evolution

All posts tagged evolution

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: Are We Smart Enough to Know How Smart Animals Are?, by Frans de Waal.

This book is primarily about discrediting false claims of human uniqueness, and showing how easy it is to screw up evaluations of a species’ cognitive abilities. It is best summarized by the cognitive ripple rule:

Every cognitive capacity that we discover is going to be older and more widespread than initially thought.

De Waal provides many anecdotes of carefully designed experiments detecting abilities that previously appeared to be absent. E.g. asian elephants failed mirror tests with small, distant mirrors. When experimenters dared to put large mirrors close enough for the elephants to touch, some of them passed the test.

Likewise, initial observations of behaviorist humans suggested they were rigidly fixated on explaining all behavior via operant conditioning. Yet one experimenter managed to trick a behaviorist into demonstrating more creativity, by harnessing the one motive that behaviorists prefer over their habit of advocating operant conditioning: their desire to accuse people of recklessly inferring complex cognition.

De Waal seems moderately biased toward overstating cognitive abilities of most species (with humans being one clear exception to that pattern).

At one point he gave me the impression that he was claiming elephants could predict where a thunderstorm would hit days in advance. I checked the reference, and what the elephants actually did was predict the arrival of the wet season, and respond with changes such as longer steps (but probably not with indications that they knew where thunderstorms would hit). After rereading de Waal’s wording, I decided it was ambiguous. But his claim that elephants “hear thunder and rainfall hundreds of miles away” exaggerates the original paper’s “detected … at distances greater than 100 km … perhaps as much as 300 km”.

But in the context of language, de Waal switches to downplaying reports of impressive abilities. I wonder how much of that is due to his desire to downplay claims that human minds are better, and how much of that is because his research isn’t well suited to studying language.

I agree with the book’s general claims. The book provides evidence that human brains embody only small, somewhat specialized improvements on the cognitive abilities of other species. But I found the book less convincing on that subject than some other books I’ve read recently. I suspect that’s mainly due to de Waal’s focus on anecdotes that emphasize what’s special about each species or individual. Whereas The Human Advantage rigorously quantifies important ways in which human brains are just a bigger primate brain (but primate brains are special!). Or The Secret of our Success (which doesn’t use particularly rigorous methods) provides a better perspective, by describing a model in which ape minds evolve to human minds via ordinary, gradual adaptations to mildly new environments.

In sum, this book is good at explaining the problems associated with research into animal cognition. It is merely ok at providing insights about how smart various species are.

Book review: Probably Approximately Correct: Nature’s Algorithms for Learning and Prospering in a Complex World, by Leslie Valiant.

This book provides some nonstandard perspectives on machine learning and evolution, but doesn’t convince me there’s much advantage to using those perspectives. I’m unsure how much of that is due to his mediocre writing style. He often seems close to saying something important, but never gets there.

He provides a rigorous meaning for the concept of learnability. I suppose that’s important for something, but I can’t recall what.

He does an ok job of explaining how evolution is a form of learning, but Eric Baum’s book What is Thought? explains that idea much better.

The last few chapters, where he drifts farther from his areas of expertise, are worse. Much of what he says there only seems half-right at best.

One example is his suggestion that AI researchers ought to put a lot of thought into how teaching materials are presented (similar to how schools are careful to order a curriculum, from simple to complex concepts). I doubt that that reflects a reasonable model of human learning: children develop an important fraction of their intelligence before school age, with little guidance for the order in which they should learn concepts (cf. Piaget’s theory of cognitive development); and unschooled children seem to choose their own curriculum.

My impression of recent AI progress suggests that a better organized “curriculum” is even farther from being cost-effective there – progress seems to be coming more from better ways of incorporating unsupervised learning.

I’m left wondering why anyone thinks the book is worth reading.

Book review: The Human Advantage: A New Understanding of How Our Brain Became Remarkable, by Suzana Herculano-Houzel.

I used to be uneasy about claims that the human brain was special because it is large for our body size: relative size just didn’t seem like it could be the best measure of whatever enabled intelligence.

At last, Herculano-Houzel has invented a replacement for that measure. Her impressive technique for measuring the number of neurons in a brain has revolutionized this area of science.

We can now see an important connection between the number of cortical neurons and cognitive ability. I’m glad that the book reports on research that compares the cognitive abilities of enough species to enable moderately objective tests of the relevant hypotheses (although the research still has much room for improvement).

We can also see that the primate brain is special, in a way that enables large primates to be smarter than similarly sized nonprimates. And that humans are not very special for a primate of our size, although energy constraints make it tricky for primates to reach our size.

I was able to read the book quite quickly. Much of it is arranged in an occasionally suspenseful story about how the research was done. It doesn’t have lots of information, but the information it does have seems very new (except for the last two chapters, where Herculano-Houzel gets farther from her area of expertise).

Added 2016-08-25:
Wikipedia has a List of animals by number of neurons which lists the long-finned pilot whale as having 37.2 billion cortical neurons, versus 21 billion for humans.

The paper reporting that result disagrees somewhat with Herculano-Houzel:

Our results underscore that correlations between cognitive performance and absolute neocortical neuron numbers across animal orders or classes are of limited value, and attempts to quantify the mental capacity of a dolphin for cross-species comparisons are bound to be controversial.

But I don’t see much of an argument against the correlation between intelligence and cortical neuron numbers. The lack of good evidence about long-finned pilot whale intelligence mainly implies we ought to be uncertain.

Book review: The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter, by Joseph Henrich.

This book provides a clear explanation of how an ability to learn cultural knowledge made humans evolve into something unique over the past few million years. It’s by far the best book I’ve read on human evolution.

Before reading this book, I thought human uniqueness depended on something somewhat arbitrary and mysterious which made sexual selection important for human evolution, and wondered whether human language abilities depended on some lucky mutation. Now I believe that the causes of human uniqueness were firmly in place 2-3 million years ago, and the remaining arbitrary events seem much farther back on the causal pathway (e.g. what was unique about apes? why did our ancestors descend from trees 4.4 million years ago? why did the climate become less stable 3 million years ago?)

Human language now seems like a natural byproduct of previous changes, and probably started sooner (and developed more gradually) than many researchers think.

I used to doubt that anyone could find good evidence of cultures that existed millions of years ago. But Henrich provides clear explanations of how features such as right-handedness and endurance running demonstrate important milestones in human abilities to generate culture.

Henrich’s most surprising claim is that there’s an important sense in which individual humans are no smarter than other apes. Our intellectual advantage over apes is mostly due to a somewhat special-purpose ability to combine our individual brains into a collective intelligence. His evidence on this point is weak, but it’s plausible enough to be interesting.

Henrich occasionally exaggerates a bit. The only place where that bothered me was where he claimed that heart attack patients who carefully adhered to taking placebos were half as likely to die as patients who failed to reliably take placebos. The author wants to believe that demonstrates the power of placebos. I say the patient failure to take placebos was just a symptom of an underlying health problem (dementia?).

I’m a bit surprised at how little Robin Hanson says about the Henrich’s main points. Henrich suggests that there’s cultural pressure to respect high-status people, for reasons that are somewhat at odds with Robin’s ally/coalition based reasons. Henrich argues that knowledge coming from high-status people, at least in hunter-gatherer societies, tended to be safer than knowledge from more directly measurable evidence. The cultural knowledge that accumulates over many generations aggregates information that could not be empirically acquired in a short time.

So Henrich implies it’s reasonable for people to be confused about whether evidence based medicine embodies more wisdom than eminence based medicine. Traditional culture has become less valuable recently due to the rapid changes in our environment (particularly the technology component of our environment), but cultures that abandoned traditions too readily were often hurt by consequences which take decades to observe.

I got more out of this book than a short review can describe (such as “How Altruism is like a Chili Pepper”). Here’s a good closing quote:

we are smart, but not because we stand on the shoulders of giants or are giants ourselves. We stand on the shoulders of a very large pyramid of hobbits.

Book review: Paleofantasy: What Evolution Really Tells Us about Sex, Diet, and How We Live, by Marlene Zuk

This book refutes some myths about what would happen if we adopted the lifestyle of some imaginary hunter-gather ancestor who some imagine was perfectly adapted to his environment.

I’m a bit disappointed that it isn’t as provocative as the hype around it suggested. It mostly just points out that there’s no single environment that we’re adapted to, plus uncertainty about what our ancestors’ lifestyle was.

She spends a good deal of the book demonstrating what ought to be the well-known fact that we’re still evolving and have partly adapted to an agricultural lifestyle. A more surprising point is that we still have problems stemming from not yet having fully evolved to be land animals rather than fish (e.g. hiccups).

She provides a reference to a study disputing the widely held belief that the transition from hunter-gatherer to farmer made people less healthy.

She cites evidence that humans haven’t evolved much adaptation to specific diets, and do about equally well on a wide variety of diets involving wild foods, so that looking at plant to animal ratios in hunter-gather diets isn’t useful.

Her practical lifestyle advice is mostly consistent with an informed guess about how we can imitate our ancestors’ lifestyle (e.g. eat less processed food), and mainly serves to counteract some of the overconfident claims of the less thoughtful paleo lifestyle promoters.

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.

RNA in our food

What you eat can influence your gene expression.

A post titled Eat Your Grains says:

RNA from our food can survive digestion, sneak into our cells, and control our genes

Researchers studied MicroRNAs from rice that affect cholesterol levels in mice. The effect appears harmful, which is a kind of defense against predation I’d expect from something that hasn’t evolved to cooperate with animals. (Grains have probably evolved some traits that help humans, but only where farmers have long been aware of the traits). Oddly, the researchers say “miRNAs may serve as a novel essential nutrient”, but I expect them to be harmful on average, except in fruits (which have evolved to attract animals).