The Selfish Gene

[GeoffP]

Its putting the cart before the horse. What came first? I consider the term adaptation to be a response [and hence a misnomer here], ie I adapted to a warmer climate. Can I "adapt" to a warmer climate before I move to a warm place?

No, but you will die, and those of your offspring that either get a lucky mutation in that generation, or that have a latent mutation that doesn't activate in the home environment, will survive.

 

[S.A.M.]

Actually, no. Not in a variable environment, they aren't. Stochasticity and randomization in genetic function or activity can be advantageous either from the perspective of individual fitness or from that of sire/dam fitness via hedge-betting offspring phenotype against local or general environment. This would be particularly true of organisms that experience their environment as 'patchy'.

The relegation of variation to anomaly or even detrimentality assumes a static environment, which is true of no living system (both generally and especially over ontogeny).

This is all retrospective masturbation. Do you really believe that specialisation is a matter of cumulative luck?

No, but you will die, and those of your offspring that either get a lucky mutation in that generation, or that have a latent mutation that doesn't activate in the home environment, will survive.

So it is a response to the environment? Or are you saying survival is a matter of chance? Somehow, studying the gestational and prenatal effects of carcinogens and mutations [not to mention, nutrients or lack thereof] makes it seem highly unlikely to me that something as critical as survival would be left to the chance of a "lucky" mutation. To give an example: there have been instances when knockouts have not culminated in the expected phenotype due to the presence of a parallel pathway being activated, o which was either pre-existing and unknown OR which arose due to the critical gene being knocked out [hard to say which is which sometimes, since detection of a 'clean' knockout presupposes that the functional code is known well enough to be identified]. Superficially, it could be assumed that a lack of change in phenotype is an indication of the gene having no effect on that phenotype, unless one knew where to look. If you see the developments in fields such as gestational metabolic syndrome, its not unrealistic to assume that environmental stimulation or changes in the milieu could induce genetic changes.

Or is that too far fetched a notion?

 

[GeoffP]

This is all retrospective masturbation. Do you really believe that specialisation is a matter of cumulative luck?

What, are you serious?

Define specialization. Explain how it would fail to work. We know gene function varies by environment, both with scalar differentiation and complete inversion of effect. We know mutation provides alternate, novel or deleted gene function.

So it is a response to the environment?

Not in all cases, but in some. That's not what we're talking about here, though.

Or are you saying survival is a matter of chance?

Frequently, yes. Are you defining pre-existing genetic completement, or variability in gene function across environmental gradients as chance?

Somehow, studying the gestational and prenatal effects of carcinogens and mutations [not to mention, nutrients or lack thereof] makes it seem highly unlikely to me that something as critical as survival would be left to the chance of a "lucky" mutation.

This is why most mutations are purportedly deleterious. Are you arguing advantageous memes allowing behavioural exploitation, followed by specialization? West-Eberhard would back you there, Pigliucci also I think.

To give an example: there have been instances when knockouts have not culminated in the expected phenotype due to the presence of a parallel pathway being activated, o which was either pre-existing and unknown OR which arose due to the critical gene being knocked out [hard to say which is which sometimes, since detection of a 'clean' knockout presupposes that the functional code is known well enough to be identified]. Superficially, it could be assumed that a lack of change in phenotype is an indication of the gene having no effect on that phenotype, unless one knew where to look. If you see the developments in fields such as gestational metabolic syndrome, its not unrealistic to assume that environmental stimulation or changes in the milieu could induce genetic changes.

Or is that too far fetched a notion?

Not at all; that would be mutation or environmental imprinting, depending on whether the change were permanent or not. But genes also have expressive lability, corresponding to "useful variation" in a natural setting. Further, multiple, stable wild-types would permit wider reproductive success in r-selected organisms; this is also "useful variation".

 

[spidergoat]

The gene does nothing to adapt itself. Or do you know otherwise?

It is either preserved through the utility of it's expression relative to the environment, or not, or it mutates. No one has suggested it adapts itself, but it appears to become better adapted over time through the passive process we call natural selection.

Useful variations? That is an anomaly, there are no useful variations, thats a retrospective outlook, only useless ones. Variations, in and of themselves have no aim or direction.

There are useful variations in relation to the environment. When random mutation, copying errors, and sex lead to a useful variation, that tends to be preserved.

 

[iceaura]

Why do you call it genetic adaptation? Is it a response to the environment?

I call it what others call it, sometimes, and appear to have little trouble communicating thereby.

Unless they run into the willfully obtuse, who insist that (for example) the various changes in their ancestral genomes that enabled dry land living in the organisms enjoying them were not "adaptations", thereby appearing to claim that none of the changes brought about by Darwinian evolution are to be described as "adaptations".

Which would require a severe editing of many thousands of books, articles, and scientific publications.

I still find very interesting the difficulty so many people have with the basic concepts of Darwinian evolution. They are not essentially complex, they do not involve years of mathematical training or other difficult intellectual endeavor, and yet we see even the well-educated and careful go weirdly spla in their presence.

 

[S.A.M.]

What, are you serious?

Define specialization. Explain how it would fail to work. We know gene function varies by environment, both with scalar differentiation and complete inversion of effect. We know mutation provides alternate, novel or deleted gene function.

Is that the effect of the gene or a function of environmental influences?

Not in all cases, but in some. That's not what we're talking about here, though.

Give me an example of a gene changing in response to the environment.

Frequently, yes. Are you defining pre-existing genetic completement, or variability in gene function across environmental gradients as chance?

Again, is this not retrospective analysis? Or are you claiming that the genetic "completement" [not familiar with this term] is a preemptive response to changes in the environment?

This is why most mutations are purportedly deleterious. Are you arguing advantageous memes allowing behavioural exploitation, followed by specialization? West-Eberhard would back you there, Pigliucci also I think.

What the hell is an "advantageous meme"?

Not at all; that would be mutation or environmental imprinting, depending on whether the change were permanent or not. But genes also have expressive lability, corresponding to "useful variation" in a natural setting.

Explain expressive lability.

I call it what others call it, sometimes, and appear to have little trouble communicating thereby.

Unless they run into the willfully obtuse, who insist ...blah blah blah

You did not respond to my question. Others do it too is simply not an adequate argument.

 

[S.A.M.]

It is either preserved through the utility of it's expression relative to the environment, or not, or it mutates.

That does not make sense, the gene does not survive or mutate. It survives or dies. Mutation is not a choice.

No one has suggested it adapts itself, but it appears to become better adapted over time through the passive process we call natural selection.

That is a circular argument. What becomes better adapted? The gene that dies? The gene that survives? The gene that is mutated or undergoes change in frequency by drift? They are not all the same gene.

There are useful variations in relation to the environment. When random mutation, copying errors, and sex lead to a useful variation, that tends to be preserved.

Variation in relation to the environment? What is that?

Preserved? How? What is the process or mechanism of preservation?

 

[spidergoat]

That does not make sense, the gene does not survive or mutate. It survives or dies. Mutation is not a choice.

Mutation is not a choice, that is correct. However, genes that have a less likely chance of surviving might get an increased chance if they happen to mutate.

That is a circular argument. What becomes better adapted? The gene that dies? The gene that survives? The gene that is mutated or undergoes change in frequency by drift? They are not all the same gene.

Certain new (mutated) sequences of genes or combinations of genes can stumble on a new solution to a problem, after which this innovation can become streamlined to work even better over time. Say, a bug gets two sets of wings instead of one, they may only work a little better than the original configuration at first, but since natural selection works on the genes that survive better, further perfection of the innovation can happen more rapidly, and soon there are no more bugs with only one set of wings and natural selection works on things that increase it's ability to fly with two wings, such as eyes and the brain.

Variation in relation to the environment? What is that?

You said variations have no aim or direction. I agree. By themselves, there is no aim or direction, but in relation to the environment, some lead to higher survival rates.

Preserved? How? What is the process or mechanism of preservation?

Variable survival rates for that gene or set of genes.

 

[S.A.M.]

Mutation is not a choice, that is correct. However, genes that have a less likely chance of surviving might get an increased chance if they happen to mutate.

But a mutated gene is not an adapted gene.

Certain new (mutated) sequences of genes or combinations of genes can stumble on a new solution to a problem, after which this innovation can become streamlined to work even better over time. Say, a bug gets two sets of wings instead of one, they may only work a little better than the original configuration at first, but since natural selection works on the genes that survive better, further perfection of the innovation can happen more rapidly, and soon there are no more bugs with only one set of wings and natural selection works on things that increase it's ability to fly with two wings, such as eyes and the brain.

Streamline? Perfection of innovation? These are all directed. How is that possible? What is the probability of hitting the jackpot so often?

You said variations have no aim or direction. I agree. By themselves, there is no aim or direction, but in relation to the environment, some lead to higher survival rates.

Variable survival rates for that gene or set of genes.

How does survival translate to specialisation? How does a random change translate to perfection of innovation?

-------------

I feel like I am unable to get my point across.

 

[spidergoat]

A mutation could be beneficial as well as (far more often) detrimental. No one is suggesting genes adapt themselves, they are only information.

Perfection of innovation is not necessarily directed. The probability of a gene leading to a successful innovation is tiny, but that's all it takes. If the innovation leads to a marked improvement in survival, then there become many more instances of that innovation, and many more opportunities for further innovation based on that theme.

Variable survival rate is just another way of saying natural selection. It is driven by random (mostly) changes. That is why sex is so successful, it helps create variations. I'm not sure what point you are trying to make either.

 

[S.A.M.]

Maybe its just the language, it seems to misrepresent what is actually occurring. It ignores for example the effect of compound allelic drift on "favorable" variations.

 

[GeoffP]

Is that the effect of the gene or a function of environmental influences?

Both, really. You could call it an innate property of the gene.

Give me an example of a gene changing in response to the environment.

??

http://en.wikipedia.org/wiki/Mutation

This is pretty common stuff. Do a search on mutations and environment on PubMed or something. Cancer, etc. If you're referring to gene activation, deactivation, then a good example is head spikes on Daphnia developing in environments with predators.

Again, is this not retrospective analysis?

No. There is little doubt that GxE exists.

Or are you claiming that the genetic complement is a preemptive response to changes in the environment?

It's an adaptation that permits varying functionality across environments. I just published a paper on GxE for growth, for instance; it doesn't mean that the gene functions well in all environments necessarily, but that it functions sufficiently for the organism to get by.

What the hell is an "advantageous meme"?

Tool use, fire, jackdaws peeling the lids off milk bottles to get at the cream, that sort of thing.

Explain expressive lability.

Gene activity that varies among environments. At the organismal level, you'd see this as GxE. In statistical analysis, this would be indicated by the significance of the interaction term in the model

y = Xb + Za + Xb*Za + e​

where y is the vector of phenotype (multiple or single), X is the incidence vector of fixed effects, b is the coefficient vector of fixed effects, Z is the incidence vector of random (that is, drawn from a theoretically infinite range of possible values) genetic effects, a is the vector of random genetic coefficients and e is error.

 

[iceaura]

Give me an example of a gene changing in response to the environment.

Why are you fixated on this? Whay aren't you talking about Darwinian evolution, like the rest of us ?

You did not respond to my question. Others do it too is simply not an adequate argument.

It is when you are talking about a common word with a well-established meaning. You apparently want the thousands and thousands of people over the years who have described the genetic changes of Darwinian evolution as "adaptations" to the environments they and their embodying organisms (or phenotyipic expressions or whatever) now fit into by consequence, to stop doing that, They won't. I won't. It's a handy word, and its meaning seems perfectly clear to me. I continue to be interested in the difficulty people have with it. (I have noticed some patterns in the matter).

That does not make sense, the gene does not survive or mutate. It survives or dies.

It reproduces with variation. Some of them occasionally "adaptive", as we call the new phenotypic expression that reproduces and spreads the newly modified gene more reliably or prolifically.

Streamline? Perfection of innovation? These are all directed. How is that possible? What is the probability of hitting the jackpot so often?

If you have run through the Hardy Weinberg calculations, you have some idea of the probabilties involved,and how one would go about calculating them. Note taht the "jackpot" comes in multiple forms and large range of "win". The streamlining and perfecting is of course not directed, in this situation. It is culled.

How does a random change translate to perfection of innovation?

By culling. Darwin's great insight.

 

[S.A.M.]

Geoff:

Both, really. You could call it an innate property of the gene.
??

http://en.wikipedia.org/wiki/Mutation

This is pretty common stuff. Do a search on mutations and environment on PubMed or something. Cancer, etc. If you're referring to gene activation, deactivation, then a good example is head spikes on Daphnia developing in environments with predators.

So mutation is a directed response to a change in environment? Going from a hot place to a cold place will cause mutations to ensure survival?

No. There is little doubt that GxE exists.

It's an adaptation that permits varying functionality across environments. I just published a paper on GxE for growth, for instance; it doesn't mean that the gene functions well in all environments necessarily, but that it functions sufficiently for the organism to get by.

The gene always functions. There is no functions well or not. Thats a matter of survival not of gene function.

Tool use, fire, jackdaws peeling the lids off milk bottles to get at the cream, that sort of thing.

Hmm so the presence of milk bottles with lids led to a mutation to peel them open? Or jackdaws had a milk bottle lid peeling gene that was activated by seeing the milk bottles with lids?

Gene activity that varies among environments. At the organismal level, you'd see this as GxE. In statistical analysis, this would be indicated by the significance of the interaction term in the model

y = Xb + Za + Xb*Za + e​

where y is the vector of phenotype (multiple or single), X is the incidence vector of fixed effects, b is the coefficient vector of fixed effects, Z is the incidence vector of random (that is, drawn from a theoretically infinite range of possible values) genetic effects, a is the vector of random genetic coefficients and e is error.

Thats just a construct used to describe the data. It does not mean that genes are interacting with the environment to change their function. That direction does not exist.

iceaura:

Why are you fixated on this? Whay aren't you talking about Darwinian evolution, like the rest of us ?

Because that is the basic premise I do not agree with. If mutations are random and genetic drift randomly changes allelic frequencies in the population, then saying that a gene changes with the environment makes no sense.

It is when you are talking about a common word with a well-established meaning. You apparently want the thousands and thousands of people over the years who have described the genetic changes of Darwinian evolution as "adaptations" to the environments they and their embodying organisms (or phenotyipic expressions or whatever) now fit into by consequence, to stop doing that, They won't. I won't. It's a handy word, and its meaning seems perfectly clear to me. I continue to be interested in the difficulty people have with it. (I have noticed some patterns in the matter).

Then they are misrepresenting the function of a gene by using a word that assumes a change in function. Genes do not adapt. They survive or die, sometimes [or quite often, rather] they mutate, which further affects their survival and demise. This is not a change in function of the gene, but a change in the gene itself.

It reproduces with variation. Some of them occasionally "adaptive", as we call the new phenotypic expression that reproduces and spreads the newly modified gene more reliably or prolifically.

The gene does not reproduce with variation, it merely reproduces or rather the organism reproduces the genes it possesses. Acquired characteristics are not inherited remember?

If you have run through the Hardy Weinberg calculations, you have some idea of the probabilties involved,and how one would go about calculating them. Note taht the "jackpot" comes in multiple forms and large range of "win". The streamlining and perfecting is of course not directed, in this situation. It is culled. By culling. Darwin's great insight.

Exactly, the ones that do not survive do not get passed on. They do not alter to ensure reproduction.

 

[GeoffP]

Geoff:So mutation is a directed response to a change in environment? Going from a hot place to a cold place will cause mutations to ensure survival?

No. But environment can cause mutations. Whether or not they're deleterious or advantageous is more a matter of chance. Why are you assuming some kind of anaturalistic purpose to mutation?

The gene always functions. There is no functions well or not. Thats a matter of survival not of gene function.

No. That is classically, and completely, incorrect. A search of functional gene-by-environment interaction on the net should generate sufficient evidence of the inaccuracy of this assumption. For example: is it of advantage for an antifreeze gene in the blood of Atlantic flounder to be active at the same rate, constantly? Or would this interfere with other elements of metabolism? Are reproductive hormones active at the same level in an infant as in a teenager, or an adult? No. And so on.

Hmm so the presence of milk bottles with lids led to a mutation to peel them open? Or jackdaws had a milk bottle lid peeling gene that was activated by seeing the milk bottles with lids?

You are confusing meme with gene. Such a mutation might be possible, over evolutionary time, if the opportunity existed for it to do so. Or it might simply be entirely learned; this might be more true of "higher" organisms which have a more complex thought process.

Thats just a construct used to describe the data. It does not mean that genes are interacting with the environment to change their function. That direction does not exist.

I am sorry, but you could not be more incorrect on this point. The existence of crossovers in genetic effect and of large scalar non-transforms unquestionably indicates the existence of changing activity of genes. I recommend de Jong, Pigliucci and West-Eberhard for an introduction to this issue.

 

[iceaura]

Because that is the basic premise I do not agree with. If mutations are random and genetic drift randomly changes allelic frequencies in the population, then saying that a gene changes with the environment makes no sense.

So? Since when is anyone except you claiming that genes "change with the environment" ?

Then they are misrepresenting the function of a gene by using a word that assumes a change in function.

Well, they don't mean that, and I don't mean that, and Dawkins doesn't mean that, and none of the people using "adaptation" in the context of Darwinian evolution mean that.

The gene does not reproduce with variation, it merely reproduces or rather the organism reproduces the genes it possesses. Acquired characteristics are not inherited remember?

I'm now baffled. You appear to be claiming that genes reproduce with perfect accuracy, that mutations are not reproduced, that recombinations of mutations never happen during reproduction, and so forth.

I'm beginning to wonder about where and how you learned about the Darwinian theory of evolution in the first place.

 

[S.A.M.]

Mutation is a relative construct. Do you know what the "original gene" looks like?

No. That is classically, and completely, incorrect. A search of functional gene-by-environment interaction on the net should generate sufficient evidence of the inaccuracy of this assumption. For example: is it of advantage for an antifreeze gene in the blood of Atlantic flounder to be active at the same rate, constantly? Or would this interfere with other elements of metabolism? Are reproductive hormones active at the same level in an infant as in a teenager, or an adult? No. And so on.

Thats its function, you recognise that a gene does not turn itself on and off. When its turned on, it does what its supposed to, when its off it doesn't. Like anything else that can be turned off and on.

Such a mutation might be possible, over evolutionary time, if the opportunity existed for it to do so

Mutations occur by opportunity? That sounds like gibberish.

No. But environment can cause mutations. Whether or not they're deleterious or advantageous is more a matter of chance. Why are you assuming some kind of anaturalistic purpose to mutation?

I didn't know there was any purpose to mutations at all.

 

[s0meguy]

It's not that we are programmed. Our genes are programmed. But, if you read to the end, you'll see that Dawkins is very careful to make the point that we are not our genes. Even if our genes are "selfish", that in no way means that we, as people, should be or must be selfish.

I still think that humans are 100% selfish all of the time. People only act altruistic when it makes them feel good about themselves. It's all about perceived reward...

 

[GeoffP]

Thats its function, you recognise that a gene does not turn itself on and off. When its turned on, it does what its supposed to, when its off it doesn't. Like anything else that can be turned off and on.

Not so. The efficiency and rate of production of a gene can be quantitatively controlled.

Mutations occur by opportunity? That sounds like gibberish.

It isn't. If the mutation has any kind of advantage or if the carrier persists in a given environment using, say, behavioral dampening of deleterious effects, a given mutation could penetrate into the rest of the population.

I didn't know there was any purpose to mutations at all.

"Purpose"? Not that I know of. Are you arguing directionality?

 

[S.A.M.]

Not so. The efficiency and rate of production of a gene can be quantitatively controlled.

By the gene?

It isn't. If the mutation has any kind of advantage or if the carrier persists in a given environment using, say, behavioral dampening of deleterious effects, a given mutation could penetrate into the rest of the population.

Thats retrospective, it only indicates the persistance of that which survives [duh?]

"Purpose"? Not that I know of. Are you arguing directionality?

I'm arguing misrepresentation.