Smeghead, you previously posted that stress does not alter mutation rate but when I googled I found a link that said there is evidence that stress does influence mutation rate.
What say you?
I want evidence that something DOES happen. I would like to see evidence that mutations are statistically random. Say take a dice : there are 6 possible outcomes for every time I roll the dice. If I roll the dice 600 times, I will come out with approximately 100 of each (100 of 1, 100 of 2 and so on). Now I would have demonstrated that the number that comes out of rolling a dice is random. However, if this does not happen, I’d show that the dice is biased or fixed.
Say I take 100 organisms and I stress each of them with the same change and I measure the mutations produced in the next generations. Are the types of mutations I observe in their progeny all have the same frequency ? or are some of the mutations occurring more than the others ?
I said that does happen in certain cases, but to claim it as a general rule is simply incorrect. For instance, it’s been shown that E. coli, when it activates its stress response pathway, turns on an alternate form of DNA polymerase that replicates its DNA with less fidelity than the normal form. In other words, when shit is going down, it cranks up its mutation rate, presumably to increase the chances that somewhere in the population, some cell will generate a mutant that can survive whatever stress they’re encountering.
Did I already post this in this thread, or was that on a different board? I forget. Apologies if I already said this.
Anyway, note that this is a very different thing from what the OP is asking about. It’s not, “Oh, crap! There are some antibiotics floating about! I’d best start mutating my efflux pump gene so that it can handle this novel molecule!” It’s “Oh, shit! What I’ve got ain’t working! Scramble! Scramble! Scramble!” There’s no directionality to it. All the mutations are still random; there are just more of them.
Actually, of course, even that is being far too anthropomorphic. What it REALLY is is that cells that have evolved the ability to take this strategy have outsurvived those that don’t.
Totally get that - was just curious about the stress and mutation rate thing.
Smeghead - Thank you for keeping up and providing this valuable info. Lets take your specific case - I take a colony of E-coli and separate it in two colonies A and B:
**Case A **: I take colony A and stress it with a mild antibiotic. I take a sample fast enough so that I minimize the effect of selection and analyze the mutations and observe that :
20% mutations are of kind X
30% mutations are of kind Y
50% mutations are of kind Z
(Just some distribution of mutations - I am just making up numbers here)
Case B : I take colony B and stress it with higher temperature. I repeat the same observations as case A and still observe that:
20% mutations are of kind X
30% mutations are of kind Y
50% mutations are of kind Z
This would offer proof that the mutations are independent of the stressor. Does published data exist proving that this is indeed the case ?
Why?
I mean, it seems kind of like requesting evidence that bedbugs aren’t engaged in a deliberate conspiracy to take over the world.
Everything we know about bedbugs definitively indicates that they don’t have the cognitive apparatus to generate consciousness or a social will: that is, there’s no mechanism by which they could generate a conspiracy to take over the world. So we don’t bother running experiments on bedbugs to demonstrate their lack of consciousness.
Likewise, everything we know about mutations in simple organisms (or cells of more complex organisms) indicates that, as Exapno Mapcase said, they have no physiological or cognitive mechanism for “desiring” a particular mutation or “choosing” to alter a particular component of their genetic material to bring it about.
You’re an intelligent adult human being with the ability to learn a lot about DNA and the consequences of particular changes to various genes and chromosomes. Can you deliberately (without medical intervention) alter your own DNA to “choose to try” a specific genetic mutation? If so, how do you do it? What muscle do you flex?
And if you can’t, then why would you assume that a much simpler organism or piece of an organism with no consciousness or volition would be able to? What mechanism would permit deliberate choice of mutation?
I don’t think so. But what do you mean by “kind”? Each mutation is, in the simplest form, a change of one base to another. E. coli has roughly 4 and a half million bases. You’re not ever going to see the same mutation in 20% of the cells. Ever. You’ll see random changes across the genome. I know you’re trying desperately, for some reason, to get around that, but that’s what happens.
Okay so say 1 million mutations are possible. Label these mutations A1 to A1000000 and make a frequency plot in Case A and Case B. Has the data been statistically analyzed and shown that they are all random ? That there are no peaks in this data ? That the peaks are different in different environments (different stressors) ?
[quote=“Smeghead, post:67, topic:622101”]
You’ll see random changes across the genome./QUOTE]
All I am asking for is data to show that it is random - that there are no peaks or valleys and these peaks and valleys (if any) do not correlate to the environment (The stressor)
I am desperately trying to see evidence - if that is what you mean. An ounce of evidence is worth a ton of theory.
Why not ? Maybe organisms have evolved far enough so that there is random mutation as well as some tried out mutations that adapt faster.
If I had a broader theory of bed bugs taking over the universe and the fundamental premise was that they were engaged in a conspiracy to take over earth first - then sure, I’d like to see evidence of that.
Exactly. So if the biologists or genetics experts here say - Ok, we think it is trivial that mutations are random. So much trivial - that we don’t bother running experiments to verify it. I think that will be a reasonable explanation that no data exists.
Hey - I am an intelligent Human being with a lot of knowledge about germ theory and diseases too. I do not know which muscle to flex when I am attached by the flu virus - **but my immune system does ** (without medical intervention). I cannot explain - how my immune system does it - that does not mean I (or my body) cannot do it.
Again - first - you have not proven that I can’t. Second - I’m a complex animal with far longer time taken to produce progeny and can produce progeny in limited number. So if I am faced with increased environmental temperature, I may seek shade or may try to cool off by taking a shower. A simple animal like a virus may not have these options and its strategy maybe to adapt quicker and may have devised ways to have more targeted mutations combined with random ones.
Ah well, pardon me for using the normal definition of the word. Ignorance fought.
You’ve mixed up the premises here. I’m asking you whether you feel you need to see evidence that bedbugs ARE NOT engaged in a deliberate conspiracy to take over the world.
We all go through life just assuming that bedbugs ARE NOT deliberately conspiring to take over the world, don’t we? But nobody’s ever run experiments or produced evidence to show that they aren’t.
So why isn’t that bothering you? Why aren’t you starting a thread to ask how we really KNOW that bedbugs aren’t engaged in a massive conscious conspiracy of world domination? We certainly don’t have any direct experimental evidence to support that position.
And the reason is, I suspect, that you’re quite willing to accept the default consensus position that bedbugs are NOT conspiring to take over the world because you more or less understand that bedbug brains just don’t have the ability to manage something so cognitively complex. In other words, there’s no physiological/neurological mechanism available to bedbugs that would let them do that.
What you seem to be failing to understand is that the same thing holds true for cells “deliberately trying” to cause a specific mutation. How could something like a cell perform that kind of function? Given that it has no consciousness or volition, what mechanism do you imagine would operate to achieve that?
Your constant repetition of “well, but what’s the evidence they’re not deliberately targeting particular mutations?” sounds kind of like somebody inquiring “well, but how do we KNOW the bedbugs aren’t conspiring to take over the world?” Simply put, they just don’t have the cognitive machinery to make something like that possible in a meaningful way.
But of course you can explain how your immune system does it. All it takes is a trivial amount of googling to find out in general terms what basic mechanism is at work in fighting off a virus. Briefly put, the infection of cells by viral parasites stimulates production of antibodies that bind to the viruses and inhibit their replication, and also of other cells that kill virus-infected cells.
None of this requires any “deliberate” action or volition on the part of your cells: it’s just that some of your ancestors by trial and error evolved genetic mechanisms for reacting to viruses in this way, and consequently they reproduced more successfully than their peers who didn’t have these mechanisms. The basic concept of “a genetic mechanism that produces certain cellular responses to some type of infection” is pretty well accepted and understood, AFAICT.
But what you seem to be trying to postulate is some sort of a genetic mechanism that requires very simple organisms and pieces of tissue actually to understand what mutational change they “want” to achieve, and to alter their genetic material accordingly. How would that even be a meaningful concept? What would they do the understanding and wanting with?
Exactly, I think there are only two ways this could be happening:
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Some kind of cognition built into the cellular machinery of organisms - which doesn’t seem to be supported by evidence, and would turn our existing understanding of evolution somewhat on its head (because if things are adapting intelligently, selection can’t weed them out).
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The solution to problems being somehow encoded into the problem, which is a nice, but absurd notion. Falling rain does not contain the design of an umbrella.
I guess I would expect that there would have been studies on relative mutation rates between base pairs.
Just looking at the possible mutations at the base-pair level between A, G, T, and C, there are twelve possible mutations. I’d expect that there’d be at least some variation between those mutation rates, based on the chemical differences between the bases. Apparently, changes between A and G, and between C and T do have significantly different rates than other changes. I think that holds for immediate* mutation rates, not just for accumulated* rates, but I’m not sure.
- or whatever the correct terms are.
Next, one of the “stressors” mentioned above was temperature. Again, it wouldn’t surprise me if those twelve mutation rates had different variations with temperature, because chemical behavior typically changes with temperature, and because the bases are different chemically.
All that is for some given organism. Those rates could be different between different organisms. Maybe the A to G mutation rate is a little higher for eukaryotes that for procaryotes because the surrounding transcription machinery is different.
It might be hard to separate the different effects, but surely someone has attempted this? I’m not a biologist or chemist, so I’m not sure where to look. I tried Googling, but most hits seem to be on accumulated mutation rates, not immediate rates.
All this, of course, is far removed from being any sort of directed evolution. This is just talking about a mutation from from one base to another, without any reference to its effect on the organism. (It also ignores other types of mutations than base changes.)
This is the type of the data I’m interested in. I am not looking for evidence for directed evolution and I do not believe in it either.