Sunday, July 06, 2014

The Mayans and the Neanderthals

Last week I was reading a news article about a new study that determined that Tibetans inherited a gene that gives them high-altitude tolerance from ancient Denisovans. Denisovans, you may recall, are an extinct human species known primarily by their DNA, that are genetically closer to Neanderthals than us. That Denisovan DNA made it into modern humans is not anything new, but apparently this particular gene variant went extinct except for among Tibetans and some Chinese.

That's interesting in and of itself. However, at the end of the article I read this:

The discovery is the second case in which modern humans have acquired a trait from archaic humans, notes paleogeneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, whose team discovered the Denisovan people. Earlier this year, another team showed that Mayans, in particular, have inherited a gene variant from Neandertals that increases the risk for diabetes.
Wait, what? How did Neanderthal DNA get into Mayans?

A paper published last February reported the results of researchers looking for genetic associations with type 2 diabetes in Mexicans and other Latin Americans. They looked at 9.2 million single nucleotide polymorphisms (SNPs) from 3,848 Mexicans with type 2 diabetes, compared with a similar number of non-diabetics. The scientists found a chunk of the genome where a certain variant containing 5 particular mutations was associated with diabetes. When they looked at other populations, they found the following:


I have simplified their table a little bit. It shows the percent of samples that had the most common version of the gene compared with the version associated with diabetes. You can see that it is hardly found anywhere except among east Asians and Mexicans. Further, when they looked at samples with over 95% Native American DNA, they found the mutant version in about half.

So let's summarize what they found so far: A gene variant associated with type 2 diabetes that is commonly found among Native Americans can also be found among east Asians, but only rarely in Europeans and Africans. That makes sense since Native Americans are descended from east Asians. But what does that have to do with Neanderthals?

Well, in looking at the variant the scientists determine that it diverged from the European version about 800,000 years ago. Modern humans didn't even exist back then, and Africans don't have it, so how could these differences have arisen? It turns out that an unpublished Neanderthal genome has a nearly identical match. Thus, it appears that ancient Asians picked up the gene from Neanderthals. It was then carried into America, and for some reason it is now common among Native Americans.

I didn't find any reference to Mayans in the paper (although I didn't look in the supplementary material) so I'm not sure where that came from, but many Mayans probably did have this gene. Lest you think that Native Americans are special in their inheritance of Neanderthal DNA, the authors point out,
...whereas this particular Neanderthal-derived haplotype is common in the Americas, Latin Americans have the same proportion of Neanderthal ancestry genome-wide as other Eurasian populations (2%)
In other words, many of us have about the same amount of Neanderthal DNA [1], just different parts.

Notes:

1. Africans have little to no Neanderthal DNA because their ancestors remained in Africa and never met Neanderthals.

Source: SIGMA Type 2 Diabetes Consortium, Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico, Nature. 2014 Feb 6;506(7486):97-101


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Thursday, July 03, 2014

Scientists: Bigfoot Still Missing

University of Oxford scientists have published--in a peer-reviewed journal--results of DNA tests for 'anomalous primates' (i.e. Bigfoot). They put out a call for people to send in hair samples and received 57. Actually, not all of the samples were hair, so after they discarded those and others from which DNA could not be extracted, they were left with 30 samples. They sequenced the mitochondrial DNA of the remaining samples and compared the sequences to those in databases. They found polar bear, horse, raccoon, porcupine, dog, and even one human. None of the results came back as not-quite-human. It wasn't a total waste of time though, because a couple of samples from the Himalayas came back as polar bear, suggesting a hybrid species of bears.

The authors conclude:

While it is important to bear in mind that absence of evidence is not evidence of absence and this survey cannot refute the existence of anomalous primates, neither has it found any evidence in support. Rather than persisting in the view that they have been ‘rejected by science’, advocates in the cryptozoology community have more work to do in order to produce convincing evidence for anomalous primates and now have the means to do so.
I think that's a diplomatic way of saying put up or shut up.

Notes:
Source: Sykes, Proc. R. Soc. B 22 August 2014 vol. 281 no. 1789


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Sunday, June 01, 2014

Watch Your Inner Animal

Back in 2008 I read paleontologist Neil Shubin's book, Your Inner Fish. (Dave at Times and Seasons invited me to do a joint review of it.) Now PBS and Neil Shubin have teamed up to make a three-part documentary. It began airing in April and is now available online in its entirety.

The three parts are Your Inner--Fish, Reptile, and Primate. It is extremely well done, and Neil Shubin conveys an infectious enthusiasm. You really should watch the whole thing. But if you only watch one, then I think the Primate episode is the best.

For me, the most important issue raised by the series is the proper pronunciation of 'opossum.' All my life I have understood the 'o' to be silent, but now I see two experts in the video saying "uh-possum." On the other hand, according to the National Park Service, the 'o' is silent. Is this a regional thing, or what?

By the way, several years ago I put together a series of posts that I titled, What Separates Humans from the Animals? I was interested to see that a couple of the examples used in the documentary are covered in my series.

I don't want to hear any excuses about how you couldn't find the documentary, so here it is again: Your Inner Fish.


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Friday, May 23, 2014

Climate Science Versus the Ether

In my last post I highlighted the release of the National Climate Assessment (NCA) and stated that I would hardly have noticed it if it weren't for some of the reaction to it. It was brought to my attention that Bret Baier on Fox News hosted a panel discussion that included George Will, Charles Krauthammer, and Mara Liasson. Will and Krauthammer spent their portion of the time throwing doubt and contempt on climate science, while Liasson played it mostly down the middle.

To be honest, I found myself thinking that if this is what conservative thought-leaders have to say about climate science, then climate science is in a good place. I say this because I thought Will and Krauthammer's opposition was frankly pathetic. Krauthammer appealed to the weather and short-term variations as an excuse to dismiss climate science as legitimate (he should have consulted the report's FAQ). Then, somewhat self-contradictory, he said he would support reductions in carbon emissions if other countries would sign on. Will's argument was that his house in South Carolina hasn't been hit by a hurricane, and that climate scientists are socially induced to support mainstream climate science.

Jonathan Chait at The New Yorker did a nice job of responding to the panel, pointing out that Will was adopting an argument that applies to all of science. (All Science Is Wrong, Concludes Esteemed Fox News Panel.) I don't want to re-do the work done by Chait, so I will refer you to his column. However, I do want to comment on a few specifics. But before doing so, I want to provide a little historical framework.

A fair-minded public cannot weigh scientific evidence themselves, so they look to experts. However, when there is a dispute among experts, the public naturally has trouble coming to a conclusion. Many special interests have discovered that if they can find even a few experts to take their side, it helps to level the playing field in the public arena. This kind of confusion was perfected by the tobacco industry. As scientists increasingly found that tobacco caused cancer, the tobacco industry decided that the best way to defend themselves from the threat of legislation was to cast doubt on the science. One way that they did so was to appeal to scientists who did not think there was a link between tobacco and cancer. It didn't matter how much those scientists were in the minority; their mere existence served to strengthen the tobacco industry's side of the debate. What the tobacco industry understood was that a loud spokesperson for the extreme minority appears equally legitimate to a spokesperson for the majority in the eyes of the public. We see this same model employed for many issues, whether it be vaccination and autism, evolution vs creationism in public schools, or any other number of fringe controversies involving science. In each case, a few clear thinkers stand against the establishment, like David and Goliath.

It is a matter of historical record that some of the same people who fought on the side of the tobacco industry went on to take up opposition to climate science and were the early pioneering skeptics, presumably because of their ideological opposition to government regulation. So perhaps it is not coincidental that some of the same tactics have been used: always emphasizing the limitations of the science, and elevating the waning number of credentialed skeptics who disagree with the mainstream understanding of the science. Whatever the case, when Dr. So-and-so says that global warming is happening because of humans, but Dr. Other-guy says it is not, what conclusion should the public draw?

This is why, to certain extent, there is a proxy rhetorical battle. The word 'consensus' is often invoked by supporters of mainstream climate science. It is an attempt to put the debate in context for the general public. In response, skeptics of mainstream climate science accuse the mainstream of being unscientific for agreeing TOO much and thinking the science is 'settled.' It is a rhetorical battle over expertise.

With that as background, let's come back to the Fox News panel.

BAIER: So you don't buy that 97 percent of scientists who studied the issue --

WILL: Who measured it? Where did that figure come from? They pluck these things from the ether. I do not. The New Yorker magazine, which is impeccably upset about climate change, recently spoke about the report from the Intergovernmental Panel on Climate Change as "the last word on climate change." Now, try that phrase, "the last word on microbiology, quantum mechanics, physics, chemistry." Since when does science come to the end? The New Yorker has discovered the end of this. Who else has?
You can see what Will has done here. First he implies that the consensus does not exist because the 97 percent number has been invented out of nothing. Actually, the number comes from a study in Proceedings of the National Academy of Sciences where the authors did a literature search in order to quantify the size of the debate in the published literature. The authors reported:
Here, we use an extensive dataset of 1,372 climate researchers and their publication and citation data to show that (i) 97–98% of the climate researchers most actively publishing in the field surveyed here support the tenets of ACC outlined by the Intergovernmental Panel on Climate Change, and (ii) the relative climate expertise and scientific prominence of the researchers unconvinced of ACC are substantially below that of the convinced researchers.
It may be that George Will has difficulty distinguishing science from the ether [1].

Having dismissed the 97 percent number, Will then sought to re-cast the meaning of consensus. Rather than a sign of experts converging on truth, Will asserts that agreement is actually a sign of closed sclerotic minds. Krauthammer joined in:
99 percent of physicists [were] convinced that space and time were fixed until Einstein working in a patent office wrote a paper in which he showed that they are not. I'm not impressed by numbers.
Put aside the fact that the kind of revolution that Einstein started is rare, and that his work did not so much invalidate Newtonian physics as incorporate it into something larger. Do you see the dilemma here? If climate scientists disagree, then we are told that we should await further research. But if scientists come to largely agree, then we are told it is a sign of scientific weakness.

My favorite part was toward the very end, when George Will was obviously caught a little off guard by Mara Liasson.
WILL: ...Again, there is a sociology of science, there is a sociology in all of this, and engaging the politics of this, we have to understand the enormous interests now invested in climate change.

LIASSON: On both sides.

WILL: Sure.

LIASSON: The fossil fuel industry has a big interest and you say environmentalists have an interest.

WILL: It pales in comparison to the money flowing from the federal government.
The transcript doesn't capture it, but in the video Will seemed to stammer a little before squeaking out that "sure." But he's a pro, so he recovered quickly by emphasizing the magnitude of the money from the federal government propping up climate science. Thus, according to Will, mainstream science is a product of a combination of financial dependence on the federal government and factors of socialization. For some reason it never seems to cross the minds of Will and Krauthammer that there just might be a powerful sociology in the conservative disbelief in climate science. In fact, their appearance on Fox News bad-mouthing climate science is itself one contributor to the sociological currents of conservatives. How many people came away from that segment thinking, "Well, if George Will and Charles Krauthammer don't buy it, then I don't either?"

Back to Will, does the interest of the fossil fuel industry pale in comparison to the federal government? A quick search turned up a GAO report showing that in 2012 the federal government spent about $2 billion on climate science, about $4 billion supporting technological research, and about $1 billion in aid to developing countries. $7 billion is a lot of money. For comparison, the NIH budget for 2012 was almost $31 billion. What about the fossil fuel industry? I'm not a business guy, so this kind of stuff isn't really my thing. But maybe this is an indicator: excluding divestments and tax-related sources of profit, Exxon Mobile made $8.4 billion in the fourth quarter of 2012. I'm not a mathematician, but if the U.S. federal government's total spending on climate-related science in 2012 was about equal to Exxon Mobile's profits in one quarter of the same year, I'm going to go with "George Will is full of hot air" on this one.

Will and Krauthammer's analysis makes for good cable TV. Their arguments have a veneer of truth (science is an imperfect and social activity, and we can't know exactly what the future will bring), and they articulate them with gravitas. This makes their skepticism emotionally appealing and helps the viewer to feel superior to the other side. But when you drill down into their assertions, it turns out that their wells of truth have run dry. Fans of Will and Krauthammer ought to demand better.

Notes:
1. Chait caught someone else trying to knock down the 97 percent claim. My favorite quote is at the end:
[Anthropogenic global warming is] not a topic of serious debate among the climate science field. It’s a topic of serious debate in American politics because one of the two major parties is controlled by a movement that resorts to bizarre, paranoid explanations for facts that complicate its ideological priors.



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Sunday, May 18, 2014

Climate Change: Still Happening

Major life changes (good) have interfered with blogging for about the last six months. Things seem to be settling down, so I'm hopeful that I'll be able to pick up the pace of my occasional commentary here.

So, what's been going on lately? Well, the National Climate Assessment (NCA) was released earlier this month and a regular reader prodded me for some discussion. So I guess that's as good a place to start as any.

The 2014 NCA website is here. However, I think the website is a little difficult to navigate. If you just want to look at PDF copies you can go here.

Why does the NCA exist? Short answer: it's the law. Wikipedia offers the following:

The National Climate Assessment (NCA) is conducted under the auspices of the Global Change Research Act of 1990. The GCRA requires a report to the President and the Congress every four years that integrates, evaluates, and interprets the findings of the U.S. Global Change Research Program (USGCRP); analyzes the effects of global change on the natural environment, agriculture, energy production and use, land and water resources, transportation, human health and welfare, human social systems, and biological diversity; and analyzes current trends in global change, both human-induced and natural, and projects major trends for the subsequent 25 to 100 years
I should also note that the NCA involves many federal agencies and was reviewed by the National Academy of Sciences. So although it was released by the White House, it is not a partisan document.

The main messages of the NCA are not anything new. Basically, human activities have released, and continue to release, carbon dioxide and other gasses into the atmosphere. These gases trap heat and have begun to warm the planet. This warming is causing changes in climate, and a variety of changes are expected for the future. In general, these changes are expected to cause problems that will need to be dealt with. However, the poor, elderly, and children will be the most vulnerable.

As I said, this is pretty straightforward and is a reiteration of the scientific message we should all be familiar with by now. As such, there's not a whole lot to say about it. If you care at all about the topic, you should at least give it a perusal. You might even want to start with the frequently asked questions (FAQ), where you are most likely to encounter the talking points found in popular discourse.

Being a little absorbed in my life circumstances, I hardly noticed that the NCA had been released. It was the reaction to the NCA that caught my attention. That's the fun part and I'll come to that in my next post.



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Tuesday, April 01, 2014

Daniel Peterson Heading to NRO

Congratulations to Dr. Daniel Peterson for being picked up as a columnist at National Review Online. The Deseret News has the details:

After he was relieved of his editorial duties with the Maxwell Institute (formerly FARMS), many thought that Daniel Peterson's involvement with apologetics was on the decline. However, the Brigham Young University professor still has a lot to say. But the pugnacious polymath will be writing less about religious apologetics, and more about politics as he joins the conservative writers at National Review Online.

Commenting on his blog, Dr. Peterson wrote, "I am, frankly, enormously pleased with this arrangement." Then with irony he added, "This is additional evidence, as my various online critics have long predicted, of my long slide to irrelevancy."
So congratulations to Dr. Peterson. I have genuinely enjoyed his contributions to Mormon studies and apologetics. I'll miss his insights and perspective as he shifts focus to politics, but I wish him well.



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Friday, February 14, 2014

D&C 77 and the World's Week

The Church has released a new Doctrine and Covenants and Church History manual for seminary. The FairMormon blog has a rundown of some items of interest, mostly how the manual deals with sensitive historical topics. What caught my attention was item number seven:

Finally, in discussing section 77 of the Doctrine and Covenants, the manual straightforwardly says, “The 7,000 years [in vv. 6–7] refers to the time since the Fall of Adam and Eve. It is not referring to the actual age of the earth including the periods of creation” (p. 280).
The document that became D&C 77 was produced in March 1832 while Joseph Smith was studying the New Testament's Book of Revelation. It was added to the cannon in 1876, long after his death. The reference in the manual is to the following passage:
6 Q. What are we to understand by the book which John saw, which was sealed on the back with seven seals?
A. We are to understand that it contains the revealed will, mysteries, and the works of God; the hidden things of his economy concerning this earth during the seven thousand years of its continuance, or its temporal existence.
7 Q. What are we to understand by the seven seals with which it was sealed?
A. We are to understand that the first seal contains the things of the first thousand years, and the second also of the second thousand years, and so on until the seventh.
This is reinforced a few verses later:
12 Q. What are we to understand by the sounding of the trumpets, mentioned in the 8th chapter of Revelation?
A. We are to understand that as God made the world in six days, and on the seventh day he finished his work, and sanctified it, and also formed man out of the dust of the earth, even so, in the beginning of the seventh thousand years will the Lord God sanctify the earth, and complete the salvation of man, and judge all things, and shall redeem all things, except that which he hath not put into his power, when he shall have sealed all things, unto the end of all things; and the sounding of the trumpets of the seven angels are the preparing and finishing of his work, in the beginning of the seventh thousand years—the preparing of the way before the time of his coming.
This all reminded me of something I discovered a while ago. Commenting on these passages, President Joseph Fielding Smith wrote:
This revelation confirms the fact that the days of creation were celestial days, and this earth is passing through one week of temporal (mortal) existence, after which it will die and receive its resurrection [1]. [italics in original]
Interestingly, the manual appears to adopt President Smith's interpretation of the length of mortal existence, while rejecting his view on the days of creation. But of greater interest to me is that the belief that the earth is passing through a week of existence has a long history. You can find references to the world-week in the religious literature in Joseph's day and earlier. For example, Scottish preacher Thomas Boston (d. 1732) wrote,
Time has run from the beginning, and is running on in an uninterrupted course of addition of moments, hours, days, months, and years. About four thousand years of it passed before the birth of Christ; and now is begun the one thousand seven hundred and thirty-second year from that happy period. So there want not three hundred years now to complete the world's week of six thousand years; after which many have thought the eternal Sabbath would come.
But it turns out that we can go back much farther to the early Christian era. The Epistle of Barnabas, thought to be written by 135 A.D., contains the same interpretation.
15:3 ...And God made in six days the works of his hands, and finished them on the seventh day, and rested in it and sanctified it.

15:4 Consider, my children, what signify the words, He finished them in six days. They mean this: that in
six thousand years the Lord will make an end of all things, for a day is with him as a thousand years. And he himself beareth witness unto me, saying: Behold this day a day shall be as a thousand years. Therefore, my children, in six days, that is in six thousand years, shall all things be brought to an end.

15:5 And the words, He rested on the seventh day, signify this: After that his Son hath come, and hath caused to cease the time of the wicked one, and hath judged the ungodly, and changed the sun and the moon and the stars, then shall he rest well on the seventh day.
It is possible that in asserting that the seven seals cover the earth's temporal history, one thousand years each, Joseph was tapping into ideas current in his culture. But it's also clear that the world-week concept is ancient, and it's worth noting that the Epistle of Barnabas and the Book of Revelation are probably only separated by 50-80 years, at most. Inasmuch as D&C 77 is about the Book of Revelation, Joseph's interpretation seems on the mark, at least in that it accords with ideas about the earth's history and future that were present just after the New Testament period.

However, we're still left with an enormous conflict with science if we take this scripture to mean that mortality began 6,000 years ago. Now I am a fan of understanding scripture within its cultural context, so I have no reason to doubt that was Joseph's intent. However, there may be other options for us. Personally, I like an interpretation that was advanced by Sterling Talmage, geologist and son of Elder James E. Talmage (himself a defender of the geological record):
...D&C 77:6 very clearly means that the Book of the Seven Seals represented the totality of scripture, to be revealed in successive dispensations; that it contained the previously unknown things regarding the plan of salvation ("the hidden things of his economy"), which were to be shown during the current seven thousand years of earth time ("its continuance") with special reference to humankind in the affairs of the present life ("its temporal existence"). This passage, then, would seem to have no reference whatever to the earth as a physical entity but refer only to the hand-dealings of God with its inhabitants [2].
On this reading, a scripture in direct conflict with science essentially becomes a summary of revealed religion as we have it in our scriptures. What it means for the future remains to be seen.

Notes:
1. Joseph Fielding Smith, Man, His Origin and Destiny, p.465. See also Doctrines of Salvation vol. 1, p. 80.
2. Sterling Talmage, Can Science Be Faith-Promoting, p.176.





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Thursday, February 06, 2014

The Church Teaches Evolution via the Book of Mormon

In what may be the most scientifically detailed explanation on LDS.org, the Church recently added a page that explains some of the basic principles of population genetics, and a few of the processes that result in changes in gene frequencies in a population (i.e. evolution). Book of Mormon and DNA Studies is another new addition to the Gospel Topics section that is meant to give a more detailed (and, ahem, accurate) answer on a controversial topic. (See also Race and the Priesthood, First Vision Accounts, and Book of Mormon Translation.)

Of course, the focus of this article is on the controversy over what lack of DNA support means for the Book of Mormon. Those familiar with the work of Michael Whiting and Ugo Perego (to which the LDS.org page provides links) will see their fingerprints in the new article. Personally, I'm pretty pleased with the result, especially coming from the Church website. As to the substance of the argument, I'm undecided whether the caveats in interpreting the state of the DNA evidence can really do the work required to make the Nephites/Lamanites genetically disappear. (I lean toward skepticism there unless it's paired with extensive intermixing from the beginning. But then we leave science and move into textual interpretation.) For now I think it's the only legitimate scientific way to argue for Book of Mormon historicity, or rather that historicity cannot be dis-proven.

But if we set the Book of Mormon aside for a moment, this article is essentially a primer on how evolution works: the creation of new alleles and their spread, as well as the loss of alleles from a population. Selection was left out of the discussion, (which is unfortunate because it might be relevant--a sensitive issue perhaps? [1]), but in a way it's just as well because natural selection usually gets all of the attention. Genetic drift, founder effect, etc, are random processes that can also play an important role.

So go study Book of Mormon and DNA Studies. As you begin to comprehend its message, you'll begin to understand how Neanderthal DNA is hanging around in many of us, and you'll begin to understand how two separate populations can begin to genetically diverge. And you'll be able to imagine how enough time and change can result in reproductive isolation, with gradual differences in form and behavior. You'll be on your way to understanding how evolution works. Thanks, LDS.org!

Notes:

1. Here's another subtle tip-toe: "Scientists theorize that in an era that predated Book of Mormon accounts, a relatively small group of people migrated from northeast Asia to the Americas by way of a land bridge that connected Siberia to Alaska." Yes, predating the Book of Mormon by about 10-15 thousand years. Some people might have difficulty squaring that with the Bible Chronology.



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