First, thank you for all the clear and intelligent answers and for taking my questions seriously. When I ask these questions elsewhere, I get treated like a heretic.

Next, I have some follow-up questions:

1.

RE the genetic mutation that benefits a species after the environmental changed, Note that the mutation is not caused by the environmental change and would have happened even if the climate had stayed the same.”

Are we certain about this directly? Or are we certain about this because it is commensurate with the secondary ideas we are certain about? Although my review of literature on this subject is infinitesimal compared to yours (which is why I am asking you), I haven’t seen anyone show the rate of genetic mutation for a characteristic showing up at unfavorable times to be the same as the rate it shows up when it finally becomes favorable. My guess is that it would simply be too hard to look back and determine which individuals were products of mutation and which were off-spring of the mutant, so there is no way to know for sure. But—if that guess is right—then that would answer my question, and that answer would be, ‘No, we are not certain about the above idea directly.’

2.

RE The reason we do not see these unfavorable traits in the fossil record is because of natural selection. Those traits, by definition, impair an individuals chances of reproduction and so they are not passed down from one generation to the next.”

I understand that we will not see generation upon generation of a given unfit characteristic (those mutants will simply fail to breed and fade out for being unfit), but since the required number of first-generation randomly UNFIT genetic mutations is astronomical compared to the very small number of first-generation randomly FIT genetic mutations, then shouldn’t we find a first-generation mutant unfit for its environment? Or even a second-generation mutant who is the off-spring of an unfit but tenacious/lucky mutant? To my (limited) knowledge, we don’t find such unfit mutants even though they are required in droves. But if I’m wrong and we do find them all the time, I would appreciate being directed to that research.

3.

RE: “Of those forms that we find, we have no way of knowing how 'fit' they were…”

This, then, does answer my question above (1.) about our level of uncertainty about the mechanism of evolution. If we can’t know whether individuals were fit or not, then we can’t say we know that random genetic mutation produces unfit individuals, and if we can’t know that, then we have to assume that a very large part of this theory is true simply because the theory is true, which, if that part weren’t true, would mean the theory would not be true. Taking the existence of astronomical numbers of individuals that have randomly unfit genetic mutations to be true without direct knowledge—holding it to be true only because it is required by a secondary truth—is worrisome to me. What am I misunderstanding here? Please set me straight.

4.

RE: “You can't have any species 'randomly unfit for its environment'; everything has been fit enough to reproduce up until the individual that is found and we can't really know the results of that individual's reproductive life in terms of average fitness.”

No, I hope I never said we must have SPECIES randomly unfit for their environments, but we must have many individuals randomly unfit for their environments.

And since the changes in evolution we are talking about are observable physical characteristics, then, yes, we can know when we come across anomalous individuals that have characteristics unfit for what we otherwise know about their environments. In theory we would find them often. In practice, (to my limited knowledge) we don’t.

But, if we disregard changes in observable physical characteristics and use only the criterion of success/failure in breeding to determine whether an individual was fit or not, then you would be right, and we could never possibly find any evidence contrary to the theory simply because we believe the un-disprovable theory to be true. But that would reduce the theory to a tautology. That would be saying that we know nature only ever selects the fit genetic mutations because that’s all we ever find, and we know that’s all we ever find because, as we said, we know nature only ever selects the fit genetic mutations.

And that’s just flat-out silly, right?

Darwinian Evolution would be easy to rescue from such a tautology simply by showing evidence for what it already calls for: astronomical numbers of individuals who have observable physical characteristics that are unfit for their environments and that are brought about by random genetic mutation. But, as above, we can’t be certain about this, and we only know it to be true because that’s what the theory calls for, then we are back to a tautology.

That species change over time and are physically suited to their environments is obvious. But the mechanism by which this happens continues to fall apart for me in the above ways. Please tell me where and how I am wrong.

5.

RE: As a related point - slightly off topic perhaps but interesting nonethless - while a "random genetic mutation" does not "receive environmental input" there is a very common phenomenon called genotype- by-environment interaction (GxE). Basically when this occurs it means that the phenotypic consequences of having a particular genotype vary with environmental conditions, or (equivalently) the phenotypic consequences of experiencing a particular novel environment differ among genotypes (individuals or lineages).

One consequence of this is that rapid environmental change can actually increase the amount of standing genetic variation within a population without any change in allele frequencies (i.e. no need to invoke new mutations). Since the amount of genetic variation for a trait determines how fast it can respond to selection, this means that GxE could play an important role in allowing rapid adaptive evolution in the context of rapid environmental change.”

Ah, now this mechanism for evolution—one that does take in and respond directly to environmental input—seems to make more sense.

However, it does mean that the initial definition of Darwinian Evolution is incorrect. It won’t be that (1.) the mechanism for evolution is solely random genetic mutation independent of environment but ultimately preferred by natural selection. It would have to be that (2.) the mechanism for evolution is sometimes random genetic mutation independent of environment and sometimes phenotypic change in direct response to environment.

If definition 2 is actually the definition that evolutionary biologists use now, then I am behind the times.



Lastly, again, I thank you for your time and sincerity. I live in the US, where there is a silly (nearly fabricated, or perhaps just instigated) battle of Creationists versus Evolutionists, and this has kept me from being able to ask my questions. Half-way through any one of my questions, Creationists dismiss me as a deluded Evolutionist, and Evolutionists dismiss me as a whacky Creationist. This is the only place I have found so far that hosts people who will simply converse sensibly. Thank you.

"I haven’t seen anyone show the rate of genetic mutation for a characteristic showing up at unfavorable times to be the same as the rate it shows up when it finally becomes favorable."

Actually there are lots of ways of measuring rates of genetic mutation and all of the evidence suggests that the rate of change for most genes is relatively constant over long periods of time. Modern sequencing techniques has allowed even more detailed analysis. This paper (http://www.cell.com/current-biology/abs … 09)01454-7) for example measured the mutation rate of the Y chromosome in humans by directly sequencing and comparing the DNA of two individuals who were separated by 13 generations. They found that the mutation rate was pretty much the same as that determined by comparing humans and chimps. That means that the mutation rate for the past 300 years or so is the same as it was about 6 million years ago (the divergence time between chimps and humans).

shouldn’t we find a first-generation mutant unfit for its environment?

You are assuming that mutations that impair fitness will always show up in the fossil record and that is simply not the case. Think of all of the genetic diseases that affect humans. Most of them would leave no fossil record at all. PKU is a good example. It is a genetic metabolic disorder that causes mental retardation. However it does not affect development of the bones or any other body part. So, if you found the fossilized remains of a human, you would have no way to tell if it suffered from PKU or most other genetic diseases.

The bottom line is that mutations are rare and when deleterious mutations happen, they don't last long because the individuals that carry them do not reproduce. So, in a normal population, the majority of individuals will be perfectly healthy. That is why we usually see fossils of individuals that we assume were normal healthy (until they died). Remember that not all organisms leave fossils. In fact, the fossil record only reflects a very, very tiny fraction of all the organisms that have ever lived. The probability of finding a fossil of an individual that carried a rare genetic trait is vanishingly small.

Re your point:

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"However, it does mean that the initial definition of Darwinian Evolution is incorrect. It won’t be that (1.) the mechanism for evolution is solely random genetic mutation independent of environment but ultimately preferred by natural selection. It would have to be that (2.) the mechanism for evolution is sometimes random genetic mutation independent of environment and sometimes phenotypic change in direct response to environment.

If definition 2 is actually the definition that evolutionary biologists use now, then I am behind the times."

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Indeed I would probably argue that the term "Darwinian evolution" is very much behind the times since Darwin for instance knew nothing about genetics. Most contemporary evolutionary biologists would actually define evolution as a change in allele frequencies over time (where time means generations). Mutation, natural selection (i.e. Darwinian), genetic drift and gene flow (migration among sub-populations) are the key processes involved. Ultimately a change in allele frequencies at coding genes (i.e. genes that make proteins) or regulatory regions translate into phenotypic change within populations and divergence among populations (that can lead to speciation). Natural selection is fundamental to this process but as I say it is certainly not the only evolutionary force in play. The environment is key because a) it is the source of selection, b) it can effect the amount of genetic variance for a trait being selected through GxE as explained previously. In some cases (e.g. an environmnet with high levels of radiation) particular environments can impact mutation too.

I'm not completely certain what you mean by "phenotypic change in direct response to the environment". This sounds to me like you mean phenotypic plasticity - which is a term we use to describe the ability of an individual (or genotype) to produce different phenotypes in different environmental conditions. Plasticity is often adaptive (i.e. individuals can change their aspects of their phenotype to better suit a new environment in which they find themselves). However plastic change is not not in and of itself considered to be evolution as it does not involve any genetic change (i.e. a change in allele frequencies).

That said - perhaps slightly confusingly - plasticity itself can and does evolve (e.g., if it is genetically variable and under selection).

Last edited by Alistair Wilson (28th Jul 2012 19:54:59)

As a secondary follow up to some of your other points - and at the risk of upsetting some of my paleontological colleagues - I'm not sure that the answers to all your questions will lie in the fossil record.

Evolution - as I defined it above - can be observed in real time using model organisms with short generation times. Classically this was done with flies, mice etc (and it still is), but increasingly we use microorganisms since its even faster. In experimental evolution studies (http://en.wikipedia.org/wiki/Experimental_evolution) we can and do observe when mutations occur, we can directly observe the fate of new alleles in a population as they are selected for or against (and/or carried by drift), and we can observe the phenotypic and fitness consequences of new alleles too.

Last edited by Alistair Wilson (30th Jul 2012 09:17:58)