Monday, November 25, 2013

More Government Overreach: 23andMe Ordered To Cease and Desist

The FDA has ordered the company 23andMe to stop providing its genetic overview and genealogy results package, which the agency describes as a "medical diagnostic device in need of approval." From the story in Popular Science:
Today, the Food and Drug Administration published a letter giving the company two weeks to discontinue marketing the kit, which the agency classifies as a medical diagnostic device in need of approval.

According to the letter, the FDA has been seeking information needed to approve the test for a while, "including more than 14 face-to-face and teleconference meetings, hundreds of email exchanges, and dozens of written communications"
Welcome to today's hyper-regulatory environment. How does this product relate to either food or drugs? They are simply providing a service by educating people with genetic information about themselves. Why would that need to be approved? 23andMe has not yet responded.This is yet another example of government overreaching because it can. 

Texas State Board of Education Chooses Scientifically Accurate Biology Textbooks

I was pointed by one of my readers to a news story on Right Wing Watch (a site I do not normally go to) that reports that the Texas State Board of Education has formally adopted the textbooks that present mainstream science and has done so without accepting any of the edits that were proposed by several groups, some of which are creationist in outlook.  Miranda Blue writes:
This afternoon, the Texas State Board of Education gave its final approval to a set of biology textbooks that include scientifically sound teachings about evolution, rebuffing a campaign by creationists to include “biblical principles” in science texts. However, the board delayed its approval of one of the books until a board of experts reviews the complaints of anti-evolutionists.

The Texas Freedom Network, which has been fighting to keep science in the state’s science textbooks, called the vote a “huge win for science education” and noted that “throughout the adoption process, publishers refused to make concessions that would have compromised science instruction on evolution and climate change in their textbooks.” People For the American Way joined TFN earlier this year to deliver 300,000 petitions to the school board urging them to reject attempts to insert creationism into science texts.
This is likely not the last that we will hear from the various groups that support the edits. People like Don McLeroy, Barbara Cargill and Cynthia Dunbar don't go away overnight and their supporters do not, either.

Sunday, November 24, 2013

PhysOrg: Research Team Discovers "Immune Gene" in Neanderthals

Neandertals once again appear to be playing a central role in modern human origins and continued viability.  From PhysOrg:
A research group at Bonn University, Germany, and international collaborators discovered a novel receptor, which allows the immune system of modern humans to recognize dangerous invaders, and subsequently elicits an immune response. The blueprint for this advantageous structure was in addition identified in the genome of Neanderthals, hinting at its origin. The receptor provided these early humans with immunity against local diseases. The presence of this receptor in Europeans but its absence in early men suggests that it was inherited from Neanderthals. The results have been published in advance online in the Journal of Biological Chemistry. The printed edition is expected in a following issue.
Whether or not it predates Neandertals will never be known but the fact that it has time-depth back that far suggests that this receptor evolved separately from the incipient modern humans and that the interbreeding between the two was sufficient enough for it to take hold in some populations of modern humans. The report also notes that this receptor is very rare in Sub-Saharan Africans but is present in at least two-thirds of Europeans. 

I think we are just scratching the surface in terms of determining how much interbreeding went on between Neandertals and modern humans.  It is clear, judging from each new study, that the species lines are becoming more and more blurred. 

Saturday, November 23, 2013

Just When You Thought It Was Safe To Go Back To Texas...

It looks like the Texas text book controversy is heating up again.  This time, ABC has noticed.  Will Weissert writes:
Publishers submitted proposed textbooks this summer, but committees of Texas volunteer reviewers — some nominated by creationists who are current and former Board of Education members — raised objections. One argued that creationism based on biblical texts should be taught in science classes, while others objected that climate change wasn't as settled a scientific matter as some of the proposed books said.

Pearson and many other major publishers weren't willing to make suggested major edits and changes. Pearson has challenged the list of alleged errors that the citizen review panel claims are in the biology book and that members raised during Thursday's meeting.

The concerns included differences of opinion on how long it took Earth to cool. Another objection called for emphasizing that modern discoveries in the fossil record reveal a "balance between gradualism and sudden appearance," suggesting that rather than developing over time, life got a boost from an intelligent designer.
These issues would not happen if people had to pass basic science competency exams before they could be elected to school boards. Of course, they would just complain that their brand of science wasn't represented in the exams and that the exams were unconstitutional and then we would be back at square one.  As long as creationist candidates for these boards are well-funded, this problem will be with us.  Kudos to Pearson and the other publishers for resisting the proposed changes.  

Thursday, November 21, 2013

John Freshwater Loses Final Appeal

The Raw Story is reporting that the Ohio Supreme Court let stand an appeals court decision to allow the termination of Mt. Vernon science teacher John Freshwater.  From the story:
“We recognize that this case is driven by a far more powerful debate over the teaching of creationism and intelligent design alongside evolution,” the court noted in its decision. “(But) here, we need not decide whether Freshwater acted with a permissible or impermissible intent because we hold that he was insubordinate, and his termination can be justified on that basis alone.”
This seems sort of anticlimactic, but boils down the termination to concrete, non-religious terms and, thus is as narrow a reading as the court can put forth.  Thus, the case that began five years ago, ends with a poof and not a bang. 

Science Daily: Neanderthal Viruses Found in Modern Humans

A year a half ago, I was sitting in a discussion group in the anthropology department at the University of Tennessee discussing the importance of the Denisova fossil and DNA that was extracted from it.  At that point, it had already been established that Neandertal DNA had been found in modern humans to the tune of between 3 and 9 % depending on the population.  I then publicly wondered when a study of endogenous retroviruses in the Neandertal genome would be forthcoming and whether that would also link them to modern humans.

It has.  Science Daily is reporting on genetic studies that have discovered Neandertal retroviral DNA in modern humans.  From the story:
The researchers compared genetic data from fossils of Neanderthals and another group of ancient human ancestors called Denisovans to data from modern-day cancer patients. They found evidence of Neanderthal and Denisovan viruses in the modern human DNA, suggesting that the viruses originated in our common ancestors more than half a million years ago.
Lets back up.  What are endogenous retroviruses, or ERVs? These are RNA-based viruses that write themselves into the DNA of an individual.  They are thought by some to be directly involved in causing things such as MS and a host of different cancers.  It is not quite clear what kind of role they play in this, however.  It has also been found that some ERV DNA has been co-opted by the reproductive system, and are involved in the creation and stability of the placenta.  They are highly conspicuous and easily recognizable.  ERVs also makes up around eight percent of modern human DNA.

If they get written into the sex chromosome, since they are part of the DNA, they get passed on and, usually over time, lose their virus-causing capabilities, ending up as non-coding parts of the genome.  Sometimes, they don't insert correctly and end up not causing trouble at all.   One of the most interesting things, though is that they insert themselves into the genome in random places.  Therefore, if they show up across related species, it is a marker of evolutionary similarity.  They have, understandably, figured into human evolutionary studies.  ERVs have been found in all of the higher apes that are also found in humans and, broadly, provide evidence of common ancestry with the higher apes.  Here is a paper in Comparative Functional Genomics by Khudosovich et al., explaining the role in detail1.

Now it seems that ERVs that are specific to Neandertals have been found in modern humans.   As with the results of the Neandertal genome, this can only mean one thing: Neandertals directly contributed, in some way, to the ancestry of modern humans.  This has broad implications not just for human evolutionary response but also for theological models involving Adam and Eve.  Conventional science posits that Neandertals appeared around 130 000 years ago in Europe and that, as modern humans moved out of Africa, they met and mated with the resident Neandertals.  The evidence further suggests that, over time, the modern human genome swamped the Neandertal genome and that, in combination with changing climatic conditions and the selective advantage of the modern human genome, Neandertals died out. 

But we know that the last Neandertal died out around 32 000 years ago.  If modern humans carry Neandertal genes (and by extension ERVs), then there must have been modern humans around at least that long.  Further, given that most of these DNA elements are non-coding and insert themselves randomly in the genome, in order to postulate a separate, non-evolutionary, special recent ancestry for modern humans, one must argue that these ERVs were separately inserted into the DNA of Neandertals and modern humans (unintelligent design).

I'm going out into left field now.

Further, if one is to argue that there were only two humans at the beginning of human history, one has to account for how the Neandertal genes got into their descendants.  One could, I suppose, argue that, in the time period between Adam and Eve to Noah, one of Adam's descendants mixed it up with the Neandertals (although one has to account for why they aren't mentioned) and that is how the Neandertal ERVs got there.  There were Neandertals in the Levant, so that is, at least within that framework, possible (Neandertals as Nephilim?).  I will be curious to see if that explanation appears in creationist' writings.

The most parsimonious explanation is that modern humans carry some Neandertal ancestry in them and that this process occurred through evolutionary means. 

1Khodosevich, Konstantin, Lebedev, Yuri and Sverdlov, Eugene (2002) Endogenous Retroviruses and Human Evolution Comparative and Functional Genomics 3(6),494-498

Monday, November 18, 2013

Slate Opines on Ken Ham, The Ark Encounter and Junk Bonds

Mark Joseph Stern has a piece in Slate that examines the new financing plan that Ken Ham and the Ark Encounter (Ark-n-Park) are enacting to raise money for the endeavor.  He writes:
Before Ham can usher in a new era of mass destruction “to separate and to purify those who believe in Him from those who don’t,” as he wrote in his newsletter to supporters, he’ll need to actually build his ark—and three years after first announcing the project, he hasn’t even broken ground. The project’s first phase will require $73 million in total, and $24 million just to commence construction. (The state of Kentucky generously offered to toss in $37.5 million worth of tax breaks, though those will expire in 2014.) The next phases will require $52.6 million. Thus far, Answers in Genesis has raised $13.6 million—just 10 percent of an optimistic estimate of the total cost. For a while, Ham maintained public silence on the delay.
Then he hatched a plan. As Josh Rosenau reported here, Ham came up with the idea of selling bonds to investors to finance the remainder of the project.  Why is this a problem? 
As Answers in Genesis readily admits, the bonds “are not expected to have any substantial secondary market” and are “not an obligation of AiG.” Somewhat alarmingly, the bonds are unrated, an indication that they’re extremely risky—and almost impossible to resell. High risk, higher yield: These, in essence, are creationist junk bonds.
It is difficult for me to believe, in the current financial climate, that a large number of investors are going to go for this.  Further, as Stern reports, the way the bonds are structured, if the enterprise never gets off the ground, investors will lose everything they invested.  This is a disaster waiting to happen.  If it were me, and I had money to invest, I would certainly steer clear. 

Saturday, November 16, 2013

A Trailer For Noah

A trailer has been released for the movie Noah.  There is still a good deal of apprehension about it, but it certainly looks like an expensive production.  Here it is:

Out March 28, 2014.  For what it is worth, it looks like they got the verse about the "fountains of the great deep" (Genesis 7:12) in there. 

Acts and Fiction: The ICR Does A Hatchet Job on Dmanisi Skull 5

The ICR has, bluntly, called the description of the new Dmanisi skull 5 a fraud.   Lets find out why.  The conclusion, based on the descriptors of the morphology of skull 5 is that it has a mix of early Homo and Homo erectus traits.  Brian Thomas of the ICR thinks it is nothing more than an ape.  In support of this, he puts together seven points, which I will take one at a time.  The analysis is somewhat repetitive at times because Mr. Thomas' points, themselves, are.

Point No. 1
It is anatomically quite different from known human skulls. The Science authors wrote, "The morphology of skull 5 stands apart from that of any other known fossil Homo specimen through its combination of a small braincase with a large prognathic face." Maybe it "stands apart from" man because it was not a man. Could it actually be an ape's skull?
Well, no.  It has no ape characteristics at all.  They are clearly hominin in nature.   For example:
  1. The foramen magnum (the hole for the spinal column) is at the base of the skull, rather than the back, as is the case for apes.  It is how we know that it was bipedal.  There is not a single ape, fossil or otherwise that has this characteristic. 
  2. On observation of the skull, there is clearly an angular torus (a ridge of bone extending from the ear to the back of the head), a trait not found in early African Homo but found in the rest of the Dmanisi skulls and all East Asian Homo erectus specimens, suggesting that this population represented a point at which there was radiation out of Africa in two directions, toward Europe and Asia. This is not a trait found in any ape. 
  3. When scaled for brain weight/body size, the brain case is too large to be an ape.  It is clearly a hominin.  Further, other skulls in the Dmanisi sample range from 601 to 730 cubic centimeters in size, a quarter more to double the size of any extant or fossil ape. 
  4. The teeth are clearly hominin in morphology (see images below).  While there is considerable procombency of the incisors (they angle forward from the face), there is no expansion of the canines beyond the tooth row, the premolars are not rotated to sharpen the canines and there is no diastema (space) between the canines and incisors to make room for an expanded canine in the opposite tooth row.  This is clearly a hominin mouth, not an ape one.
Point No. 2
It is too loosely linked with human postcranial material. The study author's phrase "probably associated" cannot substitute for solid scientific evidence.
So?   Say it isn't linked with any of the post cranial material.  That doesn't change the morphology of the skull in any way.

Point No. 3
It has a very ape-like brain volume—far smaller than that of a human. It was estimated at 546cc, similar to that of gorillas and Australopiths, but only about half the average size of a human
As Mr. Thomas so correctly notes, the cranial size is not necessarily an indication of intelligence or of hominin status.  He also doesn't define what he means by "human."  Conventional anthropologists define "human" as being bipedal (and not the weird Oreopithecus-style gait).  No other primate does this and it dates to around 4.4 million years ago.  Further, given that size is not a reliable indicator, point 3 above still stands.

Point No. 4
It has a heavily built, ape-like jaw. Skull 5 "has the largest face, the most massively built jaw and teeth and the smallest brain within the Dmanisi group," according to a news release from the University of Zurich where three of the Science authors work.4 But where is the evidence proving that all five Dmanisi skulls even belong to the human group?
There is variability in all fossil samples. For example, the Mladeč sample from central Europe that dates to between 34 and 37 thousand years ago is quite variable, with some crania resembling Neandertals and others resembling modern humans. Further, as Lordkipanidze et al. point out, the range of variation present in the Dmanisi sample is not greater than what one would find in a sample of chimpanzees or the world-wide sample of modern humans (although intra-populational differences in the modern human sample, I am quite sure, are less).

Point No. 5
It links to other material that is not clearly identified or dated. The Science authors reported, "Furthermore, the remarkably large and robust dentognathic remains of early H. erectus from Java (Trinil/ Sangiran) exhibit close affinities with skull 5." But the abstract describing the Java remains reads, "Temporal changes, within-group variation, and phylogenetic positions of the Early Pleistocene Javanese hominids remain unclear."
Additionally, experts in human evolution have a long history of assigning human and ape remains to the Homo erectus human category. By tying skull 5 to past category confusion, the Science authors muddied their own identification of skull 5 as human
The fact that some temporal changes in Homo erectus remain unclear does not diminish the importance or morphology of the East Asian Homo erectus fossils, themselves, many of which are nicely dated to between 1.5 and 1.8 million years ago.  From the paper that Thomas cites:
Further, it is absolutely clear that there are differences between these hominins and later populations:   The Bapang-AG H. erectus population is advanced, showing a similar degree of dentognathic reduction as the Middle Pleistocene Chinese H. erectus represented by the Zhoukoudian and Lantian remains. In this respect, this population is significantly derived relative to African early H. erectus and the oldest hominids of Java (Grenzbank/Sangiran group). However, it remains unclear whether these apparent similarities reflect affinities or homoplasy between the Bapang-AG and Chinese H. erectus.
Thomas' second point on tying this skull to category confusion is a terminological inexactitude.  Experts in human evolution do no such thing.  In fact, there has been a raging dispute about how expansive the Homo erectus taxon actually is, with splitters, like Ian Tattersall on one side arguing that the human fossil record between 2 million and 500,000 years B.P. is taxonomically more diverse than we think and Milford Wolpoff, who argues that we need to lump everything into Homo and dispense completely with the taxon Homo erectus.  The only person I know of who is assigning too many fossils to Homo erectus is Marvin Lubenow who, in his execrable book Bones of Contention was unable, as nearly as I could tell, to distinguish Homo erectus from anything else and who made numerous errors because of this.  Further, Lordkipanidze and colleagues did not tie the skull to category confusion, they attempted to place it taxonomically within the entire range of Homo.

But even if it were case that they were tying skull 5 to Homo erectus, that is still nothing like saying it is an ape, since no Homo erectus fossils are ape-like in any way, shape or form.  Case in point:

The top image is an African Homo erectus specimen (KNM-ER 3883) while the bottom one is a chimpanzee.  The differences are striking.

Point No. 6
The researchers' approach to skull 5 may be similar to other fraudulent or dubious finds. Dutch physician Eugene Dubois, anxious to find proof of human evolution, uncovered the famous Java "man" fossils in 1891. It was not until 30 years later that Dubois revealed the truth behind the find and admitted he had been hiding fully human skulls from the same Javan site. Some later suggested that his Java man skull cap was actually that of a gibbon. Could today's scientists be subject to the same eagerness to prove evolution, leading to skewed analyses? Because human origins research can be so subjective, one researcher of the history of paleoanthropology voiced a relevant caution: "We have only to recall the Piltdown adventure to see how easily susceptible researchers can be manipulated into believing that they have actually found just what they had been looking for."

The Science authors also wrote that skull 5 looks like the famous KNM-ER 1470 found in Africa. But skull 1470 was pieced together from so many separated fragments that it may not constitute a real, single individual. Understandably, its identification has long been difficult. Who knows which pieces were from humans and which were from apes?

Even so, the part of skull 1470 showing a forehead and human-like brow ridges differs from the apish appearance of skull 5. Did the Science authors link skull 5 to Africa's KNM-ER 1470 for evolutionary rather than anatomical reasons?
Okay, this one made me really mad because it accuses the researchers of not being competent or careful about what they have described.  The remains that DuBois uncovered were manifestly Homo erectus.  They weren't fully human and they sure as heck weren't a gibbon.   The research community refused to accept DuBois' claims because they thought he was working in the wrong part of the world, and they were susceptible to eurocentrism, a problem which dogged the discipline for decades.

Human origins research isn't any more or less subjective than any other scientific enterprise.   It grows and changes in relation to new data that is unearthed.  You might say the same thing about cosmology or cell theory or microbiology, fields that are always attempting to understand how things work.  Researchers are human and they make mistakes.  But they also try to fix them.  What is conveniently left out of Thomas' paragraph is that the Piltdown hoax was uncovered by scientists, working with scientific methods.  Science, as a self-correcting enterprise, works very well, and palaeoanthropology is no different. 

Regarding ER 1470, his reference is another young-earth creationist, Duane Gish, who has been shown repeatedly to have a severely limited knowledge of the fossil record (See Don Prothero's book Evolution: What the Fossils Say and Why it Matters for examples)  The idea that it represented pieces of humans and apes is unsupported.  The skull has many, many contiguous pieces—enough to reliably construct the cranium and the face.  Further, the pieces that were found are manifestly not from fossilized apes, none of which have ever been found in East Africa.  The primary dispute was not what it looked like, the primary dispute was how old it was. Richard Leakey said that it was 2.9 my old and everyone else said "Well, no, Richard, that can't be right."  Eventually, when stratigraphic and radiometric analysis was done, it was discovered to be around 1.9 million years old.

Point No. 7:
It is replete with ape features. Skull 5 has a U-shape dental arch, not the more parabolic shape humans present. Its chin slopes back like an ape without the forward-jutting bottom point of a human chin. There is no human nose bridge, and it has prominent attachment points for enormous jaw and neck muscles.
It most certainly does have a human-shaped dental arch.  Turn any human skull on its head and you will find dental anatomy exactly like what you find in Skull 5. Lets take a look.  On the left is a modern human from an inferior view.  On the right is Dmanisi Skull 5.  The tooth rows are very similar in shape, with similarly-proportioned teeth.

Now lets compare both of these skulls to that of a chimpanzee to see exactly what the differences are.

Well, for one, you can clearly see the diastema between the canine and the incisors.  You can also see that the maxillary tooth rows in the chimpanzee are parallel, instead of a gentle U that you see in the other two skulls.  The canine on the chimpanzee is very expansive, sharp and extends beyond the tooth row.  Further, you can see that, in Skull 5, the foramen magnum is underneath the skull, not toward the back as in the chimpanzee.   Skull 5 looks nothing like the chimpanzee skull and, in fact, shares most (if not all) of its similarities with the modern human from this anatomical position.

The lack of a chin is absolutely expected at this point in human evolutionary history and is related entirely to tooth size.  As the front teeth have shrunk in size, the bone has resorbed in the front of the jaw, creating the chin.  In fact, tooth size has continued to shrink even since the advent of modern humans, with an 11% drop since the Neolithic.  What Mr. Thomas does not seem to realize is that the chin has only appeared in the last 100 thousand years and is absent not just on early Homo but Homo erectus and archaic Homo sapiens.  The lack of a chin, in no way impairs its status as a hominin, unless you don't consider Neandertals hominins.  There is no human nose bridge on the skull because that didn't appear until archaic Homo sapiens, some 400 thousand years ago.

Thomas ends his article with this: 
Biblical creationists are not restricted to interpreting skull 5 according to evolution. Instead, they are free to exercise a healthy scientific skepticism of current interpretations. If Dmanisi skull 5 ends up not being human at all, then its titillating implications for human evolution fizzle. It would then simply become an extinct ape kind's skull found in a long-collapsed animal den into which saber-toothed cats may have dragged both human and other prey.
This is only true if the information is being treated honestly. Unfortunately, because Mr. Thomas does not possess the necessary education in either comparative primate or fossil human anatomy, he cannot do this. That he has seemingly failed to educate himself on even the basic anatomy necessary to understand these errors further compounds the problem.  His analysis is riddled with inaccuracies and unwarranted conclusions and, as such, constitutes no evidence against evolution or that the Dmanisi fossils are anything other than what the investigators say they are.

This is yet another hatchet job by the ICR.

Hat tip to Todd Wood.

Thursday, November 14, 2013

Is The Republican Party Anti-Science?

The Atlantic doesn't think so.  In an editorial called The Republican Party Isn't Really the Anti-Science Party, Mischa Fisher makes the case that the blame can be equally spread around and that rank-and-file Republicans are every bit as educated in science as democrats. I confess that I have, perhaps, fallen into this trap, profiling, almost with glee, such scientific giants as Paul Broun of Georgia, and Don McLeroy, of Texas ("I disagree with these experts. Someone has got to stand up to experts").  Indeed, Fisher writes:
I'm the first to admit that there are elected Republicans with a terrible understanding of science—Representative Paul Broun of Georgia, an M.D. who claims evolution and the Big Bang are “lies straight from the pit of hell” is one rather obvious example—and many more with substantial room for improvement. But Republicans, conservatives, and the religious are no more uniquely “anti-science” than any other demographic or political group. It’s just that “anti-science” has been defined using a limited set of issues that make the right wing and religious look relatively worse.
Perhaps this is true but that, in a way, makes them look even worse because, if they accept the rest of established, accepted science but can't wrap their brains around evolution and global warming (lets call it what it is), then the legitimate reasons for rejecting those areas scientifically crumbles. How did everybody else get the science right and the evolutionary biologists get it so wrong?

This paragraph, however, surprised me:
Numerically speaking, according to Gallup, only a marginally higher percentage of Republicans reject evolution completely than do Democrats. Yes, an embarrassing half of Republicans believe the earth is only 10,000 years old—but so do more than a third of Democrats. And a slightly higher percentage of Democrats believe God was the guiding factor in evolution than Republicans.
When one reads newspaper accounts of democrats and science, the first revelation is revealed nowhere.  Reports always indicate that democrats are enlightened and Republicans are  scientifically illiterate.  On the other hand, while the last part of this paragraph is probably true, the reason for that may be reflected in the fact that a higher percentage of Republicans think that humans were created ex nihilo around 10,000 years ago.The percentages just got shifted from one column to the other. 

To me, one of the most interesting things about the table that is quoted in the paragraph is that only 20% of those questioned think that God had no hand in either the creation or evolution of humans.  I make this statement with the understanding that I am making a large assumption here: that those that think that humans were created in the last 10,000 years think that God had a hand in it.  The reason I think it is a valid assumption is that I have yet to find anyone, anywhere that accepts the creationist account of origins and who is not a fundamentalist Christian. 

The rest of the article is damning in its examination of bad science policy on both sides of the aisle and should be read by anybody interested in this area. 

Wednesday, November 13, 2013

National Geographic Special on Denisova

National Geographic is running a special report on the importance of the Denisova hominin for later human evolution.  The timing is curious since this was big news two years ago, but “The Case of the Missing Human Ancestor” goes into the depths of the discovery, the tests done, the complex stratigraphy of the cave, and the significance of what the Max Planck Institute found.  Further, it is written by Jamie Shreeve, and he is always a good read.  He writes:
In the summer of 2010 a human toe bone had emerged, along with the enormous tooth, from Layer 11. In Leipzig a graduate student named Susanna Sawyer analyzed its DNA. At the symposium in 2011 she presented her results for the first time. To everyone’s shock, the toe bone had turned out to be Neanderthal, deepening the mystery of the place.

The green stone bracelet found earlier in Layer 11 had almost surely been made by modern humans. The toe bone was Neanderthal. And the finger bone was something else entirely. One cave, three kinds of human being. “Denisova is magical,” said Pääbo. “It’s the one spot on Earth that we know of where Neanderthals, Denisovans, and modern humans all lived.” All week, during breaks in the conference, he kept returning alone to the cave. It was as if he thought he might find clues by standing where the little girl may have stood and touching the cool stone walls she too may have touched.
Look for this site to continue to influence models of later human evolution. There seem to have been several locations at which there were both, at various times, Neandertals and modern humans.

Tuesday, November 12, 2013

"Single Evolving Lineage of Early Homo"

This was reported a month or so back.  A new fossil has been described from the site of Dmanisi, the 1.8 million year-old site in the Russian republic of Georgia.  The skull is almost totally complete and, with associated jaw, is one of the best examples of early Homo in existence.  From the abstract of the Lordkipanidze et al1 article:
The Dmanisi sample, which now comprises five crania, provides direct evidence for wide morphological variation within and among early Homo paleodemes. This implies the existence of a single evolving lineage of early Homo, with phylogeographic continuity across continents.
The idea of a single, evolving lineage is the closest you will get to someone admitting that there might be anagenetic speciation going on here. It also suggests a wide range for early Homo that extended from eastern Africa, across the upper coast, and across the strait of Gibraltar. There is evidence of early Homo at Orce, in Spain and Pirro Nord, in Italy from around 1.6 to 1.3 million years ago. No actual hominin remains exist at these sites but the stone tools that have been found found match, generally, those found at Dmanisi. Not a smoking gun but close.

What is intriguing about this is that it is not a huge intellectual leap that is making these hominins move.  The newly-described Dmanisi skull has a cranial capacity of 546 cubic centimeters, barely 100 more than the late australopithecines.  The morphological diversity also has people interested.  From the Science Daily story:
According to [Christophe] Zollikofer, the reason why Skull 5 is so important is that it unites features that have been used previously as an argument for defining different African "species." In other words: "Had the braincase and the face of the Dmanisi sample been found as separate fossils, they very probably would have been attributed to two different species." Ponce de León adds: "It is also decisive that we have five well-preserved individuals in Dmanisi whom we know to have lived in the same place and at the same time." These unique circumstances of the find make it possible to compare variation in Dmanisi with variation in modern human and chimpanzee populations. Zollikofer summarizes the result of the statistical analyses as follows: "Firstly, the Dmanisi individuals all belong to a population of a single early Homo species. Secondly, the five Dmanisi individuals are conspicuously different from each other, but not more different than any five modern human individuals, or five chimpanzee individuals from a given population."
the differences between the East African and Eurasian fossils then could be just regional variation in an evolving polytypic species. This kind of explanation certainly gives the "lumpers" a leg up and, if this explanation is the best one going, calls into our question the splitting that we have applied to other species. Is it, instead, appropriate to sink such taxonomic forms such as Homo heidelbergensis, Homo ergaster, Homo rudolfensis and Homo habilis, all of which exhibit considerable size and shape dimorphism, into one species: Homo erectus which now has taxonomic precedence?

1A Complete Skull from Dmanisi, Georgia, and the Evolutionary Biology of Early Homo David Lordkipanidze, Marcia S. Ponce de León, Ann Margvelashvili, Yoel Rak, G. Philip Rightmire, Abesalom Vekua, and Christoph P. E. Zollikofer Science 18 October 2013: 342 (6156), 326-331.

Monday, November 11, 2013

Charter Schools and Religious Entanglement

Although certainly not a new topic (witness last year's Loch Ness Monster reports), the problem of the funding of religious charter schools by state money is becoming a more visible problem.  John Turley tackles this controversy.  The article is as much as anything just a run-down of different cases that have spawned across the country but it is interesting for showing that the charter school/fundamentalist ties are strong in many different areas across the country.  Among them, he writes:
In November 2010, Jessica Meyers wrote a newspaper article about Advantage Academy in Duncanville, Texas. She said the students at this school “follow biblical principles, talk openly about faith and receive guidance from a gregarious former pastor who still preaches when he speaks.” She said Advantage Academy is typical of the “latest breed of charter schools”—those “born from faith-based principles and taxpayer funds.” She added, “Advantage markets its teaching of creationism and intelligent design. It offers a Bible class as an elective and encourages personal growth through hard work and ‘faith in God and country.’”

The academy’s founder Allen Beck is a former pastor for Assemblies of God who “hopes to instill morals and ethics in students as they learn to count and read.” Beck was quoted as saying, “America is in a battle between secularity and biblical thinking. I want to fuse the two together in a legal way.”
The more open these charter schools get in proclaiming their ID/creationism, the more scrutiny they will get to the point where the whole program will be examined and investigated. Given that the organized Texas educational system does not have a good track record for the teaching of "hard science," this will be a battleground state.

Back from Knee Surgery...

I had knee surgery a little over a week ago and have been unable to do much other than watch football games.