>By the way, I'm only a biologist "in a sense". I'm a computer scientist >by training, but I've been doing computational biology work for a few >years.
Ditto, though my other major was genetics.
>Why should you? mutations which lead to changes that increase in >frequency due to selective pressure are "beneficial", while those that >don't aren't. Of course, this classification can change overnight with >the advent of a drought or an invasion of predators.
You can have cumulative mutations, that produce some effect. I consider each step in that process a mutation, and it's a beneficial one, if a single mutation helps to benefit. But this is not necessarily the case. Say in the case of antibiotic resistance, that you needed three amino acid mutations for a specific protein that could potentially perform this function (even though it can't presently) to even begin binding the antibiotic and inhibiting it (if you'd like to work with specific examples, the one I am most familiar with are the beta-lactamases).
>And what's a "new" function, anyway? Usually mutations only >incrementally change some already-present characteristic, like >sensativity to light, resistance to antibiotics, or length of beak.
That's a new function.
>Wouldn't resistance to an antibiotic, or ability to produce viable >offspring, be new functions?
The evolution of resistance to antibiotic is a new function. The selection of it is a different story. This is the distinction I'm trying to make.
>These rarely spring into being de novo.
I am not sure if we're communicating. There is a situation where a protein inhibits an antibiotic (even feebly) and where a protein doesn't inhibit that antibiotic. Between those points, evolution (not natural selection) has occurred. Say you have two related antibiotics. Currently, in a population of bacteria you see resistance to one antibiotic, but not to the other. In a few years, you begin to see resistance to another antibiotic in that same population. Now, there are two explanations (in this context) for what happened: one, the gene for resistance to the second antibiotic was ALREADY PRESENT (as a variant of the first gene, either in the population or on the genome) in the bacterial population, and was NATURALLY SELECTED for. Two, the gene for resistance EVOLVED from the first gene, in some manner, and was THEN natural selected for. These are two different processes.
>One day, people are alive. The next day, they die. Why? Because >the bacteria in their bodies have developed the function of surviving >massive doses of a common antibiotic. Isn't that what you're after?
Nope. Because I'd argue a few bacteria (a single one will do) already had this function, and they were just selected for, and that bacteria (which is resistant) reproduced to a point where most of the bacteria in your body were not susceptible to antibiotics, thus killing the host.
>I don't understand your objection. Being selected for changes the >frequency of this character, and THAT is evolution.
That's where we disagree. To me, evolution is the evolution of the function at a molecular level, that is cumulative mutations (it could be one) that result in new function for a given protein. Natural selection is the selection (positive or negative) of that organism with that protein. Evolution operates at a molecular/genetic level. Natural selection operates on the usefuless of the evolution that has occured (at various levels).
>For example, genes which code for one protein in hemoglobin may >silently duplicate, and only over much time will that duplication >develop some functionality.
This is what I mean by evolution! Suppose our haemoglobin genes tomorrow also conferred resistance to malaria (by having a few mutations). Wouldn't you wonder HOW a new function arose from this duplication (which must've been both haemoglobin initially), and how long it took just to come up with it?
>It's pointless to insist on isolating the original duplication event, >because it was silent.
No, not the original duplication event, but the length of time (and how) it takes to come up with the new functionality (which has to happen BEFORE natural selection).
>The important point is that mutation without selection is not a >particularly interesting concept, from an evolutionary perspective.
We disagree there too, and there's quite a bit of research on this topic. Basically, the idea is, how long does it take for new function to evolve, from an existing gene, before naturally selection can operate on it. How does it evolve? Is it randomly (the current belief) or is there some directed process going on?
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