Tuesday, December 31, 2013

Acceptance of Evolution Drops Among Republicans

The Pew Forum has released the results of a new poll that seem to indicate that acceptance of evolution has stayed relatively unchanged in most demographics since 2009.  Among Republicans, however, it has dropped.  They write:
About half of those who express a belief in human evolution take the view that evolution is “due to natural processes such as natural selection” (32% of the American public overall). But many Americans believe that God or a supreme being played a role in the process of evolution. Indeed, roughly a quarter of adults (24%) say that “a supreme being guided the evolution of living things for the purpose of creating humans and other life in the form it exists today.”

These beliefs differ strongly by religious group. White evangelical Protestants are particularly likely to believe that humans have existed in their present form since the beginning of time. Roughly two-thirds (64%) express this view, as do half of black Protestants (50%). By comparison, only 15% of white mainline Protestants share this opinion.

There also are sizable differences by party affiliation in beliefs about evolution, and the gap between Republicans and Democrats has grown. In 2009, 54% of Republicans and 64% of Democrats said humans have evolved over time, a difference of 10 percentage points. Today, 43% of Republicans and 67% of Democrats say humans have evolved, a 24-point gap.
Other items of interest revealed in the poll:
  • It did not seem to matter whether or not the questions focused on humans or other animals in terms of acceptance of evolution
  • men accepted evolution more than women (65% to 55%)
  • College graduates had higher rates of acceptance than people with high school education or less (72% to 51%)
  • younger respondents had much higher rates of acceptance than retirement age people (68% to 49%)
It is not a surprise that Republicans are moving away from evolution.  The party as a whole has beeen pushing away from that position for years and most of the recent Republican presidential candidates had (usually uninformed) anti-evolutionary position.  Only Jon Huntsman and Mitt Romney deviated from this view.  As the public schools continue to degrade and more conservatives tune out public education in favor of home schooling, the acceptance rate will continue to drop and I predict a greater partisan discrepancy three years from now. 

Tuesday, December 24, 2013

Science Daily: Neanderthal Genome Shows Early Human Interbreeding, Inbreeding

More clarity.  A new study coming out of the University of California at Berzerkeley posits that not only did early modern humans and Neandertals interbreed, but Neandertals inbred, as well.  From the story:
Population geneticist Montgomery Slatkin, graduate student Fernando Racimo and post-doctoral student Flora Jay were part of an international team of anthropologists and geneticists who generated a high-quality sequence of the Neanderthal genome and compared it with the genomes of modern humans and a recently recognized group of early humans called Denisovans.

The comparison shows that Neanderthals and Denisovans are very closely related, and that their common ancestor split off from the ancestors of modern humans about 400,000 years ago. Neanderthals and Denisovans split about 300,000 years ago.
It is not clear to me when you make the species break but for two species to interbreed several hundred thousand years after they split is unusual.  Dogs and wolves, for example, don't have nearly that time depth.  The split must have been a very subtle one, then.  As to how they know that Neandertals interbred without having two related Neandertals on hand, here is the explanation:
In another analysis, Jay discovered that the Neanderthal woman whose toe bone provided the DNA was highly inbred. The woman's genome indicates that she was the daughter of a very closely related mother and father who either were half-siblings who shared the same mother, an uncle and niece or aunt and nephew, a grandparent and grandchild, or double first-cousins (the offspring of two siblings who married siblings).
Depending on how large the population was, this may have been a necessity. it may also be an artifact of sampling. This happens in modern human populations as well but is not common.  As the authors note, there are quite a few unanswered questions.  For example, they really have no idea how much interbreeding between Neandertals, Denisovans and modern humans took place.

Wednesday, December 18, 2013

Another Conservative Drinks From the Wrong Bottle

Granville Sewell has written a piece for Human Events, titled Intelligent Design Theories Gaining Steam in Scientific Circles.  As nearly as I can tell, he has gotten everything wrong.  Lets start with who Granville Sewell is.  He is a mathematics professor at the University of Texas at El Paso and a long-time supporter of intelligent design.

First, the title is indefensible.  Whether or not he, himself, came up with it, there is no evidence whatsoever that intelligent design is gaining ground in scientific circles.  In fact, there is contra-evidence.  There have been no intelligent design-based articles published in any of the mainstream journals and the only journal that is devoted to it, Bio-Complexity, has had one article and two critical reviews published for the entire year of 2013.  The article is co-written by two members of the editorial staff, to boot.

 He writes:
Darwin thought he could explain all of this apparent design through natural selection of random variations. In spite of the fact that there is no direct evidence that natural selection can explain anything other than very minor adaptations, his theory has gained widespread popularity in the scientific world, simply because no one can come up with a more plausible theory to explain evolution, other than intelligent design, which is dismissed by most scientists as “unscientific.”
This is ignorant nonsense with an arrogant tone attached to it.  The theory of evolution has gained widespread popularity because, as a theory, it is incredibly robust, with over 150 years of evidence to back it up, coming from the fields of biology, palaeontology, biogeography, microbiology, molecular biology, geology and others.  Every year, the evidence for evolution continues to pile up as we fill in more pieces of the jigsaw puzzle.  Witness recent discoveries that have shown that the first tetrapods evolved in the late Devonian in shallow seas, that feathers evolved and diversified in dinosaurs as a means of insulation before they evolved into a means of flight, or that the femur of Orrorin tugenensis shows transitional characteristics between late Miocene apes and the earliest hominins.  These are not minor adaptations.  They show selection and evolution across taxonomic levels and reflect predictions about what would be found in the fossil record IF evolution were true.

He writes: 
But, in recent years, as scientific research has continually revealed the astonishing dimensions of the complexity of life, especially at the microscopic level, support for Darwin’s implausible theory has continued to weaken, and since the publication in 1996 of Darwin’s Black Box by Lehigh University biochemist Michael Behe, a growing minority of scientists have concluded, with Behe, that there is no possible explanation for the complexity of life other than intelligent design.

Contrast the publication record of Bio-Complexity with the journal Evolution which, in 2013 alone, published 200 articles. Furthermore, Journal Citation Reports lists 29 journals that have "evolution" in the title. This does not even count those that publish articles on evolution, such as The American Journal of Physical Anthropology, Cell and Systematic Biology to name just a few.

With regard to the "growing minority of scientists,"  if he is referring to the "Dissent From Darwin" list put out by the Discovery Institute, that constitutes no evidence against evolution whatever.  When I analyzed the list a few years back, I found:
13 physicists, 1 plasma physicist, 10 biochemists, 24 chemists, 8 engineers, 7 mathematicians, 2 psychologists, 13 geneticists, and 5 medical doctors.
There are only five geologists on the list, and one lone palaeontologist on it. 

Like most ID writers such as David Berlinski, Cornelius Hunter and David Klinghoffer, he argues that there is dichotomy between accepting evolution and ID:
If you believe that a few fundamental, unintelligent forces of physics alone could have rearranged the basic particles of physics into Apple iPhones, you are probably not an ID proponent, even if you believe in God. But if you believe there must have been more than unintelligent forces at work somewhere, somehow, in the whole process: congratulations, you are one of us after all!
Here is one-dimensional, reductionistic thinking on display. it is either/or. There is no third option, the evolutionary creationist, who argues that the evidence for evolution of life, in all of its 3.5 billion year existence, can be explained as the work of a fantastically inventive and creative God, who took great joy in watching his creation unfold. It is also the thinking of someone who has taken no time to actually learn the basics of evolution and what the evidence is that supports it.  As long as this is the case, we will continue to be subjected to substandard prose such as this offering by Dr. Sewell. 

Tuesday, December 17, 2013

New Study on Neandertal Burials

Science World Report has a story on a study done by New York University. From the press release:
Neanderthals, forerunners to modern humans, buried their dead, an international team of archaeologists has concluded after a 13-year study of remains discovered in southwestern France.

Their findings, which appear in the journal Proceedings of the National Academy of Sciences, confirm that burials took place in western Europe prior to the arrival of modern humans.

“This discovery not only confirms the existence of Neanderthal burials in Western Europe, but also reveals a relatively sophisticated cognitive capacity to produce them,” explains William Rendu, the study’s lead author and a researcher at the Center for International Research in the Humanities and Social Sciences (CIRHUS) in New York City.
The subject of Neandertal burials has been debated for quite some time and there are strong opinions on both sides of the debate. The weight of evidence suggests intentional burial, however. In 1989, Robert Gargett wrote a paper called "Grave Shortcomings: The Evidence for Neandertal Burial," in which he argued that the evidence was lacking. The comments on the article were a sight to behold, some of the most caustic I have ever seen. Dave Frayer wrote, of the remains at La Chapelle aux-Saints:
...we know of no example of a naturally produced rectangular, straight- walled, flat-bottomed pit in the middle of a karstic shelter. That such a natural phenomenon would have occurred and a skeleton would have found its way into it is so unlikely as to make it impossible to consider seriously that the pit sunk into the marl was not the result of deliberate human activity. The manner in which the skeleton lay, on its back, one arm folded and legs flexed, is a strong indication of intentional burial. This seems an unlikely position for accidental death and, in any event, is one that is repeated in numerous other interments1
This seems to be the recent consensus, as well. The focus of the new research is on the cave floor, of which the authors state that the depression discovered was unnatural and suggests a burial.  The other peculiarity is that the remains were found in such good shape, showing no signs of carnivore activity or environmental degradation.  In fact, of the entire suite of Neandertal remains that we have, the La Chapelle fossils are among most well-preserved.  Filling in the pieces.

1Gargett, R. (1989) Grave Shortcomings: The Evidence for Neandertal Burial. Current Anthropology 30(2): 157-190

Monday, December 16, 2013

More on the Texas SBOE Decision to Adopt Scientifically Accurate Textbooks

Church & State has a short piece on the back story behind the adoption of the new scientifically-sound textbooks in Texas.  They write:
In the latest twist of a long-running battle, the Dallas Observer reported in October that the board has narrowed its biology textbook options down to 14 titles – and not one of those choices includes any theories that run counter to evolution.

Unfortunately, no credit is due the board for this development. Many of its members wanted creationism in the books, but textbook publishers refused to put religious concepts into secular science books.

The recent turn of events surprised some observers. Board chair Barbara Cargill is an avid advocate for creationism. In fact, she and her allies invited a few dozen people to review the textbook options this summer, including a handful of known creationists.

Critics believe the review process was stacked to aid creationists. The board has long leaned toward teaching creationism, and this year additional anti-science advocates secured spots on the oversight body.
Textbook writers are highly-tuned to the science they practice and the publishers know that the writers will jump ship rather than have their reputations ruined by putting their names on substandard textbooks. For most of them, money is not the object. It is a labor of love. To have their work watered down is unacceptable.

Judging from the article, some of the board thought that they could get the material changed.  Now that this has not happened, there is no time to go through the selection process again.  What a shame.

This, once again, underscores the need for people on these boards to be scientifically literate.  People that are anti-evolution should have to be able to articulate why, from a scientific perspective, they are that way and defend those answers.  The vast majority won't be able to and it will become clear that they know little of the subject and are basing their decisions on religious perspectives.  I am not sure how, politically, that sort of accountability structure would be set up but these problems will persist until they are.  They just need to be stopped at the door because, as one of my readers once put it, these sorts of viewpoints are religiously-motivated, will tend to persist and their adherents will not budge.   We saw this with Don McLeroy who, in the face of experts in various biological fields, remarked: "I disagree with these experts. Someone has got to stand up to experts." Hard to argue with logic like that.

Thursday, December 12, 2013

Creation Museum Not Charging Admission For Children Under 13 in 2014

The AP is reporting that the Creation Museum in Petersburgh, KY, run by Ken Ham, is not going to be charging admission for children the entire 2014 calendar year.  From the story:
The free admission to the Creation Museum is for children 12 and under and lasts the entire year.

In an online posting, museum co-founder Ken Ham says the offer is part of the museum's "Standing Our Ground — Rescuing Our Kids" theme.

Since it opened in 2007, the museum has drawn criticism for exhibits that scientists say contradict evolution science.

Ham says the museum has collected about $225,000 in child ticket admissions in 2013, so the offer "is going to significantly impact our bottom line." But Ham said he is hopeful that private donations would fill the gap.

Children must be accompanied by one paying adult.
The somewhat more jaded among us also note that the museum has had flagging attendance the last few years and that this may be a means of trying to boost that. This sort of thing is a common way to get people in the door—restaurants often have "kids eat free" days—and often will bring up profits and raise visibility despite the loss of revenue from the move.  Revenue for the museum was 5.1 million dollars in 2012, in a year in which they actually took a loss for the first time.  Assuming a status quo in revenue, $225, 000 represents 4.4% of the take, so it is not an insignificant amount.  Private donations have been drying up, which is why the construction of the Ark-n-Park is in jeopardy. The issuance of junk bonds for it and this move for the museum, itself, are risky. 

I would like to ascribe the lofty motives that Mr. Ham to the fee waiver and I hope they are purer than they look on the surface.  On the surface, it looks like they are trying to stop the bleeding. 

Tuesday, December 10, 2013

Orrorin tugenensis: As Close to the Last Common Ancestor As We Have Gotten?

Based on work by SUNY Stoney Brook, it has been learned that the femur of Orrorin tugenensis, the six-million year-old presumed hominin, also called the "millenium man," has a mix of traits that align it with not just early hominins but late Miocene apes.  Science Daily reports:
According to Dr. Almécija, their study for the first time compared the six-million-year-old Millenium Man femur (called BAR 1002'00) using state-of-the-art morphometric techniques to not only other available hominin fossils but also great apes, hylobatids (ie, gibbons and siamangs), and most importantly to fossil apes that lived in the Miocene. The analysis included more than 400 specimens.

"We discovered that
Orrorin's femur is surprisingly 'intermediate' in both age and anatomy between quadrupedal Miocene apes and bipedal early human ancestors," said Dr. Almécija. "Our paper provides quantitative results of the Orrorin femur as a unique mosaic and stresses the need to incorporate fossil apes into future analyses and discussions dealing with the evolution of human bipedalism, an investigation that should stop considering chimpanzees as default living 'starting point' models."
As the authors note, this is not so different from what was concluded about the gait of Ardipithecus ramidus and that the examination of that hominin led to the idea that, perhaps, modern apes are poor models for early hominin morphology and that the modern apes diverged from the last common ancestor (LCA) in entirely different directions. It is exciting to get to a point where there are obviously transitional characters between hominins and non-hominins. 

The other thing that is quite striking is that there is no obvious dividing line between being a quadruped and a biped and that the transition took some time and was gradual.  Don Johanson, in Lucy: The Beginnings of Humankind, word:
You don’t gradually go from being a quadruped to being a biped. What would the intermediate stage be–a triped? I’ve never seen one of these.
It appears that he may have been wrong, at least about the gradual part.

Monday, December 09, 2013

More Trouble on the High Seas

The Ark-n-Park may be in for more difficulties if animal rights organizations get a hold of it.  Gwen Pearson has written an article for WIRED in which she calls into question some of the methods the builders are using to house the actual animals that are supposed to be part of the exhibit.   She writes:
I’ve helped manage and care for a wide assortment of wild and domestic animals, big and small, over the course of my career. There is a HUGE amount of paperwork, documentation, and inspections involved in having captive animals. It is, frankly, a gigantic pain in the ass, and the animals are healthier and receive better care because of all the annoying, complex rules. That’s why the Ark project set off all sorts of alarm bells in my head.

Keeping animals in captivity is really, really difficult. By gathering animals together in an artificial environment you concentrate all the poop and pee, and just make it easier for diseases to rapidly spread. (Got a kid in daycare? You know exactly what I’m talking about.)

As caretakers we have an ethical duty to provide captive animals with the food and environment they need to stay healthy. Doing that takes specialized knowledge. If you have raptors or game birds, they can get bumblefoot just from the wrong kind of perches. Feeding an imbalanced diet, or just not noticing a raptor is off its food, can tip a bird into a metabolic crash. Ducks can get a fatal type of herpes that spreads rapidly, despite our best efforts.
Evidently, Ham has scaled back the number of animals in the exhibit, dropping the plans for exotic species.  Given that this is an amusement park and not a "real" ark, this is a good thing.  There is something deeper and more disturbing about this whole endeavor, though, that she touches on:
But the fact that how to house and care for their animals is the LAST part of their planning process — a plan to build what is supposed to be a historical artifact made specifically to hold animals — says a lot.
This is an attraction that exists to promote a religious message. It’s not about animals at all. The welfare of the animals and their biology is less important than their ability to reinforce a religious myth.

This isn’t a new issue for creationists. The Museum of Creation and Earth (formerly run by the Institute for Creation Research, and not connected to Answers in Genesis) was recently denied membership in the San Diego Museum Council, in part because of “their animal care and the protocol and care of their exhibitions…a lot of areas that were not in line with membership guidelines.”
I once listened to a lecture by Tony Campolo, How to Rescue the Earth Without Worshiping Nature, in which he lamented the fact that, as Christians, we had ceded the care of the planet and the practice of good ecology to largely secular organizations and had attained a reputation of apathy with regard to these matters.  Now we find that the creators and designers of the Ark Encounter are no better than those that came before.  I cannot find it now (help?) but I saw an interview with a city councilwoman in which she stated that there was little reason to enact conservation legislation since the earth was only six thousand years old and would not be around much longer.  These sorts of things make Christians look irresponsible and ignorant.   

Friday, December 06, 2013

Oldest Human DNA Recovered

Using the fossil material from the Sima de Los Huesos cave, at the Spanish site of Atapuerca, geneticists have recovered DNA.   From the National Geographic story by Karl Gruber:
Analysis of the bones challenges conventional thinking about the geographical spread of our ancient cousins, the early human species called Neanderthals and Denisovans. Until now, these sister families of early humans were thought to have resided in prehistoric Europe and Siberia, respectively. (See also: "The New Age of Exploration.")

But paleontologists write in a new study that the bones of what they thought were European Neanderthals appear genetically closer to the Siberian Denisovans, as shown by maternally inherited "mitochondrial" DNA found in a fossil thighbone uncovered at Spain's Sima de los Huesos cave.

"The fact that they show a mitochondrial genome sequence similar to that of Denisovans is irritating," says Matthias Meyer of Germany's Max Planck Institute for Evolutionary Anthropology in Leipzig, lead author of the study, published Wednesday in Nature.

"Our results suggest that the evolutionary history of Neanderthals and Denisovans may be very complicated and possibly involved mixing between different archaic human groups," he said.
Although the report argues that the Atapuerca remains show a greater similarity to Denisovans than Neandertals, we already know that modern Europeans and East Asians have Neandertal genes in them, indicating that admixture was occurring.  Milford Wolpoff has been arguing for decades that archaic Homo sapiens represents a polytypic species that has genetic ties to modern human groups in different parts of the Old World.  While it certainly appears that Neandertals were distinctive, this information, in conjunction with various studies (here and here) of the Denisovans and African archaics indicates that this model may be the more correct one. 

Lost in the shuffle, however, is that the ability to recover this DNA is an astounding feat of science and portends for great advances in human palaeontology in the future. 

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. 

Monday, October 28, 2013

Jonathan Turley's Thoughts on COPE et al. VS. Kansas State Board of Education

A Jonathan Turley notes, and as I reported a month back, a lawsuit has been filed in Kansas by Citizens for Objective Public Education against the Kansas State Board of Education to keep them from implementing the next generation science standards.  The focus of the complaint is that the science standards use scientific naturalism as their base for understanding science.  From the COPE press release:
The Complaint claims that the Standards lead students to ask “ultimate religious questions” like “where do we come from?” Rather than objectively inform children about these questions in an age-appropriate manner, the F&S lead them “to answer the questions with only materialistic/atheistic answers.” This indoctrination is driven by the use of a concealed Orthodoxy (or doctrine) called methodological naturalism or scientific materialism. The Orthodoxy requires that explanations of the cause and nature of natural phenomena may only use natural, material or mechanistic causes, and must assume that teleological or design conceptions of nature are invalid.
Turley suggests that neither of these are valid. He writes:
The allegations are absurd on a number of levels. First, Plaintiffs have adopted a definition of religion which eliminates any requirement for belief in a supernatural entity. Second, Plaintiffs’ reasoning, if pursued to its logical conclusion, would virtually preclude the teaching of science in the public schools because their objections go to the basis of what we understand as the scientific method. Third, Plaintiffs rely upon the same flawed dualism that taints most fundamentalist arguments, the false assumption that acceptance of the findings of evolutionary biology are incompatible with religious belief in general and Christian belief in particular. The great paleontologist and theologian Teilhard de Chardin, for example, who is quoted above, regarded evolution itself as part of the process of divine creation.
I think that what Turley is getting at in the first part is that religion is overstepping its bounds by demanding that explanations of scientific phenomena include teleological considerations. That is debatable. For the second one he is dead on. Science must proceed within the confines of scientific naturalism to explain things. That is not antithetical to religion. God has created a world that behaves within ordered bounds and is knowable. Science is how we know about it. As far as his third point is concerned, that is one of the greatest debates within Christianity right now: whether or not evolutionary biology can be subsumed within organized Christianity. Entities such as BioLogos think so. Those like AiG and ICR do not. Turley paints a rather broad brush here that is not broadly applicable.  His statement effectively does away with the controversy.  Teilhard de Chardin was a great thinker and a great palaeontologist but as anyone who has read The Jesuit and the Skull
knows, he battled with the church over issues of science his entire life. 

Wednesday, October 23, 2013

Creation Museum To Get Allosaurus Skull

The AP is reporting that the Creation Museum, in Petersburg, Kentucky, has become the recipient of a privately donated, almost complete (but plastically deformed) Allosaurus skull.  Dylan Lovan writes:

The museum said in a written statement Friday that the Allosaurus probably stood about 10 feet tall and 30 feet long, and was a meat-eater. The skeleton, nicknamed "Ebenezer," includes a skull with 53 teeth and will go on display in an exhibit next year.

"For decades I've walked through many leading secular museums, like the Smithsonian in Washington, and have seen their impressive dinosaur skeletons, but they were used for evolution," said Ken Ham, co-founder of the Answers in Genesis ministry, which operates the museum. "Now we have one of that class for our museum."
Unfortunately, they have no idea what to do with it other than put it on display. They can't do a taxonomic study because that would involve evolutionary biology. They cannot try to place it in a geological context because that would involve mainstream geology. All they can really do is sit and look at it.

The story continues:
The well-preserved condition of the Allosaurus is evidence that it died during a worldwide flood as described in the Bible's Old Testament, Andrew Snelling, a geologist at the Creation Museum, said in the statement.

Snelling said the fossil's intact skeleton is proof of an extremely rapid burial, "which is a confirmation of the global catastrophe of a flood a few thousand years ago."
That is absurd. The fact that it was buried rapidly constitutes no evidence whatsoever that it was buried during a world-wide flood. There are plenty of examples of animals that become entombed and fossilized in contexts that didn't involve water.  This happens routinely in volcanic sediments.  The Ashfall deposits in Yellowstone and the Liaoning fossil beds in China are prime examples.    Ironically, it is the deposits at Liaoning that are so damaging to the flood model because they represent multiple volcanic eruptions over  a considerable depositional thickness, something that could not possibly have happened in a world-wide flood. 

The nature of the fossil find, itself, also presents problems for Ham and Snelling (or should, at any rate).  How could something like that fossilize in four and half thousand years?  Actual, carbon-dated archaeological remains that old aren't fossilized.  These, and so many other questions about the flood model are never addressed.

For now, all they can do is put it up and say "Gee, isn't that pretty."


Tuesday, October 22, 2013

Ohio Supreme Court to issue verdict soon in Freshwater case

Here is a story that continues to have legs.  The Kenyon Collegian is reporting that the John Freshwater case, the teacher that was accused of teaching creationism in the classroom and branding the arms of at least one student is going to finally be decided by the Ohio Supreme Court.  Eric Geller writes:
Freshwater’s dismissal brought widespread attention to a local controversy over religious education in public schools that began almost a decade ago. In interviews with the Collegian, Kenyon professors recalled following the story over the years as it evolved from a rejected intelligent design curriculum into allegations of physical violence against students.

Between 2002 and 2003, Freshwater petitioned the Board of Education to adopt a lesson plan based on materials from the Intelligent Design Network, an organization dedicated to promoting creationism. Freshwater’s proposal “was turned down by the District’s science curriculum committee, and then was turned down by the Board,” said Richard Hoppe, an affiliated scholar in biology at Kenyon, who has written extensively about Freshwater’s case for The Panda’s Thumb, a science education blog.

After the last set of allegations about Freshwater’s conduct surfaced in 2008, Hoppe attended 38 of the 40 public school board meetings leading up to the 2011 termination decision. He also taught an interdisciplinary studies course at Kenyon about the conflict between creationism and evolution.

“The materials he used in support of that proposal were classical intelligent design creationism materials,” Hoppe said. “It didn’t surprise me when some of the allegations later were that he taught using those kinds of materials.”

Professor of Biology Wade Powell said Freshwater “was teaching creation science — and the fashionable version of it at that time was called ‘intelligent design’ –– and it coincided with some battles that were being fought at the level of the state board of education about the standards for Ohio education.”
The most disturbing quote from the story is this, though:
Hoppe related an incident from the administrative hearings where a student witness, when asked what he had learned about science from Freshwater’s class, reportedly replied, “I learned that you can’t trust scientists. Scientists don’t know anything. You can’t trust science.”

“That was the most striking and disheartening thing,” Hoppe said. “You can’t trust science.”
Sometimes, when I read what comes out of state legislatures with people like Paul Broun in Georgia, I think that they get these ideas from teachers like Freshwater. Rotten science education breeds rotten science legislation.

Monday, October 21, 2013

More on "Noah" From the Hollywood Reporter

Here is another article on the upcoming "Noah" film by Darren Aronovsky.  Aside from apprehensions and criticisms, we find that the production budget has gone over $125 million and:
The use of visual effects has been so extensive that in some scenes, only an actor's face is in the final image. The film relies on effects to create the flood, of course, but in addition, Noah doesn't feature any real animals. Aronofsky said the creatures in the film are "slightly tweaked" versions of those that exist in nature, and there also are fantastical beings in the mix. The director recently told DGA Quarterly that Industrial Light & Magic had said it did the most complicated rendering in the company's history for the film -- "a nice badge of honor," he said.
Might not matter. ILM did the last Star Wars film and it was awful anyway.

Stormy Seas For Darren Aronovsky and "Noah"

Somehow I missed this.  Darren Aronovsky is directing a big-budget movie adaptation of Genesis 6-9 and is running into difficulties with the studio and his audiences.  Amanda Taylor of The Deseret News reports:
Remakes are difficult enough, but when you're creating a film based on a story from the Bible that happened eons ago, the challenges increase.

Director Darren Aronofsky is creating a blockbuster version of the epic tale of Noah and his ark. Of all the problems that have arisen, the latest seems to be a clash between Paramount and the director over audience reactions. The studio has asked Aranofsky to make some changes, but he doesn't want to budge on his vision, according to The Hollywood Reporter.

An anonymous source told THR, "Darren is not made for studio films. He's very dismissive. He doesn't care about (Paramount's) opinion."

The specifics about the film remain unclear, but reactions from Jewish, Christian and general audiences are reportedly "troubling" enough for Paramount to request some alterations.
Brian Godawa, a Hollywood screenwriter referred to in the story, is extraordinarily critical of the screenplay, and writes in his movie blog:
Though God has not spoken to men or angels for a long time, Noah is haunted by recurring dreams of a rainstorm and flood that he surmises is God’s judgment on man because as Noah says, “At our hand, all he created is dying.” The trees, the animals, and the environment. “If we change, if we work to save it, perhaps he will too [save us].” Or as grandfather Methuselah reiterates, “We have destroyed this world, so we ourselves will be destroyed. Justice.” Oh, and I almost forgot, they kill people too, but it’s not really as important. In another place, “We have murdered each other. We raped the world. The Creator has judged us.” The notion of human evil is more of an afterthought or symptom of the bigger environmental concern of the great tree hugger in the sky.
Although it might reasonably be assumed that these sort of actions on the part of the humans at the time would constitute "evil," that is clearly not the primary focus of God's anger in the Genesis story.Godawa writes as much in his article, which is smack on the money in many ways.  The film is supposed to be out March 28 of next year.  It cannot possibly be as bad as the John Voight, Mary Steenburgen, "Noah's Ark" miniseries that was put out by Robert Halmi, Sr. fourteen years ago. 

No Abominable Snowman After All?

Todd Wood points in the direction of this story about the Yeti, or abominable snowman.  Alan Boyle of NBC Science writes:
After a yearlong quest, a British geneticist says he has matched the DNA from hairs attributed to Himalayan Yetis, also known as "Abominable Snowmen," to a breed of Arctic bear that lived tens of thousands of years ago. Other researchers say that might be as good an explanation as any.

The claim is being made by Oxford University's Bryan Sykes, already well-known for his research on human ancestry. Sykes says his findings suggest that sightings of the legendary Yeti may actually represent observations of a previously unknown creature in the Himalayas — perhaps a hybrid of polar bears and brown bears.

Sykes told NBC News that his aim is to bring the Yeti out of the realm of myth and fantasy. "All my colleagues think I'm taking a risk in doing this, but I'm curious, and I am in a position to actually do something to answer the questions," he said.

Outside experts didn't reject Sykes' conclusion out of hand. Tom Gilbert, professor of paleogenomics at the Natural History Museum of Denmark, told The Associated Press that Sykes' research provided a "reasonable explanation" for past Yeti sightings.
Based on the interview in the story, Sykes appears to believe that these animals exist and that the reason that they have not been found is that they are few and far between with enormous home ranges. This sounds a tad too convenient. Oddly, the new findings don't seem to have deflated his enthusiasm any.

I think that he is off the mark, anyway. As I wrote sometime back, as nearly as I can tell, the earliest stories of these huge creatures are from China and India.   I believe that their source is the extinct ape Gigantopithecus. This ape consisted of three species and the genus ranged very widely, from India to China and northern Vietnam. The largest species, G. blacki stood almost ten feet tall and is estimated to have weighed over 1100 pounds.   Put simply, if you found the fossilized remains, you would come away thinking there was a very, very large animal on the loose. Given the comparative lack of understanding of what a fossil was and how old these animals were when they were alive, it is quite conceivable, even believable that stories would have arisen about them.The earliest Gigantopithecus remains date to around 10 million years ago but G. bilaspurensis lived as recently as 100 k years ago, coeval with late archaic Homo sapiens.  When people came to the New World (from the Amur River area of China) through the Bering Strait, they brought the stories with them, which is why you get stories of Bigfoot in the Pacific Northwest. 

I have no evidence for this, only, as Mr. Spock would say, an hypothesis "which just happens to fit the facts." 

Been on Vacation

Sorry for the lack of posts.  I have been on vacation for the last week with the family down in Florida.  A nice time was had by all.

Thursday, October 10, 2013

Meanwhile, Over In South Carolina...

The South Carolina State Board of Education is about ready to approve the new school standards and some are not happy.  Ron Barnett writes this for Greenville Online:
The state Board of Education gave initial approval to a new set of science standards Wednesday, although some board members tried to overturn the vote out of concern over whether the new guidelines leave room for students’ religious beliefs on the origin of life.

“What I’m asking is to teach both,” said board member Neil Willis of Boiling Springs.

After the board approved first reading of the state’s first revision of its science standards since 2005, Willis made a motion to reconsider the move. One other board member seconded the motion, but it failed on a voice vote.

The standards now will go to the state Education Oversight Committee and come back to the state Board of Education for final action early next year.
As is typical in these debates, however, a basic understanding of how science works is not self-evident in all of the participants:
“To remove the option to believe, I think, is a mistake,” Willis said.

Board member Raye O’Neal Boyd of Winnsboro agreed.

“Where is the opening for people who believe to stick by their beliefs, but at the same time show that they understand what you’re trying to teach them, but not necessarily adopting what you’re trying to teach them?” she asked.
This kind of thing suggests that people are equating scientific evidence  with sociological or cultural debates. It just ain't the same thing. Yes, there are obviously disagreements on how some evidence is explained as theory is being worked out but  if there is scientific evidence for "A" and there is no scientific evidence whatsoever for "B" then it doesn't matter how much you "believe" in "B", it should not be taught as science. Why don't people get this?

Thursday, October 03, 2013

Ball State University: The Backlash Continues

The Muncie Star Press is reporting that now the course purporting to teach atheism that was put in the spotlight by the Discovery Institute is under investigation.  Seth Slabaugh writes:
“You can be assured that the syllabi and curricula of all of the courses you singled out, as well as those of other courses offered by the Honors College and elsewhere at the university, are reviewed and updated on a regular basis,” BSU President Jo Ann Gora wrote in a letter on Monday to The Discovery Institute.

The institute is an anti-evolution, pro-creationism intelligent design think tank in Seattle that maintains supernatural forces shaped the universe.

“Some were undergoing this process before we received the inquiry regarding Honors 296, and others are being reviewed and updated at the present time,” the letter read. “Our intent is to ensure that their content and pedagogy reflect the highest academic standards.”
It appears that Gora is concerned about the allegations but in typical fashion, the Discovery Institute is approaching the controversy in a very ham-fisted way by threatening legal action. At issue seems to be the make-up of the commmittee to evaluate Eric Hedin's class and whether or not equity is being applied across the spectrum. The story continues:
[John] West said, “We gave BSU an opportunity to clarify what it is doing, and to show that it is applying its policies in a fair and legal manner. Because BSU has refused to clarify what it is doing or answer our questions, we will be forced to seek another remedy.”

Gora said she shared the institute’s concerns and demands with the university’s board of trustees before responding to the institute by letter this week.
It seems to me that this can only come out well for the Discovery Institute, despite the fact that I still think that they are providing a mixed message in their protest. The position of the university has always been that intelligent design is not accepted science and should not be taught as such. If the Discovery Institute were protesting the straight teaching of evolutionary theory in biology class, that would be one thing. They have historically argued in an anti-evolutionary vein so that would make sense.

But that is not what they are doing. They are protesting because a strictly theological perspective is being taught in another class and they want that scrutinized. Somewhere in the back of my mind, I am thinking "ID is either science or religion. It cannot be both."

Monday, September 30, 2013

Kansas (Again)

"Who could imagine that they would freak-out somewhere in Kansas."  -Frank Zappa

The next generation science standards have been adopted in Kansas and already there has been a lawsuit filed against the Kansas State Board of Education by a conservative group to block their implementation.  From the AP by way of Fox News:
The group, Citizens for Objective Public Education, had criticized the standards developed by Kansas, 25 other states and the National Research Council for treating both evolution and climate change as key scientific concepts to be taught from kindergarten through 12th grade. The Kansas State Board of Education adopted them in June to replace evolution-friendly standards that had been in place since 2007.

The new standards, like the ones they replaced, reflect the mainstream scientific view that evolution is well-established. Most board members believed the guidelines will improve science education by shifting the emphasis in science classes to doing hands-on projects and experiments.
The complaint focuses on the idea that if the children are taught evolutionary principles, that is tantamount to teaching them atheism.  Most of the direct quotes in the story reveal a general ignorance of science on the part of the lawsuit's promoters, notably John Calvert
Calvert was a key figure in past Kansas evolution debates as a founder of the Intelligent Design Network, contending that life is too complex to have developed through unguided evolution. Joshua Rosenau, programs and policy director for the Oakland, Calif.-based National Center for Science Education, said Calvert has been making such an argument for years and "no one in the legal community has put much stock in it."
Like the folks involved in most of these lawsuits and complaints, I would be surprised if he would be capable of coming up with even a cursorily working definition of evolution.

BioLogos Post The Rise of the Neandertals, Part I is Up!

My newest BioLogos post, The Rise of the Neandertals, Part I is up, here.  Comments are welcome either here or there.

Friday, September 27, 2013

Science Daily: "Anthropologists Confirm Link Between Cranial Anatomy and Two-Legged Walking"

This sort of fits under the category of "gee, who knew" but it is nice to finally have confirmation of something that has been tacitly understood for almost ninety years.  Science Daily writes:
The study, published in a forthcoming issue of the Journal of Human Evolution, confirms a controversial finding made by anatomist Raymond Dart, who discovered the first known two-legged walking (bipedal) human ancestor, Australopithecus africanus. Since Dart's discovery in 1925, physical anthropologists have continued to debate whether this feature of the cranial base can serve as a direct link to bipedal fossil species.
Okay, first, the controversial nature of this is being massively overstated. There is very little doubt, based on comparative anatomical studies, that the placement of the foramen magnum is directly indicative of the kind of locomotor pattern that a given animal employs. That is what clued Dart in to the whole idea that the Taung child represented a biped in the first place. Its foramen magnum was not in the place that you would have expected it to be if the individual had been either a quadrupedal baboon or extinct ape (of which there were none in South Africa). It was, however, located in the same place as in bipedal humans. Further studies demonstrated that if you placed the Taung skull on a quadrupedal animal, it didn't work. The animal would have its face pointed down all of the time, instead of out, like your average quadruped. Put simply, the Taung child was an early biped and there was no reason to think anything differently.

Once again, comparative anatomical studies to the rescue!
As part of the study, the researchers measured the position of the foramen magnum in 71 species from three mammalian groups: marsupials, rodents and primates. By comparing foramen magnum position broadly across mammals, the researchers were able to rule out other potential explanations for a forward-shifted foramen magnum, such as differences in brain size.

According to the findings, a foramen magnum positioned toward the base of the skull is found not only in humans, but in other habitually bipedal mammals as well. Kangaroos, kangaroo rats and jerboas all have a more forward-shifted foramen magnum compared with their quadrupedal (four-legged walking) close relatives.
Well, now we know for sure...sort of.