Science and Religion: A View from an Evolutionary Creationist

National Geographic (and other outlets) is reporting on a new skull discovered in northern Kenya, near Lake Turkana that is 13 million years old and may reflect the morphology of a sister group to the stem group of hominoids, the group that contains modern apes and humans.  Michael Greshko writes:

“We’ve been looking for ape fossils for years—this is the first time we’re getting a skull that’s complete,” says Isaiah Nengo, the De Anza College anthropologist who led the discovery, supported by a National Geographic Society grant and the Stony Brook University-affiliated Turkana Basin Institute.

Roughly the size of a lemon, the skull belongs to a newly identified species of early ape named Nyanzapithecus alesi. Some of its features resemble those of today’s living Old World monkeys and apes, and the face bears a striking resemblance to today’s infant gibbons.

What’s more, N. alesi offers insight into early apes’ brains, the team reports in their study, published today in Nature. With a volume of about seven tablespoons, N. alesi’s brain cavity was more than double that of other Old World monkeys from the time.

The Miocene is generally thought of as the “Age of the Apes” because there were so many genera (30) and species (over 40) of apes pretty much all over the Old World. As the authors note, however, up to this point, most of the remains have been just jaws and teeth.  This skull is an incredible find and will add immensely to our understanding of this time period. 

This time, it is Rush Limbaugh, who, in one of his daily shows, questioned the wisdom of evolution.  Writing about the unfortunate incident in which the gorilla, Harambe, was shot to protect a human child, Rush stated:

A lot of people think that all of us used to be gorillas, and they're looking for the missing link out there. The evolution crowd. They think we were originally apes. I've always had a question: If we were the original apes, then how come Harambe is still an ape, and how come he didn't become one of us? "Well, that's why they're all missing link, Mr. Limbaugh. Your question is absurd." Here's one more from Ashley Byrne from PETA. "You know, the gorilla's endangered, he was 17 years old. They've had him for quite a long time."

Rush, if my children came from my wife, why is my wife still alive? This notion that evolution is strictly linear has been known to be wrong since the time of Charles Darwin, yet it is perpetuated by people who don't like evolution but won't learn anything about it.  This is why we have systematics.  As a refresher to Rush, here is a diagram that I concocted during one of my back and forths with someone about my BioLogos post on hominins of the Middle Pliocene:



In this example, there is no straight lineal relationship between any two forms.  In fact, the one salient feature of systematics is that it can only delineate taxonomic sister groups, it cannot delineate ancestor-descendant relationships.  There is no such thing as the "missing link."  Viewed within this prism,  it becomes apparent that transitional forms abound in the fossil record.  Think of the form Gerobatrachus hottoni, otherwise known as the “frogamander.”  It has the basal characteristics of both frogs and salamanders and represents the stem group to both of those forms.  Everything that follows in each node, leading to salamanders and frogs, is transitional.

This is how modern evolutionary theory is practiced.   It would sure be nice if some news people would learn this.

PZ Myers, over at Pharyngula, has some harsh words for Casey Luskin's examination of Homo naledi.  In the post, he points out something that I have pointed out in several posts for BioLogos and in my rebuttal to Luskin's post on Homo naledi: a complete lack of understanding of systematics:

I’m not going to dissect every point in Luskin’s tediously long article in detail — really, he’s just echoing every question anyone has asked about H. naledi in the last few weeks, in an attempt to construct a litany of doubt — but I have to point out the numerous ways he misrepresents evolutionary biology to pretend that H. naledi is somehow a refutation of Darwin. As I’ve pointed out many times before, Luskin is a scientific illiterate who doesn’t actually understand anything remotely biological, from genetics to embryology to molecular biology to, now, paleontology. Actually, this isn’t the first time Luskin has tripped over himself in a rush to deny — he also didn’t like Tiktaalik. So this is just more of the same.

Luskin has a bad case of missinglinkitis. This is the idea that there is a linear series of steps in a progression leading from ape to human, and all we have to do is find each frame in the movie and we can replay everything in science class. He wants a “link”, a word he uses multiple times, and he wants “transitional fossils”, unaware that every individual is a transition between parent and progeny.

The key is to focus on the traits, something that Luskin and other Intelligent Design supporters fail to do. Myers further points out, as I did, that just about every fossil that we find is a mosaic of traits and when we follow the trait patterns, we can develop phylogenies.  This line of thinking has led to remarkable understanding of the evolution of Devonian tetrapods and the transition from theropod maniraptoran dinosaurs into birds. 

He also makes light of a point that Luskin makes about the venue that Berger and colleagues took when they wanted to publish the paper:

I have to mention two other lesser points from the paper. Luskin really knows nothing.

The technical paper, “Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa,” appeared in a lesser-known journal, eLife. It’s a great find due to the sheer number of bones that were found, but to my mind its publication in eLife is an immediate hint that this fossil isn’t an earthshattering “transitional form,” because if it were, we almost unquestionably would have seen the fossil published in Science or Nature.

No. Wrong. A lot of scientists resent the tyranny of the magical CV-enhancing powers of those two journals, and think they have an inflated and dangerously dominant reputation. eLife is an entirely credible new journal which, to all appearances, has a robust reputation for good, solid peer-review…and is also open source. There are a lot of scientists who are eager to see scientific information disseminated more widely without the limiting restrictions of traditional journal publishing, and Lee Berger, the lead investigator in this work, doesn’t need the résumé reinforcement that publishing in Nature or Science provides.

This is only half-correct. While it is quite true that many scientists like to publish in open-source publications like eLife and PLoS, this is not always the perspective of the managers and department heads, many of whom would much prefer that their researchers publish in high-profile journals, like Science and Nature.  I know this to be true through my work not just in publishing but in dealing with funders.  They like flashy papers.  This often (but not always) conflicts with the desires of the researchers, themselves.  Even though there are plenty of researchers who would like just to publish and get the information out there as fast as possible, I know of quite a few researchers who don't mind padding their resumes a bit with high-profile papers because they are angling for a position higher up on the academic food chain.  We would love to think otherwise, but it just isn't always true. 

A story from the Calgary Herald sheds light on a fossil discovery that was made 85 years ago and how the conclusions about the find were recently corrected. Yohnathan Sumamo of the Edmonton Journal writes:

The species of the skeleton had been classified twice: first by Canadian paleontologist William Parks in 1924 as Dyoplosaurus, or "doublearmoured dinosaur," and later by researcher Walter Coombs, who reclassified it in the early 1970s as Euoplocephalus. The students discovered that Parks was right all along in his original identification of the species.

"We are always revising old ideas, especially in paleontology," said Arbour. "It's not that people are making mistakes, but that old ideas are just not supported any more."

The fundamentals of science essentially revolves around constantly questioning studies and taking a closer look at them, which is exactly what these students did.

As phylogenetic systematics becomes more commonplace as a way of understanding taxonomic relationships, this sort of thing may become more frequent.

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Science Daily has a report on a new technological innovation that will, according to the story, revolutionize the process of systematics. The story has this to say:

Computer scientist Tandy Warnow, biologist Randy Linder and their graduate students have created an automated computing method, called SATé, that can analyze these molecular data from thousands of organisms, simultaneously figuring out how the sequences should be organized and computing their evolutionary relatedness in as little as 24 hours.

Previous simultaneous methods like Warnow and Linder's have been limited to analyzing 20 species or fewer and have taken months to complete.

"SATé could completely change the practice of making evolutionary trees and revolutionize our understanding of evolution," says Warnow, professor of computer science and lead author of the study.

Of course, as we have learned from previous experience, such a program likely relies on input objectivity. In 1985, Cann, Stoneking and Wilson produced the groundbreaking study based on mitochondrial DNA tree analysis that showed that modern humans had originated as a speciation event in sub-Saharan Africa between 140 k and 280 k years ago. While subsequent research into other areas of the genome has tended to support (at least nominally) that finding, it was later found by David Maddison and Alan Templeton that how the data was entered largely dictated what the results were. Put simply, the African sample was added to the algorithm first, followed by the other population samples. When the samples were randomized, thirteen different trees emerged that were equally parsimonious, some of which had Asian roots.

Here's to hoping this is more objectively-based.

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