"The bad news is that we can't possibly perform the experiment."

January 4, 2020 3:39 PM

Stephen Jay Gould, after proposing the thought experiment of "replaying the tape of life" in his 1989 book Wonderful Life, despaired that his ideas about the role of contingency and chance in evolution could ever be tested. Little did he know that an E. coli experiment started one year earlier (previously, previously) would allow us to do exactly that - well, perhaps a smaller version of that, what with the difficulty of recreating the Cambrian Explosion - and that other biologists would take "can't possibly" as a challenge. 30 years on, where does his thought experiment stand?

In a series of classic papers and books, Stephen Jay Gould and his collaborators took on the excesses of over-enthusiastic adaptationism (The Evolutionary Biology of Constraint and Sociobiology: the art of storytelling), reductionism (The spandrels of San Marco and the Panglossian paradigm), and over-strict gradualism (The Return of Hopeful Monsters and Punctuated Equilibrium: An Alternative to Phyletic Gradualism) in evolutionary biology. Underlying all of his work was the idea that history matters, that chance and contingency play a role in evolutionary outcomes.

As the review paper (free to read) summarized in the above-the-fold link concludes, after reviewing the past three decades of experiments:

Unfortunately, however, the evidence boils down to one list of cases in which convergence occurred and another where it did not, rendering quantitative conclusions unsatisfactory. Nonetheless, the many impressive cases of convergence show that repeated outcomes can arise from similar environmental challenges. Conversely, the many cases in which convergence did not occur suggest that contingent effects can play a strong role in shaping divergent adaptive responses....

Where to now? Clearly, evolution can be both contingent and deterministic, and often in complicated and fascinating ways. Recognizing this mixed nature will allow future research to investigate how contingency and determinism interact. Many questions remain to be addressed; for example, what circumstances promote contingent and deterministic outcomes, how does the extent of prior genetic divergence affect the propensity for future parallelism versus contingency, what types of divergence—say, a few mutations of large effect versus the accumulation of minor variants over long periods—lead to which outcomes, and what circumstances allow convergence even in distantly related taxa?

The Long Term Evolution Experiment has recently suggested one source of contingency, after reanalyzing why it took 15 years and 33,000 generations for the experiment's signature mutation to appear: Stiff competition can force evolving populations to adopt short-sighted, incremental solutions that block or significantly delay achieving innovative breakthroughs.

posted by clawsoon (28 comments total)

Wonderful Life has aged very badly. Even when it came out paleontologist Simon Conway Morris, frequently cited in WL, got so angry about it he wrote his own book and then people wrote books about the feud.
The thesis of WL depends on the uniqueness of the fossils in the Burgess Shale. They are supposed to represent a possible route evolution could have taken but didn't, for contingent reasons. Sadly, though, it looks like the Burgess fossils are just business as usual. Hallucigenia (originally described by Conway Morris) was just a velvet worm (reinterpretation done by, yes, Conway Morris).
The strangely inept attempts to push some sort of weird demarcation of responsibilities on science and religion seemed unhelpfully crude at the time.
More amusingly, Daniel Dennett once described Gould as an "academic bully." That's an actual thing Daniel Dennett did.
posted by thatwhichfalls at 4:13 PM on January 4, 2020 [7 favorites]

This review of Conway Morris's book The Crucible of Creation by Richard Fortey (once head of paleontology at the Natural History Museum and a colleague of SJG and SCM) in the LRB will show just how bitter the feud got.
posted by thatwhichfalls at 4:24 PM on January 4, 2020 [4 favorites]

Hi! Please try to imagine being an intelligent person other than yourself, or whom you perhaps do not even know, and summarize these links for that person.
posted by nicwolff at 4:33 PM on January 4, 2020 [10 favorites]

thatwhichfalls: Even when it came out paleontologist Simon Conway Morris, frequently cited in WL, got so angry about it he wrote his own book and then people wrote books about the feud.

From the "books" link:

If one animal ancestor had not yielded the cat design, then another would have. This is not pure determinism, but the idea nonetheless retains a whiff of the Great Chain of Being. For mankind alone has access to transcendence. He does not say so in so many words, but one senses the pull of the divine in the Conway Morris version. The word ‘numinous’ appears in a footnote; how Richard Dawkins would shudder.

One of the links that I came across while putting the post together put a different spin on the relationship between the ideas of Morris and Dawkins:

Some have suggested that Morris' views are influenced by his Christianity. Brian does note that this tendency toward teleology has correspondences with the talking points of the Intelligent Design movement, but I think it is important to observe that Richard Dawkins has come down on the side of Morris and against Stephen Jay Gould on this question. So the alignments here can be rather confusing to an outsider (some critics of adaptationism argue that the Oxford school of evolutionary biology, of which Dawkins is a representative, owes a great deal to William Paley's arguments from design, simply substituting the theistic god for the blind engineer of selection).

It's interesting how much of the debate is laced through with, "No, *you* agree with creationists more!"
posted by clawsoon at 4:54 PM on January 4, 2020 [6 favorites]

Natural history is fascinating to me because, well, it sits exactly at the intersection of natural law and history. And it's right there in the name!

Roughly speaking, a natural law is "if then then that." FWIW, the inherent language of natural law is the differential equation: what change will occur then if these conditions obtain now. Moreover, the principle of relativity is inherent in natural law because we wouldn't consider something a "law" if, for instance, it had to occur under a specific tree at a specific time. That would be either history or magic (depending whether it had already happened or not). We want a law to say, "When these conditions obtain, regardless of when or where (or inertial frame, etc.), then the system will evolve as such." And that works unreasonably well.

Then there is the question of history. Some things happen and other things don't. And that leads to the conditions that feed into the natural law formulations.

So, geology can tell us about the systematic ways that landforms develop and biology can tell is how trees disperse their seeds. But in the words of Laurie Anderson, "Why this mountain; why these trees?" (Lyrics from memory and probably a bit wrong).

If you take natural law to its extreme, you get quantum mechanics, which tells you all of the possible evolutions from "cause" to "effect" and still says nothing about which possible effect obtains. It has no explanation for how (or when!) nature reduces to history.

Suffice it to say that I find Gould's arguments persuasive, yet the mystery of the intersection between nature and history remains. It may be the most important question in science.
posted by sjswitzer at 5:37 PM on January 4, 2020 [5 favorites]

Lately, I had been thinking a lot about anomalocarids (enormous terrifying protoshrimp), and I couldn't find a good new popular book about the Cambrian; instead I checked out an ebook by Conway Morris, The Runes of Evolution. It wasn't about the Cambrian as such, so I was taken aback when he started making fun of Gould (who was dead by then) on an early page. And then started whaling on "Marxians" for good measure. I dunno if I want to finish it.
posted by Countess Elena at 6:22 PM on January 4, 2020 [5 favorites]

Yeah, that was the thing. Gould was unabashedly left. So some people presumed that would inevitably color and taint his scientific work, then set out to argue that however tendentiously.
posted by sjswitzer at 6:30 PM on January 4, 2020 [7 favorites]

The way this experiment allows us to "do exactly that" is extremely limited. So limited that it isn't really addressing Gould's thought experiment at all, in my inexpert opinion. Doesn't his question depend on the initial evolution of the regulatory framework for multicellular life, and after than every organism (to a first approximation) forms part of the environment of every other one, so it isn't just a case of "we expect a particular mutation to occur every N years" but " a particular mutation has to happen before some other organism develops a different mutation that makes it inadaptive."

I'm not saying that what has been done isn't extremely interesting. Just that I'm not sure it says much about whether we might all be seven-limbed balloons with wheeled landing gear that communicate by smell if we loaded from a 3 billion year old backup and ran forward again. To go for the "biggest understatement of 2020" award early, It will be really interesting when we find independently-evolved life around another star, because that seems like the easiest way to see if things will turn out similarly.

By the way, this is a super great post. I wish I understood all this stuff better. I look forward to being mercilessly savaged by the MFers that do understand it.
posted by Gilgamesh's Chauffeur at 6:55 PM on January 4, 2020 [4 favorites]

nicwolff: Hi! Please try to imagine being an intelligent person other than yourself, or whom you perhaps do not even know, and summarize these links for that person.

I'll make the attempt. Apologies for the length.

Long Term Evolution Experiment: 30 years ago, Richard Lenski started twelve test tubes of E. coli, feeding them with a mix that was low on glucose and high on citrate. Every 500 generations or so, he'd save a sample from each tube in the freezer for later analysis. As long as there's oxygen, E. coli don't consume citrate, but after 33,000 generations, E. coli in one of the tubes - and only one of the tubes - evolved the ability to consume citrate in the presence of oxygen. This was big news. The experiment is still going, now somewhere past 70,000 generations, and still no other tubes have evolved E. coli that can use citrate with oxygen. Much analysis has gone into exactly which mutations (and there were multiple mutations) were required, and why it happened in only one tube. Other experiments using harsher conditions have been able to evolve citrate use much more quickly and reliably, suggesting that Lenski happened to pick a great set of conditions to illustrate the role of contigency in evolution, or, if you think that the big news was overblown (and are connected to an Intelligent Design foundation), suggesting that Lenski is all hype.

Gould papers are a bit hard to summarize because he pulls in examples from many subjects, all loosely organized around a theme. He is, as they say, "discursive". The theme is usually along similar lines: He's criticizing an "adaptationist program" which attempts to explain everything in nature as being ideally adapted to its environment. I'll pull an illustrative example or two from each paper as a simplifying (over-simplifying?) device.

The Evolutionary Biology of Constraint: The embryos of land animals form gill slits at some point in their development. This doesn't happen because it's an ideal adaptation; it happens because we descended from fish, and because later steps in embryonic development use gill slits as their starting point and would fail if the gill slit step was removed. [See the discipline of evo-devo for a greatly expanded version of this idea.]

Sociobiology: the art of storytelling: Adaptive stories have been created to explain everything from why fellatio and cunnilingus are more common among the upper classes, to why male panhandlers are more successful with people who are eating, to why existing social arrangements are the inevitable consequence of biology. Evolution explains the range of human behaviours, but when you start trying to explain specific behaviours with the assumption that they're ideal adaptations to some primal environment it's easy to fall into creating "Just So" stories.

The Spandrels of San Marco and the Panglossian Paradigm: Dwarf males in many crustaceans have a mix of juvenile and adult features. Many biologists have tried to explain the mix in adaptive terms, but the mix is probably just a side-effect of how quickly they mature, "leaving some features 'behind' in the larval state." When you're trying to explain something in nature, there's always the possibility that it doesn't matter itself but is a side effect of something else that does matter.

The Return of Hopeful Monsters: First, small changes in regulatory genes can have large effects. Second, transitional forms are rarely found in the fossil record. It's a Just So story to connect those two facts, but, just so, perhaps genetic micromutations occasionally lead to morphological macromutations that are successful and lead to major evolutionary transitions. Perhaps the large change doesn't result in immediate perfection, but acts as the key adaptation that sets the stage for transition to a new mode of life. [This is surely the Gould paper which has convinced the smallest number of scientists, despite occasional support.]

Punctuated Equilibria: An Alternative to Phyletic Gradualism: In allopatric speciation, a small group is isolated from the main group, evolves quickly (compared to the lifetime of the species), then spreads back into the larger range of the parent species. This process explains most of the "breaks" in the fossil record.

I haven't read Wonderful Life, but I know that's one place he made his historical contingency arguments: Given the role of constraints, chance, and the possibility of large, risky changes, things can turn out very differently in the end given small differences along the way. (sjswitzer, if you're interested in the math of it, you might find the discussion of "path dependency" in the review article interesting.)

If you look at the Long Term Evolution Experiment in a certain light, as the review paper does, it seems to illustrate many of Gould's ideas about evolutionary contingency.

You could say in general that Gould was making the same argument for the null hypothesis/neutral theory in evolution that Kimura was, but from the other end. Kimura argued (eventually very successfully) that not every DNA mutation is there because it has been selected for; some of it is just random and neutral. Gould argued that not every physical or behavioural feature is there because it has been selected for; some of it is just random and neutral. Both of them believed that an explanation for how selection could have chosen a feature isn't good enough; you have to prove that selection did choose that feature. To prove that something is selected for, you have to prove that it's selected for and not merely the result of mutation, genetic drift, random fixation, founder effects, developmental constraint, or a side effect. You also have to prove that your selective story is the correct one among all the possible selective stories.

Gould said that he believed that selection is the most important evolutionary mechanism, but he wanted to emphasize that it's not the only one.

As an aside, I've noticed - or I think I have - a personality difference of sorts in supporters of Dawkins vs. Gould. In general, if you like your explanations to lean heavily on logic and rationalism and lead to inevitable conclusions, you'll favour Dawkins. If you like your explanations to lean heavily on history and context and lead to uncertain conclusions, you'll favour Gould. As is usual with biology, the truth, as stated in the review paper, appears to be somewhere in the direction of, "Why not both?"
posted by clawsoon at 12:01 AM on January 5, 2020 [37 favorites]

Gilgamesh's Chauffeur: The way this experiment allows us to "do exactly that" is extremely limited.

No argument from me on that. All you can say is that it's the best we've got so far. :-)
posted by clawsoon at 12:03 AM on January 5, 2020 [1 favorite]

The idea of constantly being able to replay life to see what happens, seems to me, a bit reminiscent of "Go". For each game, we start with a finite board, simple set of rules and a set of game events which happen in accordance with those rules. Each move creates a constraint which may be trivial or crucial - but which cannot be undone in either case. (professional Go player Stephanie Yin briefly explains the rules of the and origin of Go). The chance events of evolution mimic various game strategies: there are lots of ways to die out given the constraints of the board and rules - just a few generic strategies are successful. In Go, while the placement of pieces in each match is likely to be unique after a few plays, we nevertheless see a number of familiar patterns which recur. It is the patterns which correlate with survival in successive games - that are the ones that become familiar.

If we were to continually rewind and replay an evolutionary tape, then I'd expect to see the kind of low level difference and high level convergence that we see with Go.
posted by rongorongo at 12:18 AM on January 5, 2020 [3 favorites]

Kimura's neutral theory is facing a lot of challenges lately:

But now some scientists are pushing back against this idea, known as neutral theory, saying that genomes show much more evidence of evolved adaptation than the theory would dictate. This debate is important because it affects our understanding of the mechanisms that generate biodiversity, our inferences about how the sizes of natural populations have changed over time and our ability to reconstruct the evolutionary history of species (including our own). What lies in the future might be a new era that draws from the best of neutral theory while also recognizing the real, empirically supported influence of selection.

posted by jamjam at 1:07 AM on January 5, 2020 [1 favorite]

I loved reading Gould and (when I was younger) Dawkins, though never quite understood their vituperative disagreements in enough detail to call a win for either side.

My favourite scientific argument was between those who thought evolution more, or less,gradual- "evolution by creeps Vs. evolution by jerks". Wonderful to see these intelligent and often subtle scientists glorying in playground taunts.
posted by Gratishades at 1:50 AM on January 5, 2020 [1 favorite]

Back in 2016, Rich Lenski and Zack Blount did respond to the paper clawsoon listed as a challenge to the evolution of Cit+ in the LTEE.
posted by Laetiporus at 5:08 AM on January 5, 2020 [1 favorite]

Stiff competition can force evolving populations to adopt short-sighted, incremental solutions that block or significantly delay achieving innovative breakthroughs.

There may be an extension of this idea to competitive systems in general: There's a theory in economics which says that the relationship between competition and innovation is an inverted U. When there's no competition at all there's no innovation because there's no selective pressure rewarding innovation and helping it spread. When competition is at its fiercest there's no innovation because to put resources toward anything other than immediate survival is a recipe for death. It's only in between those competitive extremes that you get the surplus needed to innovate combined with the pressure to make it matter.
posted by clawsoon at 5:11 AM on January 5, 2020 [3 favorites]

clawsoon : you have no need to apologise for the length of that post, it is excellent.
posted by vincebowdren at 5:35 AM on January 5, 2020 [1 favorite]

jamjam: Kimura's neutral theory is facing a lot of challenges lately:

Interesting article, thanks. The part about linked selection and genetic hitchhiking makes me think of Gould's spandrels: A bunch of genes (or, in Gould's argument, behaviours and physical traits) don't get selected on their own merits, but instead hitch a ride on a successful neighbour. When you see a gene or a trait becoming more common in a population, you can't assume that it happened because it was selected for and make up a story about why it was selected. As your link (is "link" a pun when we're talking about linkage?) puts it, most of our genome seems to have been selected indirectly, by hitching rides.
posted by clawsoon at 5:58 AM on January 5, 2020 [4 favorites]

As a biologist, I'm an avowed Gould partisan. It boggles my mind that anybody could look at the natural world and not see how many times totally random shit happened evolutionarily. I understand a layperson being sucked in by some deterministic imaginings, especially laypeople who have been steeped in creationism, but it's really hard for me to understand my fellow biologists who buy into it, especially those who prefer Just So Stories using selection alone to explain everything over just acknowledging that sometimes weird shit happens because that's just what happened.

Look at birds of paradise. Why are the males so funny looking and do such funny dances? Because the females liked it and their sons who looked like their dads passed down the genes to look like that and there was no selective pressure against looking like that. Why did the females like it? Because their mothers passed down the genes to like it. We don't need any fancier explanation than that. The natural world is a messy, odd, random place, and that is one reason I love it so much.
posted by hydropsyche at 6:52 AM on January 5, 2020 [9 favorites]

Fortey's view, from the article linked above, seems like the most reasonable one:

Earth history – a whole confection of climate and sea-level changes, plate tectonics, and extraterrestrial events – has danced a pas de deux with life. The reductionist approach to evolution, especially the unscrambling of the genetics of development, has proved enormously successful in illuminating the ultimate basis for the transformation of one organ into another, or even one species into another: but these momentous discoveries do not explain the course of biological history. The description of a cast of characters alone does not determine the shape of a drama.

(I strongly recommend Fortey's books by the way - he's a very good writer and has a deep knowledge of the subject)
posted by thatwhichfalls at 8:03 AM on January 5, 2020 [1 favorite]

I see Fortey has a bunch of books - which one would you recommend to start with?
posted by clawsoon at 8:11 AM on January 5, 2020

For anyone familiar with the British Isles The Hidden Landscape is a geological history of the islands.
Horseshoe Crabs and Velvet Worms is also good - an attempt to show through lines in evolution by looking at individual, very long lived species.
posted by thatwhichfalls at 8:22 AM on January 5, 2020

Adaptive stories have been created to explain everything from why fellatio and cunnilingus are more common among the upper classes, to why male panhandlers are more successful with people who are eating ...

w h a t

I thought I was familiar with the level of garbage in evo-psych, but neither of these begin to make sense. Can you provide a cite, or at least names I could Google?
posted by Countess Elena at 8:40 AM on January 5, 2020

Countess Elena: Can you provide a cite, or at least names I could Google?

That's straight from the Sociobiology paper. Looks like there's a version of the paper with references here. Let's see...

Lockard, J.S., L.L. McDonald, D.A. Clifford, and R. Martinez. 1976. Panhandling: Sharing of resources. Science 191: 406-408.

Weinrich, J.D. 1977. Human sociobiology: Pair-bonding and resource predictability (effects of social class and race). Behavioral Ecology and Sociobiology 2:91-118.
posted by clawsoon at 8:55 AM on January 5, 2020

I'm guessing that most of it was Wansink-level science.
posted by clawsoon at 8:57 AM on January 5, 2020

Thank you! Sorry, I misunderstood that “Sociobiology” was the name of a paper itself.
posted by Countess Elena at 8:59 AM on January 5, 2020 [1 favorite]

clawsoon, I found Fortey's book Trilobite to be an in-depth introduction to the subject. He also made an Attenborough style documentary called Fossil Wonderlands and he has several lectures and clips on Youtube.
posted by ambulocetus at 6:38 PM on January 5, 2020 [1 favorite]

Roughly speaking, a natural law is "if then then that."

Some of them. Others are more like: "if then then more likely that."
posted by Pouteria at 11:42 PM on January 5, 2020 [1 favorite]

Pouteria: Some of them. Others are more like: "if then then more likely that."

And if you're in a competition where your best move depends on predicting the next move of your opponent, and their best move depends on predicting your next move, sometimes the law degenerates into, "If... ah, screw it, just play randomly."
posted by clawsoon at 7:13 AM on January 6, 2020