-hashed from the DI “Evolution News and Views” blog and is no better than it was the first time. There is, however, a new chapter (I think it is new) by Casey Luskin, chapter 9, “Cladistics to the Rescue?” responding to me. If you don’t want to buy the book, there is a free podcast at ID the Future (heh), “Debating Darwin’s Doubt: Casey Luskin on Classification of Organisms” that interviews Luskin (although I think he wrote the questions). It has mostly the same material.

Unfortunately, I do not have time at the moment to write the introductory-level-tutorial-from-square-one that would be required to really explain the basics of cladistics and phylogenetics to Luskin et al. I have literally just moved to Australia to start as a Discovery Early Career Researcher Award (DECRA) Fellow in the Division of Ecology, Evolution, and Genetics, Research School of Biology, at The Australian National University in Canberra. Once I have a bed and a computer in my office I may be in better shape to do things more thoroughly – I have a bit of a fantasy about writing an R vignette or R package called something like BasicPhylogeneticsForCreationistsEspeciallyLuskin (I’ll take suggestions on a better name/acronym).

However, below, I can briefly hit the high points on the small bit of Luskin’s chapter that was new.


A new paper was recently published, and widely reported in the media, about a hominid skull discovered at the Dmanisi site in Georgia in 2005 (Lordkipanidze et al, 2013, Gibbons 2013). The fossil, D4500, is believed to belong to the same individual as a lower jaw fossil, D2600, previously found at the site. The combined skull, designated by the authors as “Skull 5” (the 5th skull from Dmanisi) is almost completely and perfectly preserved, making it one of the most spectacular finds in the entire hominid fossil record. And Dmanisi is rapidly becoming one of the most important sites ever found in the study of human evolution.

Skull 5’s brain volume of 546 cm3 is very small. The other Dmanisi skulls are between 600 cm3 and 730 cm3. (Earlier papers gave the size of the largest one as 780 cm3, but that estimate appears to have been reduced. By comparison, the average modern human brain size is 1350 cm3.) However the fossil also has a large and robust jaw bone, and a large and projecting face. This combination of a very small brain and a large face differs from all other known Homo fossils. The fossil is of a mature adult, and because of the robustness of the skull it is thought to belong to a male.

Scientists are naturally delighted at the discovery of such a superb fossil, but the real impact of Skull 5 comes from the conclusions that the authors have drawn from it.

The Dmanisi fossils are different enough from each other that had they been found at different locations, they might have been classified into different species. Similar differences have been used to create species such as Homo habilis and Homo rudolfensis in the past. The authors believe that the Dmanisi fossils all belong to one species, both because they all come from the same time and place, and because the pattern and amount of variability found between the skulls is similar to that found in populations of modern humans, chimpanzees, and bonobos.

Following that line of reasoning, they conclude that since a similar pattern of variation exists for all early Homo fossils in Africa, and in the absence of any evidence that the supposed different species of Homo were adapted to different ecological niches, the default and most parsimonious assumption should be that all of these fossils belong to a single highly variable lineage (though they recognize that this claim remains to be tested, and alternative scenarios exist). This would mean that Homo habilis, Homo rudolfensis, Homo ergaster and some other more obscure names did not really exist as separate species. The name of that single species would, for reasons of priority, be Homo erectus. Specimens allocated to H. ergaster would then be called Homo erectus ergaster, as a time-limited subspecies. The Dmanisi scientists had previously named a new species, Homo georgicus, for the Dmanisi fossils, but now retract that name and suggest that because the Dmanisi fossils arose from an ergaster population, they should be called Homo erectus ergaster georgicus.

So, Stephen Meyer is allegedly going to “respond” to critics of Darwin’s Doubt this afternoon on the Medved show (Medved is a DI fellow, this particular show is being broadcast from inside the Discovery Institute). They are even inviting critics to call in – it’s your very own chance to rebut Meyer’s dozens of overlapping errors and admissions with a single question or statement, and with the Discovery Institute controlling the microphone! What a deal!

Over here in real science, we mostly try to address complex scientific topics through writing and analysis. And the critics have done quite a bit of that, although you’d never know it from reading the Discovery Institute blog, where David “spin til it hurts” Klinghoffer has pushed the rhetoric-to-truth ratio to heights not seen since the Kitzmiller days.

Klinghoffer’s constant refrain is that the critics aren’t addressing Meyer’s arguments. Well, let’s make a little list, shall we? It will be convenient as a checklist for anyone who listens to the Medved show today.

Luskin’s Hopeless Monster


I’m checking in from the airport on the way back from Evolution 2013. For me, highlights of the meeting included presenting my BioGeoBEARS R package and some Ph.D. results at the Ernst Mayr Symposium, hearing about all the cool things going at NIMBioS, anticipating and thus having a seat in the room while observing the Felsenstein Effect, and meeting Jerry Coyne in person for the first time, and having a friendly conversation rather than an argument. (What will our respective readers think of us? We have reputations to uphold!)

Note: I am extremely busy this summer, finishing grad school and moving to a postdoc. But when I got this book, I realized I wouldn’t be able to focus on my real work without having gotten my 2 cents in. This is a rough-and-ready piece, so typos and missing references, and missing explanations of technical terms are to be expected, although I’m sure they can all be figured out with a wee bit of googling. I am off to Evolution 2013 tomorrow and will be incognito, writing, after that. So I may not comment much. However I expect commenters to be reasonable discussants and polite and will ban people who break the spirit of this expectation. Cheers, Nick

Review of Stephen C. Meyer’s Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design

This week, a new book came out by Stephen Meyer, Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design. Having followed the ID movement and specifically its arguments on the Cambrian ‘Explosion’ for a long time, as well being somewhat up on the recent literature, and especially on phylogenetics, I feel that I have a pretty good sense of what to look for in any work purporting to be a capable commentary on the topic. As I read through Meyer’s book, though, in case after case I see misunderstandings, superficial treatment of key issues which are devastating to his thesis once understood, and complete or near-complete omission of information that any non-expert reader would need to have to make an accurate assessment of Meyer’s arguments.

The coelacanth genome has been sequenced, which is good news all around…except that I found a few of the comments in the article announcing it disconcerting. They keep calling it a "living fossil" — and you know what I think of that term — and they keep referring to it as evolving slowly

The slowly evolving coelacanth

The morphological resemblance of the modern coelacanth to its fossil ancestors has resulted in it being nicknamed 'the living fossil'. This invites the question of whether the genome of the coelacanth is as slowly evolving as its outward appearance suggests. Earlier work showed that a few gene families, such as Hox and protocadherins, have comparatively slower protein-coding evolution in coelacanth than in other vertebrate lineages.

Honestly, that's just weird. How can you say its outward appearance suggests it is slowly evolving? The two modern species are remnants of a diverse group — it looks different than forms found in the fossil record.

Some Neil Shubin video


Neil Shubin has been out and about speaking on behalf of his recent book, The Universe Within, in a variety of venues. He summarizes his theme in this video. And as dessert, there’s this short one on Tiktaalik from the Royal Institution channel.

The gaps keep getting smaller and smaller


As we all know, Tiktaalik roseae is a magnificent example of a transitional fossil connecting aquatic critters–fish–with tetrapods, 4-limbed critters. Nevertheless, there are still gaps in that transitional sequence. A recent PNAS paper (link to abstract; full paper is behind a paywall) describes fossils of early amphibians that are later than Tiktaalik and are within Romer’s Gap. Romer’s Gap is a period around 15 million years long, from roughly 360mya to 345mya, where (up to now) there was a distinct lack of fossils of proto-tetrapods or related critters. The new PNAS paper’s senior author is Jenny Clack, one of the most prominent paleontologists studying that era, (along with people like Neal Shubin and Per Ahlberg. Per was an active commenter on the late lamented Internet Infidels Discussion Board way back when I was an administrator of IIDB.

With these new fossils, the transition from water to land animals is becoming nearly as well documented as the synapsid to mammal transition. Nobel Intent has more on the new paper.

Magnificent momma


This is one beautiful plesiosaur, Polycotylus latippinus.

(Click for larger image)

(A) Photograph and (B) interpretive drawing of LACM 129639, as mounted. Adult elements are light brown, embryonic material is dark brown, and reconstructed bones are white. lc indicates left coracoid; lf, left femur; lh, left humerus; li, left ischium; lp, left pubis; rc, right coracoid; rf, right femur; rh, right humerus; ri, right ischium; and rp, right pubis.

Xiaotingia zhengi


A lovely new dinosaur fossil from China is described in Nature today: it's named Xiaotingia zhengi, and it was a small chicken-sized, feathered, Archaeopteryx-like beast that lived about 155 million years ago. It shares some features with Archaeopteryx, and also with some other feathered dinosaurs.

That's not hyperbole. I really mean it. How else could I react when I open up the latest issue of Bioessays, and see this: Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules. Just from the title alone, I'm immediately launched into my happy place: sitting on a rocky beach on the Pacific Northwest coast, enjoying the sea breeze while the my wife serves me a big platter of bacon, and the cannula in my hypothalamus slowly drips a potent cocktail of cocain and ecstasy direct into my pleasure centers…and there's pie for dessert. It's like the authors know me and sat down to concoct a title where every word would push my buttons.

The content is pretty good, too. It's not perfect; the development part is a little thin, consisting mainly of basic comparative embryology of body plans, with nothing at all really about deployment of and interactions between significant developmental genes. But that's OK. It's in the nature of the Greatest Science Papers Ever Written that stuff will have to be revised and some will be shown wrong next month, and next year there will be more Greatest Science Papers Ever Written — it's part of the dynamic. But I'll let it be known, now that apparently the scientific community is aware of my obsessions and is pandering to them, that the next instantiation needs more developmental epistasis and some in situs.

This paper, though, is a nice summary of the emerging picture of cephalopod evolution, as determined by the disciplines of paleontology, comparative embryology, and molecular phylogenetics, and that summary is internally consistent and is generating a good rough outline of the story. And here is that story, as determined by a combination of fossils, molecular evidence, and comparative anatomy and embryology.

Turnabout is fair play


Phil Senter has published the most deviously underhanded, sneaky, subtle undermining of the creationist position I've ever seen, and I applaud him for it. What he did was to take them seriously, something I could never do, and treat their various publications that ape the form of the scientific literature as if they actually were real science papers, and apply their methods consistently to an analysis of taxonomy. So on the one hand, it's bizarre and disturbing to see the like of Ken Ham, Jerry Bergman, and Henry Morris get actual scientific citations, but on the other hand, seeing their claims refuted using their own touted methods is peculiarly satisfying.

Senter has published a paper in the Journal of Evolutionary Biology that takes their claims at face value and analyzes dinosaur morphology using their own methods. 'Baraminologists' have published a set of taxonomic tools that use as input a matrix of morphological characters for an array of animals, and then spits out numbers that tell whether they were similar enough to be related. You can guess what the motivation for that is: they want to claim that Noah didn't have to carry representatives of every dinosaur species on the Ark, but only representatives of each 'kind', which then diversified rapidly after the big boat landed to generate all the different species found in the fossil record.

The problem for them is that Senter found that it works far too well. Using creationist techniques, all of the Dinosauria reduce to…eight kinds. That makes the boat haulage problem relatively even easier.

We get mail


Recently the PT crew received an email with the subject line “A legitimate question about Evolution with no agenda.” As you might expect, the dual disclaimers–“no agenda” and “legitimate”–immediately raised a few eyebrows. “No agenda”? Hmmmmm. Well, I suppose it’s possible, though numerous previous encounters with creationists’ faux naivete have left me a dab cynical.

The email reads

Subject: A legitimate question about Evolution with no agenda
Date: Sun, 5 Jun 2011 16:48:13 -0700
From: [redacted]
To: [Enable javascript to see this email address.]

Dear Panda’s Thumb crew:

I’m not a scientist, I’m a retired history teacher with a masters in that field.

I’m not writing because I have any agendas. I’m trying to get my questions answered and I’m having trouble doing it since I don’t know any evolutionary biologists whom I could ask. Those I have written to do not reply. I’m asking for the perspective of an evolutionary biologist who might answer a student with questions who is not hostile to evolutionary biology.

If you don’t have the time to reply, or don’t want to, please write me and tell me that.

Here are my questions about macroevolution. My goal is to understand how scientists explain how macro-evolution works in a real life situation, in this case between reptiles evolving into birds, since this is postulated as occurring:

*Reptiles                 Birds*
Lay eggs                lay eggs
    fly                    fly

have feathers?      have feathers
cold blooded?       warm blooded

Would being cold blooded show up in the fossil record? If not, how and why would a reptile adapt over millions of years into warm-blooded? How would anyone know whether a feathered reptile was now a bird if one is/may be cold blooded and one is warm blooded? Where is the proof?

Same topic different question: We know that horses and donkeys can interbreed to produce a mule, which is sterile. Using this explanation for cross breeding, how does that fit with macroevolution? In other words, could a flying, feathered semi-reptile mate with a full bird (or any other combination), and not be sterile? Even over millions of years, since there would be no progeny and the variant would die.

Third question: If a reptile/bird evolved, wouldn’t it also need a reptile/bird to mate with to carry on the new species? If one, a male, for instance evolved, and no female evolved at the same time and in the same place, wouldn’t that end the cycle of macroevolution?

Thank you for your time.


You see the difficulties, and it seems clear why the evolutionary biologists to whom he claims to have written haven’t bothered to reply. I see three main reasons.



Well this is pretty cool. And apparently they interbred with modern humans, also. I can’t wait to see what Reasons to Believe has to say…

Several years ago, I saw a fantastic talk at the Evolution meeting about Intraspecific macroevolution: variation of cranial shape in dog breeds. The talk was by Abby Drake, then a grad student, and reported on a huge digital morphometric comparison of the skulls of dogs and many representatives from the order Carnivora (dogs, cats, bears, sea lions, etc.).

Morphometrics basically consists of taking digital photos of e.g. bones from different angles, and then marking the same landmarks on homologous bones across a big group. Then you can quantitatively compare the differences in shape, independent of things like body size. This is a much more sophisticated analysis than is possible with just calipers, where you can only get length, width, etc.

Early indications of bipedalism in A. afarensis


While we’re waiting to see if one of our paleo people will post at greater length on this, I will call attention to Case Western Reserve University’s Center for Human Origins’ material on the recent publication of a report on a very early specimen of Australopithecus afarensis. It shows evidence of bipedalism as early as 3.6 mya. The specimen is dubbed “Kadanuumuu,” or “big man” in Afar, the language of the region of Ethiopia in which it was found, because it is from a male over 5 feet tall. That contrasts with Lucy, a female only about 3.5 feet tall from 3.2 mya. The skeletal remains overlap Lucy’s considerably with the exception of cranial and dental material which is missing from Kadanuumuu. The work was recently published in PNAS.

Other coverage from the National Science Foundation and from the Cleveland Museum of Natural History (one of the founding partners in Case’s Center for Human Origins).

Mother of all squid!

Blogging on Peer-Reviewed Research

Well, more like great-great-many-times-great-aunt of all squid, but it's still a spectacular fossil. Behold the Cambrian mollusc, Nectocaris pteryx.

(Click for larger image)

Reconstruction of Nectocaris pteryx.

For many years, Discovery Institute spokesperson Casey Luskin has been telling the world that the genus Homo is preceded by no transitional forms, because the species typically thought to be transitional between australopithecines and Homo, Homo habilis, is actually an Australopithechus itself. Poof, there goes the transition. As I pointed out long ago, this argument about what names to apply to fossils under Linnaean taxonomy is basically pointless – the fossils stay transitional in time and in morphology no matter what names you give them – but creationists like Luskin don’t care about that (and don’t give me that silliness about ID advocates not being creationists, Luskin is arguing for the special creation of humans, for goodness’ sake!).* Instead, they love to misrepresent the terminological dispute to obscure the actual big picture of the data.

Unfortunately for Luskin, though, other creationists play the same game, and, don’t you know it, it turns out that the transitional specimens come out as transitional in their latest analysis. Bryan College creationist Todd Wood is announcing his “baraminological”** analysis of Homo habilis, Australopithecus sediba, and other fossils. He took a bunch of cladistic datasets from the paleoanthropology literature (all based on crandiodental characters) and put them through his “baraminological distance” algorithm to see where there are clusters and gaps. He concludes that the recently-discovered Australopithecus sediba should actually be Homo sediba, but this is just this is what several paleoanthropologists said after it was published. More significantly for our interests, instead of saying that habilis is just another ape far removed from Homo, Wood concludes that habilis clearly groups with the rest of Homo, and that big, unfillable, magical God-obviously-acted-here gap, which all creationists mindlessly, dogmatically believe in come hell or high water, is actually between habilis and the australopiths. Whoops!


Two spectacular new hominid fossils found in a cave at Malapa in South Africa in 2008 and 2009 have been assigned to a new species, Australopithecus sediba (‘sediba’ means ‘wellspring’ in the local seSotho language). Discovered by a team led by Lee Berger and Paul Dirks, it is claimed by them to be the best candidate yet for an immediate ancestor to the genus Homo. The fossils are between 1.78 and 1.95 million years old, about the same date of the oldest Homo erectus fossils.

The first fossil, MH1, found by Lee Berger’s son Matthew, is an almost complete skull and partial skeleton of an 11 to 12 year old boy. The 2nd fossil, MH2, is a partial skeleton of an adult female, including some jaw fragments. The boy’s brain has a typical australopithecine size of 420cc, compared to the smallest Homo brain of 510cc. Both skeletons are small, about 130cm (4’3”) tall.

Au. sediba is most similar to, and quite likely descended from, Au. africanus. The upper limbs are long, and similar to other australopithecines. Many features of the hip, knee and ankle bones show it was bipedal, like other australopithecines, but the foot bones are still quite primitive. However Berger et al. list many other features of the skull, teeth, and pelvis in which it resembles early Homo fossils.

The discoverers have suggested that Au. sediba might be ancestral to either Homo habilis or Homo rudolfensis, or that it might be a closely related sister group to Homo - not a direct ancestor, but a close cousin. As the authors admit, these two individuals existed after the earliest known Homo fossils (at about 2.3 million years), so they can’t be human ancestors. However, it’s possible that the sediba species had already existed for a few hundred thousand years and that early members of it could have been human ancestors.

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