Felix Salmon points to someone who asks, Is the European crisis good for America? A piece at Politico suggests that Midterm fury might leave Nancy Pelosi safe. Journalism of this sort would get very boring, very soon, if the journalists actually had to place any money on their musings, either directly by changing their investment portfolio, or getting involved in betting markets like Intrade.

Gene Tests For Everyone. Probably not much value in most of these tests for most people right now. Also, many of these common variants have been found in subject populations which are European, so if you are Colored it might not tell you anything relevant (i.e., the SNP which is identified as a risk has only been shown to have an effect in Europeans, or, you know you have a trait but it turns out you don’t have any of the “common” variants, perhaps because your population has different variants which are common).

Return of the Neanderchimps. Complex demographic history for one and all! I do find the genetic isolation between Bonobos and Common Chimpanzees interesting. Apparently the Congo river was an imposing enough barrier to allow for allopatric speciation. I wonder if this can tell us about the fear our own ancestors might have had in traversing water barriers.

A New Clue to Explain Existence. Physicists can always make themselves look the non-devilish scientists by inserting a reference to God.

Only Processed Meat Boosts Diabetes And Heart Disease. Medicine was quackery until the 20th century. Nutritional science seems to be quackery into the 21st.

The Microcephalin Ancestral Allele in a Neanderthal Individual. No evidence for introgression/admixture at this locus.

Mutations are as you know a double-edged sword. On the one hand mutations are the stuff of evolution; neutral changes on the molecular or phenotypic level are the result of from mutations, as are changes which enhance fitness and so are driven to fixation by positive selection. On the other hand mutations also tend to cause problems. In fact, mutations which are deleterious far outnumber those which are positive. It is much easier to break complex systems which are near a fitness optimum than it is to improve upon them through random chance. In fact a Fisherian geometric analogy of the affect of genes on fitness implies that once a genetic configuration nears an optimum mutations of larger effect have a tendency to decrease fitness. Sometimes environments and selection pressures change radically, and large effect mutations may become needful. But despite their short term necessity these mutations still cause major problems because they disrupt many phenotypes due to pleiotropy.

But much of the playing out of evolutionary dynamics is not so dramatic. Instead of very costly mutations for good or ill, most mutations may be of only minimal negative effect, especially if they are masked because of recessive expression patterns. That is, only when two copies of the mutation are present does all hell break loose. And yet even mutations which exhibit recessive expression tend to generate some drag on the fitness of heterozygotes. And if you sum small values together you can obtain a larger value. This gentle rain of small negative effect mutations can be balanced by natural selection, which weeds does not smile upon less fit individuals who have a higher mutational load. Presumably those with “good genes,” fewer deleterious mutations, will have more offspring than those with “bad genes.” Because mutations accrue from one generation to the next, and, there is sampling variance of deleterious alleles, a certain set of offspring will always be gifted with fewer deleterious mutations than their siblings. This is a genetics of chance. And so the mutation-selection balance is maintained over time, the latter rising to the fore if the former comes to greater prominence.

The above has been a set of logic inferences from premises. Evolution is about the logic of life’s process, but as a natural science its beauty is that it is testable through empirical means. A short report in Science explores mutational load and fitness, and connects it with the ever popular topic of sexual selection, Additive Genetic Breeding Values Correlate with the Load of Partially Deleterious Mutations:

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Didn’t spend enough time on the internet today for a Daily Data Dump. But,

1) ResearchBlogCast #6, sans Kevin Zelnio.

2) Noah Millman is on Bloggingheads.tv.

In the post below I pointed to various differences in regards to acceptance of evolution by demographic. One of the issues is that just because X correlates with Y, does not entail that X causes Y (and of course, if X correlates with Y, and Y correlates with Z, that does not entail that X correlates with Z). You can use the GSS to run some regressions and see what the strongest predictive variables. Because of this I know that the variable BIBLE is very predictive of skepticism of evolution. Additionally, even smart people with college educations who have a literal inerrant view of the Bible are skeptical of evolution. To show the power of Biblical fundamentalism I thought it would be useful to plot differences in regards to the Index of Creationism by various demographics for both Fundamentalists and non-Fundamentalists. So below I have a set of charts which have two series, one for Fundamentalists, and one for non-Fundamentalists, of a given demographic. So for example one chart has Fundamentalists and non-Fundamentalists separated by attainment or non-attainment of college educations.

The primary variables are BIBLE & SCITEST4.

BIBLE is:

Which of these statements comes closest to describing your feelings about teh Bible? 1. The Bible is the actual word of God and is to be taken literally, word for word. 2. The Bible is the inspired word of God but not everything in it should be taken literally, word for word. 3. The Bible is an ancient book of fables, legends, history, and moral precepts recorded by men.

I recoded so that responses 2 and 3 are classed as non-Fundamentalist.

SCITEST4:

For each statement below, just check the box that comes closest to your opinion of how true it is. In your opinion, how true is this? d. Human beings developed from earlier species of animals.

I created the Index of Creationism = (% “definitely not true”) X 3 + (% “probably not true”) X 2 + (% “probably true”) X 1, from three of the four responses to SCITEST4.

In the charts below the blue squares = Fundamentalists. The red diamonds = non-Fundamentalists. I rescaled so that 1 is the minimum for the Index of Creationism on all charts.

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My post last week about Creationism by region set off a fair number of follow up questions. I’ve actually probed the GSS evolution related variables a lot in the past, but I thought I would put it together in one post in a simple fashion for new readers. I used the SCITEST4 variable since its sample size is the largest. The question asked was: ” Human beings developed from earlier species of animals.” It was asked between 1993 and 2000.

There are four answers, definitely true, probably true, probably not true, definitely not true. I put the frequencies in a table below, but I thought it would be useful to have one number to summarize the propensity toward creationism in a demographic. Therefore, I created a simple “index of creationism.” The formula to create it is pretty obvious:

Index of Creationism = (% “definitely not true”) X 3 + (% “probably not true”) X 2 + (% “probably true”) X 1

If the Index of Creationism for a demographic was zero, that means that everyone in the demographic accepted that evolution was definitely true. In contrast, if it was three, that means that everyone in the demographic believed that evolution was definitely not true. The bar chart below has the Indices of Creationism sorted. Below it is a table with the frequencies as well (unsorted, clustered by demographic kind).

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A few preliminaries. First, if you have not updated to the new feed yet, please do do! Go into your RSS and check that your link is: http://feeds.feedburner.com/GeneExpressionBlog. If not, change it. Or if you’re too lazy to check, just follow the link and subscribe again and delete the old feed. Please.

Second, I will be traveling a fair amount over the next four weeks. I won’t post as regularly or frequently. I may not do a link round up, because whole days may pass before I get on the internet! I figured I should mention this because last fall when I didn’t post for four days (I was at the Singularity Summit) a few people made inquiries as to my health. Also, if you haven’t had a comment approved already (in which case your comment goes through automatically), there is a serious probability that you’ll be stuck in the mod queue for days for the next month. Apologies ahead, but please be chill about that.

Affluent Qataris Seek What Money Cannot Buy. This is a very amusing article. The fact is that Gulf Arabs, who have benefited from windfall wealth which they did not earn in any way, have a really minimal work ethic and maximal sense of entitlement. It’s bad form today to dismiss whole populations like this, but I don’t really care, it’s true, everyone who has worked in the Gulf knows this. The New York Times tries to maintain an air of neutral detachment, but the author of the linked article couldn’t keep it up. The piece is about the frustration that Qataris face due to discrimination in employment opportunities because employers stereotype them as relatively lazy, unqualified, and demanding (though it’s really hard to match semi-slave labor too! So “entitled” might mean “refusal to work 18 hours a day for 7 days a week” for minimal pay). Employers and coworkers treat them like the special education kid in the classroom. But that’s because that’s the rational thing to do. We all know, and can admit, that children who have large trust funds can often (though not always!) grow up to be spoiled and rendered far less productive than they would be otherwise because of wealth unearned. Same with Qataris. The final paragraph makes the journalists’ bemusement rather crystal clear:

“Moza al-Malki, a family therapist, said she was angry, too. She said that she had lost her teaching position when she complained that an Indian woman was hired to run a counseling center that she said she had set up. “We are all angry for staying at home,” she said.

A moment earlier, she turned to the Filipino woman walking one step behind her — a servant carrying bags — and told her to go look around the mall they were in while Ms. Malki ordered breakfast. Ms. Malki ordered a croissant with cheese, sent it back because it was too hard, and then settled on an omelet.”

Qataris are very fat too.

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You probably are aware that different populations have different tolerances for high altitudes. Himalayan sherpas aren’t useful just because they have skills derived from their culture, they’re actually rather well adapted to high altitudes because of their biology. Additionally, different groups seem to have adapted to higher altitudes independently, exhibiting convergent evolution. But in terms of physiological function they aren’t all created equal, at least in relation to the solutions which they’ve come to to make functioning at high altitudes bearable. In particular, it seems that the adaptations of the peoples of Tibet are superior than those of the peoples of the Andes. Superior in that the Andean solution is more brute force than the Tibetan one, producing greater side effects, such as lower birth weight in infants (and so higher mortality and lower fitness).

The Andean region today is dominated by indigenous people, and Spanish is not the lingua franca of the highlands as it is everyone in in the former colonial domains of Spain in the New World. This is largely a function of biology; as in the lowlands of South America the Andean peoples were decimated by disease upon first contact (plague was spreading across the Inca Empire when Pizzaro arrived with his soldiers). But unlike the lowland societies the Andeans had nature on their side: people of mixed or European ancestry are less well adapted to high altitudes and women without tolerance of the environment still have higher miscarriage rates.

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Check out the #bg2010 hash-tag on twitter. There’s a lot of interesting tidbits. Here are some tweets from the presentation on the Neandertal genome in relation to the Denisova hominin (a.k.a. “X-woman”):

lukejostins SP: The Denisova finger is from the Neanderthal line, but didn’t interbreed with humans, hence looking like an outgroup
…
dgmacarthur: SP claims that Neanderthals and Denisova archaics are more closely related than either are to humans; intriguing.
…
dgmacarthur: SP: next steps: generate 10-20X coverage of Neanderthal, sequence other archaic humans (e.g. Denisova).

I hope Dr. Daniel MacAthur and Luke Jostins will say more when they get back to Perfidious Albion.

Mythologist of Our Age: Why Ray Bradbury’s stories have seeped into the culture:

Science fiction dates as quickly as any genre, and Bradbury is not entirely immune to this. The futuristic rocket ships he wrote about in 1950 look a lot like the first-generation NASA rockets; the music of the future is Rachmaninoff and Duke Ellington; and in the terrifying “Mars is Heaven,” the planet bears an eerie resemblance to Green Bluff, Ill., right down to Victorian houses “covered with scrolls and rococo.” But the reason Bradbury’s stories still sing on the page is that, despite all his humanoid robots, automated houses, and rocket men, his interest is not in future technologies but in people as they live now—and how the proliferation of convenient technology alters the way we think and the way we treat each other.

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Four Nerds and a Cry to Arms Against Facebook. I kicked in some $ last week for what it’s worth.

The Euro in 2010 Feels Like the Ruble in 1998. The 1998 crisis prompted the bailout of Long Term Capital Management, who turned out to be an appetizer for the latest financial crisis. I’d recommend When Genius Failed: The Rise and Fall of Long-Term Capital Management to get on the inside of a toy model of what’s become the norm over the last few years.

Leamer on the State of Econometrics. This is a podcast, but very interesting. I’ve pulled back from getting too complicated in my data analysis with the GSS in large part because it started to become obvious how easy it was to secretly massage the model to get a statistically significant result. Instead I’ve leaned toward presenting simple descriptive frequencies and providing the variables so that readers can follow up themselves. In that way more complicated digging into the data can (theoretically) occur in the comments and so operate on a level of transparency. Otherwise I’d feel obligated to record and list all the various “quick & dirty” regressions and controls I ran, and that gets tedious.

Infectious Diseases Caused Two-Thirds of the Nearly 9 Million Child Deaths Globally in 2008. I guess the war against infection hasn’t been won.

Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times. It’s all about niches.

One of the notions implicit in most evolutionary models is that the tree of life has a common root. In other words all individuals of all species represent end points of lineages which ultimately coalesce back to the the original common ancestor. The first Earthling, so to speak. I say implicit because common ancestry isn’t necessary for evolution to be valid; after all, we presumably accept that evolutionary process is operative in an exobiological context, if such a context exists. Therefore it is possible that modern extant lineages are derived from separate independent antecedents. A “multiple garden” model. This has seemed less and less plausible as the molecular basis of biology has been elucidated; it looks like the basic toolkit is found all across the tree of life. But with a new found awareness of the power of processes such as horizontal gene transfer the open & shut case is faced with a new element of ambiguity. Or perhaps not?

Here’s a post from Wired, Life on Earth Arose Just Once:

The idea that life forms share a common ancestor is “a central pillar of evolutionary theory,” says Douglas Theobald, a biochemist at Brandeis University in Waltham, Massachusetts. “But recently there has been some mumbling, especially from microbiologists, that it may not be so cut-and-dried.”

Because microorganisms of different species often swap genes, some scientists have proposed that multiple primordial life forms could have tossed their genetic material into life’s mix, creating a web, rather than a tree of life.

To determine which hypothesis is more likely correct, Theobald put various evolutionary ancestry models through rigorous statistical tests. The results, published in the May 13 Nature, come down overwhelmingly on the side of a single ancestor.

A universal common ancestor is at least 10^2,860 times more probable than having multiple ancestors, Theobald calculates.

The paper is now on the Nature website, A formal test of the theory of universal common ancestry. They looked specifically at 23 very conserved proteins across 12 taxa from the three domains of life (those being eukaryotes, prokaryotes, and the archaea). Here’s where the author explains the philosophy behind the statistical technique: (more…)

Ancient DNA set to rewrite human history. Good overview by Rex Dalton at Nature. I assume he knows more than he’s letting on, so a bit of Kremlinology: “In March, the group reported the mitochondrial DNA sequence from this individual, an unknown hominin that, so far, does not genetically match either Neanderthals or H. sapiens and may represent a new species. The team dated the bone to about 40,000 years ago, but others say that the sediments around the bone may be as old as 100,000 years. There is speculation that the bone could be the remains of an older species of Homo, perhaps even of a remnant population of Homo heidelbergensis, known in Europe from 300,000 to 500,000 years ago, or of Homo erectus, found as early as 1.8 million years ago from Africa to Indonesia. A full sequence may help to resolve this.” I think we’ll know a lot more about X-woman and how she relates to us in the near future.

State IQ estimates (2009). Again, proximity to the Canadian border is a boon.

Neanderthals’r'us? A paleoanthropologist’s view. He claims that the genetics is finally aligning with the fossils.

The Neandertal fraction. John Hawks explains what it means to say that 1-4% of non-African ancestry is Neandertal when we always talk about how we’re 98-99% identical to chimpanzees. This came up in the comments but I didn’t address it because a little thought makes this pretty obvious, but now you can read John Hawks’ explanation if you need a boost.

Below is a video of the assault on a Swedish artist who drew Muhammad as a dog. He was at a university event celebrating free speech. People are shouting“Allahu Akbar!” Charming.
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Carl Zimmer asks “Will Anyone In Alabama Speak For Evolution?” The story is that a Republican candidate for governor in Alabama is being accused of not being a Creationist, and he is asserting that he is a Creationist. Some people might be surprised by this, but this is Alabama. It is famously well known that the general public tends to split down the middle in regards to evolution, and that there is a class aspect to the division. But what’s the breakdown by region? The GSS can help.

Let’s look at two variables:

SCITEST4: In your opinion, how true is this? Human beings developed from earlier species of
animals

REGION, which you can see on the Census Division map below:
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