You know better than that. Genes can have beneficial or negative impacts depending on what other genes they coexist with and thus be of different impact in different populations. Also there are various degrees of gene linkages.
Which is why I chose the phrase “net impact” with intention.
Yes there is lots of math.
A little-known fact is that many important techniques in statistics were first invented in order to do population genetics.
No, what I said is quite correct. Remember, I was countering the suggestion that if an individual organism is shielded from purifying selection at a particular locus, that may be good thing because the rest of its genes are “saved”. I said:
There are subtle processes like genetic hitchhiking and presence of linkage disequilibrium in a population, but bringing these up is like saying 2+2 does not equal 4 because of special relativity. Let’s get the basics principles clear first. To a first approximation, the individual genes in a sexual population may be treated as evolving independently.
I guess I am not understanding what you think you are arguing against or for.
Chronos stated something pretty straightforward to my read. There is a selection pressure on knocking out a gene that produces a protein that is deleterious in the environment of the time, or that blocks a change that would be advantageous for the time.
A subpopulation that has individuals with that “defective” gene (one that increases the survival of individuals with it through successful reproduction with the environment in which it currently exists) will cause the spread not only of that gene but of the others that are more prevalent in that subpopulation relative to others. There is I am sure complex math that models it but the other genes common within the subpopulation that that gene is more likely to spread within will also be more likely to spread while that environment exists.
Anyway. All this is interesting but what we are talking about is the a very particular case: there have been a large set of mutations that allowed for humans to develop culture, society and technology, for humans to develop increasingly less primitive tools to deal with the limitations of their biologies relative to to a variety of harsh environments. That broad set of genetic changes is what has allowed for other genetic divergences to have no meaningful impact on reproductive fitness. Genes that might decrease fitness if the first set, the set that allows for the human meta-organism, did not exist, have no meaningful impact in the context of them existing. One can imagine that humans might have to exist without human society and that humans well adapted for life within society might be poorly adapted to live without it, but the world population of blind cave catfish are much more likely to suddenly be forced to compete in the well lit world. Existing in cooperative societies in which the whole is greater than the individuals and group success drives gene success (like in ant colonies to some degree) is key to our genetic heritage.
For your interest btw some difference of opinion to your perception that LOF is invariably bad. It seems that LOF mutations have been key to becoming human.
Some very interesting examples. Enjoy!
More about the “less is more” hypothesisand how LOF is may be a fundamental pathway of genetic diversity.
A good discussion about potential reversion in the case of environmental change as well.
The best bit in it is the argument against your case for the “meaningful concept of a ‘perfect’ genotype, the optimal theoretical genotype in a population.” In this bit “wild-type” seems to the stand-in for that Platonic ideal.
I’m not arguing for anything. I’m trying to explain some basic & uncontroversial principles that would form part of a 1st year undergrad course. I readily defer to Chronos and other experts on here in physics & math, where I’m very much a wannabe amateur. But evolution and genetics is my specialty - I do know what I’m talking about.
If you prefer to persist in trying to “debate” a technical subject where you don’t understand the basic principles and resist what I’m trying to explain to you with convoluted and misconceived examples, I’m afraid this is just getting tedious, so I’m going to move on.
Regarding the research paper on primate evolution: of course I never suggested that LOF mutations are invariably deleterious. The paper on primate evolution that you linked to does not deny the general principle that you inexplicably seem to want to resist, it states it quite clearly in the introduction:
The whole reason that the paper is interesting is because it’s describing unusual circumstances and exceptions to the general rule.
Again, what you’re doing is the equivalent of refusing to accept that 2+2=4 and supporting your argument by linking to papers on Special Relativity.
Huh, is that the same Fisher who’s responsible for the Fisher information matrix? I had no clue he was a bio guy.
“Wild type” simply means the non-mutant phenotype or genotype. It is the point of reference in genetic analysis, the control. There is no subtext whatsoever of “platonic ideal”, that is complete nonsense.
Yes, Fisher, Haldane & Wright were the founders of the “Modern Synthesis” that unified genetics with Darwin’s qualitative ideas.
Fisher dabbled in other stuff, but the statistical techniques that he invented were primarily motivated by genetics.
I am sorry that you are getting upset and that you feel the dynamic here is you as teacher who should not be challenged or questioned but appreciated for the knowledge that you wish to impart.
For my part, no, I do not see any analogy to invoking special relativity. It is a fundamental basic issue that I am raising. In the real world sense considering evolution and genetics there is no “control” group; actual populations are an ongoing collection of mutant phenotypes and genotypes responding to an environment that is dynamic as well, some being selected for and some against and so on. An environment that changes sometimes as a consequence of the organism’s evolution.
Of course ALL mutations of any sort are more commonly deleterious than they are beneficial. And by definition if a mutation is neither to any degree it is neutral. What is a deleterious mutation? One that gets selected against, correct? Or is there a different definition?
You as a population geneticist have a concept of an “optimal genotype.” And I get that from the modeling perspective. And I hear that you, as a population geneticist, from the perspective of running experiments with defined populations of organisms that have a, by arbitrary definition, control genotype and phenotype and defined environment, have a concept of mutations that succeed in being passed on into future generations as commonly or more commonly than by neutral chance, accumulating, and yet, for the purposes of your models, are labelled “deleterious” … which is nice for the models even though I still do not get how a mutation that is accumulating can at that point be labelled as deleterious since deleterious is defined as that which is selected against with no judgement other than that and no foreknowledge of what the future environment may be. But the models use those terms. Okay. I’ll move along.
Yes, I read how Muller’s ratchet states that in theory “the genetic load carried by asexual populations eventually becomes so great that the population goes extinct” … but dang somehow asexual organisms did not just die off … they evolved.
In any case the conversation reminds me less of one party saying 2+2=4 with the other saying but special relativity than of a conversation that is trying to discuss how the real world works in terms of real people spending real money and saving with one party who keeps saying but models of first year econ class assume all consumers are completely rational actors trying to maximize utility with complete access to all information!
I don’t think that first year econ though, uncontroversial as it may be, actually describes the real world. To their credit the professors teaching it don’t think so either. But you’re the expert.
Bottom line? To me the interesting subject of this thread is not intro population genetics but the manner in which human culture and society, which is possible because of our individual genetics, impacts our genetics (we made genetic adaptations to agriculture’s invention, did we also to the invention of the written word? how did class structures in different cultures and group conflicts impact human evolution since civilization began, both often thought of as short time periods from an evolutionary perspective?), and, barring apocalyptic complete collapse of human society, how human society and culture has created a new environment that is both very dynamic and rapidly changing and so harsh that we are experiencing a sixth great extinction event across the planet with rapid loss of many species, and in terms of pressure on the human genome not harsh at all with that society creating tools that make what would be deleterious for most of the species history moot (I’ll avoid calling it “neutral”).
I will gladly drop deleterious in preference for that!
Your comments are littered with misconceptions about elementary evolutionary biology and population genetics, and misunderstanding and misuse of terminology. If you wish to challenge a prevailing paradigm, you first have to understand the paradigm.
Oooookay.
And have a great day!
Well, I tried politer versions, and to engage in debate where it was possible. I don’t wish to discourage your interest in the field, and you’re obviously a smart fellow, but I’m afraid at the moment in this field you’re not in a good place with respect to the Dunning-Kruger effect. You’re discovering for the first time basic ideas upon which decades of research has been built, and supposing that you can cause eveyone to re-think their mistaken ideas with a few sentences of your insight.
Actually uh no. If there is a fallacy at play here it may perhaps be “appeal to authority.”
And I did try to redirect the discussion from your positioning as someone who is acting as if (s)he is, well to put it bluntly, arrogantly, pompously, and ineffectively, lecturing a first year undergraduate class on population genetics, back to something more directly related to the op.
If you do not want to discuss those items okay fine. Don’t. But I think they have more to do with the op than does Muller’s ratchet.
If you do then I will ask the questions again in another form. Maybe others are interested even if you are not.
Human societies are possible because humans have a variety of genetic changes relative to our competition that allowed us to develop more sophisticated social groups and a human intellect that was more than just individual brains alone or even individual groups or generations of groups alone. Part of what those changes allowed was the creation of agriculture, the creation of sophisticated languages, the creation of sophisticated written languages, and the creation of technologies that allowed the species to thrive in environments that would otherwise have been too harsh and that otherwise have helped us overcome what would otherwise be limits set by our biology.
Is that a statement you agree or disagree with?
Humans have genetic adaptations to the changes in their environment that they have created. The easy examples of those include the ability to better digest starch and to digest lactose. Those genetic adaptations then allowed the cultural changes to better spread. Once humans were existing off of a diet that was heavy in starch and dairy those with adaptations to better digest those food sources reproduced more effectively which allowed that subpopulation and the ideas of farming to spread.
Do you agree or disagree with that statement?
The op recognizes that the genetic ability for learning written language was likely extant long before written languages were invented and spread as a cultural idea, and is in one sense asking if, similarly to the changes in response to the adoption of farming, there were any genetic changes in response to the similarly major culture changing event of the development of written language?
The answer is likely not to any major degree. At least not that have been identified. There is that very specualtive bit about Ashkenazi Jews having a specific period of about 800 to 1600 A.D. under which those with greater ability to become literate and to use those skills better possibly had better reproductive success with the negative consequence of increased rates of certain recessive neurodegenertive diseases. But that sort of selection pressure strong enough across the whole population for any prolonged enough period of time does not seem to have occurred.
That statement reasonable or not?
Today technology and culture creates a circumstance that, if it was static moving forward for a prolonged period of time, would not select out a variety of traits that would be selected out if we were in the world that existed prior to modernity.
Agree with that or not?
Regression from modernity to a pre-techology world could occur by way of some apocalyptic event. If so many of those features would become relevant to selection pressures. Barring that and assuming that technology only increases in sophistication, and that there are not subtle effects of those traits on reproductive fitness that will show up over many many generations either directly or by other means (linkage, epistaxis, etc.) those traits will continue to be neither selected for or against. If anything more will become moot in terms of impact on successful reproduction. Culture and group control of resources is likely to swamp those effects.
Agree or disagree there?
The world is undergoing major climate change with a consequent major extinction event, one that is thought widely to be caused by human activity. These are harsh times for most organisms on this planet and many species are unable to adapt to the rapid changes. We will adapt by way of using the same tools of culture and technology, and while many humans may die as a result of climate change the selection pressure will be more at a cultural and geographic level than based on beneficial or deleterious genes. If it qualifies as an apocalyptic event, and I think it could, it is nevertheless not one that will drive us back to pre-civilization.
Agree or disagree there? It gets to areas that more commonly provoke divergent opinions.
And the bit I’d guess you’ll most objectionable and/or ignorant: as human culture and society has become more highly developed and globalized human groups function less and less as individual genetic lines (fill in whatever is the less ignorant phrase) competing against each other and instead more similar to the meta-organism of an ant colony or a hive. The speed and efficacy of the competition and spread of ideas, technology, and culture, dwarfs changes in gene pool of the populations as a means of adaptation. That’s humanity for you.
Your, and anyone else’s, reaction to that?
Moderator Note
I’m not going to go back and try to figure out “who started it,” but these remarks are out of line for GQ. Dial it back, and drop the personal barbs. You can discuss this without the digs.
Colibri
General Questions Moderator
The way I visualize evolution is a multi-dimensional space that models the environment (dimensions being like temperature, humidity, etc.). In that space there are some bounded regions - maybe connected, maybe not, that represent the current environment in different places on Earth. Now, of course, those regions move around, hopefuly slowly, i.e. the environment gets warmer or more humid.
Now, you have a species that “lives” in a region of the environment. The population genetics will trace the movement of the region in the environment space, with a delay. Say a species of moth has a specific color to blend well with the tree bark, and if the environment changes to darken the bark with soot, the moth will, after some delay follow that movement by darkening its wings.
Here is a point in which both sex and deleterious mutations come into play. There has to be a mutation for the adaptation, and the previous allele is wrong. However, it is still maintained in the gene pool. Why ? Because the environment change may be temporary. It could be that the movement of the “region” in the environment space is oscillatory or any other type of recurring function. Then the “deleterious” allele is again best. Sexual reproduction together with the recessive/dominant mechanism enable a memory of past environments. A de novo mutation to a new environment is a probabilistic event - it may come too late to save the species. However, if the environment has already happened in the not too far-away past, a small but significant part of the population may carry the required adaptation in its genetic memory.
The next question, and for that perhaps I will start a new thread, is not “why sex ?” That has been quite convincingly answered. It is not even “why do we need all those males ?” - this question has been answered conclusively by Fischer. It is “why the sexual dimorphism ?” Why aren’t we all hermaphrodites ? This, I think is a hard question, and if we can answer it persuasively we could have answers (at least regarding humans) to some persons of the only sex that matter. 
bolding mine.
is there a variety of rhubarb I’m not familiar with? as a child, I would often pluck a stalk out of Gma’s rhubarb patch, break the leaf off, wash and then eat the stalk raw. It was the leaves that I was always told were inedible and poisonous.
I think** DSEid **said it better… but we are basically selecting for a humanity, through lack of purifying selection, that is better adapted in general for a more specialized and more fragile environment. That our population’s general survival is more fragile is probably not a good thing; because sometimes it is only localized disruptions that are the problem. Were becoming better swamp creatures, so to speak, with the risk that one day the swamp may be drained.
I specifically excluded Huntingdon’s and Type II Diabetes, as post-reproductive problems. High blood pressure may be an issue, but usually again has its most serious consequences after the children have left. (My maternal grandmother, I think, died from high blood pressure in the early 1950’s at about 55.) A quick check, the busiest clinics in the USA did almost 100,000 IVF cases last year. This is hardly trivial.
There are some fascinating long-term risks to our present homo technophilia environment that could cause problems where gene drift would add more risk. There’s the whole health care industry looking after people who are unhealthy, for example. Will that become even more of a drag on the economy?
Bio & genetics are NOT my area of expertise.
Overall your dimensional approach is useful IMO. It’s a standard technique for analyzing and visualizing any multivariate problem in any field of study. As is the idea of (at least some) recessive or neutral traits being a reservoir of “canned” adaptions that may prove beneficial at the population level under future changed circumstances.
Though you didn’t mention it, this line of thinking applies to the inter-species competitive environment just as much as the geophysical one.
Ref the snippet above, can you provide a link to further reading? Or a capsule summary of Fischer’s arguments? Thank you.
Ref hermaphrodism, I’d argue that evolution explores many paths, but not all. Each species is traveling forward through time on a vector in genetic space generally aimed towards a local environment optimum. Which target optimum, as you say, may be moving faster or slower than the species can adjust.
The mere fact hermaphrodism might (?) be more energy efficient globally doesn’t *require *that we passed through that region of genetic space some time in the past. Those species that did, are. Those that didn’t aren’t. The cause need be no more complex than that roll of the historical dice.
Clearly a feature that fundamental to organism design had to occur fairly early in the history. Hermaphrodism isn’t going to spontaneously appear in humans. Nor could we expect to create it in, say, sheep, no matter how hard we tried using conventional selective breeding techniques. With genetic engineering the future is unknowable; we may lick that problem in my lifetime or we may still be wallowing in the intractable complexity of it all 300 years from now.
It is Ronald Fisher. There’s a Wiki article on sex ratio: