Intelligent Design

Can Intelligent Design be Identified Scientifically

  • Yes

  • No

  • Possibly (explain)

  • It's a stupid question (really explain)


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kenblaster5000

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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.

Hypocrit, it sounds like the same thing evolutionary thinkers do to criticize bible thumpers like me.;)
 
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kenblaster5000

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I wonder if that primordial ooze was like the soup Jacob prepared for his father to steal the birthright of Esau, a profane, reprobate individual who did not want to listen to his father's wishes for he held the promise of birthright to be despised and was cheated of his blessing. Jacob was rightfully called the supplanter while still lying down on a rock saw the ladder with angels ascending and descending and declared surely this is the very house of God, how wonderful this place is. Esau wanted to kill his brother out of jealousy just as Cain slew Abel because Abel's offering was righteous and Cain's was not. Saul wanted to slay David because David was favored by God and by man. He was anointed and Saul lost his anointing and turned to mediums for answers. Judas had Jesus killed for money and because he thought he had a better plan. He would call him Lord but not master. Do these kinds of traits remind you of a certain person who comes in here to post and harass a child of the Most High God. This person tries to reduce this other one too his sinful level instead of striving to live a Godly life. No wonder, let he that is without sin cast the first stone. My sins are obliterated by the blood of Jesus Christ, not held against me. I will cast the first stone, it is the Rock Jesus Christ, the name above all names, and the name that everyone should and will confess, the name that everyone should and will bow to.

Brother, if you feel vindicated, then know that when the enemy comes in, the Spirit raises a standard. Enemy, we do not wrestle against flesh and blood but principalities. We forgive you for you know not what you say or do.

Bless.
 
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mark kennedy

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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?

Yes, do you ever get called on it?

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.

For those watching at home, the most important mutations are during the transcription process.

They aren't, because transcript errors occur when the transcription process gives a faulty RNA transcript.

Do tell...

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).

The transcript process being the time the replication of the DNA is being transcribed.

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.

Now a totally different cell is introduced.

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.

True but so what...

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.

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.

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.

Now he is off on one of his tangents again.



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 ...

You have not made a real statement yet...

I thought sfs told you a long time ago that the first rule of damage control was to stop digging?

You have no idea why I like that guy, it's beyond you.

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.

DNA codes for everything, that's just plain silly.

Are you sure you know the difference between DNA and proteins? (And you're thinking of telling me how life works!)

DNA has the code that becomes proteins, you seem to be grasping at straws.

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?

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.

Have a nice day :)
Mark
 
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shernren

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For those watching at home, the most important mutations are during the transcription process.

Righto, let's see some citations for that.

The transcript process being the time the replication of the DNA is being transcribed.

"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.

Now a totally different cell is introduced.

Do you know what a prokaryote is? Honest question.

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.

(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.)

DNA codes for everything, that's just plain silly.

DNA has the code that becomes proteins, you seem to be grasping at straws.

Becomes proteins, eh.

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.

No, I actually stopped making personal insults a few posts back. I'm sorry. Do they still sting? :holy:
 
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mark kennedy

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Righto, let's see some citations for that.

You mean like the ones you already ignored.

"The replication of the DNA is being transcribed"? What on earth is that supposed to mean?

And you have the nerve to act like I don't understand how DNA is reproduced.

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.

That is supposed to mean what exactly?

Do you know what a prokaryote is? Honest question.

Something a lot like a Eukaryote without a nucleous...

(Talking in third person is catchy isn't it ;) )


Well...never know who might be watching...

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.)

Yea but a mistake in the transcription process is a mutation, think about it.

Becomes proteins, eh.

Well yea....

No, I actually stopped making personal insults a few posts back. I'm sorry. Do they still sting? :holy:

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.

Have a nice day :)
Mark
 
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shernren

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And you have the nerve to act like I don't understand how DNA is reproduced.

That is supposed to mean what exactly?

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.

Something a lot like a Eukaryote without a nucleous...

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.

In eukaryotes i.e. things like you and me, the evidence isn't clear yet as to whether transcription makes DNA more or less vulnerable to mutation. At least that's what I gather from the literature thus far; if you have any papers I may have missed, I'd like to hear about them!

Yea but a mistake in the transcription process is a mutation, think about it.

*sigh*

It's not.

The product of transcription is a messenger RNA molecule.

The product of a mistake in the transcription process is a mistaken messenger RNA molecule.

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).

Like your "molecular mechanisms".

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.

Oh that's strange, that's about the point when you stopped making actual arguments too!
 
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mark kennedy

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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.

Transcription is the process of the DNA being replicated leading up to the formation of the mRNA. I think you just want to contradict me on a fundamental level because evolutionists never correct one another. The object being to make me look foolish and there is always a shernren in a creation/evolution debate. Your just here to confront and contradict, never mind the fact that you are dead wrong.

This is the process of transcription:


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!

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.

Thats because you have got the whole thing so twisted. Transcription is the whole process from the time the double helix is being unzipped until the mRNA is complete. Real basic stuff and my last ounce of respect for sfs was depleted when he agreed with you on this obviously erroneous point. They'll do that just to make a creationist look foolish, which would seem to be all you are good for.

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.

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 but you pretend to be able to contradict I don't think you are making a point, I think you are being deliberately misleading. What gets me, not a single evolutionist will correct you even though your error is obvious. I seen that clear as day with LM, he was completely wrong on a fundamental point and not once did the evolutionists correct him. There is always a you in these debates and all you do is contradict and conflate.

That will do it for now, this time I'll keep a link to this thread. Transcription has nothing to do with the copy of the DNA, boy, that's a good one.

Have a nice day spam troller :)
Mark
 
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gluadys

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Transcription is the process of the DNA being replicated leading up to the formation of the mRNA.

No, as your video shows, the DNA is not replicated. No new copy of the DNA is made.


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!

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.



Transcription is the whole process from the time the double helix is being unzipped until the mRNA is complete.

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.

Your flare for irrelevancy is unparalleled, any uncorrected copy error is a mutation, mutation are a failure of DNA repair.

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.


This copy of the genome is made during the transcription process

What copy of the genome? You mean gene, right?
 
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rcorlew

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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?

Well, in the abstract sense a transcription error can produce mutations when the resulting protein resulting from the translation of the mRNA is similar enough in tertiary structure yet different in actual attributes, that protein can be used in the replication of DNA and cause the new DNA to have different physical characteristics than the parent DNA. I do believe though that this would be extremely rare as it would take two failures of error checking to allow this product to be used, although there are other situations where a bad transcription can indirectly cause mutations.

Any change in the mRNA can cause an incorrect synthesis of that particular protein causing a change in the protein's tertiary structure and thus changing the behavior of the coded protein. Protein diseases like mad cow disease cause a change in the tertiary structure of the protein and cause the protein to exhibit different traits, these traits can become toxic to the cell or act in other ways.

All that said, a transcription error cannot directly cause mutations, the product of transcription, mRNA, is disassembled upon completing the task of synthesizing the exact protein called for, this disassembly can and usually does occur before the entire protein has been synthesized as the organic molecules for the translation process are required for other cellular funtcions.
 
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kenblaster5000

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Indeed, these things are too great for me. I think I may watch that video. I am a visual person. I need to get the mental picture, but still I do not understand all the lingo and logistics. Maybe I can cultivate myself in it and glean a bit from others. When someone points out an error, accept correction, make the change, and move on. That is just what I see. Pride and false humility can be a bad combination.

Bless.
 
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crawfish

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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.
 
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shernren

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Careful there, gluadys and crawfish, mark might lose all respect for you any time now! :p

Here's an analogy for the processes in the Central Dogma.

=========

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.
 
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mark kennedy

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Careful there, gluadys and crawfish, mark might lose all respect for you any time now! :p

Here's an analogy for the processes in the Central Dogma.

Ok, lets see....

=========

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.

The central dogma is DNA-transcription-RNA-translation. This is not in dispute, you have no rational reason to dispute this and yet you continue to argue which makes no sense. I feel sorry for you

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.

A transcript error is still a mutation, you are grasping at straws.

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.

This is truly sad, but keep working.


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.

Yea, transcription and translation are different, so what?

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.

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.

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!

Very true and absolutely meaningless.


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.

All very intersting but still gets us no closer to an actual mutation during the transcription processes.

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.)

Another one of your tangents that prove nothing.

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.

I am not on a rant, believe that. I am amused that you think this post actually means something. You wander off on one tangent after another trying to prove a point that does not exist. You are a walking strawman.

I feel sorry for you.

Have a nice day :)
Mark
 
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mark kennedy

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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.

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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shernren

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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.

Again, sources, sources, sources. You tried Wikipedia and I showed that you were misunderstanding it, please try something else. Do you have any idea how strange you sound repeating something over and over again without posting any meaningful explanation or data?

shernren said:
[stuff about reverse transcription, retrotransposons and lymphocyte antibody hypervariability]
Very true and absolutely meaningless.

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.

The reason I went on this "tangent that proves nothing" is because the majority of the papers mark cites about mutations and transcriptions involve reverse transcription.

The reason mark does not recognize this process as being relevant to the discussion is because he has no idea what is actually happening in the papers he cites.

For example:

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.

If you knew what you were citing, you would know why I introduced reverse transcription.

One more thing, mark. What is a transcript mutation?
 
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OK, just to be a neutral third party here I went and looked into this matter of a transcription error either being or causing a mutation and here is what I found:

Mutation
  • 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.
Genetics - MCAT Review

I have to say that according to what I have found thus far Mark appears to be correct. Do with that information what you will, but I figure I would chip in and see if the conversation could move along.
 
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shernren

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It seems you beat my post there good buddy.
Only just by seven minutes!

It's really a question of how mutations are defined. And I must say that the blame lies squarely on me for harping too much on the other definitions and not the definition of a mutation. For example, the Wikipedia definition of mutation is:
Mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus.
Therefore (and rightly so) the Wikipedia article doesn't list transcript errors as mutations.

I also find the MCAT review to be slightly misleading; it defines a mutation as "change in DNA sequence by means other than recombination", which is sensible, but then why would a transcript error be considered a mutation if it doesn't change the DNA at all?

By contrast, the authors of a recent study re(?)define "mutation" to simply be "error in genetic code" in the following extract:
Errors occur both during DNA replication (i.e., cell division) and during transcription of DNA to RNA and subsequent translation into protein. We call errors of the first kind genotypic mutations and those of the second kind phenotypic mutations.
Why Are Phenotypic Mutation Rates Much Higher Than Genotypic Mutation Rates? -- Bürger et al. 172 (1): 197 -- Genetics

(Note again, mark, that replication and transcription are considered distinct processes by these authors - because they are! - and so you still really do need to brush up on your understanding of cellular mechanisms. ;) )

And here's an interesting study that concludes that phenotypic mutations / transcript errors can actually make evolution easier:
If an individual acquires one of two mutations needed for a novel trait, the second mutation can be introduced into the phenotype due to transcription and translation errors. If the novel trait is advantageous enough, the allele with only one mutation will spread through the population, even though the gene sequence does not yet code for the complete trait. Thus, errors allow protein sequences to "look-ahead" for a more direct path to a complex trait.

... We have described a model demonstrating the consequences of positive phenotypic mutations on the evolution of a single gene. We have compared numerical simulations with the analytical approximations and found them to be in good agreement. When phenotypic mutations exert an effect on fitness, selection can operate on the intermediate allele of a complex trait, which otherwise (without phenotypic mutations) would be neutral. We refer to selection for the intermediate allele as the look-ahead effect, because this effect allows evolution to select for sequences not yet in the genome.​
Biology Direct | Full text | The look-ahead effect of phenotypic mutations
(By the way, is the full text of this journal accessible to non-subscribers? I'm very curious because I like the publishing model presented here - the peer reviewers are openly declared and their reviews are published in full. Yes, even the critical ones!)

I would add that if anything, phenotypic mutations would have an even stronger effect on sequences that code only for RNA (which doesn't get translated to protein) rather than sequences that code for proteins. That's because RNA is easier to "tweak" than protein: it has a standard structure which would change only a little bit (at least locally) if a single base of RNA is changed; by contrast, proteins can be very sensitive to small changes in amino acid sequence.

And guess what HAR1 codes for? ;)

So mark, you were somewhat right - and evolution is actually a whole lot easier than you thought! ;)
 
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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

There appears to be a significant difference between the two. One passes on to subsequent generations, and one does not. That is a huge difference - large enough to need to make a distinction between the two.

Your opinion is apparently also supported by some official definitions.

Personally, I think you're both arguing semantics. Yes, technically transcription errors can be called mutations, but that term could definitely become misleading when discussing the heritability of mutations.
 
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