No, they don’t. The mutations that happen in protein-coding regions are exactly the same as those that happen in junk DNA. It’s just that the genetic code may be tuned so that lots of mutations have no phenotypic effect. It isn’t the mutations that are tuned; it’s the code.
And what you’re citing there isn’t a bias of what mutations happen, it’s a bias of the mutation rate, which again isn’t any fine-tuning of what mutations happen.
They do not. Some of them do, others don’t. There is no fine-tuning mechanism that would cause such a thing to happen. Once more, your source fails to back up your claim.
You failed to quote the part that explained how it’s an example of a neutral mutation that’s beneficial. And of course such a thing is logically impossible if words actually have meanings.
No, they’re not. The genetic code being what it is has no effect on what mutations occur. The mutations that occur, occur regardless of what the mapping of codons to amino acids is like. The effect the code has is not to change or bias what mutations occur in DNA, but it does make it more likely that substitutions in protein-coding DNA are silent, and that non-synonymous substitutions result in amino acid substitutions for those of more similar properties.
That’s true in regards to the third definition of random mutations, but I primarily was arguing that the study conflicts with the second definition, where there is no way of knowing which gene will mutate in a particular cell or in a particular individual.
Well, I was not trying to offer a mechanism but describe the process. You even acknowledged that some of them do. Thus, my point stands corrected.
Yes that was my point. I am arguing that the full spectrum of mutations appear to be random but ultimately produce positive outcomes.
“Furthermore, we show that our proposed model accounts for most of the mutations at neutral sites but it is probably the predominant mechanism at positively selected sites. This suggests that evolution does not proceed by simple random processes but is guided by physical properties of the DNA itself and functional constraint of the proteins encoded by the DNA.”
You’re wrong in that too. There is no way of knowing which gene will mutate. It’s just that the distribution of probabilities isn’t uniform. Still random.
No, your point is contradicted. You have failed to describe a process. (Incidentally, describing a process and offering a mechanism are roughly synonymous. Another case of private vocabulary?)
That was word salad again. Neutral mutations are not beneficial, by definition. I have no idea what your point is supposed to be or what you were trying (failing) to say.
So I would have to show that there is an underlying causal mechanism (such as consciousness) for the distribution of mutations in order to prove that those positive outcomes I mentioned are predetermined?
What about the Toddler gene and all the function we found in the non-coding regions of Junk DNA?
@Meerkat_SK5: my question was specifically about “cancer” (based upon your statement that cancerous mutations can be beneficial).
Your response makes no mention of cancer. The abstract of the first article you link to (I could not get free access to the full contents of it, making me rather suspect that you lacked access to it as well), and the contents of the second and third, make no mention of cancer.
In what alternate universe is this an answer to my question?
I have to conclude that the word “cancerous” was tossed into your original answer with little thought and no substantiation, and you are now merely flailing around trying to obfuscate this oversight.
This conclusion is supported by the fact that, as well as it being irrelevant to my specific question, @John_Harshman and @Rumraket have deemed your response to be erroneous.
No, but you would have to show that in order to describe a process. As for the outcomes being predetermined, you would have to provide some sliver of evidence that they were.
What about it? You persist in assuming that people will understand your point when you just repeat what you said earlier. Do you know Einstein’s definition of insanity?
That does not support your claim that the genetic code affects what mutations occur. You don’t appear to have understood what you’ve read. You’re using incorrect terminology.
The genetic code is the systematic mapping of triplet codons (in RNA and DNA) to amino acids for use during protein biosynthesis (translation of mRNA). But you now seem to be using the term to describe merely all genomic DNA sequence.
What you quote has nothing to do with the genetic code, but instead with the organization of the genome. Where in the genome that genes are found in relation to each other, how repetitive this DNA is, and which genes are most actively transcribed and so on.
All it does it give an explanation for why there is such a thing as mutational hotspots, and why some pieces of DNA are more prone to mutations than others. You will generally expect more mutations in DNA that is seeing lots of active gene expression, because this DNA will be unwound and in single-strand form, and not protected by the chromatin structure. It is thus more prone to strand-breakage, and chemical alteration of individual DNA bases. And you will see more mutations in repetitive regions because these are more prone to strand slippage and unequal crossover. All of this explains why this DNA is more prone to mutations than other, more inactive parts of the genome, but it has nothing to do with the genetic code.
There is nothing in that paper that says mutations are “guided” in a sense that is different from how the path a river takes is “guided” by the happenstance of the local terrain and the gravitational attraction of the planet. That a repetitive DNA region is seeing positively selected mutations, and that mutations in repetitive DNA regions are more likely compared to other sites, is not evidence that mutations are “guided” in the completely absurd sense you’ve been arguing for in this thread. There’s no evidence that organisms(or the DNA itself, or indeed anything at all) actually know in advance what and where to mutate their DNA. And even if they somehow did know that a particular mutation in their genome would benefit their offspring in the future, the processes responsible for causing mutations are not under conscious control. No amount of mentally wanting something inside the privacy of your own mind is going to make you able to deliberately pick what mutations occur in your cells, any more than you can simply stop your intestines from digesting the food you eat by willing it not to, or make your kidneys stop making urine.
Mutations are biased by physics and chemistry, they’re not “directed”.
Can you explain how you think that paper you cited is relevant to your comment about mutations keeping the number of predators and prey low to prevent ecosystem collapse? It appears entirely unrelated.
it is unrelated come to think of it. I guess I got carried away. Anyhow, I am pretty much done with this topic already. I think the comments here cleared up my misunderstanding on the subject.