Again you are not only performing for your theater of backslapping cohorts you have no clue what I was talking about. You busted into a thread that you were intent on derailing, the way you are derailing this one. You said point blank that 'this has got to stop? Transcript errors have nothing to do with it and the whole crowd jumped right in, sfs being the one I was most disappointed in.
Oh I have every idea what mark was talking about; he just refuses to hear it.
He insistently denies that mutations can bring about large phenotypic changes, despite the simple chain of logic:
1. mutations can cause small genetic changes;
2. even small genetic changes can cause large phenotypic changes;
==
mutations can cause large phenotypic changes.
In fact, that was
exactly what I pointed out in my "derailing" post. I'll just post both my post and his response again, for emphasis:
mark kennedy said:
shernren said:
Why not? If you want to disprove it [that beneficial mutations could lead to the ASPM gene that humans have today], it's as simple as:
1. show that it is chemically impossible for the common ancestor's ASPM gene to undergo mutations that transform it into the Homo sapien ASPM gene.
You don't know what a mutation is, you don't know what a transcription error is and you have not read a word of any of the peer reviewed scientific literature quoted, cited and linked in the thread. Now you want me to prove, that something you don't understand, is impossible?
Now, mark could have engaged with my idea. He could have told me about mutations, about what he thought of them, and about why he thought particular structural changes required spooky "adaptive molecular mechanisms" instead of mutations. Instead, he chose to do nothing but attack my credibility and intelligence. Everything he said in that response was about me, and nothing was about mutations. Who's the
ad hom attacker there, folks? Who's the troll?
The fact again is that many posts were made in that thread - by everyone, even me - that had nothing to do with transcript errors, he chose not to respond to them but to keep pressing the issue of transcript errors until it dawned on him that he was wrong.
(And in fact, I didn't actually "bust into a thread that I was intent on derailing". I had posted previously on #26 and #43. I jumped on his error about transcript errors, that's true, but
he were the one who made it an issue for the next five pages.)
Now let's address the key error in mark's thought.
That's semantical double talk, any failure of DNA repair is a mutation. ...
Transcript errors is a general expression I use and I rarely use it in a technical sense. It is transcription as opposed to translation, that's really all there is to it. I'll tell you what, I'll dig it out when I get the time but on with the spam attack. ...
Oh yea, a transcript error is a mutation with sometimes devastating consequences:
Damage and transcription error
Mitochondrial DNA is susceptible to damage from free oxygen radicals from mistakes that occur during the production of ATP through the electron transport chain. These mistakes can be caused by genetic disorders, cancer, and temperature variations. These radicals can damage mtDNA molecules or change them, making it hard for mitochondrial polymerase to replicate them. Both cases can lead to deletions, rearrangements, and other mutations. Recent evidence has suggested that mitochondria have enzymes that proofread mtDNA and fix mutations that may occur due to free radicals. It is believed that a DNA recombinase found in mammalian cells is also involved in a repairing recombination process. Deletions and mutations due to free radicals have been associated with the aging process. It is believed that radicals cause mutations which lead to mutant proteins, which in turn lead to more radicals. This process takes many years and is associated with some aging processes involved in oxygen-dependent tissues such as brain, heart, muscle, and kidney. Auto-enhancing processes such as these are possible causes of degenerative diseases including Parkinson’s, Alzheimer’s, and coronary artery disease.
Human mitochondrial genetics
...
Transcript errors are mutations, that's not a silly error, it's a fact.
Let's start with the Wikipedia quote, shall we? Notice that, despite the article heading,
the extract itself says nothing about transcription errors. Instead, the article talks about (a) generic mutations, (b) DNA repair, and (c)
accurate transcription of mutated genes that produce mutated proteins. (Note: mtDNA is just "mitochondrial DNA"; it's the same kind of DNA - possibly with slightly different codon assignment, I can't remember - just in a different location.)
The essence of mark's error is that he is unable to differentiate between the different stages of the processes in the Central Dogma. Why else would he cite a Wikipedia article that says nothing about transcription to back up his claims about transcription? Why else would he say things like this?
mark kennedy said:
The chances of an amino acid seqeunce turning into one of the amino acids of life is less then one in three. There are 20 amino acids in all living things, there are 4 nucleotides that are used to make them. 4^4 is 64 and there are 20 amino acids so that's about a 1/3 ratio. I'll give you the rest of your biology primer when you digest that much.
That quote exposes a fundamental confusion between nucleotides and amino acids and the processes that go from one to another, a confusion which I don't think mark has ever really gotten over despite this quote being five years old.
Why does mark keep insisting that transcript errors are mutations? Because, apparently, most mutations occur during transcription. Now that claim in itself may be debatable. He cites a study saying that "77% of these mutations originate on the nontranscribed strand in E. coli mutants unable to repair deaminated cytosines." - but notice that these are mutants
designed to be unable to fix mutation errors. In eukaryotes the situation is a little bit murkier; some studies have indicated that transcription increases mutation rates but other studies have found the opposite.
The sad part is that in his sarcasm mark actually got it right:
A transcript error is an error in the transcript (aka RNA). An error in the DNA error is not a transcript error even if it occurs during transcription and has nothing to do with mutations but the error is a mutation.
Got it, why didn't I see it before?
Yes, mark, that's precisely what it is.
If a court transcriber dozes out and wrongly copies what the judge is saying, that's a transcript error, because the transcript goes wrong.
If a court transcriber gets shot by a sniper as he's making his transcript, it's not a transcript error, because there's nothing wrong with
the transcript itself. But it
is instead a murder.
So it is with DNA. A transcript error means that the DNA itself is unchanged but the RNA is wrongly copied. A mutation means that the DNA is changed, no matter what happens to the RNA transcript.
Does it matter? Yes, because his entire rigmarole about "molecular mechanisms" has been triggered by a fundamental misunderstanding about what happens when:
Project description:
The chloroplasts of higher plants perform oxygenic photosynthesis resulting in the transfer of light energy into chemical form, which is the basis of heterotrophic life on Earth. Photosynthesis may be dived into two sets of reactions: light reactions taking place in the thylakoid membranes, and carbon fixation reactions in soluble stroma. To ensure immaculate primary production under a wide spectrum of environmental conditions, the structure and function of photosynthetic machinery must be extremely dynamic. The molecular mechanisms behind these dynamic changes remain largely uncharacterised, although detailed knowledge of these reactions is of utmost importance for understanding the adaptation on organism level. The aim of our study is to resolve
molecular adaptation mechanisms of the photosynthetic machinery and to reveal how the information about the prevailing physiological state in the chloroplast is mediated to the nucleus (retrograde signalling).
Retrograde signalling mechanisms and adaptation of the photosynthetic machinery to environmental cues
Principal investigator:
Paula Mulo, Ph.D.
I turned a corner at some point and now I'm primarily interested in known molecular mechanisms for adaptation as opposed to the ones the logically follow Darwinian and naturalistic assumptions.
(emphasis added) See, once mark saw "adaptation mechanisms" his eyes lit up and he "turned a corner", even though
these mechanisms had nothing to do with DNA. (They change gene
expression, not gene
content: see e.g.
here.) I hope the pattern of the errors is obvious now. Transcript errors don't change DNA and yet he thinks they do; "molecular adaptation mechanisms" don't change DNA and yet he thinks they do. (Hence the comment, by the way, about him becoming a Lamarckian: he was mistakenly thinking that non-heritable changes were heritable.)
As for mutations, mark, let me ask you a very simple question. Lobsters can't swim out of a (good) lobster trap. Does that mean they can't swim
into a good lobster trap?
