kenblaster5000
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Hypocrit, it sounds like the same thing evolutionary thinkers do to criticize bible thumpers like me.
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Soooo, mark, where is this mythical thread where you were told for five pages that transcript errors have nothing to do with mutations? And where is this paper defending Darwinism that lists transcript errors with other mutations?
You basically have one post to prepare yourself before I show everyone how wonderfully proficient you are at fabricating falsehoods to criticize evolutionists.
Do I get to claim that something is true just because I've repeated it ad nauseam too, or is this a tactic that only validates creationist statements?
For those of you watching at home, here's a brief rundown of the discussion so far:
mark kennedy thinks that transcript errors are mutations.
They aren't, because transcript errors occur when the transcription process gives a faulty RNA transcript.
On the other hand, mutations involve an alteration of the DNA itself (whereas a transcript error usually involves the DNA itself being perfectly fine while the transcription factor stuffs up somehow).
In prokaryotes, it is true that the un-transcribed strand of DNA is more susceptible to mutation as the act of transcription occurs. In eukaryotes the experimental data seems to be mixed.
But even so, a mutation can happen together with a transcript error (if both the RNA and the DNA get bombed), or a mutation without a transcript error (if the DNA gets bombed, but the RNA doesn't), or a transcript error without a mutation (if the RNA gets bombed, but the DNA doesn't), or neither.
This matters because it's important for anyone talking about evolution to know the difference between heritable and non-heritable changes in biological products. If mark is confusing transcript errors and mutations - even though they occur in tandem - that may well be indicative of defective fundamental understandings of the biology involved.
It's a bit like someone believing that people go to cinemas so that they can sit down in a dark room, switch off their phones, and eat popcorn. Moviegoers do actually do that, but try telling a cinema manager that the most important part of the experience is to put truffle salt in the corn popper.
Which words did I change the meaning of, mark? Vague accusations with neither substance nor specificity are unbecoming and, may I suggest it, even histrionic ...
I thought sfs told you a long time ago that the first rule of damage control was to stop digging?
DNA doesn't code for regulatory genes (in the same way that it codes for proteins); DNA contains regulator genes which code for repressor or activator proteins.
Are you sure you know the difference between DNA and proteins? (And you're thinking of telling me how life works!)
Meh, I'm not a big fan of videos; I think videos and lectures are mostly a waste of time because often this information is conveyed better through text. Were there any particular clips of the videos that supported your strange assertions, or did you just want me to waste half an hour on YouTube?
For those watching at home, the most important mutations are during the transcription process.
The transcript process being the time the replication of the DNA is being transcribed.
Now a totally different cell is introduced.
Except that Mark is talking about mutations that happen during the transcription process already described in detail. What you are doing is spitting semantical hairs in an attempt to make two different meanings, mean the same thing. transcription can mean two different things and you blend them together just like you do the term, 'evolution', without telling anyone. Thats less then honest to put it mildly.
DNA codes for everything, that's just plain silly.
DNA has the code that becomes proteins, you seem to be grasping at straws.
You are exactly what I thought you were, a troll who does nothing but make personal insults. Not a single substantive response but you insist on being taken seriously. I feel sorry for you, I'm actually sorry I once took you seriously.
Righto, let's see some citations for that.
"The replication of the DNA is being transcribed"? What on earth is that supposed to mean?
DNA replication and DNA transcription are independent processes: the first directly manufactures two copies of double-stranded DNA, while the second manufactures a single-stranded RNA.
Do you know what a prokaryote is? Honest question.
(Talking in third person is catchy isn't it)
No, I have always meant transcription to simply be "the process by which an RNA molecule is copied out of the information present in the DNA being transcribed." It is a process that takes a sequence of DNA, throws in a few transcription factors, and produces a sequence of RNA. Show me where I have ever given any other meaning for transcription. (Other than my using it in a court context - but if you can't tell from context alone when I'm using which sense, you really have bigger problems than biology to worry about.)
Becomes proteins, eh.
No, I actually stopped making personal insults a few posts back. I'm sorry. Do they still sting?
And you have the nerve to act like I don't understand how DNA is reproduced.
That is supposed to mean what exactly?
Something a lot like a Eukaryote without a nucleous...
Yea but a mistake in the transcription process is a mutation, think about it.
I stopped worrying about you when you stopped making actual arguments. Sorry but now I'm just having some fun with you. I refuted your empty point several posts ago.
Just what it means.
When a DNA molecule is being replicated, it isn't being transcribed.
When a DNA molecule is being transcribed, it isn't being replicated.
That's why your sentence "The replication of the DNA is being transcribed" made no sense to me. You seem to be treating them as simultaneous events, when they aren't.
Yup. The reason I'm introducing them is because the paper you cited previously on errors occurring during transcriptions (the one I "ignored", remember?) only dealt with bacteria, i.e. it wasn't dealing with eukaryotes.
Transcription is the process of the DNA being replicated leading up to the formation of the mRNA.
Bear in mind folks, the process is DNA-transcription-RNA-translation, the copy of the genome is made during transcription but I'm supposed to think that replication does not happen during transcription. Are you being serious right now or are you kidding me!
Transcription is the whole process from the time the double helix is being unzipped until the mRNA is complete.
Your flare for irrelevancy is unparalleled, any uncorrected copy error is a mutation, mutation are a failure of DNA repair.
This copy of the genome is made during the transcription process
No, as your video shows, the DNA is not replicated. No new copy of the DNA is made.
Are you kidding? Transcription doesn't involve the genome, only a gene. (Perhaps you don't know the difference?) As for the rest, shernren is not kidding you, sfs was not kidding you, I am not kidding you. DNA replication does not happen during transcription.
Unzipping is not replication. No new copy of DNA is made when it is unzipped preparatory to transcription. The transcription to mRNA is made without any replication of DNA.
No, only when it is DNA to DNA. Only when it is heritable. A transcription error only affects one copy of mRNA, with a consequent failure to produce the correct protein (or even any protein). It has no effect on the DNA molecule itself, no effect on inheritance, not even an effect on the next time the same section of DNA is transcribed. The original unmutated DNA template is still there for the next time it needs to be transcribed to an mRNA molecule.
What copy of the genome? You mean gene, right?
And the reason this matters is because mRNA isn't heritable, but DNA is, so if you confuse something that happens to mRNA for a mutation, you're going to think of a lot of things as heritable when they actually aren't (directly, at least).
Careful there, gluadys and crawfish, mark might lose all respect for you any time now!
Here's an analogy for the processes in the Central Dogma.
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Imagine that our world is populated by nothing but architects and builders. Every architect has, in his house, a big Mac which stores all his architectural designs. Now the big Mac burger is pretty portable (and the architects carry them around everywhere they go) but the big Mac computer isn't. So every day, before going to work, the architect prints out the blueprints of whatever building he's working on, and brings that to the construction site where the builders are working to construct those buildings.
Here's another twist: the architects have no idea how to change their designs manually. They're all PDF files, but for some reason the code for Adobe Acrobat has been lost, and all they have is Acrobat Reader. (All the computer programmers are down in their basements playing World of Warcraft; nobody has seen them for close to ten years now.) So at the end of the day, no matter how many annotations and markings they make on their printouts in the field, none of that information manages to go back into the hard disk.
What happens when a new architect comes along? He doesn't get to start from scratch; instead, he brings his hard disk over to whichever architect is mentoring him, and simply copies everything over. (Remember, the computer programmers are downstairs playing WoW. How are the architects to know what they need to copy and what they don't need? Best to get everything.) That's what the architects do. What they don't do is grab a pile of all the printouts and try to scan them back into the computer. Hoo boy, scanners are rare and expensive pieces of junk that don't work half the time. Much better to go back to the source, unless for some perverse reason the architect involved actually wants to introduce errors into the designs he's inheriting.
=========
So that's how the Central Dogma works. (It's called a dogma only because Watson and Crick weren't creative enough to call it anything else.) The nucleus of a cell is somewhat like a big, clunky computer (clunky by the standards of the cell) with the DNA being its "hard disk". Ribosomes are the places where proteins are made (much like the builders at their building sites); information gets from the DNA to the ribosomes by means of RNA.
Why is it important for the cell to have this kind of a dual system? It's done because storage and transmission are two fundamentally different (and often incompatible) goals for an information system. When I want to store data, I want it to be untouchable in some sense. I don't want it to be too easily altered or damaged. When I want to transmit data, on the other hand, I want it to be easily seen and changed and commented on. So think of the difference between a paper printout and a hard drive. A paper printout is light and easy to carry around, and can be read at first glance; it can be written on, colored on, even folded into interesting shapes. But paper is notoriously easy to lose precisely because it's so portable; and it's easy to mess up precisely because it's so easy to alter. A hard disk, on the other hand, can only be accessed through a computer, and only "at a distance" at that. Nobody can look directly at the spinning platters of a hard disk and deduce what information is on it. But that helps keep the hard disk's information secure and controllable: an encrypted hard disk is much harder to read than any kind of encryption you could apply to a piece of paper.
So a cell needs both a "long term memory" and a "short term memory" to get protein synthesis done. DNA is a long term memory: it's massive, bulky, double-stranded (so in-built error checking). The double-stranded-ness in particular makes it hard to modify, but also hard to access: the molecule needs to be unwound physically for the information to be copied. RNA, on the other hand, is a short term memory: it's light and easily read. It can move around the cell fairly quickly (because of its size); interestingly, the unmatched bases on the single strand of RNA can pair with each other, so that RNA can already fold into base-specified 3D structures - much like how a piece of paper can be scribbled and annotated on to increase its information content.
And that's why mark's error is so important. Not just because I am a pedantic evolutionist but because you get in serious, serious trouble if you confuse DNA and RNA. They do such different things! And if the processes of replication and transcription seem similar, well, that's only because in both cases the information in DNA needs to be retrieved. It's similar to how, with computers, whether you are printing out information or copying it to another hard drive, the first step is reading it off the initial hard drive. So also the DNA molecule needs to be unwound at the location where it is being read.
But that's where the similarities end. The paper printout and the copied hard disks are headed to very different locations, for very different purposes, with very different properties. Similarly, DNA and RNA (despite their apparent similarity, both being nucleic acids) perform radically different purposes in the cell.
What's a transcript error? It's when the printer stuffs up and prints something differently from what was stored on the hard drive. What's a mutation? It's when the hard drive itself stuffs up and stores something differently from the original. Can a transcript error change the DNA? It's as simple as asking whether a printer mistake can change the data on your hard drive: the answer is obviously no. Well, there are a few indirect channels. As rcorlew points out, the proteins used to replicate DNA are themselves produced through the normal cellular process, so conceivably an error in transcribing those proteins would lead to a mutation in the DNA. Even then though, the link is tenuous and unlikely.
The more important way that DNA can be affected through transcript errors is during the process of reverse transcription. Reverse transcription is akin to the scanners introduced in the last part of the story: they have the ability to copy RNA information back into DNA format. RNA is far more prone to modification than DNA though, so reverse transcription is only applicable either when quantity is more important than quality, or when the goal is precisely to introduce some kind of variability into the genome. The former applies in the case of retrotransposons. Those are fascinating little snippets of RNA who hang around DNA for the express purpose of copying themselves into DNA: the retrotransposons that copy themselves well get to introduce more copies of themselves into the DNA, which then get expressed, leading to more of them, which leads to ... an interesting, intra-organismic evolution arms race!
The latter case (deliberately introducing variability) applies to retroviruses and immune systems. Interestingly both are two sides of the same coin: retroviruses need variability to get past the immune system, and the immune system needs variability to check the viruses. In both cases reverse transcription of error-prone transcripts does play a role in variability. This is particularly true into the production of antibodies. Antibodies are essentially proteins which contain receptor components that can "latch on" to specific proteins on the outer coats of invaders. And for every antibody to respond to a different invader, its receptor must actually be different. Reverse transcription is actually used to induce "hypermutation" in the DNA that codes for these antibodies, so that over time each B lymphocyte in the body is capable of producing wildly different antibodies, even though they started from one single copy of ancestral DNA.
But these are exceptions that prove the rule. Reverse transcription can be such a madcap process that, as far as I'm aware, it doesn't really enter into the normal replication of DNA. Normally RNA intermediates don't directly enter into the replication of DNA (imagine copying a hard drive by printing out all its bits and bytes and then scanning them into another hard drive with a scanner!); instead, each strand of DNA unwinds and becomes the template for direct production of another strand of DNA. (This has been proven in studies using radio-tagged DNA strands; when a radioactive double-stranded DNA molecule is replicated, both resulting molecules are radioactive, showing that there is some mixing; but when both molecules are replicated again to give four DNA molecules, only two molecules are still radioactive and the other two are not, showing that the individual strands still retain their identity instead of being mixed up.)
And so that's why it's critical to not confuse the two processes of transcription and replication. A lot happens to RNA (hence its usefulness as a messenger molecule), but not much happens to DNA (hence its usefulness as a storage molecule). Confusing the two is a recipe for sure disaster, and mark's amusing rants on this thread are more than ample evidence of that.
Mark, you did not seem to answer the most important piece of shernren's post:
And the reason this matters is because mRNA isn't heritable, but DNA is, so if you confuse something that happens to mRNA for a mutation, you're going to think of a lot of things as heritable when they actually aren't (directly, at least).
Is this true or not? If not, why? Because if it is, you really don't seem to have a dog in this fight.
A transcript error is still a mutation, you are grasping at straws.
You worked hard on this, I get that but the real world problem is that an error during the transciption process is a mutation. Get with the program.
Very true and absolutely meaningless.shernren said:[stuff about reverse transcription, retrotransposons and lymphocyte antibody hypervariability]
All very intersting but still gets us no closer to an actual mutation during the transcription processes.
Another one of your tangents that prove nothing.
As far as transcript errors, a mutation is a failure of DNA repair. I had not brought this up in the other thread but transcript errors are mutations, in fact:This prediction is based on a model of somatic hypermutation of rearranged V(D)J sequences in B lymphocytes which involves the production of reverse transcripts (cDNA), containing nucleotide substitutions from the error-prone processes of transcription and reverse transcription using the V(D)J pre-mRNA template, which then homologously recombine into chromosomal DNA.Recombination signature of germline immunoglobulin variable genes
There are other indicators that transcription and reverse transcription errors are effected by some unknown mechanism. Since I have to pursue this on my own and get nothing but disinformation from evolutionists it takes time. The point is that saying transcript errors have nothing to do with evolution is wrong.
Mutation
Genetics - MCAT Review
- general concept of mutation-error in DNA sequence
- Mutation = change in DNA sequence by means other than recombination.
- types of mutations: random, translation error, transcription error, base substitution, inversion, addition, deletion, translocation, mispairing
- Random mutation = random changes in DNA sequence. Can be due to radiation, chemicals, replication error ...etc.
- Translation error = even if the DNA for a gene is perfect, errors during translation can cause expression of a mutant phenotype.
- Transcription error = even if the DNA of a gene is perfect, errors during transcription can cause expression of a mutant phenotype.
- Base substitution = mutation involving a base (ATGC) changing to a different base.
- Inversion = a stretch of DNA (a segment of a chromosome) breaks off, then reattaches in the opposite orientation.
- Addition = also called insertion = an extra base is added/inserted into the DNA sequence.
- Deletion = a base is taken out of the DNA sequence.
- Addition/insertion and deletion mutations result in a frameshift mutation.
- Translocation = a stretch of DNA (a segment of a chromosome) breaks off, then reattaches somewhere else.
- Mispairing = A not pairing with T, or G not pairing with C.
Only just by seven minutes!It seems you beat my post there good buddy.
The real issue is rather or not an error during transcription is a mutation, the fact is that it is. That's all this is about and he will never be called on it. That's what gets me so worked up, you guys never correct one another and that is not science, it's foolish.
Have a nice day
Mark
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