Evolution question - Are mutations totally random ?

[Buck_Godot]

In partial answer to your second question, I don’t think that there have been a simulation exactly as you described, but there has been some analysis of data that is rather similar. In addition to the DNA that contains genes there is also a lot of “Junk”* DNA that don’t code into proteins and is just a byproduct of the evolutionary process. Like gene DNA, this junk DNA is passed down from generation to generation and undergoes mutation. However unlike gene DNA, there is no selective pressure on the junk DNA. As a result, the relative difference in this junk DNA between species can give us an indication as to how many mutations occurred since the two species separated, which in turn can give us an indication as to the time at which they separated. My understanding is that this data matches quite well with the fossil record, and is one of the clearest proofs of the theory of evolution.

• this is misnomer as the genome is a complicated place and evidence indicates that a significant portion of the non-coding DNA still play a role in the organism.

[Tim_T-Bonham.net]

@am77494

Instinctively, I feel that an organism in a new environment can provide the feedback to the genetic system (the genes) as to what might work better in the environment - so the genes as they mutate can try to produce those changes.

I don’t think this happens at a genetic level – no such feedback mechanism has been discovered. (It would be nice – imagine if you could send feedback to the cancerous cells in your body “go away – you don’t help me in this environment”.)

What you are describing is more like "instinctual behavior"or ‘basic instincts’ in animals – things that generation after generation just seems to know. Back when I was in school, it was thought that this was actually mainly learned behavior, by youngsters from parents & older animals. But this is behavior, not genetics.

[Mangetout]

@John_Mace

I haven’t heard of “paragenetics”. Are you thinking of epigenetics?

You’re right. I posted that on the train on the way home and thought I remembered the term.

[Smeghead]

@standingwave

I remember reading somewhere that the strength of the chemical bonds of the base pairs (A-T, G-C) are not equivalent, that one is more likely to mutate than the other. If this is true (and it seems likely that one or the other would be at least marginally more robust than the other), then true randomness flies out the window, does it not?

A-T pairs are held together by two hydrogen bonds; C-G pairs by three. This has nothing whatsoever to do with their tendency to mutate, because the hydrogen bonds are irrelevant to holding the actual base to the DNA backbone.

[iamthewalrus_3]

@am77494

Agreed. The question is - Is there evidence that such a mechanism DOES NOT exist ?

Yes. There’s substantial evidence that it’s a very hard problem to take a desired outcome and work backward to a necessary genetic basis. There are, for example, very lucrative and difficult problems figuring out exactly how proteins fold to create useful drugs and other chemical compounds. At the higher level, we know what sorts of shapes we want. Figuring out what sequence of amino acids is required to make those shapes isn’t at all easy. Most of our progress so far has been simulating a whole bunch of options and seeing if any of them end up in the right shape.

And that’s just one step of the process (a single protein) from “know what I want” to “get genes to express it”. For an organism to pass useful information down to a low level to “try to mutate a particular change” would require a way of solving the same sort of problem so you’d know where to direct your mutation efforts (if there were even a way to do so).

@standingwave

I remember reading somewhere that the strength of the chemical bonds of the base pairs (A-T, G-C) are not equivalent, that one is more likely to mutate than the other. If this is true (and it seems likely that one or the other would be at least marginally more robust than the other), then true randomness flies out the window, does it not?

“True” randomness usually means “as distinguished from psuedorandomness”. It’s true that you won’t get an even distribution, but the process is still just a truly random one. It’s not predetermined and computable. If you have a coin that comes up heads 51% of the time, the outcome of flipping that coin is still a random event, it’s just slightly weighted toward one possible outcome.

[am77494]

@iamthewalrus_3

Yes. There’s substantial evidence that it’s a very hard problem to take a desired outcome and work backward to a necessary genetic basis. … For an organism to pass useful information down to a low level to “try to mutate a particular change” would require a way of solving the same sort of problem so you’d know where to direct your mutation efforts (if there were even a way to do so).

I am sorry but I fail to see the line of reasoning here. If I understand you correctly, you are saying: * it is very hard for us (collective human intelligence) to compute the particular change needed in a gene to produce a desired change in the organism, so it must be impossible or equally hard for the organism to do so since it has “inferior intelligence”. * If that were correct, life in itself should be impossible since it is very hard (I do not think it has been done yet) for collective human intelligence to show how early amino acids combined to start life.

@iamthewalrus_3

“True” randomness usually means “as distinguished from psuedorandomness”. It’s true that you won’t get an even distribution, but the process is still just a truly random one. It’s not predetermined and computable. If you have a coin that comes up heads 51% of the time, the outcome of flipping that coin is still a random event, it’s just slightly weighted toward one possible outcome.

Great quote on the coin. So lets use your example of the coin and apply it to the mutations. Say you calculate the likelihood of a particular mutations based on the A-C-T-G chemical bond strengths and then observe the same mutations with organisms in different environments. Is there published data that shows that the results are the same in all these environments ? (Like the coin will show up 51% heads in all environments).

[Exapno_Mapcase]

@am77494

Great quote on the coin. So lets use your example of the coin and apply it to the mutations. Say you calculate the likelihood of a particular mutations based on the A-C-T-G chemical bond strengths and then observe the same mutations with organisms in different environments. Is there published data that shows that the results are the same in all these environments ? (Like the coin will show up 51% heads in all environments).

What would you get if you did this experiment? We already know that different physical and chemical environments lead to different physical and chemical outcomes becoming more or less likely. That says absolutely nothing about what is better for the organism. If you study water under high pressures and temperatures you will get steam; under low temperatures and pressures you will get ice. One is not better than the other. There are no “good” outcomes and “bad” outcomes; just outcomes.

[am77494]

@Exapno_Mapcase

What would you get if you did this experiment? We already know that different physical and chemical environments lead to different physical and chemical outcomes becoming more or less likely. That says absolutely nothing about what is better for the organism. If you study water under high pressures and temperatures you will get steam; under low temperatures and pressures you will get ice. One is not better than the other. There are no “good” outcomes and “bad” outcomes; just outcomes.

What it tells about the organism is that it tries different mutations under different environments which as I understand contradicts the part of the evolution theory which says it is random. I totally agree with you - there maybe no good or bad outcomes - but are they random and not correlated to the environment. Maybe evolution theory just assumes randomness as a convenience - or is it necessary for the rest of the theory to work ?

Allow me to give an example :

Say I have a large petridish of adult healthy organisms that reproduce every 6 hours and are adapted to a pH of 7. Now I divide them into 3 petridishes. In the first one, I raise the pH a notch (not to kill the organisms, just to make them uncomfortable) say to 7.2 , in the second one I lower the pH a notch say to 6.8 and the third one I keep the same pH of 7. I wait for 6 hours and check for mutations in the 3 petridishes. Are the differences in the mutations in all three petridishes statistically insignificant ?

[Exapno_Mapcase]

@am77494

Maybe evolution theory just assumes randomness as a convenience - or is it necessary for the rest of the theory to work ?

Yes, it is both implicit and necessary.

Allow me to give an example :

Say I have a large petridish of adult healthy organisms that reproduce every 6 hours and are adapted to a pH of 7. Now I divide them into 3 petridishes. In the first one, I raise the pH a notch (not to kill the organisms, just to make them uncomfortable) say to 7.2 , in the second one I lower the pH a notch say to 6.8 and the third one I keep the same pH of 7. I wait for 6 hours and check for mutations in the 3 petridishes. Are the differences in the mutations in all three petridishes statistically insignificant ?

This experiment, in principle, not only has been done millions of times but is currently being done in a million labs all over the world. Of course there will be differences. And exactly the same thing happens in the real world every day.

What does not happen is that the organism looks around at the environment and thinks, hmm, I better change my genes because that will fit the pH better. That’s Creationism, literally.

[John_Mace]

@Exapno_Mapcase

Yes, it is both implicit and necessary.
This experiment, in principle, not only has been done millions of times but is currently being done in a million labs all over the world. Of course there will be differences. And exactly the same thing happens in the real world every day.

What does not happen is that the organism looks around at the environment and thinks, hmm, I better change my genes because that will fit the pH better. That’s Creationism, literally.

Well, it’s certainly possible for the environment to influence the rate of mutations, and that a change in the environment can result it an increase or decrease in them.

[Exapno_Mapcase]

@John_Mace

Well, it’s certainly possible for the environment to influence the rate of mutations, and that a change in the environment can result it an increase or decrease in them.

Yes, that’s exactly what I’ve been saying. But I’m also saying that the increase or decrease won’t be directed toward better or worse mutations.

[Blake]

@am77494

Say I have a large petridish of adult healthy organisms that reproduce every 6 hours and are adapted to a pH of 7. Now I divide them into 3 petridishes. In the first one, I raise the pH a notch (not to kill the organisms, just to make them uncomfortable) say to 7.2 , in the second one I lower the pH a notch say to 6.8 and the third one I keep the same pH of 7. I wait for 6 hours and check for mutations in the 3 petridishes. Are the differences in the mutations in all three petridishes statistically insignificant ?

That’s a devilishly complicated question to actually answer.

The first point is that stressful environments all by themselves will increase the rate of mutations. When an organism is in its optimal environment, it wastes a lot of energy shielding the DNA from damage. Move it to a sub-optimal environment and it transfers that energy use to simply surviving, leading to increased mutation rates

So we would expect the rate of mutations in the sub-optimal conditions to be higher regardless of any other factors.

The next complictaion is the role of prions as genetic shepherds. What you find in many organisms is that if you apply stress, the conformation of the prions will change and you will start getting heritable changes in the DNA instantly. So you will find that in stressful conditions organisms will start to produce novel proteins, and that the production of those proteins will continue in their offspring even if the offspring are produced in non-stressful environments. Until about 10 years back it was assumed that this was evidence of mutation having occurred Now we know that this isn’t the case, and the only way to actually detect mutations is to do a complete DNA sequence, which is damn near impossible for the average researcher.

The changes in prion conformation also has a secondary effect of changing mutation rates. The prions normally act as “caps” for certain sections of DNA, which prevents them being transcribed and also protects them form damage. With a change in the prion the cap no longer fits and the DNA is not only expressed, it is also open to damage. Essentially where you used to have a single gene regulating trait X, you now have two, which of course doubles the chance of a mutation occurring that affects that trait.

Note that none of this is anything other than random. there’s no evidence that a change in pH will cause a change in genes related to pH as opposed to genes related to size, for example. It has been hypothesized that such a mechanism *could *exist, but I have to stress that we have no evidence for it. The hypothesis relies on the fact that some stretches of the genome or more prone to mutation than others. So an organism in a stable pH environment would place the primary “pH gene” (whatever that may be) in a high fidelity region of the genome where it is unlikely to mutate. Then it would place copies of it in low fidelity regions but inactivate them using prions that change conformation when exposed to low or high pH. If you then place that organism into a sub-optimal pH medium the prions will change conformation and the copies of the genes will be expressed. However they will also be prone to mutation because of their mutation. So the organism will then start undergoing rapid mutation of the pH gene.

It’s an interesting theory, but it has a few problems, not least of which is the total lack of evidence. But it’s not inconceivable that such a system has evolved.

[iamthewalrus_3]

@am77494

I am sorry but I fail to see the line of reasoning here. If I understand you correctly, you are saying: * it is very hard for us (collective human intelligence) to compute the particular change needed in a gene to produce a desired change in the organism, so it must be impossible or equally hard for the organism to do so since it has “inferior intelligence”. * If that were correct, life in itself should be impossible since it is very hard (I do not think it has been done yet) for collective human intelligence to show how early amino acids combined to start life.

Intelligence isn’t necessary for life or evolution. They clearly have been shown to work quite well via the process of random mutation and selection.

You, however, are suggesting that an organism can try to mutate in a particular direction. In order to do so effectively, intelligence is required.

Your example with the three petri dishes isn’t going to be measuring the total number of mutations. It’s going to be measuring the level of different mutations present under the selection pressure of the environment.

Imagine for a moment that there are only two possible mutations, one that makes the organism ideally adapted for 6.8 pH, but die in 7.2, and one that does the opposite. Both mutations occur exactly once in each of the three petri dishes. But when you go to measure the organisms, you’ll see only mutation 1 in one dish, both in the middle dish, and only mutation 2 in the third dish, because the other organism died immediately. The organisms have mutated in exactly the same way, but when you measure, you get distortion from the environment.

This survivorship bias is why it often appears that evolution is “directed” toward a particular solution. Failures die off and aren’t measured.

[BrainGlutton]

@panache45

How on earth would that work? How would a process of intention or goal-direction come about? The word “try” doesn’t make sense here.

Of course it does. Teleology, y’know. That’s how we climb the Evolutionary Levels.

[brujaja]

@njtt

Mutations jiving in the environment.

Hahahaha! I was waiting for something like that!

[am77494]

@iamthewalrus_3

You, however, are suggesting that an organism can try to mutate in a particular direction. In order to do so effectively, intelligence is required.

I don’t quite follow the rationale behind this assertion (the one in bold). Are you saying that the organism is “intelligent” enough to understand that the new environment is hostile and hence increased mutations are required to protect its progeny but not “intelligent” enough to know which mutations are good ? Even if we forego this argument, the question was if the mutations are willful - not necessarily intelligent. Are they willful or random ? Now the will can be intelligent or stupid - but thats a different discussion

Also - why is the measure to mutate in a certain direction a measure of intelligence ? Can’t it be argued that the organism in previous evolution saw a pH increase and “remembers” which mutations work ? (I guess you consider memory as intelligence too - right ?) Also can’t it be argued that the organism “observes/communicates with” other organisms and learns from them which mutation is needed ?

@iamthewalrus_3

Intelligence isn’t necessary for life or evolution.

I do not understand what you mean by intelligence here. If you are saying that willful mutations implies intelligence - I do not quite get it since willful mutations can still turn out to be stupid mutations. Also its like saying it isn’t necessary to paint a car for it to be driveable. Agreed - but the question in this context is: are they painted ?

@iamthewalrus_3

They clearly have been shown to work quite well via the process of random mutation and selection.

I do not dispute that random mutation can explain it. (Look at Car analogy) However, willful mutation also can explain it. So what evidence is there to choose the former over the latter ?

@iamthewalrus_3

Your example with the three petri dishes isn’t going to be measuring the total number of mutations. It’s going to be measuring the level of different mutations present under the selection pressure of the environment.

I beg to differ here. Notice that I measure at 6 hours. Selection has not yet taken place - its the first generation of progeny.

@iamthewalrus_3

Imagine for a moment that there are only two possible mutations, one that makes the organism ideally adapted for 6.8 pH, but die in 7.2, and one that does the opposite. Both mutations occur exactly once in each of the three petri dishes. But when you go to measure the organisms, you’ll see only mutation 1 in one dish, both in the middle dish, and only mutation 2 in the third dish, because the other organism died immediately. The organisms have mutated in exactly the same way, but when you measure, you get distortion from the environment.

If you read carefully, the experiment was designed to not to kill the organisms, just to make them uncomfortable - so your reasoning may not apply here . Also - as I pointed out, we are looking at the first generation - so selection has not yet played its part.

@iamthewalrus_3

This survivorship bias is why it often appears that evolution is “directed” toward a particular solution. Failures die off and aren’t measured.

Are you saying - Failures dying off and not getting measured - proves that evolution is random ? It can be also argued that evolution got it wrong and the mutations it pushed for did not win but other mutations though smaller in number initially, won in the long run. We are not ruling out natural selection here.

[Mangetout]

@am77494

I am sorry but I fail to see the line of reasoning here. If I understand you correctly, you are saying: * it is very hard for us (collective human intelligence) to compute the particular change needed in a gene to produce a desired change in the organism, so it must be impossible or equally hard for the organism to do so since it has “inferior intelligence”. * If that were correct, life in itself should be impossible since it is very hard (I do not think it has been done yet) for collective human intelligence to show how early amino acids combined to start life.

What you’re describing is a process that would require analytical functions though - and though you’re trying to describe it in a way that would not require actual sentient intelligence, you’re describing something like Searle’s Room.

It’s not just that we find it hard to compute the effect of a particular change to a particular gene, it’s also that the relationship between genes and traits is not simple or consistent across the genome.
As a (hypothetical) example, you might tweak a gene for hair colour and it just effects a change in hair colour, but when you perform a similar tweak on a gene that is responsible for eye colour, and it affects eye colour, but also results in the organism developing with no kidney function (these aren’t real scenarios, but reality is like this).

So in order for an organism to rewrite its genome to cope with environmental changes, it would have to:
a)Analyse what the problem actually IS (i.e. a short-necked giraffe is hungry, but why?)
b)Determine or select a workable solution to the problem
b)Compute a change to the genome that delivers the solution in the adult organism, at the same time as not having any deleterious side-effects.

How can this be done without intelligence? (well, it’s done at the moment by evolution, without intelligence, but the process isn’t one of design, but rather, multiple trial and error).

[BowlOfDucks]

The line between reptile and bird is arbitrary, and so when the change happened would depend on where you drew the line.

It’s not like lizard, lizard, lizard, BANG, parrot, parrot…

[Mangetout]

@Mangetout

a)
b)
b)

Or even C)

[iamthewalrus_3]

@am77494

I don’t quite follow the rationale behind this assertion (the one in bold). Are you saying that the organism is “intelligent” enough to understand that the new environment is hostile and hence increased mutations are required to protect its progeny but not “intelligent” enough to know which mutations are good ?

I think we might be getting off track into what constitutes “intelligence”, which is sort of a philosophical question. I interpreted the below sentence of your OP as something like “Organism desires to be able to run faster and somehow transmits that desire: ‘Genes, evolve faster legs!’”

Instinctively, I feel that an organism in a new environment can provide the feedback to the genetic system (the genes) as to what might work better in the environment - so the genes as they mutate can try to produce those changes.

The problem with this model isn’t that it requires the organism to be intelligent. It’s that it requires some way of translating an end goal (being faster) into a possible useful set of mutations, so that the genes can work toward that end goal. My evidence that this isn’t happening within an organism is that that translation process is really hard. So far, even with our intelligence we can’t really do much better than it appears evolution is doing, which is to try random things and see what happens.

Can’t it be argued that the organism in previous evolution saw a pH increase and “remembers” which mutations work ?

This seems quite possible, and intriguing. It also sounds like it would be a testable proposition. Take some organisms and repeatedly alternate them between two environments. If the organism can remember, then it should adapt more rapidly to the new environment each time.

However, this test doesn’t necessarily indicate that the mutations are non-random. One way that the adaptation would become more rapid is that the genetic sequence for some adaptation is still present in the organism, but is turned off by a simple genetic switch. Instead of re-evolving the whole sequence, the switch could simply mutate to on, which would make for quicker adaptation, but still wouldn’t imply directed mutation.

I do not dispute that random mutation can explain it. (Look at Car analogy) However, willful mutation also can explain it. So what evidence is there to choose the former over the latter ?

Occam’s razor is one. Random mutation is much simpler than directed. Plus, we can observe random mutation. Based on simple physical and chemical models, we can predict that random mutations would occur. So far there’s no suggested mechanism for directed mutation.

I beg to differ here. Notice that I measure at 6 hours. Selection has not yet taken place - its the first generation of progeny.

Populations of real organisms aren’t as discrete as you’d like. It’s not like populations that reproduce every six hours do exactly nothing for the first 5 hours 59 minutes, then all of a sudden double. The process of development is a continuous one, and you could see a maladaptive mutation get quashed any time during the development process.

Are you saying - Failures dying off and not getting measured - proves that evolution is random ?

No. I’m just saying that you have to be very careful in your experimental design and realize what you’re counting. It’s easy to design an experiment in which you think selection isn’t occurring (like the one you’ve proposed :)), but where it actually is, and furthermore explains the apparent directed outcome you observe.