The Nature of Mutations

Some minor technical errors here. Mutation is change in the sequence of base pairs of DNA. This can be addition, deletion, substitution, and also translations; in which a segment of DNA is reversed or moved from one place to another. There are also some gross chomosomal mutations, which need not concern us.One of the most important functions of DNA is to synthesize proteins, and it is proteins which are made up of amino acid sequences. So a mutation in DNA can have a carry over effect in synthesized proteins. But it can also disable any expression at all of some protein, or introduce a new protein altogether, by mutation of the basepair sequences to introduce or remove the start codon which makrs the point in DNA where protein expression begins.This is all just a matter of getting the terminology correct and understanding the difference between DNA, and basepair, and amino acid, and protein, and so on. The qualification you make for "beneficial" applies just as much for deleterious. Suppose you have a mutation which you are willing to label as deleterious. What do you call a mutation which reverses the deleterious mutation? You miss the point. The mutation has some effects which are beneficial, and other effects which are detrimental. How, then, can you label it as deleterious? There are some environments in which it is a benefit.(There is a subtle point here also, in that the major deleterious effect is in homozygotes for the mutated allele.)What this demonstrates is that beneficial and deleterious are both defined with respect to an environment. This is merely berwildering. What do you think variation means? Of course mutations lead the variation. How could they not? Mutations occur all the time. This is observed. We both probably have around 60 mutations which were not in our parents, and a couple of those are not silent, having an effect on the amin acid sequences of expressed proteins. And there are even more mutations difference with your grandparents, of course. Etc. This is not an assumption. This is an observation. It is a repeatable experiment to observe that mutations arise in bacterial cultures, and that advantageous mutations get selected, and the result is a population in which new mutations become fixed. This is not a change from active to inactive sites. It is (for example) a change in the sequences of DNA, and hence in the sequences of expressed proteins. You even define it above more or less appropriately, if we skip over the minor confusion between a sequence of basepairs in DNA, and a sequence of amino acids in proteins.The mutations change the DNA sequence, which changes the protein sequence, which has an effect, which is sometimes advantageous and hence tends to spread through the bacterial culture as generation pass. Shrug. Any biologically heritable change is evolution, by definition. Give a lot of time, inherited changes accumulate, driving copies further and further from the parent form. Selection is the process which weeds out deleterious changes; the end result is organisms which are different, but which remain adapted. Speciation is what happens when sufficient change has accumulated betwee two populations that they no longer breed together. Once that occurs, the populations simply continue to diverge as time passes.Sure; a small observed mutation arising in a petri dish and becoming fixed in a bacterial culture is not speciation. It is demonstration of the processes of variation and selection. How are you going to stop change from accumulating over time? We observe the processes involved in evolutionary (inherited) change over small time scales, and we observe the fact changes in lineages over long time scales in the traces they leave behind. We observe the nested patterns of similarity between existing species, and note that it conforms to the patterns produced by cummulative inherited variation.Cheers -- Chris

quote:

---

Second, environment has nothing to do with the catagory, nor the effects of deleterious mutations. They are deleterious no matter what, and can cripple an organisms life processes or outright kill it within days or weeks. The only place where environment comes into play is with the so-called beneficial side effects of the mutation.

---

You are wrong. Deleterious and beneficial are both defined with respect to evironment.The source of your confusion may be those mutations that so badly disrupt the organism that it does not survive in any environment. We can ignore these in practice, since they have a 100% negative selection; they do not persist in future generations.But this is not definitional; this is just an extreme case. What is of more interest are mutations that arise and persist and may have an effect on future generations, for good or for ill. And that is defined with respect to environment.The way deleterious and beneficial are actually defined is by measuring selection effects; and that can only be done in a particular environment.It is quite usual to have mutations which are beneficial in one environment and deleterious in another. There is a discussion of this by Joe Boxhord as a part of the Are Mutations Harmful? FAQ at talkorigins, which examines mutation studies in bacteria. There are many examples there of what I am describing. Here is one in particular, using work by Chao and other in 1977. They grew E coli. cells, and innoculated them with a bacteriophage T7 that would kill the E. Coli. In time a mutation arose in the E. coli which gave them resistance to T7. Then the T7 virus mutated to infect the mutated E. Coli, and then a new mutation arose in E. coli to give resistance to the mutated virus. The experiment had 3 strains of E coli and 2 strains of the T7 virus co-existing. But the beneficial mutations came with a cost; the E. coli tended to take up nutrient more slowly. Hence these mutations were beneficial in one environment (with T7 present) and deleterious in another (with no T7 present).Also, why do you say "so-called" beneficial "side-effects"? The existence of beneficial mutations is unambiguous, and acknowledged by groups like Answers in Genesis.

quote:

---

On this part I not only disagree, but so does the observations of genetics. There is no observational evidence anywhere which states that variation has its origin within mutations. Think about that for a minute, if the only mutations that have an effect upon the genotype as well as the phenotype are deleterious (because we both know that neutral mutations have no effect) and only some very rare ones hold any kind of beneficial side effects depending upon the environment in which the organism lives, how many are left that could really lead to variation? Every deleterious mutation shortens the life span of the organism in which it occurs, as well as conferring genetic illness which is usually the reason the organism dies.

---

Actually, you are wrong again. It is certainly not the case that neutral mutations have no effect. Neutral only means that the effects are neither beneficial or deterimental in the existing environment. The terms beneficial, deleterious and neutral are all defined by the selective effect of the mutation in a particular environment.If the effect makes no apprecial difference to the fitness of an organism, then it is neutral. This still gives rise to diversity. Furthermore, because these terms are most emphatically defined with respect to environment, note that neutral variations can become beneficial or deleterious when the environment changes. Again, the FAQ I cited above discusses this phenomenon with a mutation in E. coli that gives resistance to a T5 bacteriophage; but which is neutral when there is no T5 present. This was measured by tracking the levels of T5 resistance over time in a culture which had no T5 present.

quote:

---

Yes, as defined by evolutionary theorists when they could not produce a viable beneficial mutation.

---

You are behind the times. The existence of viable beneficial mutations is so solidly established by many different studies and direct observations that even groups like Answers in Genesis acknowledge they occur. Their new line of argument (which is just as counter factual, of course) is that mutations cannot add information. But there is no point discussing that until you catch with the basic and trivial fact that yes, there most certainly are beneficial mutations.

quote:

---

To the quick - any biological change, heritable or not, is NOT evolution in progress. It is only a biological change. The sooner mainstream science understands this, evolutionary theory will disappear over the horizon. It's day is coming, and coming fast.

---

It has been coming fast now for well over a hundred years.Glenn Morton may be known to some people here. Glenn is a geologist, and an evangelical Christian, and he used to be an active young earth creationist. Some of his creationist writings are still being cited by creationists now, although Glenn has long since acknowledged that they are completely incorrect. Glenn has recently produced a new document called The Imminent Demise of Evolution: The Longest Running Falsehood in Creationism. In it, he documents a trail of claims about evolution and related science being on the verge of rejection, starting way back in 1825.Glenn's title is a bit misleading, in that many of his earliest extracts refer not to evolution but to geology -- which is Glenn's own area of real expertise. However, from 1878 they start to focus upon biological evolution. The 1904 extracts are especially hilarious.

The above is incorrect.The apoA-1 Milano mutation does not destroy the capability of forming HDL. In fact, the HDL (High densisty lipoprotein) formed with the mutated form of the expressed protein appear to be more effective at their task of removing cholesterol.My reference is: This is a study of the HDL particles formed by the mutated protein.It is certainly true that HDL counts are low, but since the HDL particles are more effective, it is unambiguously false to infer that the low HDL would lead to an early death in the absense of an anti-oxidant effect.The anti-oxidant effect is an additional benefit of the mutation, and cannot be a replacement for HDL particles, which are essential to the cycles of cholesterol transport in the body.I do not know why HDL counts are low, but one contributing factor may be that the mutated proteins form a dimer, which means that two protein molecules bind together and work as a unit. HDL particles require protein molecules to form. With the wild type, the HDL particles seem to come in two main sizes, using two and three monomeric protein molecules respectively. The mutated form works as a dimer, using one and two dimeric protein molecules respectively. This means that effectively the same number of monomeric protein molecules give a smaller number of HDL particles. The chemistry of body metabolism is extraordinarily complex, and this simplistic model is certainly not adequate as a real explanation, but it may be one contributing factor.So far, no negative effects of the mutation are known. Low HDL counts are not a negative effect, since the HDL is so much more effective. HDL is used for transport of "bad" cholesterol out of the body, and this occurs just fine in individuals with this mutation. The benefits of this mutation are not confined to the additional anti-oxidant effect, which is proposed as another benefit of the mutation.A study of this mutation is a useful way to appreciate just how intricate and complex is the human body. A new protein does not just have one effect; it gets added into the mix of metabolism and body chemistry, and changes can have many different consequences. This stands as an example of a "random" change in which the mutated protein fitted in very well, with a number of desirable consequences. Effectively, the mutation seems to give an immunity to heart disease.The talkorigins archive has a new FAQ available on this mutation, at Apolipoprotein AI Mutations and Information. I helped with this FAQ (not as an author, though I did write the glossary), and this post is based on my own direct investigations from the primary literature.[This message has been edited by cjhs, 04-25-2003]