Tag: Statistics

The power of false positives in behavior genetics

By Razib Khan | November 23, 2011 9:57 am

Genomes Unzipped, Size matters, and other lessons from medical genetics:

Smaller studies, which had no power to detect these small effects, were essentially random p-value generators. Sometimes the p-values were “significant” and sometimes not, without any correlation to whether a variant was truly associated. Additionally, since investigators were often looking at only a few variants (often just one!) in a single gene that they strongly believed to be involved in the disease, they were often able to subset the data (splitting males and females, for example) to find “significant” results in some subgroup. This, combined with a tendency to publish positive results and leave negative results in a desk drawer, resulted in a conflicted and confusing body of literature which actively retarded medical genetics progress.

An easy thing to pick on is the reliance on “p-values,” thresholds of statistical significance. Just because something is statistically significant doesn’t mean that it is substance. Statistical significance is just a number, and blindly adhering to a numerical standard in most human endeavors often results in a creeping bias and “gaming” of the measurement. There’s going to be a random distribution of p-values, and for publication you just need to fish in the pool below the 0.05 threshold. It just goes to show that you can’t beat taking a step back, and actually thinking about what your results mean and how you came to them.

(as indicated in the post, this is a problem in many domains, probably most worryingly in medical and pharmaceutical studies)

MORE ABOUT: Statistics

Asian Buddhists are not atheists

By Razib Khan | November 19, 2010 3:10 pm

In response to my two posts below on atheism statistics, people in the comments and around the web (e.g., Facebook) have pointed out that Buddhism is necessarily/can be atheistic, and that Buddhism, is not/not necessarily a religion, and therefore that explains the statistics. Some of these people are lazy/stupid judging by the way the argument is delivered, but they are clearly grounded in a reality which is expressed in books and documentaries which introduce people to Buddhism. There is a small issue which confounds this analysis of the atheism statistics: most East Asians do not identify as Buddhist. This is mostly because most citizens of the People’s Republic of China do not identify with Buddhism. That being said, Buddhism is clearly the dominant organized religion historically in many East Asian nations (though that has not been true in South Korea for the past generation). I reject the equivalence between the role of Catholicism in much of Europe and that of Buddhism in East Asia (the Church was a much more powerful, prestigious, and influential institution than the Buddhist sangha with only a few exceptional periods), but it can be argued that these are Buddhist cultures, just as they are Confucian societies.

But there’s a bigger issue with this objection: most Asians who identify as Buddhist are themselves theists. This is also the case for American Buddhists. Some people have objected that theism in a Buddhist context is not equivalent to theism in a Hindu, and especially Abrahamic sense. There is no creator god obviously. That is fine, but I think it is important to point out that no matter the theological details of their beliefs, most Buddhists do seem to accept the existence of supernatural entities which we would term “gods.” I was aware of this personally because I’ve encountered several people of Chinese origin who tell me that they’re Buddhist, they believe in god, when I tell them I’m an atheist (usually in response to the question about whether I am Muslim).

The previous question as to whether someone was a “Religious person,” “Not a religious person,” or a “Convinced atheist,” can be broken down by religion. I did so. Below are the data for Buddhists alone. I also provided the sample size for Buddhists. The overall N’s were on the order of 1,000-2,000. So you can see that only a small minority (5% actually) of Chinese in the People’s Republic identify as Buddhists. The other values are obviously percentages.

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CATEGORIZED UNDER: Data Analysis, Religion

Life is One, universal common ancestry supported

By Razib Khan | May 13, 2010 3:01 am

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 102,860 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: Read More

CATEGORIZED UNDER: Genetics, Genomics

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