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Humans are evolving rapidly
December 10, 2007 3:53 PM   Subscribe

Humans are evolving more rapidly than in the distant past, according to a new study published in PNAS. "The massive growth of human populations has led to far more genetic mutations, and every mutation that is advantageous to people has a chance of being selected and driven toward fixation. We are more different genetically from people living 5,000 years ago than they were different from Neanderthals", says lead author John Hawks.

PNAS has not published the abstract as of today, but it can be read on John Hawks blog under the second link. A more "popular press" story released by the AP is making its way around the wire, here is a copy. It's a little more entertaining:
Science fiction writers have suggested a future Earth populated by a blend of all races into a common human form. In real life, the reverse seems to be happening. People are evolving more rapidly than in the distant past, with residents of various continents becoming increasingly different from one another. "I was raised with the belief that modern humans showed up 40,000 to 50,000 years ago and haven't changed. The opposite seems to be true."
posted by stbalbach (136 comments total) 19 users marked this as a favorite

 
abstract (from the second link)



Recent acceleration of human adaptive evolution



John Hawks, Eric T. Wang, Gregory Cochran, Henry C. Harpending, and Robert K. Moyzis



Genomic surveys in humans identify a large amount of recent positive selection. Using the 3.9-million HapMap SNP dataset, we found that selection has accelerated greatly during the last 40,000 years. We tested the null hypothesis that the observed age distribution of recent positively selected linkage blocks is consistent with a constant rate of adaptive substitution during human evolution. We show that a constant rate high enough to explain the number of recently selected variants would predict (i) site heterozygosity at least 10-fold lower than is observed in humans, (ii) a strong relationship of heterozygosity and local recombination rate, which is not observed in humans, (iii) an implausibly high number of adaptive substitutions between humans and chimpanzees, and (iv) nearly 100 times the observed number of high-frequency linkage disequilibrium blocks. Larger populations generate more new selected mutations, and we show the consistency of the observed data with the historical pattern of human population growth. We consider human demographic growth to be linked with past changes in human cultures and ecologies. Both processes have contributed to the extraordinarily rapid recent genetic evolution of our species.
posted by acro at 4:04 PM on December 10, 2007


This seems kind of sketchy right now. I'm looking forward to the additional posts and FAQ Hawks promises in his blog.
posted by beagle at 4:05 PM on December 10, 2007


We're changing more quickly than we ever have, but that doesn't mean we're getting better. Evolution rewards only reproduction, period, and the most successful at that are often the people we would least consider 'evolved'.



Idiocracy, people. Idiocracy.
posted by Malor at 4:09 PM on December 10, 2007


De-evolution of humor: I always giggle when someone says something was published in penis.
posted by not_on_display at 4:11 PM on December 10, 2007


Especially when it was written by a Wang and a Cochran.
posted by brain_drain at 4:12 PM on December 10, 2007


OW! My balls!
posted by Floydd at 4:13 PM on December 10, 2007 [3 favorites]


Humans may be mutating more rapidly than in the past, but I'm not convinced that this means the same thing as "evolving".

Evolving would require some kind of natural selection causing more advantageous genes being passed on more often than their less advantageous cousins, leading to a gradual change in our genetic makeup.

As it is, the barriers to procreation are probably at an all-time historical low, with perhaps no particular genetic characteristic guaranteeing any individual a better or worse chance of success than any other. The things that determine whether or not one procreates are more likely to be geographical accidents of birth (ie not being born into a poor African country with high mortality) or social factors (eg westerners holding off marriage & childbirth in order to pursue careers or afford real estate).

In other words, it's currently a bit of a genetic free-for-all, with all kinds of mutations & combinations being produced, and perhaps no particular genes winning out over others.

Interestingly, if there is any natural selection going on, it may be determined by largely social factors, since the "lower classes" are apparently reproducing at a far higher rate than those higher up on the socioeconomic scale.
posted by UbuRoivas at 4:20 PM on December 10, 2007 [5 favorites]


Someone laffed in my face about 10 years ago when I said I thought humans were "speciating".
posted by uncanny hengeman at 4:22 PM on December 10, 2007


(hm, if higher socioeconomic status correlates with intelligence & attractiveness, Malor might be right, but it won't just be an idiocracy, but also an uglocracy)
posted by UbuRoivas at 4:23 PM on December 10, 2007


U-P-G-R-A-Y-E-D-D. Two Ds for a double dose of pimpin'.
posted by amuseDetachment at 4:28 PM on December 10, 2007


What makes humans unique from other animals is that our ability to change the environment to better suit us far outweighs our ability to adapt to our environment. I think that essentially eliminates vast swathes of selection pressures and many maladaptions that would have caused us to not reproduce successfully (myopia, for example) are no longer selected against. In a thousand years or so, it may be that no one is born with 20/20 vision any more.

We're certainly becoming more genetically diverse, but I think that will largely manifest in the form of more chronic diseases and genetic deformities which we can manage medically and don't prevent reproduction. What will be interesting to see is if certain genetic deformities after a few generations manage to turn into something incredibly useful-- for example, a form of autism that makes it easier for us to interface cybernetically with computers.
posted by empath at 4:31 PM on December 10, 2007 [8 favorites]


Someone laffed in my face about 10 years ago when I said I thought humans were "speciating".

I think we most certainly are. And the difference will be when we interface with machines to the point where we can no longer survive without them.
posted by empath at 4:32 PM on December 10, 2007


The way things are going we'll be up to our knees in morlocks by teatime.
posted by Kattullus at 4:35 PM on December 10, 2007 [7 favorites]


Here's the paper: Recent acceleration of human adaptive evolution (PDF).
posted by homunculus at 4:42 PM on December 10, 2007 [2 favorites]


the difference will be when we interface with machines to the point where we can no longer survive without them

You mean like the trucks that deliver the genetically-modified factory-produced corn syrup drinks to my grocery store, or were you thinking more of the syringe that I use to get my insulin?

For what it's worth, I'm not sure I could live without my iPod either.
posted by sy at 4:43 PM on December 10, 2007 [1 favorite]


Humans may be mutating more rapidly than in the past, but I'm not convinced that this means the same thing as "evolving".

Evolving would require some kind of natural selection causing more advantageous genes being passed on more often than their less advantageous cousins, leading to a gradual change in our genetic makeup.

Yeah--i'm confused by this--we're mixing far far more than ever before and sharing our genes more, it seems to me--thru immigration and global travel, etc. And we're diversifying more in terms of variations and blends (like the old colonial/invasion/raping and pillaging thing but voluntarily usually this time).

But does that equal evolving? Evolving in what way? Do people have more immunities? more robustness? more fertility? Doesn't any evolution have to help/protect the species as a rule or else it gets called something else?
posted by amberglow at 4:45 PM on December 10, 2007


or is it that simply by becoming more diverse and branching out more we do help the species by ensuring more opportunities for survival of at least one or more of the groups?
posted by amberglow at 4:47 PM on December 10, 2007


Greg Laden thinks the paper makes some faulty assumptions about population size and change in human population over time.
posted by homunculus at 4:52 PM on December 10, 2007


How do we know agriculture was not invented a few times over the last 100,000 years, but fell totally out of use in many areas?

Application of Occam's Razor in conjunction with archaeological studies which provide no evidence for the alternate hypothesis.
posted by Upgrayedd at 4:56 PM on December 10, 2007


hengeman, empath: we're almost certainly doing the reverse of speciating. All human groups are mixing genetically a lot more than they used to. (Probably this is driving the increased evolution— haven't read TFA yet.)
posted by hattifattener at 5:11 PM on December 10, 2007


Application of Occam's Razor in conjunction with archaeological studies which provide no evidence for the alternate hypothesis.

Yes, sedentary agriculturalism leads to permanent settlements, leaving archaeological evidence, which can be dated with reasonable accuracy. From memory, the spread of agriculture was continuous & sustained.

Yeah--i'm confused by this--we're mixing far far more than ever before and sharing our genes more, it seems to me--thru immigration and global travel, etc. And we're diversifying more in terms of variations and blends

Well, there are at least two theories that claim we may not be diversifying more: one which says that we are heading towards some kind of slightly brown average as all the races mix; and another which talks of a polarisation into rich, intelligent, educated & attactive v poor, stupid, uneducated & ugly.
posted by UbuRoivas at 5:15 PM on December 10, 2007 [1 favorite]


amberglow, there are several mechanisms of evolution. The help/protecting the species would fall under natural selection. My memory is foggy, but you've got genetic drift and plain ole mutation as other mechanisms. So you can have a population that mutates a whole lot, but if there isn't any selection, none of those mutations are necessarily going to become more prevalent. But they are still evolving... that is, the genes are changing and being passed on. It's weird. It seems I was taught evolution in a way that takes into account geographic location and populations moving about when it seems that the general populace sees evolution as somehow being worldwide.

This quote is interesting:

"And every mutation that is advantageous to people has a chance of being selected and driven toward fixation."

So we're getting more mutations than before. That's evolution, but people associate evolution more with natural selection. What's key is the assertion of the article that those mutations have "a chance of being selected." That's a chance, not a given.

One thing that's clear to me is that this isn't surprising. There are a lot of humans. A whole lot of them, which means there's going to be an absolute increase in mutations. What would surprise me is a small segment of the population with a higher rate of mutations.
posted by Mister Cheese at 5:16 PM on December 10, 2007 [1 favorite]


hattifattener: i'm not talking about speciating based on race. I'm talking about speciating based on socio-economic strata and technology-- the haves are becoming post-human.
posted by empath at 5:28 PM on December 10, 2007


slightly brown average as all the races mix

Genetically, there is no such thing as "race" - there is more genetic diversity between some tribes in Africa a few miles apart than there is between Europeans and Asians. In fact most genetic diversity is in Africa, which makes sense, we started there and have been there the longest, only outside of Africa 60k years or so. Ironically, the "brown average" person that has all the worlds features can best be seen in the "Bushmen", which are thought to be the oldest genetic human line - one can look at their face and see European lips, Asian eyes, Indian skin, African hair. It only makes sense that the oldest line would contain the most features of the world, since it was from this that the rest of the world came from. The future will probably look like something different as evolution selects for new traits. Blond hair (in adults widely dispersed) is thought to be only about 15,000 years old.
posted by stbalbach at 5:32 PM on December 10, 2007 [8 favorites]


Doesn't any evolution have to help/protect the species as a rule

Evolution is blind. Natural selection is more directed, but it tends only to increase the frequency of alleles within a population that are reproductively adaptive to the environment in which they circulate. If the environment changes, what was an adaptive mutation can become maladaptive. For example, many of our common adaptations to a food-scarce environment in which we evolved are now maladaptive in our obesogenic environment. We call these maladaptations diabetes, metabolic syndrome, obesity, and so on.
posted by meehawl at 5:42 PM on December 10, 2007 [2 favorites]


Of course humans are evolving more rapidly, some more than others. I could have told you that, not that you'd understand it.
Speaking of evolving toward 'smug' that picture of Hawks from the first link is a dead giveaway. (Look how much smarter I am than this dead guy)

Funny, I wonder how you go off lactase. That gene must've gotten shut off in me, I drank a huge glass of milk before bed every day for years. Suddenly I can't tolerate the stuff.
posted by Smedleyman at 5:43 PM on December 10, 2007


Ironically lactose tolerance has probably popped up sporadically throughout human existence and before but in every case it was maladaptive because it would have meant adults competing with infants for female breast milk - thus tending to reduce the survivability and size of the infants and reducing the kindred's reproductive success wrt others. Only in the era of the domestication and cultivation of cows and other non-human milk producers did the lactose tolerance mutation begin to confer a reproductive advantage that outweighed its disadvantages and its frequency increased throughout some populations.

Another gene is one kind of recessive mutation that causes cystic fibrosis. This is much more common in some populations of northern Europeans than can be explained by random probability. Like the sickle cell trait in West Africans and Indians, this was probably selected for some adaptive advantage as a recessive trait in the European populations. It's speculated that it helped reduce the mortality from diarrhea of single allele carriers within a population chronically exposed to diseases like cholera.
posted by meehawl at 5:52 PM on December 10, 2007 [2 favorites]


ahhhh....thanks, all.

It seems I was taught evolution in a way that takes into account geographic location and populations moving about when it seems that the general populace sees evolution as somehow being worldwide.
Not worldwide, but specieswide, i think, is how most of us are taught (and taught very very little in general. Since people are everywhere and are all the same species, that is worldwide, as opposed to some specific turtle that only exists on one isolated island in the whole world, or something maybe?)

there is more genetic diversity between some tribes in Africa a few miles apart than there is between Europeans and Asians.
There was a really interesting thing on tv recently--from the results of this DNA search along the Silk Road, i believe--some guy found a family he identified as direct descendants of the very first Europeans (or something like that--they were this little modest family--very goodlooking tho)...
posted by amberglow at 7:02 PM on December 10, 2007


Evolving would require some kind of natural selection causing more advantageous genes being passed on more often than their less advantageous cousins

I think the Homo S.S. is seeing muchmore sexual selection in the last 5000 years than the time before.

Plus all those nasty bugs that urban congestion and living with domesticated animals have produced.
posted by panamax at 7:09 PM on December 10, 2007


Evolution is blind.
That seems weird to me. (beside my mistake of evolution=natural selection, doesn't the word "evolve" itself imply if not directly mean to develop or achieve? like a progression or attainment? That's not neutral or blind.)
posted by amberglow at 7:11 PM on December 10, 2007


I think the Homo S.S. is seeing much more sexual selection in the last 5000 years than the time before.

I'm not sure what you mean by this.

The broad historical trend has been from polygamy to almost universal monogamy. That would many more men are able to pass on their genes now than before. This might be what you're saying, but I don't understand what you mean by "sexual selection".
posted by UbuRoivas at 7:18 PM on December 10, 2007


(that would mean many more men)
posted by UbuRoivas at 7:19 PM on December 10, 2007


Humans may be mutating more rapidly than in the past, but I'm not convinced that this means the same thing as "evolving".

Evolving would require some kind of natural selection causing more advantageous genes being passed on more often than their less advantageous cousins, leading to a gradual change in our genetic makeup.

As it is, the barriers to procreation are probably at an all-time historical low, with perhaps no particular genetic characteristic guaranteeing any individual a better or worse chance of success than any other.


The article indicates that resistance to disease is the biggest area of change.

Also, beware of the idea of "gradual change." The theory of punctuated equilibrium holds that much of evolution is driven by rapid changes over a short period of time followed by slow periods of almost no change. Usually the rapid changes occur as a result of huge changes in the environment.

Hmmm any major changes in the environment we inhabit in the last 5,000 years?

Evolution is blind because a highly adaptive creature could be quickly felled by a rapid change in the environment. Note that we are not "better" than the dinosaurs or other forms which came before. The circumstances of life changed and new forms came to dominate. And when we are gone, other forms will take our place.
posted by Ironmouth at 7:21 PM on December 10, 2007


i am glad to hear this. i'm tired of people laughing when i tell them my daughter was born with tattoos and piercings.
posted by kitchenrat at 7:28 PM on December 10, 2007


Ubu, I'm thinking of more abstract human ideals of beauty / aesthetical selection, plus how the social institution of marriage has affected the dynamics.
posted by panamax at 7:31 PM on December 10, 2007


Evolution is blind because a highly adaptive creature could be quickly felled by a rapid change in the environment. Note that we are not "better"

I find this position to be somewhat dogmatic, btw. I think IQ -- the ability to plan, see connections, make predictions, reason with rigor -- and related emotional capacities are both "better" and driven by evolutionary presssures.
posted by panamax at 7:36 PM on December 10, 2007


Interesting point you've brought up, amberglow. In strict biological terms 'evolution' means 'change', not necessarily 'advancement' or 'improvement'. Evolution + Natural Selection = Advancement (of a particular form).

I suspect, without foundation, that the modern understanding of the word to mean 'advancement' has a lot to do with misunderstanding the writings of Darwin, Wallace, et al.
posted by Pinback at 7:41 PM on December 10, 2007 [2 favorites]


amberglow: doesn't the word "evolve" itself imply if not directly mean to develop or achieve? like a progression or attainment?

In laymen's English, maybe. But in the science of Biology, the definition is simply a change. If some particular part of the genome changes by a random walk (for something unrelated to survival, say earlobe shape) then it's still considered "evolution." It's not evolution by natural selection in that instance, it's evolution by genetic drift.

"Evolving" a particular trait as we think of it is usually adaptive to the organism's situation, and under natural selection, which is why we think of evolution as progress. But it doesn't have to be.

And even in everyday English, I can see "evolve" being used for a neutral kind of shift. "The botany hike eventually evolved into a birdwatching tour," or "Their kitchen table evolved into a homework workstation," would be valid, and basically free from connotations of advancement or achievement.

panamax: I'm thinking of more abstract human ideals of beauty / aesthetical selection

I'd disagree. Sexual selection seems pretty low to me -- even the extremely unattractive seem to manage to reproduce. Those who don't reproduce seem to be from all ranges of the attractiveness spectrum. But this is pretty subjective. There might be something to it.
posted by lostburner at 7:42 PM on December 10, 2007 [2 favorites]


what about dogs? we've created all these breeds--would that be considered evolution too, or just mutation (forced by us?) And, if not, why is it evolution when it's us?
posted by amberglow at 7:43 PM on December 10, 2007


Go to a Wal-Mart and observe the mutation of human morphing with water buffalo. Giagantic rumps, vaguely human, yet not.
posted by 45moore45 at 7:44 PM on December 10, 2007 [1 favorite]


Humans are evolving more rapidly than in the distant past, according to a new study

This is nonsense, because

and every mutation that is advantageous to people has a chance of being selected and driven toward fixation.


Does not really apply to the Human race since most of us practice birth control. Do people who are billionaires or win the Noble prize breed more (what they probably could) than the average John Doe? Nope. But with generous wellfare and social aid you basically get people who are less able to perform in this society to have more children.

I neither say this is good or bad or Dawins principle should be applied 1:1 to a human society but the statement that "and every mutation that is advantageous to people has a chance of being selected and driven toward fixation." is only true in a very broad sense. You would have to define "advantageous" that an unemployed drug dealer who fathers 10 children is more successfull than a Nobel prize winner with only one child. From a biological perspective he is.
posted by yoyo_nyc at 7:51 PM on December 10, 2007 [1 favorite]


UbuRoivas: Well, there are at least two theories that claim we may not be diversifying more: one which says that we are heading towards some kind of slightly brown average as all the races mix; and another which talks of a polarisation into rich, intelligent, educated & attactive v poor, stupid, uneducated & ugly.

These theories are, to put it mildly, bunk. They both rest on false assumptions about how inheritance works. The fuck-till-we're-all-brown theory assumes that all genetic traits will spread evenly in the population resulting in a homogeneous mixture of genes in all humans. Inheritance is not chocolate milk.

The polarization theory assumes that good traits will adhere to all other good traits and bad traits to all bad. We will not be up to our necks in morlocks by teatime because humanity doesn't segregate very well, even during times of legal segregation. Also, the son of dullards might not be a dullard himself. Same goes for the daughter of a pair of smarty-pants. Furthermore, there's nothing that says that social traits, like wealth or education, go together with attractiveness or intelligence. Lastly, I just want to make absolutely clear that good traits, such as, say, the ability to hold one's liquor, will not necessarily go with other good traits, such as good, natural posture or 20/20 eyesight.
posted by Kattullus at 7:58 PM on December 10, 2007


Ubu, I'm thinking of more abstract human ideals of beauty / aesthetical selection, plus how the social institution of marriage has affected the dynamics.

Well, the shift to monogamous marriage has enabled a greater proportion of people (men) than ever before to pass on their genes. In the past, it would have been the alpha males (kings, chieftains etc, in other words, the strongest & most powerful) with hundreds or thousands of concubines passing on their genes far more than the common men.

Beauty & aesthetic selection might be a bit more of a factor in choice today than in previous eras (?), but the fact that we now have one-to-one pairings, with roughly a 50/50 gender split, means that every single person - from the most to the least beautiful - has the potential to procreate, even assuming a model in which beauty is the only determinant of partner selection. That model, combined with monogamous partnering, would just mean that all the 1s pair up with each other, as would the 2s, etc. The 10s might want 1s, but settle for 10s. Everybody still wins, in terms of passing on genes.

Also, beware of the idea of "gradual change." The theory of punctuated equilibrium holds that much of evolution is driven by rapid changes over a short period of time followed by slow periods of almost no change. Usually the rapid changes occur as a result of huge changes in the environment.

True. Many mutations offer little or no evolutionary advantages until something momentous happens. I wonder what the imminent / already under way rapid changes in the environment are likely to result in, other than geopolitical nastiness? Darker-skinned people are probably already at an advantage against skin cancers exacerbated by the holes in the ozone layer, no? - although most people could probably pop out a few kids before the cancers get them.
posted by UbuRoivas at 8:01 PM on December 10, 2007 [1 favorite]


You know, sooner or later it will become impossible to ignore the fact that the human genome probably changes over time -- in other words, selection pressure isn't all that's going on, there are systems in us that are actively adapting to environmental influences, selecting, designing, and absorbing constructs that yield useful traits.

The recent discovery of retroviral fossils tends to support this assertion.
posted by effugas at 8:06 PM on December 10, 2007


I think IQ -- the ability to plan, see connections, make predictions, reason with rigor -- and related emotional capacities are both "better" and driven by evolutionary presssures.

Abstract reasoning is better for one mode of life. Sharp claws and good night vision are better for another mode of life. These big brains and nimble fingers do seem to have done pretty well for us, but you have to keep in mind that according to basic principles, each species is equally well adapted for their role in the environment, barring recent environmental change. Evolution really isn't an "up, up, up" process, though it's easy to think of it that way. It's more a process of species constantly adapting to shifting environments.
Note that lots of other creatures have very complex brains, but none have developed them quite to the point that we have. It's because big brains are expensive to maintain and make you physically vulnerable to trauma, and they just haven't been adaptive in the majority of cases. Minds like ours aren't the inevitable result of evolution. They're just an accident of an environment that for whatever reason rewarded incremental increases in intelligence. The big brains have indeed improved our reproduction, though, as evidenced by the population boom. I might even argue that on the 200,000-year timescale, they're likely to be a liability to the species in another way: they have enabled us to develop an efficient means of killing ourselves all off.

If you want to define "better" on an emotional level, that's cool, but it's a different topic. Personally, I think it's awesome to have been born with a human mind. The range of emotions and experiences, and just sitting around being interested in things and arguing about evolution, is a really enjoyable adaptation.

what about dogs? we've created all these breeds--would that be considered evolution too, or just mutation (forced by us?) And, if not, why is it evolution when it's us?

It's evolution by artificial selection. It's still evolution, and the dogs aren't particularly more fit to survive in the wild as a result.
posted by lostburner at 8:08 PM on December 10, 2007 [5 favorites]


The idea that evolution has a direction is a popular teleological fallacy, but is the essence of Lamarckism, intelligent design and other deist reifications of evolutionary theory such as the omega point, Professor X, the singularity, the übermensch, or the New Socialist Man.
posted by meehawl at 8:09 PM on December 10, 2007


These theories are, to put it mildly, bunk.

I never said I agreed with them. Just trying to embiggen the discussion.

Having said that, my gut reaction to both is that they tend towards truthiness:

The fuck-till-we're-all-brown theory assumes that all genetic traits will spread evenly in the population resulting in a homogeneous mixture of genes in all humans.

Not even over one hundred million generations?

Furthermore, there's nothing that says that social traits, like wealth or education, go together with attractiveness or intelligence.

I think there's a reasonably plausible nexus between wealth, education & 'intelligence'. Attractiveness can be thrown in because anybody wealthy, intelligent & 'educated' enough can maximise their attractiveness, and attractiveness has been (controversially) demonstrated to be advantageous to career success. I can imagine these to be a cluster of things that tend to correlate, without implying strong causation, and definitely without implying that one cannot be, say, incredibly stupid & incredibly wealthy. Plenty of celebrities prove that this is far from an absolute rule.
posted by UbuRoivas at 8:15 PM on December 10, 2007


there are systems in us that are actively adapting to environmental influences, selecting, designing, and absorbing constructs that yield useful traits

That doesn't really make sense, according to the modern understanding of evolution. The body can't modify the genome in direct response to outside traits. See Wikipedia for a discussion of Lamarckian evolutionary theory, in which species develop according to environment in the same way a body develops in response to its environment (eg. strengthening muscles which are often used). Darwinian theory replaces that notion entirely.
posted by lostburner at 8:20 PM on December 10, 2007


Whoops. that should be:
in direct response to outside conditions.
posted by lostburner at 8:22 PM on December 10, 2007


wow, comment deletion #2. metafilter, who has been put in charge of things to have such heavy hands? i have been a member of this website for many years and have a fine posting record. i do not take lightly to having my comments deleted and i think you will only alienate perfectly good members of the site by being so censorial. i will certainly not let my comments be deleted silently and without protest.
posted by PigAlien at 9:04 PM on December 10, 2007


i have been a member of this website for many years

In which case, you will know that you should take it to MeTa instead of protesting in-thread.
posted by UbuRoivas at 9:12 PM on December 10, 2007


Not when my comments are deleted, UbuRoivas... My comments were relevant to the threads and their deletion shall be pointed out in thread.
posted by PigAlien at 9:14 PM on December 10, 2007


That would be a change to the way things are normally done, and also best discussed in MeTa.
posted by UbuRoivas at 9:26 PM on December 10, 2007


*bows with respect to lower usernumber*
posted by UbuRoivas at 9:26 PM on December 10, 2007


I thought we already decided the Anunnaki were responsible for all of this.

Man, you are all educated stupid.
posted by eritain at 10:39 PM on December 10, 2007


I'm gonna tell y'all my big biology idea, it's about recent selection in humans, but I've never seen it fully articulated by anyone else, though it probably has somewhere.

The idea is that if a species develops culture, the cultural environment will be able to push evolution above and beyond the natural environment. Since humans have a culture vastly more complicated and important than any other species, it is probable that cultural changes played a large role in Human evolution.

How does the cultural environment trump the natural environment? Lets say their are three identical species of predators. Species A lives in an environment without a lot of prey. In this environment genes for being a good hunter would be selected for as poor hunters would starve out. Species B lives in a prey rich environment. Genes for hunting prowess would not face selective pressure. Species C lives in the same environment as species B, but has developed culture. In this culture coming home with a large prey carcass brings status, which means better reproductive opportunities. So in species C, genes for being a good hunter are culturally selected for with no input from the environment. If it did not have culture it would be just like Species B. But evolutionarily it looks more like species A. Since cultural change happens much faster than environmental change, it can affect evolution more quickly as well.

How would this work in humans? Take the evolution of blond hair, When this was recently announced, most of the theories as to why it happened involved environmental or biological reasons; Blonde's had mess melanin and were better at producing vitamin D in the sparse sunlight North Europe. Blonds have better reproductive ability so they out breeded their counterparts. But the most obvious answer was only provided as a joke explanation: "Gentlemen prefer Blonds." It is quite possible that in Northern Europe at that time, a cultural, and completely arbitrary, preference for Blonds could have developed. In a culture with a few powerful men producing the most offspring, their cultural preference for blonds could have quickly led to the proliferation of the gene without any environmental or biological pressure at all. Notice that this is almost Lamarkian evolution, conscious people seeing what they like and deliberately deciding to make more people like that.

Another example of cultural evolution is the largest change in human population genetics of recent times, the European and African replacement of the native population in North America. This would never have happened without boats, cultural artifacts. In fact all genocides are cultural and evolutionary events.

This makes human evolution really hard to figure out because there are infinite cultural stories you could make up about why a particular trait occurred. However I think taking cultural evolution seriously will be key in understanding human evolution, particularly in figuring out how language developed, since language and culture are so closely tied.
posted by afu at 10:46 PM on December 10, 2007 [1 favorite]


Well, with genetic engineering, natural evolution becomes kind of meaningless. Memes take over, genes take the backseat.
posted by empath at 10:55 PM on December 10, 2007


yes, we're all missing heroes
posted by atomicmedia at 11:12 PM on December 10, 2007


or is that hiro
posted by atomicmedia at 11:13 PM on December 10, 2007


People act like Lamarck and Darwin are mutually exclusive. They're not. We can simultaneously evolve according to selective pressures, and exchange/evolve genetic sequences within ourselves and with the vast amount of bacteria that populate us. If there's one thing I've noticed about genomics, it's that the system repeatedly rejects convenient simplifications.

Viruses may be more complex signaling mechanisms than they're given credit for being.

We won't know about the fundamental stability of the genome until completing a full genome map is affordable enough to do repeatedly across the lifespan of a higher mammal. Until then, a bit of scientific humility about the exclusive nature of natural selection would be prudent.
posted by effugas at 12:48 AM on December 11, 2007


I'm excited to see this in the news because I do research on identifying positive selection in the human genome. I'm glad someone dug up the original paper too. The first news story I saw didn't even mention PNAS, and then I found that it wasn't even on the early edition of PNAS yet.

You would have to define "advantageous" that an unemployed drug dealer who fathers 10 children is more successfull than a Nobel prize winner with only one child. From a biological perspective he is.

Generally yes, but not necessarily. When the next flu pandemic comes about, the poor children of the drug dealer might all die, while the Nobel laureate's child will be safely preserved with top medical care.

afu: Theories of sexual selection have been around since Darwin. The idea that mate choice could increase the prevalence of traits that would otherwise be deleterious does not require any concept of culture.
posted by grouse at 1:57 AM on December 11, 2007


We won't know about the fundamental stability of the genome until completing a full genome map is affordable enough to do repeatedly across the lifespan of a higher mammal.

No, we already know. The genome of some of your cells changes during your lifespan. There are dramatic changes in cancerous cells, which the cancer genome project is studying. And your B cells modify their own genomes to produce different kinds of antibodies. But of course, this doesn't affect evolution in the main very much since it doesn't occur in the germline.

Also, it's incorrect to call humans "higher mammals." The higher mammals are giraffes and bats.
posted by grouse at 2:07 AM on December 11, 2007


Let's all upload ourselves into computers quick so we can stop having fuzzy subjective arguments like which is the best skin color, and start having precise technical arguments like which is the best OS. Wait...
posted by hoverboards don't work on water at 2:32 AM on December 11, 2007


I think IQ -- the ability to plan, see connections, make predictions, reason with rigor -- and related emotional capacities are both "better" and driven by evolutionary presssures.

Sure. Let's see how long your capability to plan and predict and reason with rigor will keep you alive while naked in the middle of the Atlantic ocean. It's all useful to us where we live, but not where we don't - environment determines how useful a given mutation is, and it's only criteria for usefulness is 'is it, in conjunction with everything else about you, enough to keep you alive long enough to get your genes propagated?'. 'Better' is an anthropocentric determination. Nifty, on the other hand, I'll give you - but then so are cephalopods, who can do some really freaky stuff a heck of a lot better than we can - often, in fact, naked in the middle of the Atlantic ocean.
posted by Sparx at 2:45 AM on December 11, 2007 [4 favorites]


grouse--

My argument is that it is at least possible more complex things are going on with the germline than we expect. From where I sit, there's an overwhelming hostility to the concept that our experiences could shape our genome. I think more of this hostility is driven by politics and the difficulty of comprehending the beauty of natural selection, than it is by actual science.

We can simultaneously lack the ability to conclusively measure Lamarckian effects, and have strong evidence that Darwin was mostly right.

I suspect there are mechanisms by which the germline is patched, and that these mechanisms are tied to the lifespan of an organism. A short lived organism doesn't have long to modify its code, but a long lived one will not adapt to its environment fast enough if it doesn't patch along the way -- if not itself, then its children.

Clearly, the germline can change over time -- how else would the retroviruses get in? We're effectively colonies for bacteria; you don't think we can't extract useful sequences living inside us? Is it not remotely possible a lactase-consuming bacterium became rampant around the time humans started being able to consume milk? As you mention, we've already found cells that adapt their sequences to external influences. Many things are possible. It's just a question of what actually happens.

Question: Would we even be able to *detect* asymptomatic viruses? Isn't it interesting that cross-lifeform genomic injection units exist, and function quite well?
posted by effugas at 3:00 AM on December 11, 2007


effugas: it's certainly possible that foreign genes can transfer into the germline. It's happened before. Some researchers think that bacterial genes have transferred recently into the human lineage. I'm not saying that what happens in the rest of the body can't affect the germ line. Even if it were perfectly isolated genetically, you'd still be able to influence the mutation rate by controlling radiation exposure.

On the other hand, this:
there are systems in us that are actively adapting to environmental influences, selecting, designing, and absorbing constructs that yield useful traits
is a real stretch. Horizontal gene transfer is too rare for this to be an active germline-affecting process.

Would we even be able to *detect* asymptomatic viruses?

Through laboratory techniques, yes. Through patient reporting, no.
posted by grouse at 3:33 AM on December 11, 2007


When the next flu pandemic comes about, the poor children of the drug dealer might all die, while the Nobel laureate's child will be safely preserved with top medical care

Universal.

Healthcare.

Can we dig it? I can't understand why people in the US don't riot in the streets about this.

(And sincerely apologise for the derail, but I sometimes see red.)
posted by Wolof at 3:55 AM on December 11, 2007


grouse--

Given our relatively weak visibility into the state of the genome in 2007, we wouldn't really know what was being injected where, especially if an active sequence was being transcoded into a place or format we weren't analyzing.

My fundamental problem with pure natural selection is that it doesn't yield enough information transfer from generation to generation. You get, what? A couple of bits, regarding how many children and when they're born? I don't think that sufficiently accounts for the number of positive adaptations found within any complex lifeform. The idea that a malfunctioning protein somehow causes its source to be actively inhibited, and that large amounts of inhibitor eventually has an effect all the way into the germline, is the sort of feedback loop that would not surprise me if eventually found to exist.

Now what would be interesting is if mothers deliberately delivered non-reproducing viruses as a genomic communication channel between somatic cells and the germline.
posted by effugas at 4:00 AM on December 11, 2007


Generally yes, but not necessarily. When the next flu pandemic comes about, the poor children of the drug dealer might all die, while the Nobel laureate's child will be safely preserved with top medical care.

Fails to matter. From an evolutionary standpoint, the only thing that counts is that genes were passed on. Adaptation is a different subject altogether (and 10 to 1 odds at further procreating combined with exponential growth seems like a safer bet no matter the environment).
posted by quintessencesluglord at 4:16 AM on December 11, 2007


We are more different genetically from people living 5,000 years ago than they were different from Neanderthals.

My anthropology's a little rusty, so let me a(nthrop)ologize in advance, but aren't Neanderthals now considered to be an entirely separate sub-species that died out or were crossbred into homo sapiens 50,000 years ago, or so?
posted by fairmettle at 4:43 AM on December 11, 2007 [2 favorites]


We'll all be bald! I'm just ahead of the curve is all. More evolved than you filthy hirsuit buggers, in a manner of speaking.
posted by The Monkey at 4:51 AM on December 11, 2007


Given our relatively weak visibility into the state of the genome in 2007, we wouldn't really know what was being injected where, especially if an active sequence was being transcoded into a place or format we weren't analyzing.

You seriously underestimate how much we know about genetic variation already.

mothers deliberately delivered non-reproducing viruses as a genomic communication channel between somatic cells and the germline.

Doing it "deliberately" implies some sort of consciousness about it, so I'm pretty sure this isn't the case. I'll ask my mom next time I talk to her.

From an evolutionary standpoint, the only thing that counts is that genes were passed on.

Well, what matters is who is around at the end. I agree that in most circumstances a human with 10 children will have a greater chance of passing on his genes than one with 1, which is an extreme case. Limiting offspring, however, can sometimes be a good strategy. Producing an order of magnitude more offspring than other members of your species isn't an automatic win, although it's probably one of the best single predictors.
posted by grouse at 5:04 AM on December 11, 2007


Could everyone please stop referring to some mythological history where elite males were the only ones to pass along their genes? That type of culture has been rare in human history. Even in polygamous societies the number of wives men had was normally not more than a few. Plus, in most circumstances where there was in fact some sort of high poobah with hundreds of wives and concubines, that was an outlier. (And don't get me started on other-side-of-the-bed births.)

Realized that's a bit off subject but it's something people tend to parrot when discussing evolution without really thinking about it.

This seems like a fascinating study-- I do wonder, however, whether what they're seeing is a lot of spontaneous mutations that will never be selected for, and will just die out.
posted by miss tea at 5:30 AM on December 11, 2007 [1 favorite]


I do wonder, however, whether what they're seeing is a lot of spontaneous mutations that will never be selected for, and will just die out.

There's already evidence that the alleles in question are under positive selection.
posted by grouse at 5:40 AM on December 11, 2007


Actually, I'm pretty sure we seriously overestimate our knowledge of genetic variation. I've been watching the various discussions on gene expression, nonlinear genomic logic functions, RNA, and the like. The more I investigate the field, the more respect I have for nature -- with no requirements for global comprehensibility, the system has collapsed towards an order more chaotic than anything we can hope to accomplish.

You abuse my use of the word deliberate. If I can say something like, "the cell uses this protein to denature toxic particles", I can ascribe intent to biological processes. Viruses being a legitimate comm channel gone sour wouldn't be so shocking, would it?

I think my point is that a lot of people -- you, as well -- need to stop pretending we know exactly how everything works. We don't. Our tools suck right now, and we're attacking a problem more complex than anything else we've tried to comprehend. You want to say there's no good evidence for systemic Lamarckian influences? Sure, go right ahead. You want to act like any suggestion of the like is impossible and utterly disproven by the amazing and all-evolving natural selection? That's when I think you've overextended your position.
posted by effugas at 6:05 AM on December 11, 2007


I'm pretty sure we seriously overestimate our knowledge of genetic variation.

Let's be clear. We don't know everything about genetic variation. And there are a lot of unknown unknowns, to borrow the phrase from Donald Rumsfeld. But there are some things we do know.

You want to act like any suggestion of the like is impossible and utterly disproven by the amazing and all-evolving natural selection? That's when I think you've overextended your position.

That's a misstatement of what I am saying. I'm sorry, I don't think your particular suggestion is disproven because of the theory of natural selection. It's disproven because we have collected massive amounts of data on human genetic variation worldwide, and the evidence is totally inconsistent with an active mechanism in humans to drive horizontal gene transfer into the germline.

Could horizontal gene transfer happen sometimes? Yes, and it has. Is there machinery actively driving horizontal gene transfer on a large scale? No. That sort of machinery working over millions of years would produce variation on a scale that it would have been ridiculously obvious by now.

* * *

The problem with your use of the word "deliberate" or "legitimate" when you describe a communication mechanism is that the sense you are using it in is ill-defined. How do you distinguish a deliberate communication mechanism from an accidental one? What makes communication illegitimate? Consciousness is one way. You obviously have some other distinction in your mind but you haven't specified it.
posted by grouse at 6:37 AM on December 11, 2007


Theories of sexual selection have been around since Darwin.

Yes, but those theories deal with sexual selection in a purely biological situation. Peacocks have their tails only because it is a reliable indicator of biological fitness. In an organism with culture, sexual selection can happen regardless of if the trait is a sign for fitness or not. With culture, selection can occur without the influence of biological or environmental conditions, which can never happen in a species that does not have culture.

Could everyone please stop referring to some mythological history where elite males were the only ones to pass along their genes? That type of culture has been rare in human history.


The percentage of male humans who have successfully reproduced is much less than the percentage of females. This implies that there were a few males who had many mates, at the expense of unsuccessful ones. This is particularly true in a harsh environment like Northern Europe during the ice age, where the death rate for males was very high.
posted by afu at 7:16 AM on December 11, 2007


Assuming there is more genetic diversity in the population now, one can make the argument that humans are evolving faster. However, this is not the evolution you commonly think of as survival of the fittest. This is evolution as a result of random genetic drift.

The chance that an allele of a gene becomes fixed in the human population (i.e. the only allele) is equal to the frequency of that allele in the population. This is in the absence of any selective pressure. Therefore the more genetic diversity in a population, the increased chance that some of those alleles will become fixed in the population. Given the size of the human population, this kind of evolution is over an enormous time scale.
posted by batou_ at 7:51 AM on December 11, 2007


This does not mean I am buying what the authors are selling. I need to read the manuscript. I am wary of this statement "We are more different genetically from people living 5,000 years ago than they were different from Neanderthals". Sounds like soundbite BS to me.
posted by batou_ at 7:58 AM on December 11, 2007


Searching for ineffable Lamarckian qualities within eukaryotic gene transmission comes uncomfortably close to Vitalism. If our lactose tolerance mutation resulted from the insertion of a bacterial or viral genome, we could detect this because the sequence signature of such an inserted gene would be very different from our normal set. On a base pair level, it would have a different completely nonhomologous sequence of CG and AT pairs that could be seen to arise de novo. It would especially have very different CG repeats flanking it. It would have genomic markers characteristic of bacterial, retroviral, or DNA viral insertions. Finally, it would lack introns and use a protein code optimised for a slightly different set of tRNAs and polymerases. These are easy to see - we can identify inserts within human and other eukarotic inserts, and we can see that the mitochondrial DNA resulted from a bacterial infection because of its similarity to some extant species.

The varieties of the human lactose tolerance genes lack any of these characteristics. Therefore, any reasonable person can only conclude that lactose tolerance arose in all extant cases from spontaneous mutations.

Extraordinary claims require extraordinary proof.

This is particularly true in a harsh environment like Northern Europe during the ice age, where the death rate for males was very high.

Is there some research that demonstrates that the death rate here was higher than in, say, ancestral Africa where humans co-evolved with large carnivorous mammals (mainly cats) that regarded humans as prey for most of our existence? Also, in areas where human population density was higher, we could expect internecine warfare and territorial disputes to have been at a higher density and frequency, comparable to chimpanzee warfare over contested territories today.

I like the theory of sexual selection for blondness as a recognition factor for blond parents. Blondness is recessive. Therefore, in a mating between two blonds, any dark-haired children have a higher probability of being the offspring of someone other than the blond father and might have been culled. A few generations of this and you have a blond population. It makes about as much sense, and is as provable, as most of the other blondness origin theories.
posted by meehawl at 8:03 AM on December 11, 2007


Is there some research that demonstrates that the death rate here was higher than in, say, ancestral Africa where humans co-evolved with large carnivorous mammals (mainly cats) that regarded humans as prey for most of our existence?

The theory I have read is that in ice age Northern Europe most of the calories came from hunting because there so few plants to be foraged. Hunting was dangerous and since men were the main hunters it lead to them dying at a higher rate than average. I'm not saying this is the truth, but it is plausible. I'm not saying for sure that my theory on blondness is true, I was just using it as example of cultural genetic selection outside of biological selection.
posted by afu at 8:12 AM on December 11, 2007


To clarify some things with amberglow's questions. In biological terms, evolution is the change in gene frequencies over time within a population, and the factors that influence those changes.

"Population" is often used instead of "species" for two reasons, first the definition of "species" is ambiguous and problematic, and secondly evolutionary biologists are often interested in how local populations differ from each other. For example the Tsavo lions often do not have manes, because Tsavo lions experience significantly higher heat stress. Or microbiologists might be interested in identifying a particular strain that makes a particularly good batch of lambic.

Within a population individuals will have a distribution of phenotypes for a given trait that approximates a bell curve. Cases in which a phenotype is all or nothing is relatively rare, and environmental factors will also influence the resulting phenotype. For example, the average width of the human thumb is approximately one inch. Some people have wider thumbs, some people have thinner thumbs. Selective pressure determines which individuals will pass on their genes. If the selective pressure is biased, or not centered on the mean, then the population distribution of that phenotype will shift over generations.

So as an example with domestic dogs, one model is that within wild dog populations there were a distribution of behaviors. Some dogs tolerated sharing food, other dogs did not. Some dogs can learn human body language, others can't. Some dogs aggressively attack anything that could be food (including infants), others don't. The cultural symbiosis of human-dog relationships involved selective pressure that changed multiple gene frequencies in the dog populations that lived alongside humans.

And it should be noted that selective pressure can serve to reinforce the status quo. "Living fossils" are structurally similar to their fossil ancestors not because of a lack of selective pressure, but because the selective pressure acting on them selected against deviations from the mean.
posted by KirkJobSluder at 8:30 AM on December 11, 2007 [1 favorite]


"...and there are even rumors, Miss Grey, of mutants so powerful that they can enter our minds and control our thoughts, taking away our God-given free will. Now I think the American people deserve the right to decide if they want their children to be in school with mutants. To be taught by mutants! Ladies and gentlemen, the truth is that mutants are very real, and that they are among us. We must know who they are, and above all, what they can do!"
posted by iamck at 8:56 AM on December 11, 2007


Assuming there is more genetic diversity in the population now, one can make the argument that humans are evolving faster. However, this is not the evolution you commonly think of as survival of the fittest. This is evolution as a result of random genetic drift.

It's not just that there's a lot of genetic diversity. The researchers here are specifically claiming the patterns of this diversity are only consistent with positive selection. The phrase "adaptive evolution" in their title specifically means positive selection. I hate the term "adaptive evolution," because it makes it even more difficult to discuss evolution as a process which includes more than just selection.

afu: Regardless of whether Darwin considered human culture in sexual selection, this stuff has been done by evolutionary psychologists (not the same as evolutionary biologists). David Buss has done much research on human mate choice.
posted by grouse at 9:25 AM on December 11, 2007


I don't have anything to add to the biological debate - a lot of what you's guys is talking about, what with viruses causing DNA mutation and whatnot I've read about casually (mostly in Survival of the Sickest - some lovely airplane reading!), but I don't have anything new to say about it.

I can however comment about me! Yes, me! Ohboy!

Also, the son of dullards might not be a dullard himself. Same goes for the daughter of a pair of smarty-pants. Furthermore, there's nothing that says that social traits, like wealth or education, go together with attractiveness or intelligence. Lastly, I just want to make absolutely clear that good traits, such as, say, the ability to hold one's liquor, will not necessarily go with other good traits, such as good, natural posture or 20/20 eyesight.

I might not be a good example of evolution as a whole, but I am the attractive child of two homely parents and the only member of my extended family (on both sides!) with 20/20 vision. On the downside, I have epilepsy, which no one else in my family on either side suffers from. Hopefully, when I breed I will have pretty children neurologically normal with 20/20 vision, but it's just as likely that I'll have some seizure-rific nearsighted babies with faces that only I, as their mother, will be able to love.
posted by grapefruitmoon at 9:39 AM on December 11, 2007 [1 favorite]


I will buy that we can likely detect insertions, due to distinct statistical properties from wholesale insertion. However, nature does not care if something comes close to a disliked theory ("vitalism").

What neither you, meehawl, or you, grouse, are addressing is my assertion that the feedback loop from survival or r non-survival is just too damn slow to account for the rate of adaptions that have non-disastrous effect. Natural selection is great and all, but I don't buy that all changes need to be random. The "offers a 5% survival advantage, so everyone has it after a few generations" logic works great for one trait, and totally fails for hundreds of thousands at once. A large number of systems working in parallel, being modulated, inhibited, and perhaps migrated into the germline through competitive pressures makes more sense, given the amount of information at stake.

Anyway, it's a prediction, one that can be experimentally disproved by showing only statistically random changes across germline cells from birth through death on a moderate sample of individuals. Faster sequencing will make this experiment possible.
posted by effugas at 10:20 AM on December 11, 2007


Vitalism is not just disliked, or right. It's not even wrong. It's just not science. It made predictions, and constraints, and those predictions and constraints were conclusively demonstrated to not be in accord with observed phenomena. Therefore it was rejected as a theory.

I'm not aware that anyone has argued that sexual selection cannot accelerate or increase the number of phenotypic variations within a species. Scandinavian blondes, for example, are a often presented as a classic example. But this is not speciation, and it is not Lamarckianism, or intelligent design. Within the human species we breed for pedigreed breeds, not overt adaptations. Our "races" are not incipient, directed speciations or genetically distinct on any meaningful aggregate level, but instead are just mild phenotypic variations on the level of the difference between poodles and mastiffs.

A large number of systems working in parallel, being modulated, inhibited, and perhaps migrated into the germline through competitive pressures

Why should a large number of systems working in parallel (presumably uncoupled and individually seeking maximal propagation) produce anything other than a reversion to the mean phenotype within the aggregate vector of their expression through natural selection (ie, us)? This is not an easy problem to overcome in the theory of speciation. The only way you can impute direction to this statistical chaos is to introduce teleology, or intelligent design. Or all the mechanisms of puncuated equilibrium, founder effects, allotropism, pleitropism, gene flow, and the esoterica of evolutionary theory.

Take HIV for example. HIV mutates many millions of times faster than us in the time dimension. Within an infected individual being treated with single drugs, the mutated, resistant HIV clades quickly proliferate because their non-resistant kin are eliminated. Yet rotate treatments, or use multi-drug treatments, and the HIV infection becomes controllable because each clade quickly reverts to the mean infection clade when the stressor abates. This holds true even in case of superinfection with extremely divergent clades. The HIV genome is many orders of magnitude less complex than our eucaryotic genome - why should HIV exhibit an averaging and ours does not?
posted by meehawl at 10:48 AM on December 11, 2007


I neither say this is good or bad or Dawins [sic] principle should be applied 1:1 to a human society but the statement that "and every mutation that is advantageous to people has a chance of being selected and driven toward fixation." is only true in a very broad sense. You would have to define "advantageous" that an unemployed drug dealer who fathers 10 children is more successfull than a Nobel prize winner with only one child. From a biological perspective he is.
posted by yoyo_nyc at 7:51 PM on December 10 [1 favorite +] [!]


Well, there may be a disconnect about the word "advantageous" here. Also, time scales seem to present difficulties to some thinkers. Oh, well...
posted by Mental Wimp at 11:19 AM on December 11, 2007


the feedback loop from survival or r non-survival is just too damn slow to account for the rate of adaptions that have non-disastrous effect.

What rate is that, anyway? How are you defining it? What would be a rate that you would accept as low enough to fit?

The "offers a 5% survival advantage, so everyone has it after a few generations" logic works great for one trait, and totally fails for hundreds of thousands at once.

It's not just a few generations. It's hundreds to thousands of generations. And through genetic drift, this will happen whether the fixated character is adaptive or not.

Anyway, it's a prediction, one that can be experimentally disproved by showing only statistically random changes across germline cells from birth through death on a moderate sample of individuals.

Your prediction has already been disproven. You are arguing that humans (and presumably other mammals) may have active mechanisms to encourage horizontal gene transfer from bacteria into the germline. If this had been going on for millions of generations, it is virtually impossible that we would not have seen telltale signs of this already. Among other things, such a mechanism would introduce several orders of magnitude more variation into human or primate populations than what we have observed repeatedly.
posted by grouse at 12:39 PM on December 11, 2007


Or all the mechanisms of puncuated equilibrium, founder effects, allotropism, pleitropism, gene flow, and the esoterica of evolutionary theory.


Needs to be repeated. It's unfortunate that with the rise of "The Selfish Gene" speciation doesn't get the attention it deserves, but it is really were all the really interesting things happen in evolution, especially in multicellular organisms. Though I tend to think allotropism and pleitropism don't do all that much.

Regardless of whether Darwin considered human culture in sexual selection, this stuff has been done by evolutionary psychologists (not the same as evolutionary biologists). David Buss has done much research on human mate choice.

Regardless of whether Darwin considered human culture in sexual selection, this stuff has been done by evolutionary psychologists (not the same as evolutionary biologists). David Buss has done much research on human mate choice.

I was just using the blond thing as a proof of plausibility, I don't mean it to be a definitive explanation. Most evolutionary psychologists put too much weight on biological factors and not enough on cultural. It's one of the reasons I find their work so mundane.
posted by afu at 12:44 PM on December 11, 2007


Additionally, I wonder if this is damaging to the get-out-of-jail-free card that evolutionary psychologists like to employ; namely, that findings that do not fit in to their models are classified as "recent evolutionary developments."
posted by proj at 1:43 PM on December 11, 2007


Generally yes, but not necessarily. When the next flu pandemic comes about, the poor children of the drug dealer might all die, while the Nobel laureate's child will be safely preserved with top medical care.

Fails to matter. From an evolutionary standpoint, the only thing that counts is that genes were passed on.


That is completely nonsensical. If all the drug dealer's children die, then, no, it doesn't "matter" that the genes were passed on, because the kids are now dead and are unable to pass THEIR genes along. The father's genetic line is ended.

From an evolutionary standpoint, what matters is that genes continue to exist AFTER they're initially passed on, so that they can be passed on AGAIN. That's why humans don't just abandon babies immediately after birth- because, in order to pass on our genes, we need to protect the kids until they themselves are old enough to breed.
posted by showbiz_liz at 2:01 PM on December 11, 2007


So as an example with domestic dogs, one model is that within wild dog populations there were a distribution of behaviors. ... The cultural symbiosis of human-dog relationships involved selective pressure that changed multiple gene frequencies in the dog populations that lived alongside humans.
Thanks--I notice you don't use the term "evolution" tho--to describe how dog populations have changed (and it seems you should, no?)...i often find that it's only used for humans, and fossils of all sorts--and not often used to describe poison-resistant rats or labradoodles or anything like that.
posted by amberglow at 2:12 PM on December 11, 2007


The higher mammals are giraffes

That makes sense.
posted by UbuRoivas at 2:34 PM on December 11, 2007


Evolution is descent with change. Most models of evolution involve the change occurring in a population over time. An increased population of poison-resistant rats would definitely be the product of evolution. On the other hand, it's not really that useful to refer to a single example of the crossing of a labrador with a poodle as evolution.
posted by grouse at 2:44 PM on December 11, 2007


Could everyone please stop referring to some mythological history where elite males were the only ones to pass along their genes? That type of culture has been rare in human history. Even in polygamous societies the number of wives men had was normally not more than a few. Plus, in most circumstances where there was in fact some sort of high poobah with hundreds of wives and concubines, that was an outlier. (And don't get me started on other-side-of-the-bed births.)

Although my phrasing wasn't the best, the point was more that elite males had a higher chance of passing on their genes in the past, whereas today it's much more egalitarian. I never meant to imply that only elite males passed on their genes.

It's also far from mythical. There are tribes in existence today where chiefs have dozens of wives, and lesser men go without. In feudal times, the lord of the manor (in some places & times) apparently had the legal right to spend the first night with any peasant woman on his lands who got married.

And you can also see the process of higher status males being advantaged at work in modern India: due to female infanticide & male children being generally more valued, there's about a 55-45% split between the sexes. With strict limitations on sex outside of marriage, and with most marriages arranged & depending largely on social status & life prospects, this means that at least 18% (10/55) of men are pretty much excluded from procreation, and you can safely assume that the ones who miss out are generally lower on the socioeconomic scale. I'd guess that something similar happens in China, and with those two countries we're talking about nearly half the population of the world.

Also, in more ancient times, when medicine was poorly understood & people were more exposed to droughts & famines, it's also pretty safe to assume that wealthier men tended to live longer and therefore be able to father more children than poorer men, even if they didn't practice polygamy.
posted by UbuRoivas at 2:53 PM on December 11, 2007


Even in polygamous societies the number of wives men had was normally not more than a few.

Um, so assuming a 50-50 gender split, that means for every man who has three wives (for example), two other men go without, right?
posted by UbuRoivas at 2:58 PM on December 11, 2007


this means that at least 18% (10/55) of men are pretty much excluded from procreation

It's hard to measure these things without getting a lot of people angry, but I've seen estimates for the number of children with different fathers than their presumed ones to be anywhere from 2-5%. Culturally specific, but most of the genetics researchers based in the West that I've taken lessons from incline towards the high end of that range.
posted by meehawl at 3:04 PM on December 11, 2007


I've seen estimates for the number of children with different fathers than their presumed ones to be anywhere from 2-5%

I recall a Kinsey-era study that suggested it was much higher. Based on blood-type inheritance, they found that something like one in three or four could not possibly have been fathered by the man taking that role in the family.

It's probably pretty hard to get to the bottom of such things, as they'd be very culturally specific. You'd imagine that in the 50s plenty of people were marrying young & finding themselves in unhappy marriages, but keeping up appearances & avoiding the stigma of divorce. In the Indian context, I'd find it pretty hard to imagine that bored housewives would be seeking much sexual action from the 18% of men at the bottom of the social pile, especially because caste & religious issues can mean that the sexy pool cleaner might be literally untouchable.
posted by UbuRoivas at 4:24 PM on December 11, 2007


amberglow: Oh, I thought that was obvious. But yes, the domestication of canines (and the development of the various breeds) is an example of evolution. Although with boutique hybrids like labrapoodles you run into a problem of defining the population, because I don't think breeders fancy second-generation hybrids at this point in time.

In regards to: "i often find that it's only used for humans, and fossils of all sorts--and not often used to describe poison-resistant rats or labradoodles or anything like that." Well, I have to wonder what the heck you are reading, because all of the examples I used of evolution have been discussed in rather pedestrian sources like National Geographic, and Scientific American. And perhaps more importantly, just about any biological examination of populations of more than a dozen is going to hinge on evolutionaly theory. So perhaps sometimes biologists take evolution for granted and focus on selection mechanisms and models, but that's just the details of Darwinian evolution as a framework.
posted by KirkJobSluder at 4:52 PM on December 11, 2007


caste & religious issues can mean that the sexy pool cleaner might be literally untouchable.

Is sex dirty? Only if it's done right!

Never underestimate the attraction of the taboo.
posted by meehawl at 5:04 PM on December 11, 2007


Yes, but also never underestimate the disincentive value of total social ostracism in a country with no real social security! Even not-at-fault (female) divorcees in India can typically expect their own family to disown them, as a rule that applies to all but the most westernised of urban elites.
posted by UbuRoivas at 5:38 PM on December 11, 2007


Your prediction has already been disproven. You are arguing that humans (and presumably other mammals) may have active mechanisms to encourage horizontal gene transfer from bacteria into the germline. If this had been going on for millions of generations, it is virtually impossible that we would not have seen telltale signs of this already. Among other things, such a mechanism would introduce several orders of magnitude more variation into human or primate populations than what we have observed repeatedly.

Actually, I've been convinced by you and meehawl that direct horizontal transfer is a lot rarer than I believed.

What I think you've insufficiently addressed is the usefulness of mutations. I'm a cryptographer to some extent, and we take the concept of randomness quite seriously. I don't think we change entirely randomly. Non-random change does not require some sort of grand teleological vision (frankly, it betrays biases to think that it does). Randomness is hard, especially if you want useful output in the end. Some sort of germline changes based on long periods of expression regulation (either positive or negative) by as-yet undiscovered systems would provide a much better feedback signal than survival or lack thereof.

Complex lifeforms are all about massively parallel self-adaptation -- everything figures out how to work with everything else. That selection needs to only occur between generations, and not over the course of a repeatedly rebuilt lifespan, is not at all obvious. There are political implications to this that I think make people uncomfortable.

Hell, people are uncomfortable with animals having emotions. Doesn't mean it isn't true.

You could level the critique against me -- that I'm uncomfortable with the minimal information transfer inherent in selection leading to complex multicellular organisms with long lives. I just don't think there's enough bits to go around in the serial model, whereas there's more than enough to go around in a parallel model.
posted by effugas at 6:35 PM on December 11, 2007


The HIV genome is many orders of magnitude less complex than our eucaryotic genome - why should HIV exhibit an averaging and ours does not?

Because the HIV genome is many orders of magnitude less complex than our eukaryotic genome? Because maybe in nature multicellular organisms with long lives and sexual reproduction work differently than a floating unit of genetic material?

You're making some good arguments, but this ain't one of 'em.

What data do we have on germline stability, and on the actual entropic decay of the genome?
posted by effugas at 8:28 PM on December 11, 2007


Some sort of germline changes based on long periods of expression regulation (either positive or negative) by as-yet undiscovered systems would provide a much better feedback signal than survival or lack thereof.

Well, that happens. In many vertebrates, such as humans, DNA methyltransferases travel along the genome finding CG sequences and methylating the cytosine. But 5-methylcytosine spontaneously deaminates into thymine, so now the sequence is TG. So if you look at the frequency of dinucleotides, CG is significantly less than what one would expect from the frequency of C times the frequency of G, and TG is found significantly more than what one would expect.

If these genes are actively being expressed, however, transcription factors will bind the DNA near the beginning of the gene, and prevent the methyltransferases from gaining access. So, for many genes expressed in the germline you can see a significant increase in CG sequences over what you would see in the rest of the genome, or even the beginnings of tissue-specific genes not expressed in the germline. These areas of increased CG frequency are called CpG islands, with the p indicating that the C and the G are on the same strand covalently linked to each other by a phosphate backbone rather than being on opposite strands connected by base pairing.

I think that's pretty cool, and it's possible that there are other mechanisms like this. But it isn't necessary to explain adaptation. This particular phenomenon isn't even universal in the vertebrates. And the work was done in the first half in the twentieth century to prove that adaptation was possible even with just random mutations and Mendelian inheritance.
posted by grouse at 3:02 AM on December 12, 2007


effugas: Two things.

First of all, I think it's really difficult for us to understand Deep Time, in the same way that it's really difficult to understand the scales involved in Deep Space.

Secondly, I think there are inklings that some of the key things that make this species different from that species involves more than just random mutation of gene sequences. Mutuations that influence gene regulation can be quite powerful.
posted by KirkJobSluder at 11:09 AM on December 12, 2007


Mutuations that influence gene regulation can be quite powerful.

Right, very astute. And it goes beyond just regulation of expression. Transcribed exons can be assembled differently and the choice of imprinted genes can greatly influence phenotype.
posted by Mental Wimp at 11:26 AM on December 12, 2007


What data do we have on germline stability, and on the actual entropic decay of the genome?

Paradoxically, the phenotype can remain stable as the germline genotype "boils", owing to the redundant properties of protein encoding and the fact that some sequence changes have no functional implication. This has been observed in very old species that are with us today.
posted by Mental Wimp at 11:29 AM on December 12, 2007


What data do we have on germline stability, and on the actual entropic decay of the genome

I'm not entirely sure what this means. Is it something like this?

Identification of conserved lentiviral sequences as landmarks of genomic flexibility

New maximum likelihood estimators for eukaryotic intron evolution

Codon bias as a factor in regulating expression via translation rate in the human genome

Binding energy and the information content of some elementary biological processes

Power law exponents characterizing human DNA

Statistical information characterization of conserved non-coding elements in vertebrates

And especially for teleological people:
A non-adaptationist perspective on evolution of genomic complexity or the continued dethroning of man.
posted by meehawl at 11:59 AM on December 12, 2007 [1 favorite]


An NYT story on this topic with slightly critical comments from a couple of scientists.
posted by grouse at 2:32 PM on December 13, 2007


thanks for that article, grouse...i guess now that we're identifying and tracking genes we'll see from now on what changes occur? (it wouldn't have been possible until now, no? unless there's enough buried genetic material from all our ancestors?)

totally out of my league, but still fascinated:
how does the change of regular cells into cancer cells figure into this "germline" thing -- or is that just regular mutation? or the normal deterioration of all cells during aging and the loss of efficiency in so many areas like healing and recuperation and strength, etc? or when a virus invades and changes blood cells and/or others while also sometimes changing itself during the process? ... (which all happen during one life and may or may not be transferable to offspring?)

and also, the whole genes acting in concert or only being activated in the presence of other genes(?) things, and the hit-or-miss nature of some genetic diseases and conditions (like the breast cancer genes--shouldn't they give men breast cancer in the same rates, if the family history is the same too?) ... our mixing of genes more and more would lead to both more protection but also weird/deadly new combinations, no?
posted by amberglow at 7:20 PM on December 13, 2007


grouse--

Fascinating information. Just to complete the picture though, is it generally accurate that external factors (stress, hormone rates, peer groups, whatever) can modulate gene expression? For example, I understand that various substances bind to receptors, and these receptors cause changes inside the cell. I'd just like to validate that receptor binding can directly modulate gene expression.

Given that, a transition from CG to TG -- this alters codons, but it isn't apparent to me that it deactivates unused genes. I do see that TGA is a stop codon while CGA is not; does this mean there's a greater likelihood for unused protein sequences to be disabled?

meehawl--

I'm not a teleologist. I just suspect, strongly, that the "deep time" model fails to account for sufficient complexity for creatures with long lifespans, and that those creatures that could adapt over the course of their lives would have a significant survival advantage over those that couldn't. Nature seems to like having one system stop scaling as another starts.

(Side note: Man, the trouble that Dotplots get me into...)
posted by effugas at 8:29 PM on December 13, 2007


i guess now that we're identifying and tracking genes we'll see from now on what changes occur?

Not really. This stuff takes many generations to show up, so we won't see new human selection in our lifetimes, assuming that we aren't going to live for hundreds of years. What we will see is increased data about the genomes of individual humans, which we'll be able to use to see what happened in the past, much in the way that we can conclude that Queen Victoria carried the hemophilia allele without sequencing her genome.

We do have the technology to get some sequence data from animals that have been dead only a few thousand years (used in the Neanderthal Genome Project), so I've always thought it would be fascinating to see how our predictions matched up with reality there. But for the near future I think most of the substantial resources needed at present for genome sequencing will probably go to study living humans, not dead ones. So it might be a while before we get that data.

how does the change of regular cells into cancer cells figure into this "germline" thing

The germline is the line of cells starting with the zygote and ending with a gamete. So a mutation in a benign skin cancer will not on its own cause mutations in your sperm, although mutations there could perhaps be caused indirectly. Mutations would be less likely in eggs because they are already produced before birth.

There are also ways of passing epigenetic information on other than in the DNA. See maternal effects. It's possible, but very unlikely that this information passed this way will continue to propagate over several generations. I believe I saw an experiment once where researchers got maternal effects to pass through two generations but no more.

or the normal deterioration of all cells during aging and the loss of efficiency in so many areas like healing and recuperation and strength, etc?

Telomerase is expressed in the germline, and counteracts the most notorious cellular aging process of telomere shortening. So, different rules here. I thought that sperm viability was still affected by aging, however.

(like the breast cancer genes--shouldn't they give men breast cancer in the same rates, if the family history is the same too?

This review of male breast cancer says that the same sorts of mutations that are risk factors for female breast cancer are also risk factors for male breast cancer. But it's multifactorial, and men are much, much, less likely to get breast cancer for a lot of other reasons (hormones and amount of breast tissue just to start), so the risk won't be the same.

our mixing of genes more and more would lead to both more protection but also weird/deadly new combinations, no?

An interesting thing about mammalian biology is that most of the weird/deadly new combinations are selected against before birth. That's what a miscarriage is.
posted by grouse at 2:53 AM on December 14, 2007 [1 favorite]


is it generally accurate that external factors (stress, hormone rates, peer groups, whatever) can modulate gene expression?

Yes, definitely.

Given that, a transition from CG to TG -- this alters codons, but it isn't apparent to me that it deactivates unused genes.

I explained this poorly. First, this sort of thing will be most important upstream of genes, where transcription begins, so it's less likely to actually affect any codons. It's not the change to TG that prevents transcription. It's the methylation of C that has two effects: (a) it makes transcription less likely, and (b) it makes a mutation to T much more likely. However, not only does methylation block transcription, but transcription blocks the methylation process as well. So if you find an unexpectedly high amount of CG, you can conclude that the C was less likely to be methylated, and therefore that transcription was much more likely to be happening at that position in the germline.

Anyway I think this is all really cool stuff, but I just want to underscore that it's not necessary for evolution to proceed. I only know of this mechanism being found in vertebrates, and not even all vertebrates.
posted by grouse at 3:01 AM on December 14, 2007 [1 favorite]


grouse--

Obviously evolution can occur without resorting to mechanisms such as this, and almost certainly it happens without any sort of explicit teleological desire. However, it's cool to see some rather explicit non-random activity occurring. I just took a look as some random sample of a human chromosome, and the effects aren't exactly subtle:

1grams for ACTG:

'A' => 2553,
'C' => 2462,
'T' => 2447,
'G' => 2524,

2grams for ACTG:

'AC' => 484,
'CC' => 797,
'TG' => 805,
'AT' => 514,
'AA' => 724,
'CT' => 767,
'CG' => 62,
'TA' => 360,
'GC' => 583,
'CA' => 835,
'GT' => 481,
'AG' => 830,
'TC' => 597,
'GA' => 634,
'TT' => 685,
'GG' => 826,

This is indeed cool stuff. Where can I learn more?
posted by effugas at 10:57 AM on December 14, 2007


thanks, grouse : >

this thread keeps reminding me of a wonderful book by Geoff Ryman: The Child Garden
posted by amberglow at 4:55 PM on December 14, 2007


Meehawl,

Your links are pretty cool too. The paper on Codon Bias appears to imply that a highly expressed sequence will be optimized to reduce production cost / error rate.

Nothing teleological -- just a strong suspicion that survival rates on the overall organism aren't all that's modulating the codebase, at least in some instances.
posted by effugas at 5:46 PM on December 14, 2007


In other science news: High School Students Drink to Escape and Other Obvious Science
posted by homunculus at 7:17 PM on December 14, 2007


Yes, the various scaling patterns for genome efficiencies surprised me as well. You may like reading about aptamers or glycobiology - there are undoubtedly network effects going on in the organism, but regarding whether those creatures that could adapt over the course of their lives would have a significant survival advantage over those that couldn't, well, the division between somatic and germline cells has already been made. Natural selection has undoubtedly experimented with organisms that could improve themselves, and their germ line, but beyond maternal and paternal imprinting of various chromosomes in different eukaryotes, anything beyond this seems to be selected against. The old must give way to the new, after all. Some organisms take especial care to sequester parental germline information - there's a mussel, for instance, that secretes away the male-derived mitochondria in its gonads for propagation through the male line, as do some other euks. Nature has overwhelmingly selected against this, however, finding it more successful to transmit the mitochondrial infection through the female line. This seems to hold in general (not all, but close to) in animals and plants with very different sex determining mechanisms.

If you're looking for examples of eukaryotic genomes being reprogrammed on a vast scale, see Wolbachia. Certain Drosophila species also seem to be inthe process of being colonised by relatively new retroviral infections. But these are more like environmental toxins than goal-directed individual adaption.
posted by meehawl at 11:21 PM on December 14, 2007


If you want to learn more about CpG sites in general, I'm not sure if there's a good way other than delving into the literature. Search on PubMed for CpG and click on the review tab. This looks like an interesting review of the repair processes that cause this phenomenon.

Just so you know, scientists don't universally recognize the existence of significant codon bias in the human genome. I'm not saying I don't, I'm just saying that many do not.

If you want to read about the kinds of tests done in the article that is the subject of this post, there is a truly excellent review by Sabeti and co-workers.

About evolution in general, Understanding Evolution is a great resource. At a more advanced level, I've been going through the third edition of Evolution by Mark Ridley, and it is very good. Beware: there is another book with the same title by the same author which is a TOTALLY DIFFERENT BOOK consisting in classic papers by various authors. I'm told it's pretty good too, but it's totally different.
posted by grouse at 8:14 AM on December 15, 2007 [1 favorite]


those creatures that could adapt over the course of their lives would have a significant survival advantage over those that couldn't

Indeed, all that is required according to my information-theoretic critique is that the next generation adapt to conditions experienced during its parent's life, not that the parent itself rewrites its code.

grouse, how is codon bias controversial? CG was missing from the random sample I picked up. Have there been experiments were CG is found to be stripped after major environmental changes to parents? Does anything invert the process?

I'll be reading everyone's links. Thanks! Here's some of what got me into this research:

Law is Code (and yes, that's my own work).
posted by effugas at 12:00 PM on December 17, 2007


how is codon bias controversial?

I don't think there's a raging controversy or something, it's just that not everyone agrees that it plays an important role in human biology the same way that it does in other species. Look at this table from Ridley. Compare the arginine codon bias in human against Drosophila or E. coli. It's a different order of magnitude. This means that it's much more likely that Drosophila or E. coli biology is affected by tRNA abundance, while in human I don't know of any evidence that there is. There might be some that I don't know about since I don't pretend to be an expert on codon bias, but even if there is, it's not as significant as in Drosophila or E. coli.

CG was missing from the random sample I picked up.

If you limit to only coding sequence, then there is still some depression for CG, but not the. I used BioMart to download the coding sequences of all Ensembl 48 protein coding transcripts (ambiguous dinucleotides excluded) and got the following frequencies:

AA 5103287
AC 3897144
AG 5718212
AT 3685737
CA 5633980
CC 5426275
CG 2208216
CT 4956415
GA 5407510
GC 4835956
GG 5077539
GT 3206126
TA 2250795
TC 4065130
TG 5532290
TT 3586949


There's still less CG, but not the order of magnitude you would get if you did this across the whole genome. Why? Purifying selection. That CpG→TpG transition happens at the same rate, but when it disrupts the amino acid translation of coding sequence, the offspring is no longer viable. So it's not passed on.

Law is Code

Interesting, I didn't realize that non-biological fields used dot plots.
posted by grouse at 1:50 PM on December 17, 2007


grouse--

I've been pushing dotplots further than almost anyone, though there's some precedent using it for audio analysis. My own version of a dotplot audio analyzer can be seen here.

Regarding there being less CG, what are the odds a given CpG->TpG transition will lead to a fatal translation failure?
posted by effugas at 7:03 PM on December 17, 2007


In coding sequence:
 ACG (T) --> ATG (M)
 CCG (P) --> CTG (L)
 CGA (R) --> TGA (*)
 CGC (R) --> TGC (C)
 CGG (R) --> TGG (W)
 CGT (R) --> TGT (C)
 TCG (S) --> TTG (L)
 GCG (A) --> GTG (V)
CG -> TG: 8/8

 ACG (T) ... ACA (T)
 CCG (P) ... CCA (P)
 CGA (R) --> CAA (Q)
 CGC (R) --> CAC (H)
 CGG (R) --> CAG (Q)
 CGT (R) --> CAT (H)
 TCG (S) ... TCA (S)
 GCG (A) ... GCA (A)
CG -> CA: 4/8
Looks like 12/16 CG→TG transitions (don't forget that CG→TG on the minus strand looks like CG→CA on the plus strand) are nonsynonymous, including one nonsense mutation leading to a premature stop. Most amino acid changes are deleterious, and probably almost all nonsense mutations are.
posted by grouse at 2:07 AM on December 18, 2007


grouse,

If the transition was synonymous, why methylate at all? Seems an expensive system to keep up if it's not going to cause an actual change.

Also, are the environmental effects that drive gene expression equally impactful on germline cells, as opposed to the somatic cells that are actually exhibiting desired/undesired behavior?
posted by effugas at 12:46 PM on December 18, 2007


why methylate at all

Methyls are used all throughout biochemistry. The methyl group is small and easy to transfer and to hang off the DNA chains. The methyls are used to protect against retrovirus attack, and in complex creatures to recruit factors that regulate histone protein attachment and others used in an acetylation/deacetylation cycle that helps to up- and down-regulate gene expression.
posted by meehawl at 3:54 PM on December 18, 2007


Meehawl--

What I meant by "why methylate" was that if CG->TG methylation was fatal to the genome, we wouldn't see evidence that we'd survived so much of it. That we specifically incur this methylation damage in unexpressed genes -- could this not imply that the reason we survive is because the damage is only hitting (mostly) unused code?

As for retrovirals, I gather they inject their code anywhere along the genome, meaning they miss transcribed sections, meaning their more vulnerable to methylation? Or is there another mechanism in play?
posted by effugas at 4:05 PM on December 18, 2007


s/their/they're

(pedantic)
posted by effugas at 4:20 PM on December 18, 2007


effugas, the methylation process does not change CG→TG on its own. Methylation itself is not damage. It is an essential part of mammalian gene regulation. It changes the C to m5C, which suffers a much higher rate of mutation (specifically to T) than any other commonly found nucleobase. But it's not automatic, just a matter of probability.

If the genes were truly unexpressed, then they'd evolve away pretty quickly. They are likely to have less expression in the germline. Methylation is thought to control some genes that are tissue-specific. It's why your neural cells act differently from spermatocytes.
posted by grouse at 4:22 PM on December 18, 2007


grouse--

Automacity is just a probability of 1 :) The presumption of damage comes from you, when you wrote that non-synonymous transitions are deleterious. If we've evolved a system that targets deleterious effects on unexpressed genes in the germline -- or, to argue to the inverse, preferentially deploys protections on highly expressed genes in the germline -- and germline expression is environmentally modulated, then environmental influences during the life of an organism have a direct effect on the germline.

There is no teleology -- just a better source of selective pressure than mere reproduction. My problem with survival being the exclusive metric is that one sequence with a significant survival advantage would let everything else descend into chaos, since the system could only select for one thing at a time. Nature seems to hate doing just one thing at a time -- the methylation scenario you describe is inherently parallelized.

One interesting note is that if you accept that unexpressed genes evolve away quickly, then CG->TG transition creating broken genes would also create unexpressed genes, which would evolve away quickly using whatever method was available.

Is there anything that reverses the methylation, moving back from TG to CG?
posted by effugas at 5:42 PM on December 18, 2007


The presumption of damage comes from you, when you wrote that non-synonymous transitions are deleterious.

C→m5C is not a transition. C↔T and A↔G are transitions. In no way is the methylation of cytosine a kind of damage. There is a very small chance that m5C will transition to T, but it is much higher than the probability of C→T, or really any other kind of common mutation.

Also, the protection from methylation is around the transcription start site, which in lots of genes is far away from the coding sequence. So in many genes this phenomenon does not affect the rate of coding mutations whatsoever.

My problem with survival being the exclusive metric is that one sequence with a significant survival advantage would let everything else descend into chaos, since the system could only select for one thing at a time.

Yes. That's what would happen if we didn't have sex*. Even then, it still happens, because nearby sequences are linked and don't recombine independently. One of the ways in which we discover selection is by finding selective sweeps where the selective advantage of one sequence has eliminated most diversity from the surrounding sequence.

One interesting note is that if you accept that unexpressed genes evolve away quickly, then CG->TG transition creating broken genes would also create unexpressed genes, which would evolve away quickly using whatever method was available.

Universally unexpressed genes would evolve away quickly. Not ones that are just unexpressed in the germline. The sequence that decides whether the gene is expressed is substantially different from the protein-coding sequence. In most cases an amino acid substitution is not going to affect the level of transcription.

Is there anything that reverses the methylation, moving back from TG to CG?

The methylation is transient, so it is reversed all the time. This is m5C&arr;C, not a T→G change (see above).

* Recombination to be specific, but sex is more fun. Someday I'm going to write a bunch of bad pickup lines for evolutionary biologists. "Hey baby, want to reverse Muller's ratchet?"
posted by grouse at 2:10 AM on December 19, 2007


grouse--

Why would recombination allow parallelized selection? (I have other comments, but that's the immediate question at hand.)
posted by effugas at 3:15 AM on December 19, 2007


Because it means the forces of selection can act independently on different characters. Given a sufficiently large effective population size, a new allele on one chromosome under strong positive selection won't carry a deleterious allele on another chromosome to fixation.
posted by grouse at 4:16 AM on December 19, 2007


we wouldn't see evidence that we'd survived so much of it

Well, strictly speaking, "we" are not so much surviving it as using it as part of our gene metabolism (it's a legacy from our bacteria-like ancestors). It's the least bad option for many things among a bunch of potential strategies. We actually use selection deamidation (ammonia removal) of unmethylated bases both as as a destructive strategy to combat viruses (APOBEC3G) and as "sloppy repair" within our own genes to replace double-strand breaks of our DNA that have stalled DNA synthesis *and* as a method of "somatic hypermutation" within constrained portions of our immune system's antibody producing cells using positive and negative feedback from other cells as a way of creating more efficient antibodies. Methylation provides a quick way to regulate many of these similar processes. Think of it as using comments in a computer program to remove a code block without actually deleting it. Further down the line, someone else might remove that commented block inadvertently and notice no immediate effects. Later code refactorers would not see that eliminated code block at all so it simply gets lost. Uncommented code tends to enjoy protection against accidental deletion.

There's a lot of publicly available high-quality info on DNA biochemistry. This book's a little old but is a standard undergrad textbook: Molecular Biology of the Cell.
posted by meehawl at 12:40 PM on December 19, 2007


NOVA scienceNOW Podcast profile on Pardis Sabeti, who works in genomic evolution and wrote the review I referred to above.
posted by grouse at 4:18 AM on December 20, 2007


Is Homosexuality an Evolutionary Step Towards the Superorganism?
posted by homunculus at 9:39 AM on January 4, 2008


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