genetics

All posts tagged genetics

Book review: Warnings: Finding Cassandras to Stop Catastrophes, by Richard A. Clarke and R.P. Eddy.

This book is moderately addictive softcore version of outrage porn. Only small portions of the book attempt to describe how to recognize valuable warnings and ignore the rest. Large parts of the book seem written mainly to tell us which of the people portrayed in the book we should be outraged at, and which we should praise.

Normally I wouldn’t get around to finishing and reviewing a book containing this little information value, but this one was entertaining enough that I couldn’t stop.

The authors show above-average competence at selecting which warnings to investigate, but don’t convince me that they articulated how they accomplished that.

I’ll start with warnings on which I have the most expertise. I’ll focus a majority of my review on their advice for deciding which warnings matter, even though that may give the false impression that much of the book is about such advice.
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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.