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Is there a reason why the TOE paragraph is at the top instead of the paragraph explaining what mutations are?--TimS 22:27, 8 May 2007 (EDT)

There are some serious mistakes in this article. First off, RNA is not found in the nucleus of the cell unless its mRNA, and in that case would not be mutated or affect the genetic makeup of the organism in question. mRNA is copied from the DNA structure itself and thus cannot alter DNA. Second, ribosomes are not responsible for correcting the DNA structure, they are responsible for protein synthesis and production of tRNA. It should also be mentioned that most mutations have no effect on the codons read to synthesis proteins due to similar 3 base codes. —The preceding unsigned comment was added by Biology (talk) June 2007

Gain-of-Function Mutations

Sickle hemoglobin is a gain of function mutation Conservative.--TimS 17:05, 5 September 2007 (EDT)

I have to ask, after reading this article and having much background knowledge of Sicklic hemoglobin, why anyone one would label it as a gain or a loss of function mutation? Heterozygous carriers of the Sicklic hemoglobin trait have hemoglobin that binds O2 just as regular hemoglobin does the only difference is in low O2 environments where the sicklic hemoglobin changes to a sicklic shape, otherwise it functions just like normal hemoglobin. I am not a biologist so I do not know how this relates to functional mutation grouping but I am a biochemist and I know for a fact that the sicklic hemoglobin is caused by a point mutation, where there is a change in the beta subunit to the amino acid valine at position 6 instead of the glutamic acid that is found in normal hemoglobin. As for homozygous carriers it has been found that the degree of anemia varies widely between patients. In general, patients with sickle cell disease have hematocrits that are roughly half the normal value (e.g., about 25% compared to about 40-45% normally). Patients with hemoglobin SC disease (where one of the beta globin genes codes for hemoglobin S and the other for the variant, hemoglobin C) have higher hematocrits than do those with homozygous Hb SS disease. The hematocrits of patients with Hb SC disease run in low- to mid-thirties. The hematocrit is normal for people with sickle cell trait. So depending on the variant of the disease caused by the homozygous carriers the disease does not have to be life threatening.

If anything I believe that a good example of a gain of function mutation would be found in HIV. SIV Vpu is not a viroporin, HIV-1 O Vpu is not a viroporin, however HIV-1 M Vpu is a viroporin (gated cation channel specific to Na+). This is a new activity that evolved in HIV after the split from SIV over a 10 year timeframe and is part of the reason that the HIV-1 M clade is the most common type of HIV in the world. This cation channel is gated and therefore more complicated than just a simple ion channel, considering that this is a new viral component found only in the HIV-1 M clade it is a safe conjecture to say that this is an example of a gain of function mutation considering that the HIV clades before HIV-1 M did not contain a gated cation channel specific to Na+.

Apolipoprotein AI is another example of what I believe would classify as a gain of function mutation. The Apolipoprotein AI Milano allele is the mutated allele. In an experiment where reconstituted HDL particles made of Apolipoprotein AI were infused into arteriosclerotic rabbits, the rabbits had fewer and less extensive plaques. There was decreased aortic cholesterol, and decreased cell proliferation (both of which improve cell wall flexibility. These experiments all point to the Apolipoprotein AI as a lipid-binding protein that is a major component of High Density Lipoprotein particles, and therefore play an important role in removing cholesterol from cells. Subsequent detailed research of the Apolipoprotein AI mutation has demonstrated that it has improved biological function that directly contributes to lowering the incidence of cardiovascular disease in the individuals carrying it.

Perhaps the two examples I listed above should be placed into the article since they are well researched in the scientific community due to the amount of press heart disease and HIV both get.--Able806 15:40, 12 November 2007 (EST)

Feel free to add them, although keep in mind the target audience.
The sickle hemoglobin is sometimes used as evidence for evolution (as opposed to creation), and I suspect that is why it was included in this article. However, leading creationists only dispute information-gaining mutations, and accept that there are information-losing mutations, such as apoliproprotein AI, which result in a gain of function or a benefit in some circumstances.[1]
Philip J. Rayment 20:54, 12 November 2007 (EST)
I will look into the APO-AIM but for now if it does not meet the standards then it should be left out. The HIV example though I know meets because it also increased the size of the genome of HIV. So I will add it in.--Able806 09:59, 15 November 2007 (EST)

No new genetic info?

The statement that "mutations that create new genetic information have never been observed" is simply false, unless you're using some unusual definition of genetic information, in which case that should be explained. Dadsnagem2 21:55, 7 January 2008 (EST)

No, it's not false, and I would consider it a usual use of "information", although not the meaningless (literally) definition that evolutionists often use (i.e. any change (except perhaps a deletion) is by definition new information). However, I do take your point that the definition wasn't explained. As a partial answer to that, I've linked "information", and although that article doesn't specifically mention genetic information, it's better than nothing. Philip J. Rayment 04:24, 8 January 2008 (EST)

According to Molecular Pathology

There are three main classes of mutation with several subclasses.

  • Deletions
Deletions of DNA ranging from 1 bp to megabases.
  • Insertions
Insertions of DNA including duplications.
  • Single base substitutions
  • Missense Mutations
Replacement of one amino acid with another in the gene product.
  • Nonsense Mutations
Replacement of an amino acid codon with a stop codon.
  • Splice Site Mutations
Create or destroy signals for exon-intron splicing

Within these main classes a mutation can be consided a loss of function or gain of function. There are also Frameshifts and Dynamic Mutations. Since I did not start this article I want to know if anyone would object if I made these corrections as well as provide some background information about what exactly these mutations trully are?--Able806 09:07, 12 February 2008 (EST)

Ok, I am assuming that this is fine and will start adding it in.--Able806 16:15, 15 September 2008 (EDT)

Sounds good. Philip J. Rayment 22:32, 15 September 2008 (EDT)

Mutations don't lead to evolution? New genetic information?

What's this about no new genetic information never being observed? Is it talking about a whole new genetic code? Mutations change DNA, which changed RNA, which changes proteins. This has been observed numerous times such as the nylon eating bacteria who have evolved to produce nylonase. To say that mutations are produced, but that they are neither new information nor beneficial is wrong and naive. Mutations simply create differences in bonds, in physical properties, it may make a protein more hydrophobic or change it's stability. Inherently they are neither good nor bad, it is only to the organism to whom these differences apply that may have worse or better effects depending on the circumstances of the molecule. Also, mutations don't cause evolution on their own. It is only with natural selection that mutations can cause evolution to occur. Also, bacteria and viruses evolve all the time. They may not meet most people's definition of "evolved", but they are some of the most successful organisms on earth. For instance it would be a lot easier to wipe out humans as "highly evolved" as they seem to be than bacteria as the current problems with antibiotic resistance show. And please that Mayr quote is taken out of context, Mayr gave many examples of how such complex organs could be improved by mutations, surely you could replace it with something from AIG or something that doesn't go against the life's work of the author. --Rainedaye 22:43, 25 October 2008 (EDT)

When talking about genetic information, we are talking about data with meaning. If you randomly change a sentence, for example, you don't introduce any new meaning; you only corrupt the sentence. There is evidence that the nylon-eating bacteria is not a random change, but something that appears to have been designed for[2].
The article does not say that beneficial mutations are not produced, only that ones with new information are not produced.
"Also, bacteria and viruses evolve all the time. They may not meet most people's definition of "evolved", but they are some of the most successful organisms on earth.": First you assert that it happens, then you admit that it may not be evolution, then you try and justify that it is evolution on the grounds that they are successful! That's a series of non-sequiturs.
You would accept a quote from AiG? Why do I have my doubts? Nevertheless, you have a point, and although I'll leave the quote in, I'll clarify it.
Philip J. Rayment 02:52, 26 October 2008 (EDT)
So you admit genetic information can change, but not obtain new meaning? I really don't understand your concept of "new meaning". If you have the sentence THE HAT WAS RED a H->C mutation occurs THE CAT WAS RED. I would call this new meaning, although you could probably argue that it was 'corrupted' from it's earlier version in that it no longer carries the same meaning, but I don't see that as a problem. And I was commenting on that people have different concepts of what is "evolved", a lot of people believe that dogs are somehow more evolved than worms. Bacteria are successful, in that they are not static. There happens to be a site that refutes that very article [[3]], and I'm very glad they have since I have little time to go through and pick it apart myself. Honestly, I find it hard to go through their lines of reasoning, it seems as if they don't fully grasp the idea of plasmids.
And I wouldn't myself accept a quote from AIG as a satisfactory argument, I have very little respect for their work. However, they are used commonly on this site as an appropriate if not authoritative source. It's just that if a preacher spent his whole life studying the bible and said once: "It must be admitted, however, that it is a considerable strain on one’s credulity to assume that an invisible supernatural being exists which was able to create everything we know." despite explaining afterwards what he meant, and backing up his claims in numerous books, it would be misleading to use this quote single-handedly to try and discredit his life's work. Although, I do thank you for changing it to read a little more accurately. Perhaps you should pick up What Evolution Is by Mayr, it's written for the general reader (I assume you haven't taken undergrad biology courses?) and sums up Mayr's reasoning well. --Rainedaye 10:54, 26 October 2008 (EDT)
A mutation is a random change. Did you randomly change a letter in the sentence "THE HAT WAS RED", or was some intelligent design involved on your part? How about trying that again with a random change, and see what you get. I've done the same sort of thing a number of times before, but I always make a random change (close my eyes, move the cursor back an arbitrary number of spaces, then press a key at random, before opening my eyes). And you know what? I've never had to repeat that because I've actually added new information!
Furthermore, information is not normally found in isolation. If your sentence was in a discussion about a person and their clothing, then "THE CAT WAS RED" would make no sense, despite it being grammatically correct.
Now it is theoretically possible that the sentence is in a context where there is a cat, and elsewhere creationists have admitted that the odd extremely rare information-gaining mutation might occur, so even if the Nylon bug is one, it's about the only one (and it's about the only one people keep telling me about), whereas if evolution was true, there should be many examples. And the odd very rare such mutation is going to be swamped by all the information-destroying ones, so it offers little comfort to evolution. By the way, the article you linked to is not a response to the one I linked to, although it does have a link to such a response.
Philip J. Rayment 06:51, 27 October 2008 (EDT)
Oh, dear I was really hoping the "random" thing wasn't going to be a problem. You see I could have ran that sentence through a program that randomly changed one letter in the sentence to any others in the alphabet and listed them all. Of all of these one would be "THE CAT WAS RED" which in this example let's consider a beneficial mutation along with others such as "THE BAT WAS RED", and "THE MAT WAS RED" that still make plausible sentences in English. If we consider these sentences as mRNA and each word as a codon for a protein (reading left to right) in this four protein molecule then these mutations in the first base of the second codon will change the type of amino acid to be inserted into this protein. In the proteins for the "beneficial" mutations that I have stated above the new amino acid would do something like alter the configuration of the protein or change it's hydrophobicity in a way that would enable it to carry out it's function more effectively (it could have other consequences, but this is an example so let's keep it simple). We can say that mutations such as "THE PAT WAS RED", "THE SAT WAS RED", and "THE NAT WAS RED" that are all made up of English words, but don't make grammatical sense as mutations that may change the amino acid sequence, but change it to something similar (like Asn->Glu, both negatively charged with similar pKa values) to where it's function is not affected. Also third base pair changes such as "THE CAN WAS RED" would still code for the same amino acid (in this case) since their is redundancy in the the genetic code and would therefore have the same protein produced as from the original sequence. That mutation would have little or no effect on the fitness of the organism, unless for a complex biochemical one (such as changing the stability of the DNA by going to a G/C->A/T base pair). All the other mutations that make nonsense sentences "THT HAT WAS RED", "THE GAT WAS RED", and "THE HAT WAS NED" let's call harmful mutations that make the protein less effective at what it does. When natural selection works on these mutations the positive ones get selected for and the harmful ones start declining in the population. So after many generations some may be left with "THE CAT WAS RED" which despite being random in the first place looks like it was designed, since all the much more likely harmful mutations occurred and were selected against.
And I do apologize for linking the wrong article, tabbed browsing is a boon and a curse. ^^ --Rainedaye 10:49, 27 October 2008 (EDT)
Using intelligent design to demonstrate evolution is a problem, and always will be. Including systematically trying all combinations. And stopping the "mutations" there. No microbes-to-man evolution is going to stop at a single mutation. How about randomly making one mutation (even trying every combination), then another random (not systematic) mutation to the sequence that already has a mutation, then another random mutation to that, and so on. And then see how many still make sense.
Further, you didn't address the point about whether the "mutated" sentence actually did make sense in context.
Lenski's research involved bacteria going through about 44,000 generations before he got one that he could claim was novel (not that it truly was). Humans, if they evolved from apes, must have had thousands of information-gaining mutations, and there's been nowhere enough time for that to happen (44,000 generations is about one million years). And with sexual reproduction there's only a 50% chance that any beneficial mutation will be passed on anyway! (See here for more on that.)
Philip J. Rayment 10:10, 30 October 2008 (EDT)
I was not stopping the mutations there, nor "systematically" trying them all. In a large populations over a large period of time the improbable is possible, all combinations might arise. Mutations can arise on top of each other, but given the occurrence rate of mutations and the size of most genomes, mutations happening in the same gene aren't likely (but yes, they do happen! improbable is not impossible!). As for whether or not the sentence made sense in context, the changing of one base pair in a gene isn't the same as changing a letter in a sentence. It might be my fault for trying to use an example to make things simpler, but addition before algebra. I'm not sure what you mean by the "context" a protein might find itself in, but a single amino acid change can do a lot or a little. Changing the hydrophobicity for example can make it more or less effective at what it does, but not necessarily take it "out of context". And before we start discussing on the accumulation of mutations, just how much time are you talking about here for age of the earth? --Rainedaye 21:11, 2 November 2008 (EST)
You may not have intended to stop the mutations there, but that's as far as your example went, and continuing it would have changed the result.
Time is not the magic wand that saves the argument. Trains run on tracks. Not when there are active processes working to weed out misfits, etc.
Not every combination of letters—even just three letters—constitutes a valid English word. And not every combinarntion of valid English words makes sense. And not every combination of valid English sentences make sense. And so on. In the case of DNA, there are only 64 possible "words", and, unlike English, every single one of them "makes sense", i.e. codes for an amino acid. But does every combination of amino acids make sense? And every combination of proteins? And so on all the way up the chain, even to the whole organism. A brain cell in a liver doesn't make sense, for example. This is what I mean by context. You would have wondered what my reference to trains was there for. The words of that sentence are all valid. The sentence itself makes sense. But the sentence in this context doesn't make sense. (It even disrupts the flow of thought, as the next sentence seems to refer to it, although it's not meant to.) A random change in a very small unit (e.g. a gene) might well make sense locally, but not in the wider context, especially the wider you go. The wider you go with the context, the greater the chance that it makes no sense at all.
I'm out of time now, but I hope that's clear enough.
Philip J. Rayment 02:52, 3 November 2008 (EST)
Well a sense of the time in which these processes occur in does help with the understanding, as does knowing how often mutations do occur. However, I don't think that your argument about context works against the idea of beneficial mutations. A mutation that doesn't "make sense" in a larger context and decreases the fitness of an organism is selected against. But not all mutations do that. The likelihood of a series of mutations rapidly occurring to make brain cells appear in the liver is not likely. And even if you may not think that it is "in context" it doesn't mean it couldn't be beneficial in some way. Lots of structures have lost their original function and are used for something else, such as legs becoming mouth parts in lobsters. --Rainedaye 20:41, 4 November 2008 (EST)

KathrynMonroe's edit

I've reverted KathrynMonroe's edit because most claims of information-gaining mutations having been observed turn out to be bluster or misunderstanding the issue, and because:

  • The first reference, to "Susumu Ohno 1984" is not elaborated on, so it can't be checked.
  • The second reference, to Sean Carrol, appears, from the abstract, to be to a claimed mutation that occurred "prior to the emergence of the adaptive immune system in vertebrates", so could not possibly have been observed.
  • The third reference, from a quick read, also doesn't appear to make any claims about actual observation of such mutation.

It also makes unsubstantiated claims about old and mined quotes.

Philip J. Rayment 10:28, 30 October 2008 (EDT)

I apologize since my wikifying is a new skill I"m trying to develop. I've fixed the wording and provided a better example of the first point - the creation of the nylon-digesting enzyme complex. I also clarified the quote by Grasse. Hope those help!
You've now provided a different first reference, but haven't addressed the comments I made about the other references.
Also, your revised comment about quotes is slightly better, but still not good enough, and implicitly falsely treats creationists and scientists as two mutually-exclusive groups. Your comment near the end about some claims being opinion is factually incorrect.
I'll do some work on it.
Philip J. Rayment 08:21, 31 October 2008 (EDT)

Mutation Types

A point mutation is in the same class as a deletion and an insertion mutation, however it is classified as a subsitution mutation (there are some subsitution mutations that change more than one base). I will try to work out the formating.--Able806 10:28, 4 February 2009 (EST)

However, mutations that create new genetic information have never been observed.

What does the above sentence actually mean? In other words, what is "genetic information"? This page is woefully incomplete without such a definition, and the page on information does not define it, either. TaKess 16:59, 7 May 2009 (EDT)