Friday, August 31, 2012

More on Modern Human Origins

Scientific American is running a story on more news from the Max Planck Institute. Now, the entire genome of the hominins represented by the material from Denisova Cave has been sequenced. Here is what we find:
Unfortunately, the Denisovan genome doesn't provide many more clues about what this hominin looked like than a pinky bone does. The researchers will only conclude that Denisovans likely had dark skin. They also note that there are alleles "consistent" with those known to call for brown hair and brown eyes. Other than that, they cannot say.

Yet the new genetic analysis does support the hypothesis that Neandertals and Denisovans were more closely related to one another than either was to modern humans. The analysis suggests that the modern human line diverged from what would become the Denisovan line as long as 700,000 years ago—but possibly as recently as 170,000 years ago
.
Given the amount of genetic similarity in the three groups, it makes more sense that the number is closer to 170,000, especially since there is evidence of hybridization between the three groups. What also seems to be true is the Denisova group shows some level of founder effect in the sense that the genetic variability is more restricted than that found in modern humans. Who the population split off from is anybody's guess right now.

Monday, August 27, 2012

Bill Nye on Evolution

Here is a YouTube clip by Bill Nye on the denial of evolution.



It is short and doesn't include a whole lot of information but it is heartfelt and some of the warnings are certainly good.

ABC News covered this here. The best quote is:
“And I say to the grownups, if you want to deny evolution and live in your world, in your world that's completely inconsistent with everything we observe in the universe, that's fine, but don't make your kids do it because we need them. We need scientifically literate voters and taxpayers for the future. We need people that can - we need engineers that can build stuff, solve problems.”
The parents don't get this information in a vacuum. It is groups like the ICR and AiG that should be held accountable for the distortions of science. They are the ones that are doing so much harm.

Friday, August 24, 2012

Baton Rouge Advocate on Louisiana and the Loch Ness Monster

In an editorial dated August 19, the editors of the Baton Rouge Advocate address the controversy surrounding the Louisiana voucher program and the Loch Ness Monster. They write:
The state has no intention, apparently, of launching any serious investigation of the Loch Ness monster in school curriculums. Instead, it will pay and pay, for years, and — if students do poorly on science tests at some future date — the state Department of Education might raise the question of why mythology is part of a school’s curriculum.

“In the event that there is basic academic incompetence, the state (education) department can intervene,” White says. “The most effective way of testing all of this is to literally see what do the students know and what do they achieve, and we’re doing that through the state test.”

A more-effective way would be for the department to open its eyes to this kind of educational malpractice before children’s futures are endangered.
The problem, of course, is by the time you get academic incompetence, how do you go about re-educationg these kids? By then the damage is done. Then what you have is kids that go to college (if they go to a mainstream college) who get their faith rocked by the scientific “real world.”

Then supposing you do find academic incompetence because of the curricula. How do you go about getting rid of the bad curricula without lawsuits, court cases, injunctions, and other delay tactics?

“Darwin just made it up.” Great googlymoogly!

Hat Tip to Glenn Branch.

Science News: Tangled Roots

Bruce Bower of Science News has written a great column that highlights all of the current discoveries/revelations/uncertainties in modern human origins research. The article focuses on the new developments in genetics that have revealed mating patterns between Neandertals and modern humans and the existence of the third strand of humanity, the Denisovans. It is modern human origins research in a nutshell. He writes:
The question is no longer ‘When did ancient populations such as Neandertals go extinct?’ but ‘What happened to those populations and to modern humans as a result of interbreeding?’ ” says anthropologist John Hawks of the University of Wisconsin–Madison.

Clear signs of interbreeding have left archaeologists and other students of the Stone Age scrambling to revisit existing ideas about Homo sapiens’ evolutionary past. A dominant theory holding that humans evolved in Africa and left on neat one-way routes to Asia and Europe has to be revised. Instead, these ancient people must have followed a tangled web of paths taking them to other continents and sometimes reversing course. During these travels, humans encountered Neandertals, Denisovans and probably other humanlike populations that were already traipsing interconnected avenues through Asia and Europe.
Even though it seems likely that modern humans as a whole, owe their ancestry to these African populations, it is gratifying to see genetic evidence in support of what some of us have been hanging onto for all these years—some variant of the multi-regional evolution model. I don't think that a strict center/edge model will work but it is obvious that there was considerable interbreeding between population groups, be they Neandertals, moderns or Denisovans. More and more, everyday, it looks my former adviser, Fred Smith, was right. Some form of assimilation seems to be the best model to go with.

I am also reminded that, once upon a time, Geoff Pope argued that there were traces of Neandertal characteristics in some of the Chinese archaic Homo sapiens material. If, as John Hawks remarks, Neandertals interbred on a grand scale, then Pope's position, which was largely rejected at the time, has some credence.

“Not Responsible”

A friend of mine sent me this. Here is a sign seen at a restaurant.


It reminds me of a sign I saw in Rocky Mountain National Park that read “Mountains Don't Care!” I saw a similar sign in Japanese climbing Mount Fuji. Heartless, perhaps, but true nonetheless.

Friday, August 17, 2012

Shocked! Simply Shocked!

An amusing (or not) story is coming out of Kentucky where some state representatives have discovered that students are actually being tested in evolutionary theory. Kentucky.com reports:
Kentucky's Senate Republicans pushed successfully in 2009 to tie the state's testing program to national education standards, but three years later, they're questioning the results.

Several GOP lawmakers questioned new proposed student standards and tests that delve deeply into biological evolution during a Monday meeting of the Interim Joint Committee on Education.

In an exchange with officials from ACT, the company that prepares Kentucky's new state testing program, those lawmakers discussed whether evolution was a fact and whether the biblical account of creationism also should be taught in Kentucky classrooms.

"I would hope that creationism is presented as a theory in the classroom, in a science classroom, alongside evolution," Sen. David Givens, R-Greensburg, said Tuesday in an interview
.
Oh, I would certainly hope not.

This is at once an example of two things: 1. the general cluelessness of state (and national) lawmakers as to what, exactly, is in the bills that they pass and 2. the complete lack of adequate science education on the part of representatives like Mr. Givens. Two idiocies for the price of one. How can you top that? Here's how:
Another [House Education] committee member, Rep. Ben Waide, R-Madisonville, said he had a problem with evolution being an important part of biology standards.

"The theory of evolution is a theory, and essentially the theory of evolution is not science — Darwin made it up," Waide said. "My objection is they should ensure whatever scientific material is being put forth as a standard should at least stand up to scientific method. Under the most rudimentary, basic scientific examination, the theory of evolution has never stood up to scientific scrutiny."
And Mr. Waide is a member of the House Education Committee????? How does something like that happen when he cannot even identify what a theory is or have any familiarity with the evidence for evolution? Who puts these people in office? Why is there not at least a rudimentary test for people who seek to be on these committees? Why has this ignorant individual not been asked to step down immediately for these comments? The Kentucky legislature has a mess on their hands.

Tuesday, August 14, 2012

Todd Wood on the Neandertal Interbreeding Question

Todd Wood has weighed in on the Neandertal hybridization results in ArXiv with some of his own thoughts and he raised the spectre of incomplete lineage sorting...something that entirely escaped my thought process when I was waxing about the ArXiv paper yesterday. But as he, himself, points out, there are problems with this explanation. He writes:
Since incomplete lineage sorting is a random process, I would not expect to see any modern human population significantly more similar to Neandertals than any other modern human population. Modern human populations diverged well after the Neandertal divergence, so whatever genes were still very similar to Neandertals should have been evenly divided. Even more interesting is the geography: the ancestors of the modern humans with Neandertal-like genes come from the same geographic region as the Neandertals. If incomplete lineage sorting is to blame for Neandertal-like genes in modern humans, that geographic pattern would just be a weird coincidence. That's not to say that one couldn't make a case for incomplete lineage sorting, but we would need some new evidence to really seal the deal (such as new samples of Eurasians that don't have Neandertal-like genes or Africans that do).
He is right. If modern humans and Neandertals diverged as much as 250 ky BP as many people think, then drift would ensure that the two genomes would be more highly divergent than they appear to be. He is also correct about the geographical coincidence. As I wrote yesterday, the interbreeding conclusion would tend to be supported by the appearance of Neandertal-reminiscent traits in the earliest moderns from the area.

The authors argue that linkage dis-equilibrium, which is when you have allele combinations that are present in two related populations in higher percentages than can be accounted for by chance, supports the recent interbreeding model, a conclusion that Wood agrees with (although how a young-earth creationist can agree with that kind of model, I will never know).

Monday, August 13, 2012

More on Neandertal Interbreeding from ArXiv

For some time, Cornell University has been running a pre-print server for physicists so they can bounce papers off of each other. It now seems that geneticists are getting into the act. As a result of this, the good folks at Max Planck have written an abstract of a forthcoming paper, in which they describe research involving more on the Neandertal genome. Here is the abstract in its entirety:
Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans. This could be due to interbreeding between Neandertals and modern humans when the two groups met subsequent to the emergence of modern humans outside Africa. However, it could also be due to population structure that antedates the origin of Neandertal ancestors in Africa. We measure the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals (or their relatives) into Europeans likely occurred 37,000-86,000 years before the present (BP), and most likely 47,000-65,000 years ago. This supports the recent interbreeding hypothesis, and suggests that interbreeding may have occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.
This corresponds to the range of dates of the classic Neandertals from La Chapelle, La Ferrassie, Feldhofer Cave and La Quina, and may in fact partly explain the morphology of the earliest modern humans from Europe that people like Dave Frayer have been arguing for years have Neanderthal-reminiscent traits. It certainly refocuses interest on sites like MladeĨ (34 ky BP), where the faces are modern but the vaults for some of the individuals are long and low, with small buns.

I think the demographic picture in central and western Europe is a whole lot more complex than we currently understand. I look forward to reading this paper when it comes out.

Friday, August 10, 2012

Not As Off-Topic As It Might Seem...

The Tennessean ran a story today about how Thomas Nelson publishers, famous for their line of bibles, is dropping a new book on Thomas Jefferson by David Barton because the book “contains historical errors.” Bob Smietana writes:
Barton’s book, The Jefferson Lies, claims to expose liberal myths about Thomas Jefferson, author of the Declaration of Independence and the nation’s third president.

But a group of conservative scholars says Barton’s take on Jefferson is factually untrue. And a group of ministers from Cincinnati called on Nelson to cancel the book.

Casey Francis Harrell, director of corporate communications for Thomas Nelson, said the publisher had gotten several complaints about the book and found enough errors to cancel it.

“Because of these deficiencies, we decided that it was in the best interest of our readers to cease its publication and distribution,” Harrell said.
The story goes on to detail some of the disputed information in the book, none of which I am remotely qualified to assess. That is not why this is important. I bring this up because Barton has also been active in the creation/evolution debate. Those of you who read up on that might remember this exchange:



Now, it is quite true that the idea of biological change has been around for some time but it was only with Lamarck in the very late 1700s and early 1800s that any sort of mechanism was attributed to biotic change and even then, the vast majority of people believed in fixity of species. Even Darwin did when he set out on his trip aboard the Beagle in the 1830s. But that is not what Barton is getting at here.

In his own writings on the subject, Barton consistently confuses evolution at a cosmic level with evolution at a biological level. These are not the same. Did the founding fathers debate whether or not the cosmos had a grand design? Yes they probably did. Did they debate the theory of biological evolution? No they did not. Yet that is how Barton frames his response. Subsequent to his thoughts on cosmic evolution, he writes:
As confirmed by Dr. James Rachels, professor at the University of Alabama at Birmingham: Mivart [1827-1900, a professor in Belgium] became the leader of a group of dissident evolutionists who held that although man’s body might have evolved by natural selection, his rational and spiritual soul did not. At some point God had interrupted the course of human history to implant man’s soul in him, making him something more than merely a former ape. . .
Lost in the shuffle is that Dr. Rachels lived and wrote in the 1800s, quite some time after the founding fathers debated “intelligent design versus evolution.”

Barton spends a good bit of ink writing about how many of the founding fathers have argued that the universe looks designed. That is a very different thing from the idea that evolution, even in a cosmic sense, does or does not happen. I doubt that there is a person alive that does not accept evolution of some kind. One only has to look at the changes in a river's path or the location of the shoreline at Ephesus (where once Paul gave a speech but that is now twenty miles inland). Evolution, after all, is change over time.

I do think that, based on what Barton has said in public and what he has written in more in-depth fashion, that he is being misunderstood. The problem is that neither are very clear. To his credit, Barton seems to view the theistic evolution perspective in a not-unkind light, although it is not clear what, exactly, he thinks from this post. He is also quite correct that the four viewpoints he delineates have not altered much in recent years in their adherents. He just needs to articulate his viewpoints more clearly with regard to evolution in general and biological evolution in specific. He may agree with one and not the other but there is no way to tell from what he has either written or said.

This might just be my own personal take on what I find in Barton's writings. If your take is different, let me know.

Thursday, August 09, 2012

The Discovery Institute vs. The Peppered Moth

The Discovery Institute claims that a new paper in the Journal of Evolutionary Biology has “debunked” the peppered moth icon of natural selection. They write:
A new paper in the Journal of Evolutionary Biology helps debunk the peppered moth icon, and cites Discovery Institute's Jonathan Wells in the process.

You wouldn't know it from the summary on PhysOrg, or from the abstract of the paper in the
Journal of Evolutionary Biology, but some South Korean scientists have joined in the cause to dismantle a celebrated "Icon of Evolution," the myth of the peppered moth. That's right; in the first paragraph, Kang, Moon, Li and Jablonski set right to work, pulling the rug out from Kettlewell (1955) and all his copycats who made the peppered moth Exhibit A for the power of natural selection.
The focus of the post is that the Korean authors observed the moths Hypomecis roboraria and Jankowskia fuscaria to see where they rested on tree trunks and concluded that once they rested, they moved around on the bark, changing their orientation in order to more carefully conceal their appearance. Thus, they argue that it is a combination of color and resting behavior that contribute to their camouflage, not just the color alone. To this, the writer of the post responds:
In the real world, as opposed to the staged peppered-moth photos we have all seen in textbooks, the moths would not have stood out like sore thumbs on the tree trunks. They would have wandered about for a place to blend in; most likely, they would not have landed in such conspicuous spots in the first place (Wells, p. 148). Letting the moths do what comes naturally is what the experimenters should have done. The old peppered moth experiments, consequently, have been invalidated (again).
First, the authors seem to forget that Majerus (whom they cite) actually conducted comprehensive experiments that did not involve nailing moths to trees and his results corroborated earlier results that wing color was highly selective. The DI post author even admits that.

The odd thing about this post is that the author(s?) have made the logical non sequitur that behavior and morphology are completely divorced from each other. I know of no evolutionary biologist that would make that claim. Behavior always plays a role in evolution. If you take any animal out of its environment, it behaves differently. Sometimes that behavior can adapt to new environments, sometimes it cannot.

When Homo ergaster started using stone tools as weapons and started hunting, it changed what they could eat (and reduced the number of animals that could eat them), which allowed them to expand their home range. It also allowed them to outcompete their neighbors, in this case Australopithecus boisei, which likely caused the latter's extinction. Behavior and selection have always been intricately linked and there are literally thousands of examples of this.

The post writers argue that supporters of natural selection have “yielded some highly significant ground.” How? We already know from Majerus' work that the earlier results, if not technically or scientifically rigorous, were corroborated. The work of the Korean scientists simply adds the explicit role of behavior. Nobody doubts that selection is acting on wing color.

The author ends by writing:
And finally, the paper shows that criticisms of Darwinism by ID writers like Dr. Wells are having an impact -- even in the Journal of Evolutionary Biology.
It does no such thing. Wells is cited three times, and only in passing. His work is never discussed in any depth. The author remarks that the Korean scientists have picked up the word "iconic" from Wells. So? When I write for BioLogos, I regularly cite anti-evolution authors. I might even use one of their phrases. That does not mean that I agree with them or endorse their views. To say that Wells is having an impact might be true and it might not be. From this paper, however, that, like the claim that the peppered moth research has been debunked, is not in evidence

Wednesday, August 08, 2012

Two Hominin Species Running Around At 1.9 Mya

Meave Leakey and some colleagues1 have unearthed and described some new fossil hominins from Koobi Fora that seem to confirm that, yes, there were two very different critters running around 1.8 to 1.9 million years ago on the plains of eastern Africa. From the Turkana Basin Institute:
Found within a radius of just over 10 km from 1470’s location, the three new fossils are dated between 1.78 million and 1.95 million years old. The face KNM-ER 62000, discovered by field crew member Elgite Lokorimudang in 2008, is very similar to that of 1470, showing that the latter is not a single “odd one out” individual. Moreover, the face’s well-preserved upper jaw has almost all of its cheek teeth still in place, which for the first time makes it possible to infer the type of lower jaw that would have fitted 1470. A particularly good match can be found in the other two new fossils, the lower jaw KNM-ER 60000, found by Cyprian Nyete in 2009, and part of another lower jaw, KNM-ER 62003, found by Robert Moru in 2007. KNM-ER 60000 stands out as the most complete lower jaw of an early member of the genus Homo yet discovered.
The skull being referenced (heavily throughout the press release) is that of KNM-ER 1470, discovered by Richard Leakey in 1972 and dated to 1.9 million years ago. 1470 has a very flat face and is large, so much so that when it was discovered and compared to the Homo habilis material that Richard's dad, Louis Leakey and Napier and Tobias were pulling out of the ground, it was felt that it represented a new species, Homo rudolfensis.

For a short run-down on the material from this time period, go to my BioLogos post, The Human Fossil Record, Part 7: The Rise of Early Homo.

Anyhow, these new fossils add a new level of what Bernard Wood2 calls “complexity.” For quite some time, 1470 existed in its own little world, with no fossil remains being similar to it in size or in shape. Questions began to rise about the veracity of its reconstruction and its provenance. These new fossils fit 1470 to a “T” and it now seems clear the 1470 does, in fact, represent a different form than that represented by skulls like ER 1813, which is small and gracile and gives support to the idea that there were two competing species of hominin on the landscape even before Homo erectus/ergaster arrived on the scene some two hundred thousand years later. Below, on the top is KNM-ER1813 and below it is KNM-ER 1470















As you can see, there is considerable difference in overall size and robusticity between the two and when the new material is compared to the mandible KNM-ER 1802, which is similar to 1813, there is a considerable mismatch. What remains to be seen is where Homo ergaster came from.

1Leakey, M. G., Spoor, F., Dean, M. C., et al. (2012). New fossils from Koobi Fora in northern Kenya confirm taxonomic diversity in early Homo. [10.1038/nature11322]. Nature, 488(7410), 201-204.
http://www.nature.com/nature/journal/v488/n7410/abs/nature11322.html#supplementary-information

2Wood, B. (2012). Palaeoanthropology: Facing up to complexity. Nature, 488(7410), 162-163.
http://dx.doi.org/10.1038/488162a

Thursday, August 02, 2012

Is Noah's Ark Sinking?

A reader pointed out a story in Leo Weekly about the newest troubles of the Ark-n-Park, the Noah Ark theme park being built (mostly) by Answers in Genesis next to its fabled Creation Museum. Joe Sonka writes:

The first phase of the project will cost $73 million to build, and $6 million has already been spent on land acquisition and design. So far, Answers in Genesis has raised $7.5 million, with private investors pitching in an additional $15.5 million to the LLC, leaving $22 million left to raise before they have enough money to break ground, and $44 million left to complete the project. [Joe] Boone estimates it will take 12-24 months to secure the funding to break ground, then it will take another 24 months to complete construction.

The company will then have to raise $53 million for additional phases of the park throughout next decade.

Such a delay in construction makes the potential for a full $43 million in tax incentives impossible, as the state will only rebate sales taxes for 25 percent of what they’ve spent constructing the project by May 2014. This in turn could hurt private investment for the park, as there is no longer the virtual guarantee of $4 million in rebates every year.

The loss of the tax revenue will be a serious blow to the park construction since it was the center of focus not even a year ago and raised so much controversy. It is an interesting article, with a few hair-raising anecdotes about a visit to the Creation Museum thrown in, just to show how borderline-cult this group is. I truly hope the project hits a dead end but I would bet money that the park will wind up being built. Read the whole thing.

Wednesday, August 01, 2012

Gee, This'll Look Good...

Another Republican has clearly aligned himself with YEC sympathies by holding his fundraiser at the Creation Museum in Kentucky. Steve Daines is the politician and the truly interesting thing is that he is running his race in Montana, so he had to go pretty far afield to get support.

In other words, he is not just a local pol raising support from the area, he targeted the museum as a resource. This was noticed by Don Pogreba, who runs a blog in Montana. He proceeds to confuse the Creation Museum with the up-and-coming Ark-n-Park, which undercuts his argument, and then he makes a weird statement about tree-ring dating, but he is right to point this out and the fact that a candidate for congress is holding his fundraiser there is truly amazing.

The Republicans can't hitch their wagon to this cause...they just can't.