genetics

All posts tagged genetics

Book review: Aging is a Group-Selected Adaptation: Theory, Evidence, and Medical Implications, by Joshua Mitteldorf.

This provocative book argues that our genes program us to age because aging provided important benefits.

I’ll refer here to antagonistic pleiotropy (AP) and programmed aging (PA) as the two serious contending hypotheses of aging. (Mutation accumulation used to be a leading hypothesis, but it seems discredited now, due to the number of age-related deaths seen in a typical species, and due to evidence that aging is promoted by some ancient genes).

Here’s a dumbed down version of the debate:
<theorist>: Hamilton proved that all conceivable organisms age due to AP and/or mutation accumulation.
<critic>: But the PA theories better predict how many die from aging, the effects of telomeres, calorie restriction, etc. Also, here’s some organisms with zero or negative aging …
<theorist>: A few anomalies aren’t enough to overturn a well-established theory. The well-known PA theories are obviously wrong because selfish genes would outbreed the PA genes.
<critic>: Here are some new versions which might explain how aging could enhance a species’ fitness …
<theorist>: I’ve read enough bad group-selection theories that I’m not going to waste my time with more of them.

That kind of reaction from theorists might make sense if AP was well established. But AP seems to have been well established only in the Darwinian sense of being firmly entrenched in scientists’ minds. It got entrenched mainly by being the least wrong of a flawed set of theories, combined with some poor communication between theorists and naturalists. Wikipedia has a surprisingly good[1] page on the evolution of aging that says:

Antagonistic pleiotropy is a prevailing theory today, but this is largely by default, and not because the theory has been well verified.

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Book review: The Vital Question: Energy, Evolution, and the Origins of Complex Life, by Nick Lane.

This book describes a partial theory of how life initially evolved, followed by a more detailed theory of how eukaryotes evolved.

Lane claims the hardest step in evolving complex life was the development of complex eukaryotic cells. Many traits such as eyes and wings evolved multiple times. Yet eukaryotes have many traits which evolved exactly once (including mitochondria, sex, and nuclear membranes).

Eukaryotes apparently originated in a single act of an archaeon engulfing a bacterium. The result wasn’t very stable, and needed to quickly evolve (i.e. probably within a few million years) a sophisticated nucleus, plus sexual reproduction.

Only organisms that go through these steps will be able to evolve a more complex genome than bacteria do. This suggests that complex life is rare outside of earth, although simple life may be common.

The book talks a lot about mitochondrial DNA, and make some related claims about aging.

Cells have a threshold for apoptosis which responds to the effects of poor mitochondrial DNA, killing weak embryos before they can take up much parental resources. Lane sees evolution making important tradeoffs, with species that have intense energy demands (such as most birds) setting their thresholds high, and more ordinary species (e.g. rats) setting the threshold lower. This tradeoff causes less age-related damage in birds, at the cost of lower fertility.

Lane claims that the DNA needs to be close to the mitochondria in order to make quick decisions. I found this confusing until I checked Wikipedia and figured out it probably refers to the CoRR hypothesis. I’m still confused, but at least now I can attribute the confusion to the topic being hard. Aubrey de Grey’s criticism of CoRR suggests there’s a consensus that CoRR has problems, and the main confusion revolves around the credibility of competing hypotheses.

Lane is quite pessimistic about attempts to cure aging. Only a small part of that disagreement with Aubrey can be explained by the modest differences in their scientific hypotheses. Much of the difference seems to come from Lane’s focus on doing science, versus Aubrey’s focus on engineering. Lane keeps pointing out (correctly) that cells are really complex and finely tuned. Yet Lane is well aware that evolution makes many changes that affect aging in spite of the complexity. I suspect he’s too focused on the inadequacy of typical bioengineering to imagine really good engineering.

Some less relevant tidbits include:

  • why vibrant plumage in male birds may be due to females being heterogametic
  • why male mammals age faster than females

Many of Lane’s ideas are controversial, and only weakly supported by the evidence. But given the difficulty of getting good evidence on these topics, that still represents progress.

The book is pretty dense, and requires some knowledge of biochemistry. It has many ideas and evidence that were developed since I last looked into this subject. I expect to forget many of those ideas fairly quickly. The book is worth reading if you have enough free time, but understanding these topics does not feel vital.

Book review: The Intelligence Paradox: Why the Intelligent Choice Isn’t Always the Smart One, by Satoshi Kanazawa.

This book is entertaining and occasionally thought-provoking, but not very well thought out.

The main idea is that intelligence (what IQ tests measure) is an adaptation for evolutionarily novel situations, and shouldn’t be positively correlated with cognitive abilities that are specialized for evolutionarily familiar problems. He defines “smart” so that it’s very different from intelligence. His notion of smart includes a good deal of common sense that is unconnected with IQ.

He only provides one example of an evolutionarily familiar skill which I assumed would be correlated with IQ but which isn’t: finding your way in situations such as woods where there’s some risk of getting lost.

He does make and test many odd predictions about high IQ people being more likely to engage in evolutionarily novel behavior, such as high IQ people going to bed later than low IQ people. But I’m a bit concerned at the large number of factors he controls for before showing associations (e.g. 19 factors for alcohol use). How hard would it be to try many combinations and only report results when he got conclusions that fit his prediction? On the other hand, he can’t be trying too hard to reject all evidence that conflicts with his predictions, since he occasionally reports evidence that conflicts with his predictions (e.g. tobacco use).

He reports that fertility is heritable, and finds that puzzling. He gives a kin selection based argument saying that someone with many siblings ought to put more effort into the siblings reproductive success and less into personally reproducing. But I see no puzzle – I expect people to have varying intuitions about whether the current abundance of food will last, and pursue different strategies, some of which will be better if food remains abundant, and others better if overpopulation produces a famine.

He’s eager to sound controversial, and his chapter titles will certainly offend some people. Sometimes those are backed up by genuinely unpopular claims, sometimes the substance is less interesting. E.g. the chapter title “Why Homosexuals Are More Intelligent than Heterosexuals” says there’s probably no connection between intelligence and homosexual desires, but there’s a connection between intelligence and how willing people are to act on those desires (yawn).

Here is some evidence against his main hypothesis.

Book review: The Beginning of Infinity by David Deutsch.

This is an ambitious book centered around the nature of explanation, why it has been an important part of science (misunderstood by many who think of science as merely prediction), and why it is important for the future of the universe.

He provides good insights on jump during the Enlightenment to thinking in universals (e.g. laws of nature that apply to a potentially infinite scope). But he overstates some of its implications. He seems confident that greater-than-human intelligences will view his concept of “universal explainers” as the category that identifies which beings have the rights of people. I find this about as convincing as attempts to find a specific time when a fetus acquires the rights of personhood. I can imagine AIs deciding that humans fail often enough at universalizing their thought to be less than a person, or that they will decide that monkeys are on a trajectory toward the same kind of universality.

He neglects to mention some interesting evidence of the spread of universal thinking – James Flynn’s explanation of the Flynn Effect documents that low IQ cultures don’t use the abstract thought that we sometimes take for granted, and describes IQ increases as an escape from concrete thinking.

Deutsch has a number of interesting complaints about people who attempt science but are confused about the philosophy of science, such as people who imagine that measuring heritability of a trait tells us something important without further inquiry – he notes that being enslaved was heritable in 1860, but that was useless for telling us how to change slavery.

He has interesting explanations for why anthropic arguments, the simulation argument, and the doomsday argument are weaker in a spatially infinite universe. But I was disappointed that he didn’t provide good references for his claim that the universe is infinite – a claim which I gather is controversial and hasn’t gotten as much attention as it deserves.

He sometimes gets carried away with his ambition and seems to forget his rule that explanations should be hard to vary in order to make it hard to fool ourselves.

He focuses on the beauty of flowers in an attempt to convince us that beauty is partially objective. But he doesn’t describe this objective beauty in a way that would make it hard to alter to fit whatever evidence he wants it to fit. I see an obvious alternative explanation for humans finding flowers beautiful – they indicate where fruit will be.

He argues that creativity evolved to help people find better ways of faithfully transmitting knowledge (understanding someone can require creative interpretation of the knowledge that they are imperfectly expressing). That might be true, but I can easily create other explanations that fit the evidence he’s trying to explain, such as that creativity enabled people to make better choices about when to seek a new home.

He imagines that he has a simple way to demonstrate that hunter-gatherer societies could not have lived in a golden age (the lack of growth of their knowledge):

Since static societies cannot exist without effectively extinguishing the growth of knowledge, they cannot allow their members much opportunity to pursue happiness.

But that requires implausible assumptions such as that happiness depends more on the pursuit of knowledge than availability of sex. And it’s not clear that hunter-gatherer societies were stable – they may have been just a few mistakes away from extinction, and accumulating knowledge faster than any previous species had. (I think Deutsch lives in a better society than hunter-gatherers, but it would take a complex argument to show that the average person today does).

But I generally enjoyed his arguments even when I thought they were wrong.

See also the review in the New York Times.

Book review: The 10,000 Year Explosion: How Civilization Accelerated Human Evolution by Gregory Cochran and Henry Harpending.

This provocative book describes many recent genetic changes in humans, primarily those resulting from the switch from hunter-gatherer lifestyles to agricultural lifestyles. Large changes in diets and disease are the simplest causes of change, but the book also describes subtler influences that alter human minds as well.

I had believed that large populations rarely evolve very fast due to the time required for a mutation to spread. This is true for mutations which provide negligible selective advantage, but the book shows that it’s plausible that a number of mutations have recently gained a large enough selective advantage that the rate at which they become widespread is only modestly dependent on population size. Also, the book makes a surprising but plausible claim that the larger supply of mutations in large populations can mean large populations evolve faster than small populations.

The book is occasionally not as rigorous as I would like. For instance, the claim that Ashkenazi “must have been exposed to very similar diseases” as their neighbors is false if the diseases were sexually transmitted.

Most of their claims convince me that conventional wisdom underestimates how important human genetic differences compared to cultural differences, but leave plenty of room for doubt about the magnitude of that underestimation.

They provide an interesting counterargument to the claim that differences within human populations are larger than the differences between populations. Their belief that differences between populations are more important seems to rest on little more than gut feelings, but they convince me that the conventional wisdom they’re disputing is poorly thought out.

They convinced me to take more seriously the possibility that some Neanderthal genes have had significant effects on human genes, although I still put the odds on that at less than 50 percent.

Most experts were surprised at the news that human DNA seems to contain less than 25000 genes.
Since then signs have emerged that the rest of the DNA (often called junk DNA is quite active, with about 80% of the DNA being transcribed into RNA even though only 1-2% constitutes protein-coding genes.
There’s a lot of mystery about what, if anything, most of that RNA does, but it’s not all junk. One such RNA molecule, HOTAIR, appears to control expression of some genes. RNA has an ability to fold into shapes that may rival proteins in their diversity, so there’s no good reason to think that creating proteins comes close to describing the set of functions that RNA performs.

I recently took a simple genetic test to determine whether I have genes for fast or slow caffeine metabolism. The result says that I’m a fast metabolizer, which indicates that caffeine use reduces my risk of heart attacks rather than increasing it.
This kind of testing is just becoming affordable, and it seems like many more tests of this nature should become common soon.

Book review: Evolution’s Rainbow: Diversity, Gender, and Sexuality in Nature and People by Joan Roughgarden
This book provides some good descriptions of sexual and gender diversity in nature and in a variety of human cultures, and makes a number of valid criticisms of biases against diversity in the scientific community and in society at large.
Many of her attempts to criticize sexual selection theory are plausible criticisms of beliefs that don’t have much connection to sexual selection theory (e.g. the belief that all sexually reproducing organisms fall into one of two gender stereotypes).
Her more direct attacks on the theory amount to claiming that “almost all diversity is good” and ignoring the arguments of sexual selection theorists who describe traits that appear to indicate reduced evolutionary fitness (see Geoffrey Miller’s book The Mating Mind). She practically defines genetic defects out of existence. She tries to imply that biologists agree on her criteria for a “genetic defect”, but her criteria require that a “trait be deleterious under all conditions” (I suspect most biologists would say “average” instead of “all”), and that it reduce fitness by at least 5 percent.
Her “alternative” theory, social selection, may have some value as a supplement to sexual selection theory, but I see no sign that it explains enough to replace sexual selection theory.
She sometimes talks as if she were trying to explain the evolution of homosexuality, but when doing so she is referring to bisexuality, and doesn’t attempt to explain why an animal would be exclusively homosexual.
Her obsession with discrediting sexual selection comes from an exaggerated fear that the theory implies that most diversity is bad. This misrepresents sexual selection theory (which only says that some diversity represents a mix of traits with different fitnesses). It’s also a symptom of her desire to treat natural as almost a synonym for good (she seems willing to hate diversity if it’s created via genetic engineering).
She tries to imply that a number of traits (e.g. transsexualism) are more common than would be the case if they significantly reduced reproductive fitness, but her reasoning seems to depend on the assumption that those traits can only be caused by one possible mutation. But if there are multiple places in the genome where a mutation could produce the same trait, there’s no obvious limit to how common a low-fitness trait could be.
Her policy recommendations are of very mixed quality. She wants the FDA to regulate surgical and behavioral therapies the way it regulates drugs, and claims that would stop doctors from “curing” nondiseases such as gender dysphoria. But she doesn’t explain why she expects the FDA to be more tolerant of diversity than doctors. Instead, why not let the patient decide as much as possible whether to consider something a disease?

Book Review: Race, Evolution, and Behavior: A Life History Perspective by J. Philippe Rushton
Rushton has a plausible theory that some human populations are more k-selected than others. He presents lots of marginal-quality evidence, but that’s no substitute for what he should be able to show if his theory is true.
Much of the book is devoted to evidence about IQs and brain sizes, but he fails to provide much of an argument for his belief that k-selected humans ought to have higher intelligence. It’s easy to imagine that it might work that way. But I can come up with an alternative based on the sexual selection theory in Geoffrey Miller’s book The Mating Mind that seems about as plausible: r-selected humans have more of their reproductive fitness determined by success at competition for mates (as opposed to k-selected humans for whom child support has a higher contribution to reproductive fitness). Since The Mating Mind presents a strong argument that human intelligence evolved largely due to such competition for mates, it is easy to imagine that r-selected humans had stronger selection for the kind of social intelligence needed to compete for mates. Note that this theory suggests the intelligence of k-selected humans might be easier to measure via standardized tests than that of r-selected humans.
Rushton’s analysis of the genetic aspects of IQ makes the usual mistake of failing to do much to control for the effects of motivation on IQ scores (see pages 249-251 of Judith Rich Harris’s book The Nurture Assumption for evidence that this matters for Rushton’s goals).
He also devotes a good deal of space to evidence such as crime rates where it’s very hard to distinguish genetic from cultural differences, and there’s no reason to think he has succeeded in controlling for culture here.
Rushton mentions a number of other traits that are more directly connected to degree of k-selection and less likely to be culturally biased. It’s disappointing that he provides little evidence of the quality of the data he uses. The twinning data seem most interesting to me, as the high twin rates of the supposedly r-selected population follow quite clearly from his theory, it’s hard to come up with alternative theories that would explain such twinning rates, and the numbers he gives look surprisingly different from random noise. But Rushton says so little about these data that I can’t have much confidence that they come from representative samples of people. (He failed to detect problems with the widely used UN data on African AIDS rates, which have recently been shown to have been strongly biased by poor sampling methods, so it’s easy to imagine that he uses equally flawed data for more obscure differences). (Aside – the book’s index is poor enough that page 214, which is where he lists most of his references for the twinning data, is not listed under the entry for twins/twinning).
Rushton occasionally produces some interesting but irrelevant tidbits, such as that Darwin “affirmed human unity” by ending the debate over whether all humanity had a common origin, or that there’s evidence that “introverts are more punctual, absent less often, and stay longer at a job”.
Edward M. Miller has a theory that is similar to but slightly more convincing than Rushton’s in a paper titled Paternal Provisioning versus Mate Seeking in Human Populations.

Book Review: The God Gene : How Faith Is Hardwired into Our Genes by Dean H. Hamer
This book is entertaining but erratic. To start with, the title is misleading. The important parts of the book are about spirituality (as in what Buddhists seek), which has little connection with God or churches. He does a moderately good job of describing evidence that he has identified a gene that influences spirituality. He makes plausible claims that spirituality makes people happy (that part of the book resembles the works of Csikszentmihalyi and Seligman). He makes a half-hearted attempt to argue that spirituality has evolutionary advantages which isn’t very convincing by itself, but in combination with the sexual selection arguments in Miller’s book The Mating Mind it becomes moderately plausible.
About halfway through the book, he runs out of things to say on those subjects and proceeds to wander through a bunch of marginally related subjects.
His descriptions of psilocybin, prozac, and ecstasy were interesting enough to make me want to learn more about those and similar drugs.
His claims that placebos are effective seem very exaggerated (see this abstract).