Wednesday, November 30, 2011

Slightly Off-Topic: Why Science Works Even When People Behave Badly

Ars Technica has a fascinating story about scientific misconduct involving a retrovirus and how the whole thing came apart like a cheap suit. A cautionary tale.

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Tuesday, November 29, 2011

Dear Svante, I am a Neandertal

The Guardian's Notes and Theories has a column on the mail that Svante Pääbo received after delivering the revelation that Neandertals and Early modern humans interbred. They write:
In the months after the paper was published, Pääbo began to receive letters and emails from people who had read about the work. He decided to keep track of the correspondence, at least until September that year, to see if any trends appeared. He wasn't disappointed.

Some 45 men wrote in to declare themselves fully or partially Neanderthal and several asked if they should provide saliva samples for Pääbo to analyse. Over the same few months, only two women wrote in to declare themselves of Neanderthal stock.
I think that it was Dave Frayer who once said that, on an individual trait basis, you could see the remnants of Neandertals in the modern European populations but that if you took the whole suite of Neandertal traits, there wasn't a person alive who had them. I wonder what led the women to think they were Neandertals? “Evening vear. Svimvear. Very nice!”

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Monday, November 28, 2011

British Muslim Students and Evolution

There is, apparently, a growing problem in Great Britain right now with Muslim medical students—they are skipping the lectures on Evolution. According to the Mail Online:
Professors at University College London have expressed concern over the increasing number of biology students boycotting lectures on Darwinist theory, which form an important part of the syllabus, citing their religion.

Similar to the beliefs expressed by fundamentalist Christians, Muslim opponents to Darwinism maintain that Allah created the world, mankind and all known species in a single act.
This was foreseeable given the changes that England has gone through in the last two decades, leading one author to call London “Londonistan.” Young earth creationism has been growing in importance and influence in Islamic countries. Part of the problem is Adnan Oktar, nee Harun Yahya:
Sources within the group Muslims4UK partly blame the growing popularity of creationist beliefs within Islam on Turkish author Harun Yahya who, influenced by the success of Christian creationists in America, has written several books denouncing Darwinist theory.

Yahya associates Dawinism with Nazism and his books are and videos are available at many Islamic bookshops in the UK and regularly feature on Islamic television channels.
That his books have no evidence to support them and are very pompously written does not detract from their influence. I am curious to see how the British press view this, given their reluctance to draw any negative attention to anything Islamic. When Christians reject evolution, they are considered rightwing fundamentalist nuts.

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Lynn Margulis Has Died

From the University of Massachusetts at Amherst:
Margulis was best known for her theory of symbiogenesis, which challenges central tenets of neo-Darwinism. She argued that inherited variation, significant in evolution, does not come mainly from random mutations. Rather, new tissues, organs, and even new species evolve primarily through the long-lasting intimacy of strangers. The fusion of genomes in symbioses followed by natural selection, she suggests, leads to increasingly complex levels of individuality. Margulis was also acknowledged for her contribution to James E. Lovelock’s Gaia concept. Gaia theory posits that the Earth’s surface interactions among living beings sediment, air, and water have created a vast self-regulating system.
The notion of symbiogenesis has come under some guarded acceptance in recent years, her work with Lovelock, not so much. R.I.P.

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Tuesday, November 22, 2011

A Short History of Humans and Vitamin D

The Philadelphia Enquirer has an article on the research done by Nina Jablinski on humans’ evolution of skin color as a response to the need for vitamin D. Most of this is not unknown, the higher in latitude a population is, the lighter the skin color to maximise the amount of Vitamin D that is absorbed from the sun. In a nut shell, this is why equatorial populations are dark-skinned as well. Response to the amount of Vitamin D that is needed for a given population is subject to very high degrees of selection. Faye Flam writes:
Originally, humans made more than enough in skin, Holick said. When some of our ancestors left Africa, they adjusted their skin tone to allow in more sunlight. Penn State's Jablonski found that around the world, the skin color of native people maps almost perfectly onto a map of UV radiation; the more UV, the darker the average skin.

In 2005, Penn State professor Mark Shriver and colleagues isolated a genetic mutation that contributed to Europeans' having white skin, a mutation that in zebra fish leads to absence of the characteristic stripes.

Shriver, a professor of anthropology and genetics, said the original human skin color was probably light, because other apes are light-skinned under their fur. Dark skin became advantageous in Africa when we lost our fur.

Genetic evidence suggests that light-skin-related mutations arose recently, less than 15,000 years ago, and spread fast through Europeans.

Jablonski said that when scientists scraped bits of DNA from Neanderthal skeletons, they found a mutation of another skin-color-related gene. Neanderthals lived in Europe and the Middle East long before our ancestors left Africa, and apparently they independently evolved light skin.

In the Arctic, the Inuit never developed light skin, which scientists at first considered a paradox until they discovered how much Vitamin D is in a traditional Inuit diet, which included oily fish and whale blubber.
That Neandertals underwent a slightly different mutation and selection to the need for Vitamin D suggests that there was at least some separation between them and the incoming modern humans. One wonders what gene was involved in the Denisova DNA.

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Monday, November 21, 2011

The Mind of Neandertals

Nature has a review of a book called How To Think Like a Neandertal by Thomas Wynn and Frederick Coolidge. Curiously, the authors spell “Neandertal” correctly but the Nature editors do not. They still spell it the old way, with the “h” in it. The Germans dropped that over a hundred years ago. Clive Gamble writes:
Wynn and Coolidge conclude that today, Neanderthals would be commercial fishermen or mechanics, based on their enormous strength and ability to learn the motor procedures needed. Their capacity for empathy might even have made them competent physicians, the authors say, although a lack of mathematical ability means that they would never have been able to graduate from medical school. Neanderthals would also make excellent army grunts, with their high levels of pain tolerance, and would be good tacticians in small combat units. They would never rewrite the tactical manual — although tearing it up, however thick, would not be a problem.
Without having read the book (and I plan to), it is difficult for me to accept that we could know these sorts of things based on the fossil record that we have. I am also skeptical of the limitations that are attributed to Neandertals. Once again, your life would be different if you lived in the U.S. when the tundra line extended into southern Ohio and there was no Canada. I would also like to know how they have figured out that Neandertals liked “slapstick humor.”

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Saturday, November 19, 2011

Neandertals Found on the Greek Islands

They are sunny, tranquil and surrounded by gorgeous blue-green ocean. They are the Greek isles and now, it seems, they were also home to a population of Neandertals. The Greek Reporter writes:

Meganisi – a small and beautiful strip of land four miles south-east of Lefkada- is part of the group of small islands called Prighiponisia, among which is the famous Skorpios owned by the Onassis family.

On the basis of elements brought to light during excavations, Meganisi’s first inhabitants – according to archaeologists – were Neanderthal men and women living in that part of the Ionian Sea 100,000 years ago in a period scholars call the Mid-Paleolithic Era. The archaeological discovered on the island of Meganisi provide evidence of the presence of human beings in the Mesolithic Period, which with small intervals cover many millennia to the late Roman period.

This is not much of a surprise. The Greek islands are not very far apart and we already know that archaic Homo sapiens were in Greece some 250-300 thousand years ago as represented by the Petralona skull (below) and some other finds.

If I had the chance to live on those islands, I would, too.

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Friday, November 18, 2011

Slightly Off-Topic: The Nature of Moths

Harriet Walker writes about the nature of moths in this column and, while I am convinced that God does not hate us in the least bit, I am reminded that the world in which we live is not as tame as we would like to think. After all, moths will be moths.

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Thursday, November 17, 2011

What Gigantopithecus Ate

A story in PhysOrg reports on research done on the diet of Gigantopithecus blacki, the immense primate that lived during the late Miocene in southern China and Vietnam. They write:
Drs. ZHAO LingXia, ZHANG LiZhao and WU XinZhi, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Ac of Sciences, and ZHANG FuSong from Institute of Geology and Geophysics, Chinese Academy of Sciences, analyze enamel stable carbon isotope values of G. blacki and the associated mammalian megafauna from two sites in South China, and find that this giant ape and other large mammals solely fed on C3 biomass, and lived in forest habitats, as reported in the journal of Chinese Science Bulletin, 2011(56), No.33:3590-3595.
C3 biomass sources are more primitive than C4, which include the canes and more open-field grains. This is not a surprise, just confirmation of what we suspected.

This was a truly unusual and majestic ape, standing some eight to ten feet tall. There were two species, G. bilasporensis and G. blacki, the latter of which lasted until around 300 k years ago. It is this form that is likely the impetus behind the Sasquatch and abominable snowman stories. Here is an artist' sketch, based on accumulated jaws and teeth.

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Wednesday, November 16, 2011

New BioLogos Post is Up

My new post on early Homo is up at BioLogos. As always, comments are welcome here and there.

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Peter Hess is “Clearing the Middle Path”

Robert Luhn, the Director of Communications for the National Center for Science Education sent me a link to an American Scientific Affiliation profile of Peter Hess. Hess is the staff theologian for the NCSE. The profile is written by Emily Ruppel. She writes:
Two years ago, ASA member Peter Hess participated in a colloquium on Intelligent Design at the University of St. Thomas in Minneapolis. He argued that science can neither discover nor rule out the existence of God. A few days later, in the online discussion sparked by this event, a blogger labeled him the Anti-Christ.
Gotta love that Christian tolerance on full display.If he is the Anti-Christ, then there are a whole bunch of us running around. Onward.
“The problem with Biblical literalists is that they are ignorant of exegetical history,” says Peter, “and are generally unaware that an insistence on a woodenly literal understanding of scripture is a relatively recent invention imposed on the Church’s traditional four-fold interpretation. They’re as ignorant of theology as they are of the sciences they presume to critique…

“On the other hand, the issue with some scientists who are atheists is that they fail to see that they are actually making a theological claim by declaring that there is nothing to believe in. Scientists who feel they are qualified to comment authoritatively on religious faith because they have apprehended some of the truths of the natural world are putting on a very ill-fitting philosophical hat.”
The four-fold sense of scripture interpretation (if I understand it correctly) is that scripture should variously be interpreted in a literal sense, where actual events have been recorded, an allegorical sense, where seemingly actual events are not meant in a literal sense but in an allegorical one, a moral sense in that all scripture is good and useful for teaching a Godly way of approaching life, and an anagogical one, in which a truth or event signifies something greater or points us to Heaven. This is yet another area of my theological education that is severely wanting.

It is also hard not to read the second part of that quote and think of The God Delusion by Richard Dawkins and how badly it fared at the review table. Hess, indeed, wonders why Dawkins has been so ignorant of contemporary issues in Christianity. He is so for the same reason that Ken Ham is so abysmally ignorant of basic evolutionary biology and the fossil record. It is much easier to maintain a hostile position to the other side if you perceive them as promulgating lies and misinformation. That honest, thought-provoking scriptural interpretation or education about the natural history of the earth get lost in the process is simply collateral damage.

The entire article is very good and profiles someone who is honestly struggling to find a common ground where all can discuss the issues. This is, or should be, our fervent prayer.

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Tuesday, November 15, 2011

New Post Up at CFSI

My new post is up at CFSI. It is called Can You Practice a Science You Don't Believe? and deals with the question of whether or not you can practice science with integrity and deal honestly with the evidence and yet not believe the results it provides. As always, comments are welcome.

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Thursday, November 10, 2011

John Evans — “Science and Religion: A False Divide?”

I missed this when it came out. John Evans of the L.A. Times (not normally a newspaper I pick up) wrote an interesting column about the controversy between science and religion and his contention that the whole thing is overhyped. He writes:

On most issues, there is actually very little conflict between religion and science. Religion makes no claims about the speed of hummingbird wings, and there are no university departments of anti-resurrection studies — scientists generally are unconcerned with the vast majority of religious claims and vice versa.

There are, of course, a few fact claims in which conservative Protestant theology and science differ, such as the origins of humans and the universe. Here we find that typical conservative Protestants are likely to believe the teaching of their religion on the issue and not the scientific claim.

We could complain that they are being inconsistent in believing the scientific method some of the time but not always. Yet social science research has long shown that people typically are not very consistent. The people who are more consistent are those who are punished for inconsistency: philosophers, media pundits, political activists and politicians.

I have often marveled at how much emphasis this topic has taken up in the media and religious world. As I pointed out in my post on the Miss America pageant, that the contestants were asked whether or not evolution should be taught in public schools had very little relevance to them. All it did was single out the religious conservatives and also point out that science education had all but failed them in this area. For your average person, the creation-evolution controversy has little traction and most view it as a curiosity of modern society. Consequently, when my church friends ask me about it, I always ask them why it is important to them to learn the science behind the old earth model since such knowledge will needlessly complicate their lives. That doesn't seem to stop them, though.

Evans has one other nugget:

The greatest conflict between fundamentalists, evangelicals and science is not over facts but over values. While scientists like to say that their work is value-free, that is not how the public views it, and conservative Protestants especially have homed in on the moral message of science.
This is a slow realization for most scientists. I tend to view evolution in much the way that I view nuclear energy: regardless of what values we attach to it, it exists—independent of those values. David Klinghoffer, over at the Discovery Institute, argues that “Darwinism” has ruined society and caused evils of all sorts, as if somehow if we brand it as evil, it will just go away.

It is also not just that the vast majority of scientists tend to view science amorally, they view attempts to infuse scientific discourse with morality with repugnance. It is the few here and there that seek to venture beyond the bounds of science to argue for or against the existence of God and even if they are highly regarded in their fields (for example Richard Dawkins), their efforts to do this are not.

The problem is these few are very highly visible and, unfortunately, set the tone for the discourse and the understanding of the scientific enterprise. After all, if Richard Dawkins is an eminent evolutionary biologist and he claims, vociferously, that God doesn't exist, why shouldn't evangelicals attach morality to his science?

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Wednesday, November 09, 2011

Jonathan Dudley Wonders “Why Evangelicals Believe Weird Things”

Author of Broken Words: The Abuse of Science and Faith in American Politics, Jonathan Dudley writes:
Lay evangelicals evaluate the arguments made by “experts” in a manner different from many non-evangelicals. The latter will often ask: How prestigious is her academic pedigree? Is she representing the consensus of similarly credentialed experts? Insofar as I can understand her arguments, do they convince me? Lay evangelicals ask different questions: How good of a Christian is this guy? (Or, in evangelical parlance, “How is his walk with the LORD?”) How closely do his arguments line up with my understanding of the Bible? Is this guy one of us?
Despite the “Blunt stick” approach of this statement, comments made here and in the BioLogos comments sections seem to bear this up to some extent. Ken Ham recently also broadcast this idea far and wide in his address on the “Unbiblical teachings of BioLogos.” It is Their science, not Biblical science. He outlines the problem that is growing in political and evangelical circles as the rift between fundamental evangelicalism and the academy increases. Read the whole thing.

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Wednesday, November 02, 2011

Denisova Update

John Hawks does not think that the recent data from the paper by Skoglund and Jakobsson holds up under scrutiny. He cites striking discrepancies between the analysis presented by these two with a paper that came out by Reich et al. ( called “Denisova admixture and the first modern human dispersals into southeast Asia and oceania.” Their salient finding is that there were very few Denisovan markers in mainland Asian populations.

Hawks suggests that the reason the two papers differ so greatly is that in the paper by Skoglund and Jakobsson, the analysis is picking up only slight differences in gene frequencies between populations, and that, while there is hybridization and migration into the area by Denisovans, it is small in amount. He writes:
We aren't very far from a more definitive answer of this question, as the data continue to accumulate every day. What I find interesting is the way that models can generate these 1% differences in ancestry proportions, depending on sampling and the pattern of migration assumed to have happened in the past. Two estimates that differ by less than a percent are not really different. This paper provides the suggestion of a more widespread Denisovan legacy, and I accept that as a possibility.
It is clear that there was some interbreeding between these populations. How much remains to be seen.

Hat tip to Paul Pavao.
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One Big, Polytypic Family

Science Daily has a story on research from Uppsala University that the Denisova genome is showing up in East Asia. They write:
"Our study covers a larger part of the world than earlier studies, and it is clear that it is not as simple as we previously thought. Hybridization took place at several points in evolution, and the genetic traces of this can be found in several places in the world. We'll probably be uncovering more events like these," says Mattias Jakobsson, who conducted the study together with Pontus Skoglund.
Given that we have evidence of Neandertal hybridization as well, it is appearing as if there was a good deal of gene swapping among many late Pleistocene populations. This is certainly what many researchers think that the fossil material reflects, especially that from South East Asia and China. My guess is that, as they uncover more events, the level of hybridization between Neandertals (and other archaic Homo sapiens populations) and moderns will be found to have been higher than thought.

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