Filed under: deep time, evolution, Hot Earth Dreams | Tags: deep time, evolution, Hot Earth Dreams
I’m not following the primary journals as much as I used to, so this pop-science article in Quanta on the rate of evolution caught my attention. It claims, apparently on the grounds of several different lines of evidence, that rates of mutation and evolution appear to run faster at short time scales than long time scales. In other words, there’s more genetic and morphological variation over short time spans than over long ones.
Paradoxical? Not quite. Useful? Very.What the article is talking about and what I’m interested in are two slightly different things. The article is about the humorous practice of using the number of single base-pair changes in the genetic sequences of two organisms to work out how far back their last shared ancestor lived, aka the molecular clock. The idea is to use neutral DNA sequences (such as spacers between genes) where there is presumably no selection pressure, so that mutations accumulate at random. You simply make some estimate of how often mutations happen on average, multiply that by the number of base pair differences you see, and voila, that’s how long they’ve been separate. If you’re a good/well-funded scientist, you do this with a bunch of different sequences to see if they all give the same answer. Back in the 90s when I was in school, we callow grad students were warned not to believe clock estimates without a fossil backing the date up. I actually contributed to the genesis of a paper when I heard someone talking about how old they thought a group of mycorrhizal fungi were, and heard another researcher talking about how they’d found fossil spores of that fungus in a road cut in Wisconsin, and they happened to be exactly the same age as Dr. Molecular Clock had found. I got them talking to each other, and the rest is entombed in university libraries around the world. But I digress.
It turns out that in a variety of data sets: fossil horse teeth, long-term mammalian studies, viral DNA studies, there is more variation over the short term than the long term. According to the article (and it’s similar to what I learned in school) there are two causes for this variation in rates. One is simple natural selection: if a mutation is deleterious in a particular environment at a particular time, it gets weeded out. Now you may complain that fossils have a much longer timespan than do viral genes, and you’re right. Part of this is that you have to look at time in generation time, rather than clock time, and you can have many generations of viruses in a single big animal generation. The second is that the environment is variable at all scales, from bacterial interactions to Milankovitch cycles, so it’s probable that different records show the effects different rates of changes due to different environmental fluxes.
The second problem is sequence saturation. Basically, if you have 100 base pairs, and you have a chance of a single base pair changing over X generations, then eventually, you’re going to see a particular base pair mutate more than once. Since we can only detect changes, not how often a particular base pair changed, a genetic sequence over time will systematically and increasingly downgrade the amount of change it has undergone. The Quanta article celebrated a technique for figuring out how much older a sequence difference is than it appears to be, at least in viruses, and that’s a step in the right direction.
Still, the end result is that evolution over a few generation times seems to be full of sound and fury, rarely signifying anything, and in the long term, stasis tends to prevail, except when it doesn’t. Assuming this is truly as widespread as it appears to be, it has all sorts of implications.
One is that it explains why there are species. Remember that species are not (unless they’re very unlucky) single genetic individuals. They’re populations containing a certain amount of variation. While at any given time, the characteristics of that population are going to vary based on whatever their parents experienced, over the longer term, the population is going to (generally) stay cohesive and “orbit” within a fairly defined envelope: the species. Apparently, species are basically good general sets of strategies for producing offspring in a particular environment, with some variation, and you’d expect selection to weed out the individuals who couldn’t hack it, for whatever reason (note that I’m not including sheer bad luck here).
Of course, not every clade subscribes to the notion that there are distinct, reproductively isolated species. The wheat tribe is notorious for inter-generic hybrids, and oaks, ceanothus, and manzanita are notorious for hybridization within subgenera, just to pick three easy examples. Hybrids don’t disprove the species concept, but they do suggest that populations aren’t all equally reproductively isolated. Instead of occupying isolated peaks in the adaptive landscape, these genera tend towards ridges and mountain ranges.
Then there’s the second issue: rapid evolution. This is also something we see, most notably on islands, but also after mass extinctions. It’s when the weedy little tarplants somehow go from California to Hawai’i and go through an adaptive radiation to form everything from alpine rosettes (the silverswords) to trees and shrubs, all of which can still hybridize with mainland tarplants, at least in the greenhouse (the half tree/half weed looks weird). What’s happened here is that the fast rate of short-term evolution has taken over as the plants invade a novel environment. There’s no strong selection pressure, and so what was originally a single population diverges fairly rapidly into a bunch of novel forms. This is happening now with mullein, a common eurasian weed in the US, which over the last few decades started not just invading in Hawai’i, but showing high numbers of odd structural features, like overly thick inflorescences and subsidiary rosettes (pdf link or USFS report) (picture of normal mullein here, fasciated mullein here). Getting back to the central point, change can happen very quickly when selective pressures slack off, and that’s why you get so many weird species on islands, and probably why speciation explodes after a mass extinction. These are places and times when selection pressures slack off, and hopeful monsters flourish. Inevitably selective pressures strengthen, and the slow rate of long term evolution reasserts itself.
A related issue is what this says about the whole human domestication thing. Some people seem to think that we’re all godly and such, because we’ve created so many weird breeds of everything from dogs to tulips in the last few centuries, using selective breeding of hopeful mutations. It seems that all we’re doing is creating a particular selective environment that allows particular, weird forms to flourish, that domestication is a phenomenon of rapid, short-term evolution, not long-term, conservative evolution. We know this, of course–who expects a teacup poodle to survive in the wild?–but we get into trouble when we try to extrapolate from the rapid changes achieved by the breeders working with small, genetically uniform populations, in contrast to the evolution of the species as a whole. In the long term, species disappear, and we know this. For example, few, if any, of the Roman horse or dog species still exist (mastiffs may be a rare example), and many so-called ancient breeds are very often modern recreations. However weird and crazy dog breeds get, if civilization collapses, probably their descendants will look like modern feral dogs, which are variable, but much less so than breeds, even most mutts. I suspect this is true for most domestic breeds of most species. Breeds, while extravagantly exotic, are likely to be ephemeral in deep time.
Finally, we can look at human evolution this way too. People have speculated on future human evolution from probably before Olaf Stapledon’s Last and First Men. Dougal Dixon took his shot with Man After Man, and it’s a staple subject of science magazines and the internet. To me, the problem with most of this speculation (ignoring, for a second, the real problems I wrote about in Hot Earth Dreams) is that it falsely extrapolates short term variability into long-term change. This is one of the roots of the notion that in, say, 50 years, we won’t be human. Now it’s always possible that this will be true, but I’d suggest that it’s quite possible that most of the wild variety we see now will disappear in the long term, and that over the long run we may be less variable than we think. This also ignores the effect of culture and civilization, which allow us to be wildly ecologically variable without changing physiologically or genetically. You can train a woman to fish for her livelihood without forcing her family to evolve into mermaids.
Now, fun as this theory is, it doesn’t necessarily say that everything will stay the same going forward. If we do go through a mass extinction, the survivors of that event will see life go wild around them, and some of those sports, like the fasciated mullein, may well go on to become stable new species in themselves. Still, it’s worth remembering that evolution is noisy, in that short term fluctuations don’t necessarily let you forecast either long term trends or abrupt changes. Life’s complicated that way, I guess.
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Putting the life back in science fiction 
This might explain punctuated equilibrium (evolution by jerks), although I am skeptical. The article was about the accuracy and limitations of the molecular clock (and how to correct for it), not about the underlying rate of actual evolution which is more about selecting for beneficial changes which can be in a variety of mechanisms – functional proteins, transcription control, etc, etc.
Then, of course, the fossils are about chance too – large successful populations are more likely to be fossilized, and which population is captured depends on what caused fossilization of the organism. It is like trying to follow a plot in a novel with most of the pages missing.
Comment by Alexander Tolley April 6, 2017 @ 10:21 pmFossils are about what fossilizes well, which is why we know so much about clam and reef evolution, and so little about things that lived in mountains. Numbers play a role, but most life on Earth (bacteria) leaves behind no useful fossil trace.
Anyway, thanks for bringing up punctuated equilibrium. That’s another aspect to this whole issue. Still, I think there’s good evidence for evolution slowing down over longer generation times. For me, it was watching my friends work on DNA from Hawaiian plants and not find anything they could use to make a good phylogeny. Even though the plants were morphologically very distinct, their genes said they were very close cousins.
Comment by Heteromeles April 7, 2017 @ 4:00 pm“This might explain punctuated equilibrium (evolution by jerks), although I am skeptical.”
There’s a whole lot of hidden variability. Most of the time expression of the hidden genes is selected against, so the wolves all look pretty much alike etc.
We’re capable of changing fast, but usually we don’t because our environments don’t encourage it.
I like to think of it like a room that’s completely filled with balloons. Each balloon is stuck in a particular place in the room, and squeezed out of shape by the balloons around it. That’s its ecological niche. It’s stuck there because of the other balloons. It can’t change its location or its shape because they push back.
If half the balloons get popped, then the remaining ones can quickly settle to the floor and turn kind of round. They aren’t squeezed in place any more. It doesn’t take long for that at all. Random events can bounce them around. But when enough balloons get added that they start squeezing each other, then they are trapped again, held in one place and deformed.
Comment by jethomas5 April 8, 2017 @ 3:14 pmNow I’m wondering whether there are conditions where teacup poodles or other toy breeds (probably toy crossbreeds) might survive in the wild. After all, there *are* small predators.
My assumption is that if we’re in some sense not human in fifty or a hundred years, it will be because of bioengineering and that isn’t going to resemble evolution all that much. Or at least it’s evolution plus memes.
Comment by nancylebovitz April 7, 2017 @ 4:07 amThis is what I was trying to get at in the article. For one thing, being human is both cultural and genetic. There is no gene for being American or Australian, nor is there a gene that makes you a computer programmer, a forager, a jet pilot, or a molecular ecologist. These are all solely due to culture. Culture changes *fast,* and that allows humans to adapt to all sorts of weird environments (office cubicles, for instance) without having to change our genes. The flip side to this is that cultural changes insulate our genes from all sorts of selective pressures.
Now, everyone gets all starry eyed about the promises of Technology X to make us More Than Human (as we have since forever, going back to the alchemists and before), but as we’ve found so far, it’s easier to let Technology X make cultural changes and for us to stay human. For example, it might be possible to engineer humans to not get diabetes no matter how much sugar we eat and how little exercise we get. On the other hand, treating diabetes is a (what?) multi-billion dollar industry that’s only growing? Something like that? You’re going to destroy that sector of the industry with your genetic meddling? Why shouldn’t they spend a few million dollars discrediting your research? And furthermore, if you did create those humans, it would take generations (at 28 years-plus per generation) to prove that it worked well. Aren’t pills and shots easier than all that?
Comment by Heteromeles April 7, 2017 @ 3:56 pm“There is no gene for being American or Australian, nor is there a gene that makes you a computer programmer, a forager, a jet pilot, or a molecular ecologist. ”
True, but there are genes that allow the individual to excel at the general skills needed for the job – good eyesight, patience, the ability to concentrate for long periods, aggressiveness, body shape, etc, etc. It might be possible to determine which sets of genes/alleles work best for certain types of desired abilities.
Comment by alexandertolley April 7, 2017 @ 4:11 pmMy assumption is that fear about genetic engineering for humans won’t win forever, and eventually there will be a lot of parents who chose to have children who look like celebrities.
And that eventually there will be genetic engineering for adults, not just before conception, and then things will get genuinely weird. Humanity will split into a large number of overlapping types.
This assumes that nothing else gets us first, but we’re a pretty capable species.
Comment by nancylebovitz April 7, 2017 @ 6:46 pmWhile there are genes (or alleles like sickle cell) which disqualify people from particular jobs, I suspect that most of what you’re talking about is a combination of many genes shaped by epigenetic signals. Technically it’s heritable, but practically, it’s simpler to run skill and suitability tests than to try to deduce what part of a genome or epigenome makes someone suitable for a particular job at a particular time.
Comment by Heteromeles April 7, 2017 @ 4:59 pmWith a lot of data, I think we could pick out sets of genes that would bias you in particular directions. It might be very hard, but ML and AI techniques should be able to do the heavy lifting. Some will be easier than others, so these low hanging fruit will be first. Others may prove almost intractable until there is enough data. But given billions of human genomes, plus information from near relative animals, I see no reason why you couldn’t eventually order up a tailored genome that works approximately as advertised. If the epigenome proves important, we can already influence that today, so tailoring that as well should be feasible.
It isn’t possible today, but it may well be in the future.
We are just at the very start of this technological revolution that will likely impact parts of the biosphere, not just humans and the species we pay particular attention to.
There will always be other technological solutions for many desired attributes. No matter how well designed you are, you can never out lift a forklift. OTOH, physical beauty might be equaled by technology, but not exceeded by it.
A “Gattaca” type culture would be very undesirable for a true meritocracy, even as we are slouching our way towards it. Leveling the playing field might be important, even given the obvious downsides.
Comment by alexandertolley April 7, 2017 @ 5:22 pm“No matter how well designed you are, you can never out lift a forklift.”
If the natural gas that runs a forklift gets expensive, it might turn out that a well-designed human can outlift a forklift when measured in pounds per dollar.
Comment by jethomas5 April 8, 2017 @ 3:03 pmGive me an appropriately sized block and tackle, I’ll do it myself right now.
Comment by Heteromeles April 8, 2017 @ 5:04 pm“If the natural gas that runs a forklift gets expensive, it might turn out that a well-designed human can outlift a forklift when measured in pounds per dollar.”
Large draft animals have always had that role. You really think humans will compete with them?
Comment by alexandertolley April 8, 2017 @ 5:14 pm“Large draft animals have always had that role. You really think humans will compete with them?”
I hope not.
I can imagine humans outcompeting forklifts on price, when forklifts get expensive.
I can imagine humans outcompeting draft animals on price, and I would prefer it not go that way.
Comment by jethomas5 April 9, 2017 @ 8:34 pmThis cephalopod RNA study throws in another variable:
‘RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose.
Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events.
We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites.
Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology.
The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage.
Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions.
This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function.’
http://www.cell.com/cell/fulltext/S0092-8674(17)30344-6
Comment by SFreader April 7, 2017 @ 5:22 pm“Give me an appropriately sized block and tackle, I’ll do it myself right now.”
You have just proved my point. Block and tackle is a technology that is used to extend human capabilities. Technology trumps any likely human genetic engineering in certain domains.
Even today, blade runners like Pistorious are capable of outcompeting regular runners. Technology improving capabilities beyond genetic programs.
Comment by alexandertolley April 8, 2017 @ 8:51 pm