Thursday, March 31, 2016

Louisiana Votes To Keep the LSEA

The Times-Picayune is reporting that the Louisiana legislature passed up an opportunity to repeal the Louisiana Science Education Act.  Julia O’Donoghue writes:
State Sen. John Milkovich, D-Shreveport, made the case for teaching creationism in schools Tuesday night (March 29).

"Scientific research and developments and advances in the last 100 years -- particularly the last 15, 20, 10 years -- have validated the biblical story of creation," the freshman state senator said.

Milkovich, who is the vice chairman of the Senate Education Committee, said archeologists and scientists have verified the origin story of the Christian Bible. He said archeologists had found the remnants of Noah's ark recently. A study of rocks had verified that the earth was created in a week, Milkovich said.

Milkovich isn't the only member of Senate Education Committee who thinks creationism should be taught in schools. The panel voted 4-2 to reject legislation that would have repealed an unconstitutional -- and unenforceable -- law that requires creationism be taught in schools.
Archeologists have found the remnants of Noah's ark recently? Really? Here is what he is what he is referring to (BTW, read Todd Wood's ideas in that link of why we will never find Noah's Ark.  It is ingenious without quite rising to the level of conspiracy theory).  That boat's never going to be found.  The other thing that caught my eye was the letter in front of Milkovich's name, “D.”  This suggests that the teaching of creationism is so ingrained in this area of the south that it crosses party lines.  In fact, there is a healthy mix of Ds and Rs in the story, on both sides. 

Monday, March 28, 2016

A Tour of The Ark Construction

Brandon Ambrosino writes about a tour of the construction site of the Ark Encounter.  He remarks that he was “one of a handful of journalists being led through the empty structure by Ken Ham, president and founder of Answers in Genesis, or AiG.”

The Ark Encounter (Ark-n-Park) is scheduled to open on July 7, 2016, a date that has been chosen because it corresponds to Genesis 7:7, the verse where Noah, his wife, their sons and wives entered the ark.  Ambrosino writes:
Throughout the tour, an armed guard sticks close to Ham, which, we’re told, is standard for media visits. Ham shows us where Noah’s bedroom will be as well as photos on his phone of what some of the other exhibits are expected to look like. AiG boasts that the ark is the world’s largest timber-frame building. Based on the dimensions given in the Bible, the structure is 510 feet long*, 85 feet wide, and 51 feet high. If you laid all this timber end to end, it would stretch from its home in Williamstown to Philadelphia. After the ark opens its doors in July, AiG plans to eventually work on a replica of the Tower of Babel, described in Genesis 11. The entire project will cost more than $150 million, with the first phase costing $91 million. According to estimates from America’s Research Group, the Ark Encounter will host between 1.4 million and 2.2 million visitors in its first year.
Ambrosino is then treated to the general philosophy behind the Ark Encounter and a defense of young earth creationism:
In the world of creationism, any counterfactual is taken to be evidence in the creationists’ favor. When the science complements AiG’s interpretation of the Bible, the science is right. When it challenges it, the science is wrong. What is never wrong, though, is the Bible. According to one article on AiG’s website, “When a scientist’s interpretation of data does not match the clear meaning of the text in the Bible, we should never reinterpret the Bible. God knows just what He meant to say, and His understanding of science is infallible, whereas ours is fallible.”

I asked
[Nathan] Jeanson why he thought virtually all scientists accept evolution and an old age of the earth. He gave me two reasons. The first, he said, is answered by Scripture, which says that wicked people suppress the truth in their ungodliness. The context of that passage from Romans, he says, speaks directly to the origins issue, since it comes from a larger Pauline discussion of nature. “Why do they believe in evolution?” asks Jeanson. “Because Romans 1 tells us they’re going to.”

The other reason he gives for the small number of creationists is that, simply, the majority of scientists haven’t read AiG’s research. Answers in Genesis has created an entire organization dedicated to studying the science and history contained in the opening chapters of Genesis. The group has spent money opening a museum, and now an Ark, and has launched peer-reviewed publications, and has hired dozens of thinkers — none of whom, it should be noted, are idiots; Jeanson is a very sharp, poised man — to demonstrate how modern-day science proves the truth of the Bible.

Jeanson says he’s pleaded with evolutionists to read AiG’s literature, but none of them want to. They’re so biased, he says, that they don’t even want to consider the arguments of creation science.
There are a few things about this passage that really bother me. First, the notion that if science comes up with a finding that doesn't agree with the narrow six-day reading of Genesis, that they are "ungodly" and committing sin by suppressing the “truth.” This cuts to the heart of AiG's core philosophy, that if you don't agree with their interpretation of scripture, you are guilty of sin. This is abhorrent. No other Christian organization that I am familiar with is this arrogant and haughty about their beliefs.  The second statement about scientists not reading their literature, is simply wrong.  There are plenty of scientists who don't want to bother with it but there are quite a few that do.  The only reason that I know that Elizabeth Mitchell's articles on human fossils are full of garbage is because I read them.  Other people do, as well, and you can find reviews of AiG's literature all over the net.  They have, indeed, considered the arguments of creation science and found that they don't have any support.  Nice try, Jeanson.

The article covers all bases, though, to its credit.  Interviewed are Pete Enns and Brad Kramer, of BioLogos, both of whom argue that creationism is harmful because it sets people up for a crisis of faith later when they encounter real science.  They are correct, and I wonder how many people have been led astray and lost their faith by the teachings of AiG.  

*Actually, this is not the correct length given in the Bible. This length is based on the Sumerian cubit.

Thursday, March 24, 2016

More Evidence of Hybrization Between Archaics and Moderns in Africa

Nature's Research Highlights points to a paper written for the journal Genome Research, in which the authors, using whole genome analyses, argue that, for the first time, conclusive evidence of admixture between archaic Homo sapiens and early modern Homo sapiens occurred in Africa.  From the Nature blurb:
Michael Hammer at the University of Arizona in Tucson and his team analysed the entire genomes of seven individuals from two contemporary Western African Pygmy groups. The researchers identified 265 regions of the Pygmy genomes that may have been acquired through ancient interbreeding with other species, events that could have happened as recently as 9,000 years ago.
The article, itself, points out the nature of introgression in hominin evolution, thus:
Introgression, the transfer of genetic material between closely related species through hybridization, is an important and ubiquitous evolutionary force in both plants and animals (Mallet 2007). Although hybrids are often nonviable or infertile, hybridization can be an important driving force for the origin of novel traits and new species (Mallet 2007; Zinner et al. 2011). Within our genus, Homo, there is strong evidence for multiple introgression events between our own species, H. sapiens, and now extinct sister taxa outside Africa (Pääbo 2014). Neanderthal whole-genome sequencing (Green et al. 2010; Prüfer et al. 2014) revealed that Neanderthals contributed an average of ∼2% of the genetic variation of present-day humans living outside of sub-Saharan Africa. This gene flow likely took place 37–86 thousand yr ago (kya), after early modern humans emigrated from Africa and before archaic forms went extinct in Eurasia (Sankararaman et al. 2012), and it may have occurred multiple times (Vernot and Akey 2014, 2015; Kim and Lohmueller 2015).
It has been found, for example, that aspects of our immune system owe themselves to Neandertal introgression. This is an often overlooked aspect of how evolution proceeds.  There is continual debate about whether or not Neandertals represent a separate species from modern humans but the evidence that they interbred and exchanged genes is pretty good at this point.  The authors suggest that introgression of archaic genes occurred continually from the period of one million years down to less than 5 thousand years ago. That says something about the depth of the hybridization as well as the persistence of archaic genes in the modern human genome. 

Wednesday, March 23, 2016

Humans and Meat

New research by Dan Lieberman and Katherine Zink strongly supports what we have suspected for quite some time, that a substantial change in diet of early hominins led to rapid evolution in brain size and social structure.  Brian Handwerk of Smithsonian writes:
After measuring chewing and biting in modern humans, scientists found that a diet that includes one-third raw meat requires far less chewing and bite force exertion than meals of tubers alone. The researchers suggest that with the advent of stone tools, ancient human relatives were able to tenderize their food and make it far easier to chew and digest.

“An important step was just using a simple stone tool to cut our meat and bash our vegetables,” says Harvard University evolutionary biologist Daniel Lieberman.
The idea that fire allowed humans to cook their food and soften it that way has been around for quite some time and arguments usually point to the widespread use of fire toward the end of the Middle Pleistocene as the point where this begins to happen. This is the first time I have seen this argument extended to the early Pleistocene.The article continues:
“If I gave you a piece of raw goat, you would just chew and chew it, like a piece of bubble gum,” Lieberman explains. “Human teeth don't have the kind of shearing ability that, say, dogs' teeth have, and that is necessary to break down meat. With human chewing it just stays in a clump, and studies have shown how that makes digestion far less efficient.”

Cooking makes it easier to chew meat, but evidence suggests that the regular use of fire for cooking didn't pop up until perhaps half a million years ago—far later than the changes to H. erectus. Also, evidence from archaeological and paleontological research points to a spike in human meat consumption by at least 2.6 million years ago.

However, we have plenty of evidence that hominins had begun making stone tools some 3.3 million years ago. Those tools could have been used as pounders to tenderize foods, a practice seen in modern chimps. Flaked tools can also slice foods into easily chewable pieces or remove skin, cartilage and other bits that are harder to chew.

“It's not a coincidence that the oldest evidence for eating meat shows up around the same time as tools,” Lieberman says. “We know that the evolution of meat-eating basically required stone tools. And that had a huge effect on our biology.”
When my wife makes a dish involving chicken breasts, the first thing she does is pound them.  This makes it much softer and easier to eat. 

This is one of the principle reasons I tend to regard arguments in favor of vegetarianism somewhat warily. It is simply not in our nature or physiology to be that way. You can be one, if you wish, but that is not the natural state of things.

Tuesday, March 22, 2016

More Stones Thrown at the Phrase "Theistic Evolution"

Forbes has a post by John Farrell, the science and technical writer, about the inadequacy and inappropriateness of the term “Theistic Evolution.”  He points out that those who label themselves as such are often pariahs not just to modern young-earth creationists but to atheists as well.  Both sides regard them as “compromisers.” But, beyond that, he notes that there are problems with the appropriateness of the term, as well.  He quotes Stacy Tracanos, who writes
“Think about it. If you are a believer, it is already implied that you see all biological and physical processes as created and held in existence by God. You do not need “theistic” in front of biological terms. Who speaks of theistic reproduction? Or theistic gestation, theistic meiosis, or theistic menstruation? Plus, to qualify a biological process as ‘theistic’ implies that the opposite is possible, that God may not be involved in creating certain laws of nature.”
She is correct about this. This is why I tend to favor the term “evolutionary creationist.” It takes the emphasis off the “evolutionist” and puts it on the “creationist.”  This differentiates it from “progressive creationist” or “young earth creationist.” Farrell finishes with this:
The main point is Christian scientists who accept evolution have a much broader understanding of God than—chief engineer. And ‘theistic evolution’, as its summarized for example at Wikipedia, simply misrepresents their position.

Atheists have voiced many arguments for wondering how Christians can maintain belief in a benevolent deity in a world that features so much apparent waste and suffering ‘built in’ to the program, as science has revealed.

But ‘theistic evolution’ isn’t one of their answers, at least not among the serious scientists I know who are theists. And it’s well past its sell-by date.
Probably true.

Thursday, March 17, 2016

Nuclear DNA From the Simo de los Huesos Fossil Material

Nature has a paper that focuses on DNA that has been extracted from the Sima de los Huesos fossil material from the site of Atapuerca, in northern Spain.  The letter does not appear to be behind the pay wall, at the moment.  In 2014, researchers completed a mitochondrial genome sequence for a hominin and the results were interesting, to say the least.  Here is the abstract from the 2014 paper:
Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene1. One of these sites, the ‘Sima de los Huesos’ (‘pit of bones’), has yielded the world’s largest assemblage of Middle Pleistocene hominin fossils2, 3, consisting of at least 28 individuals4 dated to over 300,000 years ago5. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits6, 7, 8. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans9, 10, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.
The authors argued at the time that Denisovans and the population from Sima de los Huesos shared a common ancestor, with a split of about 700 kya, and that both are more closely related to each other than either is to Neandertals.  This strongly suggests that Neandertals are a later derivation from a common crown group that represented the progenitors of all three groups.  The authors suggest that these findings are unexpected because of the incipient Neandertal traits found in the Sima collection, including occipital bunning in the back of the head and some mid-facial prognathism (it looks like the maxilla is puffed out).  Arsuaga and others have stated previously that they thought all of the Sima de los Huesos material belonged to the Neandertal lineage. That, apparently, is not the case.  As these authors point out, there may have been more than one evolutionary lineage roaming the valleys and forests of Europe.

Now the nuclear DNA has been  sequenced and these results strongly suggest that the people represented by the SH population were, in fact, early Neandertals.  From the paper by Meyer et al:
The nuclear DNA sequences of femur AT-5431 and the incisor show that they belonged to the Neanderthal evolutionary lineage, and the limited data available for the molar suggest that the same is true for this specimen. Thus, the results show that the SH hominins were early Neanderthals or closely related to the ancestors of Neanderthals after the divergence from a common ancestor shared with Denisovans. Although it is difficult to determine the age of Middle Pleistocene sites with certainty, geological dating methods1, as well as the length of the branches in trees relating the mtDNAs from femur XIII and an SH cave bear to other mtDNAs2, 12, suggest an age of around 400,000 years for the SH fossils. This age is compatible with the population split time of 381,000–473,000 years ago estimated for Neanderthals and Denisovans on the basis of their nuclear genome sequences and using the human mutation rate of 0.5 × 10−9 per base pair per year7

These authors now suggest that, in combination with the MtDNA results from last year, that the SH hominins are ancestral to Neandertals and that the MtDNA found in later Neandertals is derived relative to that in the SH hominins and that the SH hominins may have had several different MtDNA strands. 

It appears that the evidence supports a model in which the classic Neandertals from France and Germany, which are dated to between 50 and 70 kya, represent a more stabilized, homogenous genome relative to that of earlier hominins.  I have always been struck by the similarities between the Atapuerca 4 cranium and Petralona, from Greece, and this suggests that there may have been extensive migration between regions and considerable gene flow between groups (J. Lawrence Angel, again).  We know that the range of Neandertals extended from the lower Iberian peninsula to Teshik-Tash, north of the Taurus Mountains and Okladnikov, in Siberia.  It does not seem like a stretch that their precursors did the same thing. 

Hat tip to Todd Wood.

Friday, March 11, 2016

Welcome Back My Friends to the Show That Never Ends...

Keith Emerson, formerly of the rock band Emerson, Lake and Palmer, has passed away.  Reports are that he had been in spotty health and had a degenerative neurological disease in his right hand that was robbing him of his ability to play the keyboards, and there is speculation that this led him to take his own life.  That is such a great loss.

I got plugged into ELP in the early 1970s, when I was 12 and followed them through their break-ups and reunions.  Rolling Stone has put together a “Ten Essential Songs” page with commentary on each song.  Of those, probably Emerson's adaptation of Aaron Copeland's Hoedown shows off his technical skill the best.

It has been a bad last twelve months for those of us that grew up in the 1970s. Chris Squire, Paul Kantner, Glenn Frey, David Bowie, and now Keith Emerson. I saw Todd Rundgren in Atlanta last month. Who knows how many more shows he is going to do, as he is pushing 70. Going to the Steve Hackett show in April. He is 66. Time marches on.

Rest in Peace.

Sunday, March 06, 2016

Klinghoffer Responds to the Retraction

David Klinghoffer followed up his initial post about the grasping hand paper with a post involving its inevitable retraction.  Called Censorship in Real Time, he writes:
That was fast. The sound of one hand clapping? Now, it's no hands. Besieged by a furious mob of censors, the editors at the peer-reviewed journal PLOS ONE have retracted a paper on the "architecture" of the human hand that repeatedly invoked notions of "design" and a "Creator."
This was in the works so it is not a surprise that it happened. It is true that there was a good deal of hand-waving in the process but the claims had no place in a paper of that sort. Then Klinghoffer writes this:
I must note here that the theory intelligent design does not infer a "Creator," a religious idea that goes beyond what the scientific evidence says. ID infers a source of intelligence, and leaves it to others to argue about the identity of the source.
This comment is illogical on its face and cuts to the heart of the position that the Discovery Institute has tried to take.  Something either arose by chance or it was created.  It cannot be neither.  If it did not arise by chance, which is the position of many of the DI fellows on different aspects of our anatomy (eye, blood-clotting cascade), then it was created.  If it was created, then by whom or what?  ID absolutely does infer a creator.

While it is quite true that they do their best to deflect attention away from the Christian God as the source of these creations,  it was shown pretty conclusively at Dover that the two are linked at the hip.  This is further exacerbated by public pronouncements by prominent ID proponents such as William Dembski that ID represents the Logos of John's Gospel restated in information theory (1999) as well as their preferred choice of venues for conferences.

That being said, whether or not it is the Christian God or Cosmic Muffin,  it is a “creator.” 

Saturday, March 05, 2016

That Didn't Take Long...

Sure enough, the Discovery Institute's David Klinghoffer has penned a response to the ruckus involving the retracted paper in PLoS ONE about the human grasping hand.  Called Mob with Pitchforks Forms as Science Journal PLOS ONE Acknowledges "Proper Design by the Creator", complete with picture of an angry mob from what looks like the 1930s. In this post, he recounts some of the comments that appeared in response to the publication of the paper:
Another self-identified editor: "As an editor of PLOS ONE, I am ashamed this ever got to be published, and I am ready to resign if this is not retracted immediately."

Still another: "There is no room in the scientific literature for Intelligent Design. This is more than just a 'language issue'."


"Plos One must here intervene to avert damage from all Plos ONE publishers."

"I published three times in P One. Is my career ruined?"

"It is assumed by the scientific community that PLoS ONE is a science-driven journal. If so, this manuscript must be retracted."

"PLoS must remove this article in total, along with the Editor who handled the manuscript."

"I am appalled by this paper and its reference to a 'Creator'. This paper should be retracted immediately."

It goes on. The note of career anxiety -- no, panic -- is telling. These folks don't want to be rendered ritually impure by contact with a bit of injudicious language. Predictably, Twitter is aflutter. And the ever-useful website Retraction Watch has already reported on it. The paper's editor apologized: "I am sorry for this has happened. I am contacting PLoS one to see whether we can fix the issue."
To be sure, a good bit of this is hyperbolic. This paper ruined nobody's career. It did, however, give pause because, briefly, science is in the business of explaining the natural world in terms of natural causes. As Dennis Lamoureux once remarked (paraphrased), it is quite possible that the socks that are missing from my dryer were taken by fairies, but it is much more likely that they got sucked out the drain tube and that is something we can test.

The position that the grasping hand reflects the genius of the creator is broadly analogous to the claim made by Ray Comfort that the Banana must have been crafted by God rather than by evolution because it fits perfectly in the hand, although no such anti-evolutionary claim was made by the authors of the hand paper and Ray Comfort's claim was idiotic, in light of what we know of artificial selection of the banana.

The problem that is giving people the vapors is that the grasping hand claim is baldly non-scientific.  Science is simply not capable of determining whether or not the hand's ability to grasp is divinely bestowed or not.  That is a matter of faith.

And Just In Case You Wondered...

...what the major scientific organizations think about Intelligent Design, here are short, paragraph-long summaries of their positions.  For example:

National Academy of Sciences:
Those who oppose the teaching of evolution in public schools sometimes ask that teachers present evidence against evolution. However, there is no debate within the scientific community over whether evolution occurred, and there is no evidence that evolution has not occurred. Some of the details of how evolution occurs are still being investigated. But scientists continue to debate only the particular mechanisms that result in evolution, not the overall accuracy of evolution as the explanation of life's history.
The American Association for The Advancement of Science:
The [intelligent design] movement has failed to offer credible scientific evidence to support their claim that ID undermines the current scientifically accepted theory of evolution... the lack of scientific warrant for so-called intelligent design theory' makes it improper to include as a part of science education.
The Paleontological Society:
Because evolution is fundamental to understanding both living and extinct organisms, it must be taught in public school science classes. In contrast, creationism is religion rather than science, as ruled in recent court cases, because it invokes supernatural explanations that cannot be tested. Consequently, creationism in any form (including scientific creationism, creation science, and intelligent design) must be excluded from public school science classes. Because science involves testing hypotheses, scientific explanations are restricted to natural causes.
There are many more on the page, as well as links to the statements of other organizations.  One might almost get the idea that they don't think too highly of it as a scientific theory.

St. Paul's Cathedral Ceiling Shows Evolution?????

Really? That would be quite something, if true. Hannah Tooley writes in Premier:
Google Cultural Institute's feature means that online visitors can explore the building on Streetview and see of in-depth details that are usually too far away in the high ceilings to be seen with the naked eye.

The access is significant because, for more than 1,000 years, the three domes in London's famous Cathedral were thought to show beasts, birds and fish as God created them - however, new technology appears to suggest the images portray something different.

The images, painted by William Blake Richmond in 1890, could appear to depict the theory of evolution.

The cathedral's head of collections, Simon Carter, told The Times newspaper that the mosaic appears to support Darwin's theories about the survival of the fittest - which he said is shown through a depiction of a fish with teeth "fighting for survival."

This will not sit well.

Friday, March 04, 2016

PLoS ONE Intelligent Design Paper on Grasping Hand Retracted

A paper published in the journal PLoS ONE has raised a huge ruckus with the scientific community and has led to (apparently successful) calls for its retraction.  Doug Bolton of the Independent writes:
The paper, titled: 'Biomechanical characteristics of hand coordination in grasping activities of daily living' was written by a team of four researchers, three from Huazhong University in China, and one from Worcester Polytechnic Institute in Massachusetts.

Published in the PLOS ONE journal, the fairly conventional study looked at the mechanics of how we grasp things, and involved the measurement of the hand movements of 30 participants.

However, members of the scientific community have demanded the paper be retracted, for its several perceived references to the pseudoscientific theory of intelligent design and a possibly divine 'Creator'.

In the opening sentences of the study, it claims the link between muscles and hand movements is the product of "proper design by the Creator."

Later, it says human hand coordination "should indicate the mystery of the Creator's invention," and concludes by again claiming the mechanical architecture of the hand is the result of "proper design by the Creator."
If you want a copy of this paper, you should probably hurry. It is going through the retraction process even as we speak:
“In light of the concerns identified, the PLOS ONE editors have decided to retract the article, the retraction is being processed and will be posted as soon as possible. We apologize for the errors and oversight leading to the publication of this paper.”
The authors, themselves, have retreated to the excuse that the uses of language that appear to support intelligent design were “translation errors.”

Hat Tip to Rob Mitchell.

UPDATE: There is now a retraction notice on the page that reads thus: 
Following publication, readers raised concerns about language in the article that makes references to a 'Creator', and about the overall rationale and findings of the study.

Upon receiving these concerns, the PLOS ONE editors have carried out an evaluation of the manuscript and the pre-publication process, and they sought further advice on the work from experts in the editorial board. This evaluation confirmed concerns with the scientific rationale, presentation and language, which were not adequately addressed during peer review.

Consequently, the PLOS ONE editors consider that the work cannot be relied upon and retract this publication.

The editors apologize to readers for the inappropriate language in the article and the errors during the evaluation process.

4 Mar 2016: The PLOS ONE Staff (2016) Retraction: Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living. PLoS ONE 11(3): e0151685. doi: 10.1371/journal.pone.0151685
I am quite sure the Discovery Institute will weigh in at some point about this.