SCIENCE JANUARY 24, 2014
This year’s Edge question, which John Brockman distributes to a stable of scientists and other scholars, is given below, and you could do worse than scanning the 174 answers and reading the ones that intrigue you (the short titles of the posts are the answers to the question):
WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT?
Ideas change, and the times we live in change. Perhaps the biggest change today is the rate of change. What established scientific idea is ready to be moved aside so that science can advance?
Some answers I really like, others I disagree with but still find provocative, while still others are, I think, misguided. Two in the last class are about evolution.
The first is by Roger Highfield, editor of New Scientist from 2008-2011 and now “Director of External Affairs of the Science Museum Group.” While he was editor, New Scientist got a reputation for overblowing new findings about evolution and using them to cast doubt on the entire neo-Darwinian paradigm. This was most prominent in New Scientist‘s “Evolution is Wrong” cover, which I posted about here, and to which several of us responded by sending a letter to the journal. “Darwin was Wrong” was simply wrong.
At any rate, I see that Highfield, who has provided an answer to the Edge question, is still on his crusade against the truth of neo-Darwinism, for the idea he wants to retire—as given in the title of his post—is ”Evolution is true.” In other words, he’s suggesting that modern ideas about evolution are wrong. I will reprise and expand a shorter comment I made on my website about Highfield’s piece (excerpts from Highfield’s piece are indented):
I had a severe attack of gastritis this morning when I saw Roger Highfield’s answer to the Edge Question. What he wants to discard is the idea that “evolution is true”.
Here’s part of what he says:
If evolutionary biologists are really Seekers of the Truth, they need to focus more on finding the mathematical regularities of biology, following in the giant footsteps of Sewall Wright, JBS Haldane, Ronald Fisher and so on.
The messiness of biology has made it relatively hard to discern the mathematical fundamentals of evolution. Perhaps the laws of biology are deductive consequences of the laws of physics and chemistry. Perhaps natural selection is not a statistical consequence of physics, but a new and fundamental physical law. Whatever the case, those universal truths-’laws’-that physicists and chemists all rely upon appear relatively absent from biology.
Little seems to have changed from a decade ago when the late and great John Maynard Smith wrote a chapter on evolutionary game theory for a book on the most powerful equations of science: his contribution did not include a single equation.
Yet there are already many mathematical formulations of biological processes and evolutionary biology will truly have arrived the day that high school students learn the Equations of Life in addition to Newton’s Laws of Motion.
Moreover, if physics is an example of what a mature scientific discipline should look like, one that does not waste time and energy combating the agenda of science-rejecting creationists, we also need to abandon the blind adherence to the idea that the mechanisms of evolution are Truths that lie beyond discussion.
Highfield’s problem seems to be that he wants mathematical laws that describe how evolution proceeds that are as accurate as the mathematical laws characterizing physical processes. Well, although evolution has become considerably more mathematical than when Darwin proposed it in 1859 (On the Origin of Species doesn’t contain a single equation), Highfield’s dream won’t be fulfilled. And that is because evolution is contingent on unpredictable (and unknowable) things like the occurrence of new mutations, environmental changes, and the invasion of predators and parasites. While in many ways evolution is just as deterministic as physics (and could even be somewhat indeterministic if new mutations involve quantum effects), we simply won’t be able to know or measure the things that can be enfolded into overarching “laws” of evolutionary biology. While I applaud the mathematization of my field, I contend that the important principles of that field will largely remain nonmathematical, and can be expressed in a few declarative sentences:
1. Evolution happens: populations change genetically over time.
2. That change is gradual and transformative rather than instantaneous; that is, individuals don’t change, but the genetic constitution of populations changes—and substantial change requires substantial time.
3. Lineages also split, creating the diversity of life on Earth today from the first Ur-organism (and yes, there is, rarely in eukaryotes, horizontal movement of genes, which was the basis of New Scientist’s claim that “Darwin was wrong”).
4. That splitting of lineages is what creates common ancestry, so that any pair of species on Earth had a common ancestor at some time in the past.
5. The “designoid” features of organisms arose through the process of natural selection, although random processes like genetic drift can cause evolution (but not the appearance of design).
These are things about evolution that are true. No math needed.
What we need to abandon is not the idea that “evolution is true”, but Highfield’s claim that a “mature” scientific discipline of evolutionary biology will rest on the same type of predictive equations as does physics. It would be futile, for instance, to try to use “evolutionary laws” to predict what will happen to the gene pool of, say, the African elephant or the white oak. Evolution, like nearly all fields of biology, will inevitably become more mathematical, but to say that it’s “not true” because it doesn’t comprise a series of inviolable laws shows a deep misunderstanding of both evolution and biology
Kevin Kelly is a smart guy who’s had an interesting career. He was editor of the Whole Earth Catalogue (remember that?), founder of Wired Magazine, and someone who writes extensively on technology and other subjects. A bit over three years ago, I reviewed his book What Technology Wants for the New York Times, and found it less than satisfactory.
But what’s even less satisfactory is his response to the Edge question, for what Kelly wants tossed into the dustbin of science is the idea of ”Fully random mutations.” Here’s part of what he says:
What is commonly called “random mutation” does not in fact occur in a mathematically random pattern. The process of genetic mutation is extremely complex, with multiple pathways, involving more than one system. Current research suggests most spontaneous mutations occur as errors in the repair process for damaged DNA. Neither the damage nor the errors in repair have been shown to be random in where they occur, how they occur, or when they occur. Rather, the idea that mutations are random is simply a widely held assumption by non-specialists and even many teachers of biology. There is no direct evidence for it.
On the contrary, there’s much evidence that genetic mutation vary in patterns. For instance it is pretty much accepted that mutation rates increase or decrease as stress on the cells increases or decreases. These variable rates of mutation include mutations induced by stress from an organism’s predators and competition, and as well as increased mutations brought on by environmental and epigenetic factors. Mutations have also been shown to have a higher chance of occurring near a place in DNA where mutations have already occurred, creating mutation hotspot clusters—a non-random pattern.
While we can’t say mutations are random, we can say there is a large chaotic component, just as there is in the throw of a loaded dice. But loaded dice should not be confused with randomness because over the long run—which is the time frame of evolution—the weighted bias will have noticeable consequences. So to be clear: the evidence shows that chance plays a primary role in mutations, and there would be no natural selection without chance. But it is not random chance. It is loaded chance, with multiple constraints, multi-point biases, numerous clustering effects, and skewed distributions.
So why does the idea of random mutations persist? The assumption of “random mutation” was a philosophical necessity to combat the erroneous earlier idea of inherited acquired traits, or what is commonly called Lamarckian evolution. As a rough first-order approximation, random mutation works pretty well as an intellectual and experimental framework. But the lack of direct evidence for actual random mutations has now reached a stage where the idea needs to be retired.
This is, as the physicists say, “not even wrong.” For Kelly gets the biological meaning of “random mutations” wrong from the outset, and that makes the rest of his essay irrelevant. What biologists mean when they say “mutations are random” is not that they don’t occur more often at some genes than others, nor that some errors in DNA replication aren’t more frequent than other errors. We’ve known for years that some genes are more “mutable” than others, and that some types of lesions are far more frequent than others. Nor do we mean that mutation rates are impervious to environmental factors, which is also wrong (you can jack them up, for instance, by feeding organisms mutagens like ethidium bromide, or dosing them with X-rays).
What we mean by random mutations is simply this:
“The chance of a single mutation being “adaptive” for the organism (i.e., promoting the replication of the gene in which it occurs) does not depend on the environment in which it finds itself.”
In other words, the genome does not somehow “know” that a mutation would be adaptive, so there is no way that it can produce a higher proportion of ”good” mutations when the environment changes in a certain way. When it gets colder, for example, we don’t see a higher proportion of mutations in mammals that give them longer fur or shorter ears. Most mutations are deleterious in all environments, and a few are useful, but the proportion of useful ones doesn’t increase when the environment changes.
(If you don’t like the term “random” because it’s confusing, then you might use an alternative term suggested by my friend and colleague Paul Sniegowski at Penn, who studies “adaptive mutation.” He suggests that we replace the sentence “mutations are random” with “mutations are indifferent.” What he means is that the proportion of adaptive mutations is indifferent to the environment encountered by the organism. It means the same thing as “random” as I’ve defined it above, but may be less confusing.)
And there are a lot of data that testify to this, particularly in microorganisms. Further, we know of no genetic or biochemical mechanism for jacking up the proportion of useful mutations when the environment changes.
There are some controversial data in microorganisms that the overall mutation rate can rise in times of stress, and you can show via population-genetic theory that—in principle—such an increase, by promoting an increased number (not proportion) of adaptive mutations, will keep the mutation rate higher than it would be otherwise. (To use technical jargon, the new “adaptive” mutations will be physically linked on the chromosome to those mutations that simply cause an overall increase in mutation rate. The adaptive mutations, when they rise in frequency, will then drag along, by genetic “hitchhiking,” the mutations that jack up the mutation rates of all genes, so what we get at the end is an evolved increase in the overall mutation rate in response to environmental stress. This is called “adaptive mutation.”)
But that is a very special case, is still (as I said) controversial, and at any rate hasn’t been found in eukaryotes, where the data still say that mutations are random in the way I defined above.
And Kelly’s claim that we cling to an erroneous idea about mutations as a bulwark against Lamarckism is simply wrong. Many scientists who believe in truly “nonrandom” mutations are trying to overthrow the “randomness” paradigm, and aren’t clinging to any dogma! I suspect Kelly got things wrong here because he isn’t trained as a biologist (the idea of “random mutations” is not intuitive) and didn’t ask any evolutionists for feedback before he submitted his answer.
There is no “peer review” of the answers to Edge questions, and I guess I’m the first question-answerer who has decided to criticize the answers of other respondents. But, as always, the laws of physics have determined that I must be a pain in the tuchus by criticizing folks who spread misconceptions about evolution.
Jerry A. Coyne is a Professor of Ecology and Evolution at The University of Chicago and author of Why Evolution is True, as well as the eponymous website. A version of this post first appeared on WhyEvolutionIsTrue.
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