What is the solid evidence for random (meaning not epigenetic) causes for successful gene mutation?

[Delta1212]

Overtone: thank you for your long answer.

 

Line one. Chaos theory, as far as I understand it, often describes systems comprised of many individual elements which seem to be behaving randomly, and yet, as a whole, or viewed from a different perspective, exhibit some kind of order. Can you explain how you have ruled out any kind of order in mutating genes or any kind of environmental influence?

 

This is not what chaos theory describes. Chaos theory describes systems in which very small differences in initial starting conditions lead to drastically different outcomes. If chaos theory were in play, the difference between the conditions in the lab and the natural environment would lead to very different, very noticeable, differences in mutation rates and evolutionary changes. Since we don't see that massive difference, chaos theory is not a good argument for why we may have missed something.

 

As for what evidence we have that mutations aren't responding directly to the environment in some way, well, we have a fairly good handle on how rapidly mutations accumulate in a population. We can track how long ago in time two species diverged based on a comparison of their genomes. If there were a novel mechanism for producing mutations that not only functioned solely when the organism is in the natural environment out of the lab, but produced mutations specifically beneficial for survival in that environment at a higher rate than random chance, our models for mutation rates and how quickly evolution happens would be horribly mismatched with our observations in the lab, and they are not.

 

We may have less control over observing the specific mechanism producing each individual mutation in a population in the wild than we do when observing in the lab, but we can still readily observe the overall rate at which mutations, and specifically beneficial mutations, are accumulating in a population, and it simply doesn't match against what we'd expect to see if mutations were happening in response to the environment in a way we don't see in the lab.

 

You are, in effect, asking how we have ruled out a phenomenon for which we have no proposed mechanism and which has no observable effect. There just isn't any evidence to support the idea that this is happening, and plenty of evidence that it isn't necessary for what we do observe to happen.

 

Also, you say you have observed none of the predicted patterns specific to environmentally guided genetic alteration. Is not the outstanding appropriateness of just about every organism to its environment a sufficiently compelling reason to assume that the environment has some impact on genetic evolution?

 

It would be we're it not for the fact that all of the variation matches very well with our models of evolution using entirely random mutations filtered through natural selection. If mutations were being guided by the environment specifically, we would expect to see much, much faster rates of evolution than we actually do.

 

From what you say, I gather that we have not ruled out some means for the environment to influence mutations.

 

I am not suggesting that there are no such things as random mutations. What I am endeavouring to understand is if the environment might have some means of influencing genes, or if cells might have some means of genetically responding to the environment. I gather that science has not found such a mechanism, but I am also starting to think it has definitely not ruled out that it might be there.

 

All further thoughts welcome.

Again, we have a fairly good understanding of how the environment interacts with DNA. It'd be like a physicist being handed a car to take apart. Without a background as a mechanic, he might not immediately understand what every piece of the car does, but he'd at least be able to tell that the machine probably doesn't fly.

 

You are, in effect, asking whether the car might be able to fly when we can't see it because it got from one place to another very quickly. Based on what we've observed, there is no way for this to happen, and the time it took the car to reach its destination actually did take approximately the amount of time we'd expect based on speed tests in the lab, but sure it's difficult to specifically rule out that something is happening when we aren't looking. It's just that your evidence for why it might be happening (be it the speed of the cars travel or the variation found in nature) matches very well with what we've observed in the lab and so isn't actually evidence of it happening at all.

 

When something has no proposed mechanism for how it might happen and no evidence that it is actually happening, we tend to rule it out as something that happens pending future evidence to the contrary.

[lordcheesehorn]

Delta 1212, thank you!

 

If mutations were being guided by the environment specifically, we would expect to see much, much faster rates of evolution than we actually do.

Why? Could there not be a slight influence from the environment, a weak magnetic pull, or ‘a very small difference in initial starting conditions leading to a drastically different outcome’, if you will?

 

...all of the variation matches very well with our models of evolution using entirely random mutations filtered through natural selection.

 

Could you explain how biologists can be sure that their models match what we see? Let’s say it took x years for a wasp to evolve an extremely complex set of venoms and behaviours required to stun a caterpillar and bury it for its eggs to feed on. How can biologists be sure that it only requires random, survival-selected incremental mutations to get from one behaviour to another in x?

 

a phenomenon for which we have no proposed mechanism

 

Are you sure that there is no proposed mechanism for cells [responding to the environment] and influencing genes? I’m sure I’ve read in a couple of places that this might be possible – I forget where now [and will investigate forthwith]. Nevertheless, surely it is theoretically possible that a hitherto undiscovered mechanism in the cell might be able to influence (again, influence, not flat out write) genetic code?

 

You are, in effect, asking whether the car might be able to fly when we can't see it because it got from one place to another very quickly.

 

No, I’m not. I’m asking whether the speed, direction and handling of the car might not necessarily be entirely down to what’s in the engine.

 

Another question, if you have a moment. Bit off topic: but how do developing cells know what to become? I’ve read that biologists do not yet know how a cell in a foetus knows to turn into, say, a nerve cell in the thigh, develop precisely all the architecture required to do its job and set up shop in just the right place… that this info cannot possibly stored in the genes. Any thoughts?

[chadn737]

Overtone: thank you for your long answer.

 

Line one. Chaos theory, as far as I understand it, often describes systems comprised of many individual elements which seem to be behaving randomly, and yet, as a whole, or viewed from a different perspective, exhibit some kind of order. Can you explain how you have ruled out any kind of order in mutating genes or any kind of environmental influence?

 

Line two. I am intrigued about ‘recent genetic engineering advances [that have] provided us with the first known instances [of “successful” genetic change]’. Can you elaborate?

 

Also, you say you ‘have observed none of the predicted patterns specific to environmentally guided genetic alteration.’ Is not the outstanding appropriateness of just about every organism to its environment a sufficiently compelling reason to assume that the environment has some impact on genetic evolution?

 

From what you say, I gather that we have not ruled out some means for the environment to influence mutations.

 

I am not suggesting that there are no such things as random mutations. What I am endeavouring to understand is if the environment might have some means of influencing genes, or if cells might have some means of genetically responding to the environment. I gather that science has not found such a mechanism, but I am also starting to think it has definitely not ruled out that it might be there.

 

All further thoughts welcome.

 

The environment is in constant interaction with an organisms genetics and does shape responses, however, these responses occur with in a range of possible phenotypes are determined genetically. Through alteration of gene expression levels, timing or location of gene expression, protein modification, etc; there will be an altered response. The thing about such a response is that it is rarely ever heritable, meaning that rarely will it be passed on to the next generation. In the few true cases of epigenetics, where a response is passed on to the next generation, it rarely persists for more than a couple of generations. Such short term alterations means that these non-genetic responses do not have the permanence to be of long term evolutionary consequence.

 

Because of the stability and reproducibility of DNA, this is ultimately the substrate upon which evolution acts over long term.

 

The environment does have the effect through Natural Selection of eliminating deleterious alleles and promoting the spread of beneficial alleles, however, the environment did not induce these specific changes. One way to think about it is in terms of what is called the fitness landscape.

 

 

Here peaks are viewed as variants underlying beneficial traits, the higher the peak, the higher the fitness of that allele. In contrast, valleys represent deleterious alleles. The landscape represents all the possible phenotypes. If mutation were non-random and environmentally induced, we would expect an organism to maximize its fitness and so adapt by developing phenotypes with the highest peak. That is not the case however, as organisms often get trapped on the smaller peaks. While these peaks still represent beneficial phenotypes, they are not the maximally fit phenotype. Once trapped on one of these lesser peaks, the organism would typically have to have cross one of the valleys to the next highest peak, a process which requires accumulating multiple deleterious mutations.

[overtone]

 

 

Can you provide an actual paper or data that supports the claim "nutritionally abetted larger size human babies tend to make larger size babies in their turn, regardless of genetics". I find this highly suspect, especially the assertion that they have eliminated genetics as a root cause.

Stuff like this is common on the net:

http://everydaylife.globalpost.com/causes-high-birth-weights-newborns-diabetic-moms-6005.html

http://care.diabetesjournals.org/content/26/2/343.long

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025254

http://www.theguardian.com/science/2014/feb/17/birth-weight-mother-diet-child-pregnant

 

 

 

If it is simply a matter that "nutritionally abetted" babies happen to live in an environment that provides such conditions and that that subsequent generations also live under such advantageous conditions, then this neither heritable nor adaptive. Its simply a result of positive environmental factors enabling a population to achieve its full genetic potential.

We are not talking about an advantageous situation, or any benefits. We have a growing percentage of babies being born too big (like the increase in height, too fast for genetic alteration), and big babies 1) suffer a variety of ills 2) are more likely to bear big babies in their turn.

 

Of course genetics is the "root cause" in some sense of all physiology, but the crucial role of environment is pretty clear.

 

 

 

What I am endeavouring to understand is if the environment might have some means of influencing genes, or if cells might have some means of genetically responding to the environment. I gather that science has not found such a mechanism, but I am also starting to think it has definitely not ruled out that it might be there.

As noted above:

 

 

Very general and abstract theories based on the mere presence of such guidance, without even specifying a mechanism (and thus able to incorporate almost any), have been proposed and diligently investigated many times for hundreds of years now (varieties of Judeo-Christian Creationism, Lamarckian Evolution, etc) but have yet to acquire any support in evidence or in theoretical calculation; instead, they have proved to be unhelpful in suggesting research or predicting fruitful investigation, contradicted by the calculations of mathematical description, and in very poor agreement with field observation, at all appropriate scales.

Note that the proposals of guided genetic (evolutionary) change have none of them specified a mechanism - they have been refuted on very general grounds, as necessarily resulting in patterns different from any seen.

 

In addition to the observation above that environmentally guided change would result in much faster and less jury-rigged adaptation than we see, for example, notice that even the basic statistical distributions of taxons matches the predictions of various models founded on selection from "random" (careful) mutation rather than guided alterations of genomes. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2982224/

So the burden of evidence is on those who assert taht somewhere, somehow, there is guidance of evolutionary progress - in particular, they need a mechanism that avoids the problems of even very general proposals so far, a quite new and unimagined (to date) means by which guided evolution could produce the patterns we see.