Replies to comments that attempted to point out a numerical parameter that’s increased by evolution. (I’d be more interested in comments pointing out a deep reason why we can’t find such a numerical parameter, but there were no such comments.)
lmm:
Life “wants” to spread, so perhaps an increase in the volume in which life can be found?
That’s been steady for awhile now.
ChristianKl:
Organisms like bacteria that have much more iterations behind them then humans also tend to have less waste in their DNA.
Evolution can both add and remove junk DNA. Humans are descended from bacteria.
David_Gerard:
Total number of species (including extinct).
That can’t decrease by definition, and will increase under any mechanism that gives nonzero chance of speciation, e.g. if God decides to create new species at random.
Lumifer:
The chances of successful transmission of genes across generations given a stable environment.
Evolution can both add and remove junk DNA. Humans are descended from bacteria.
More particularly, the equilibrium size of the DNA is very roughly inversely correlated with population size. A larger population size is better at filtering out disadvantagous traits. It’s not linear—there are discontinuities as decreasing population size eliminates natural selection’s ability to select against different things. And those things sometimes can even go on to be selected for for other reasons—there are genomic structures that are important for eukaryotes that could probably never have evolved in a bacterium because to get to them you need to go through various local minima of fitness.
Soil bacteria can have trillions of individuals per cubic meter of dirt and they actually experience direct evolution towards lower genome size—more DNA means more sites at which something could mutate and become problematic and they actually feel this force. Eukaryotes go up in volume by a factor of ~1000 and go down in population by at least as much, and lose much of the ability to select against introns and middling amounts of intergenic DNA and expanding repeat-based centromere elements.
Multicellular creatures with piddlingly tiny population sizes compared to microbes lose much of the ability to select against selfish transposon DNA elements, gigantic introns and gene deserts, and their promoter elements get fragmented into pieces strewn across many kilobases rather than one compact transcriptional regulation element of a few dozen to a few hundred base pairs (granted, we’ve also been able to make good use of some of these things for interesting purposes from our adaptive immune system to the concerted regulation of our hox gene clusters that regulate our body plans). They also become very sensitive to the particular character of the transposons or DNA repair machinery of their particular lineage and wind up random-walking like crazy up and down an order of magnitude or two in genome size as a result.
Thanks! I was hoping you’d show up, it’s always nice to get a lesson :-)
Going back to the original question, are there any “general purpose adaptations” that never disappear once they show up? Does evolution act like a ratchet in any way at all?
Closest thing I can think of from what I know without going through literature is the building up of chains of dependencies. Once you have created a complex system that needs every bit to function, it has a tendency to stay as a unit or completely leave.
You can see that in a couple contexts. One is ‘subfunctionalization’. Gene duplications are fairly common across evolution—one gene gets duplicated into two identical genes and they are free to evolve separately. You usually hear about that in the context of one getting a new function, but that’s actually comparatively rare. Much more likely is both copies breaking slightly differently until now both of them are necessary. A major component of the ATP-generating apparatus in fungi went through this: a subunit that is elsewhere composed of a ring of identical proteins now has to be composed of a ring of two alternating almost identical proteins neither of which can do the job on its own. Ray-finned fish recently went through a whole-genome duplication, and a number of their developmental transcription factors are now subfunctionalized such that, say, one does the job in the head end and the other does its job in the tail end.
Another context is the organism I work in, yeast. I like to call yeast “a fungus that is trying its damndest to become a bacterium”. It lives in a context much like many bacteria and it has shrunk its genome down to maybe 2.5x that of an E. coli and its generation time down to 90 minutes. But it still has 40 introns hanging out in less than 1% of its genes so it needs a fully functional spliceosome complex to be able to process those transcripts lest those 40 genes utterly fail all at once, and it has most of the hallmarks of eukaryotic genome structure and regulation (in a neat, smaller, more research-friendly package). That being said it has lost a few big eukaryotic systems, like nonsense-mediated RNA decay and RNA interference, and they left relatively little trace behind.
Sure, but mostly because evolution’s so good at it. The fact that evolution so quickly filled a tidal pool, so quickly filled all the tidal pools, so quickly filled the oceans, so quickly covered the land, is evidence of strength rather than weakness.
There does seem to be a “punctuated equilibrium” effect here; life fills a region, appears static for a while, but then makes a breakthrough and rapidly fills another region. It could be argued that this is also true of things that humans optimize for: human population growth has abruptly rapidly accelerated at least twice (invention of agriculture, industrial revolution). Slavery was everywhere in the ancient world, then eliminated across most of it in the space of a century. Gay marriage went from hopefully-it-will-happen-in-my-lifetime to anyone who opposed it being basically shunned. Scientific and technological breakthroughs tend to look a lot like this.
Generalizing this to all optimization processes would be very speculative.
Evolution can both add and remove junk DNA. Humans are descended from bacteria.
From bacteria that lived a long time ago. Not from those that live today that had many iterations to optimize themselves. Different bacteria species can also much better exchange genes with each other than vertebrates that need viruses to do so.
Implying that humans evolved from the kind of bacterias that are around today might be more wrong than saying that the bacteria we see know evolved from humans. There more evolutionary distance between todays bacteria and those from which humans descended and humans and those bacteria from which they descended.
Yeah, and there are often bacteria in a single flower pot that are less related to each other than you are to the potted plant. But both bacteria still have a much smaller genome than you or the plant, maybe because genome size matters for reproduction speed for them, but is insignificant for us.
That can’t decrease by definition, and will increase under any mechanism that gives nonzero chance of speciation, e.g. if God decides to create new species at random.
Just apply Occam.
That seems to be contradicted by the possibility of evolutionary suicide.
Possibility wouldn’t contradict anything, a high enough probability would.
That seems to be contradicted by the possibility of evolutionary suicide.
Evolutionary suicide seems to be someone’s theoretical idea. Is there any evidence that it happens in evolution in reality?
In any case, are you basically trying to find the directionality of evolution? On a meta level higher than “adapted to the current environment”? There probably isn’t. Evolution is a quite simple mechanism, it just works given certain conditions. It is not goal-oriented, it’s just how the world is.
However if I were forced to find something correlated with evolution, I’d probably say complexity.
Damn it. It was going to be a better example because I was going to give the actual genera (Aspidoscelis and Cnemidophorus) of whiptail lizards whose species keep going down this path and then I got distracted and didn’t do that. Oops.
Depends on your time frame. Looking at the whole history of life on Earth evolution certainly correlates with complexity, looking at the last few million years, not so much.
I understand the argument about the upper limit of genetic information that can be sustained. I am somewhat suspicious of it because I’m not sure what will happen to this argument if we do NOT assume a stable environment (so the target of the optimization is elusive, it’s always moving) and we do NOT assume a single-point optimum but rather imagine a good-enough plateau on which genome could wander without major selection consequences.
But I haven’t thought about it enough to form a definite opinion.
I think you just don’t give an amoeba much credit because it’s no multicellular organism. It’s genome is 100-200 times the size of the human. As it’s that big it seems like we haven’t sequenced all of it so we don’t know how many genes it has.
We also know very little about amoeba. Genetic analysis suggests that the do exchange genes with each other in some form but we don’t know how.
Amoeba probably express a lot of stuff phenotypically that we don’t yet understand.
Replies to comments that attempted to point out a numerical parameter that’s increased by evolution. (I’d be more interested in comments pointing out a deep reason why we can’t find such a numerical parameter, but there were no such comments.)
lmm:
That’s been steady for awhile now.
ChristianKl:
Evolution can both add and remove junk DNA. Humans are descended from bacteria.
David_Gerard:
That can’t decrease by definition, and will increase under any mechanism that gives nonzero chance of speciation, e.g. if God decides to create new species at random.
Lumifer:
That seems to be contradicted by the possibility of evolutionary suicide.
Humans don’t have more offspring than bacteria in average conditions, and have much fewer offspring in ideal conditions.
More particularly, the equilibrium size of the DNA is very roughly inversely correlated with population size. A larger population size is better at filtering out disadvantagous traits. It’s not linear—there are discontinuities as decreasing population size eliminates natural selection’s ability to select against different things. And those things sometimes can even go on to be selected for for other reasons—there are genomic structures that are important for eukaryotes that could probably never have evolved in a bacterium because to get to them you need to go through various local minima of fitness.
Soil bacteria can have trillions of individuals per cubic meter of dirt and they actually experience direct evolution towards lower genome size—more DNA means more sites at which something could mutate and become problematic and they actually feel this force. Eukaryotes go up in volume by a factor of ~1000 and go down in population by at least as much, and lose much of the ability to select against introns and middling amounts of intergenic DNA and expanding repeat-based centromere elements.
Multicellular creatures with piddlingly tiny population sizes compared to microbes lose much of the ability to select against selfish transposon DNA elements, gigantic introns and gene deserts, and their promoter elements get fragmented into pieces strewn across many kilobases rather than one compact transcriptional regulation element of a few dozen to a few hundred base pairs (granted, we’ve also been able to make good use of some of these things for interesting purposes from our adaptive immune system to the concerted regulation of our hox gene clusters that regulate our body plans). They also become very sensitive to the particular character of the transposons or DNA repair machinery of their particular lineage and wind up random-walking like crazy up and down an order of magnitude or two in genome size as a result.
Thanks! I was hoping you’d show up, it’s always nice to get a lesson :-)
Going back to the original question, are there any “general purpose adaptations” that never disappear once they show up? Does evolution act like a ratchet in any way at all?
Closest thing I can think of from what I know without going through literature is the building up of chains of dependencies. Once you have created a complex system that needs every bit to function, it has a tendency to stay as a unit or completely leave.
You can see that in a couple contexts. One is ‘subfunctionalization’. Gene duplications are fairly common across evolution—one gene gets duplicated into two identical genes and they are free to evolve separately. You usually hear about that in the context of one getting a new function, but that’s actually comparatively rare. Much more likely is both copies breaking slightly differently until now both of them are necessary. A major component of the ATP-generating apparatus in fungi went through this: a subunit that is elsewhere composed of a ring of identical proteins now has to be composed of a ring of two alternating almost identical proteins neither of which can do the job on its own. Ray-finned fish recently went through a whole-genome duplication, and a number of their developmental transcription factors are now subfunctionalized such that, say, one does the job in the head end and the other does its job in the tail end.
Another context is the organism I work in, yeast. I like to call yeast “a fungus that is trying its damndest to become a bacterium”. It lives in a context much like many bacteria and it has shrunk its genome down to maybe 2.5x that of an E. coli and its generation time down to 90 minutes. But it still has 40 introns hanging out in less than 1% of its genes so it needs a fully functional spliceosome complex to be able to process those transcripts lest those 40 genes utterly fail all at once, and it has most of the hallmarks of eukaryotic genome structure and regulation (in a neat, smaller, more research-friendly package). That being said it has lost a few big eukaryotic systems, like nonsense-mediated RNA decay and RNA interference, and they left relatively little trace behind.
Sure, but mostly because evolution’s so good at it. The fact that evolution so quickly filled a tidal pool, so quickly filled all the tidal pools, so quickly filled the oceans, so quickly covered the land, is evidence of strength rather than weakness.
There does seem to be a “punctuated equilibrium” effect here; life fills a region, appears static for a while, but then makes a breakthrough and rapidly fills another region. It could be argued that this is also true of things that humans optimize for: human population growth has abruptly rapidly accelerated at least twice (invention of agriculture, industrial revolution). Slavery was everywhere in the ancient world, then eliminated across most of it in the space of a century. Gay marriage went from hopefully-it-will-happen-in-my-lifetime to anyone who opposed it being basically shunned. Scientific and technological breakthroughs tend to look a lot like this.
Generalizing this to all optimization processes would be very speculative.
From bacteria that lived a long time ago. Not from those that live today that had many iterations to optimize themselves. Different bacteria species can also much better exchange genes with each other than vertebrates that need viruses to do so.
Implying that humans evolved from the kind of bacterias that are around today might be more wrong than saying that the bacteria we see know evolved from humans. There more evolutionary distance between todays bacteria and those from which humans descended and humans and those bacteria from which they descended.
Yeah, and there are often bacteria in a single flower pot that are less related to each other than you are to the potted plant. But both bacteria still have a much smaller genome than you or the plant, maybe because genome size matters for reproduction speed for them, but is insignificant for us.
Just apply Occam.
Possibility wouldn’t contradict anything, a high enough probability would.
Evolutionary suicide seems to be someone’s theoretical idea. Is there any evidence that it happens in evolution in reality?
In any case, are you basically trying to find the directionality of evolution? On a meta level higher than “adapted to the current environment”? There probably isn’t. Evolution is a quite simple mechanism, it just works given certain conditions. It is not goal-oriented, it’s just how the world is.
However if I were forced to find something correlated with evolution, I’d probably say complexity.
Species of nightshade tend to evolve to become self-fertile, before dying out due to lack of genetic diversity.
Is this your source?
Link? Lots of plants are self-fertile and do quite well...
Better example: parthenogenic lizard species.
What makes that example better?
Damn it. It was going to be a better example because I was going to give the actual genera (Aspidoscelis and Cnemidophorus) of whiptail lizards whose species keep going down this path and then I got distracted and didn’t do that. Oops.
This doesn’t seem to be the case either
Depends on your time frame. Looking at the whole history of life on Earth evolution certainly correlates with complexity, looking at the last few million years, not so much.
I understand the argument about the upper limit of genetic information that can be sustained. I am somewhat suspicious of it because I’m not sure what will happen to this argument if we do NOT assume a stable environment (so the target of the optimization is elusive, it’s always moving) and we do NOT assume a single-point optimum but rather imagine a good-enough plateau on which genome could wander without major selection consequences.
But I haven’t thought about it enough to form a definite opinion.
Complexity in what way? Kolmogoroph complexity of DNA?
No, complexity of the phenotype.
How would you go about measuring that complexity?
I don’t know. Eyeballing it seems to be a good start.
Why do you ask? Do you think that such things are unmeasurable or there are radically different ways of measuring them or what?
I have a hard time trying to form a judgement about whether a human is more or less complex than a dinosaur via eyeballing.
Is a grasshopper more of less complex than a human?
Well, would you have problems arranging the following in the order of complexity: a jellyfish, a tree, an amoeba, a human..?
Yes.
I think you just don’t give an amoeba much credit because it’s no multicellular organism. It’s genome is 100-200 times the size of the human. As it’s that big it seems like we haven’t sequenced all of it so we don’t know how many genes it has.
We also know very little about amoeba. Genetic analysis suggests that the do exchange genes with each other in some form but we don’t know how.
Amoeba probably express a lot of stuff phenotypically that we don’t yet understand.
Sabre-toothed tigers and mammoths.
Huh? Sense make not.