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Author Topic:   Adding information to the genome.
Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 1 of 280 (531849)
10-20-2009 8:41 AM


It has been estimated that the size of the functional genome has increased 7.8 fold every billion years. Whether that figure is right or wrong, molecule-to-man evolution certainly requires a steady and substantial nett increase in genomic information.

The occasional point mutation can be "seen" by natural selection, but these generally switch an existing gene on or off, so they don't constitute additional information. So what is the absolute minimum novel genetic structure required to be "seen" by natural selection and added as new information to the genome?

Is it a protein? An enzyme? A gene? What must be created by random processes in order to be seen and conserved by selection?


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
Replies to this message:
 Message 3 by Wounded King, posted 10-20-2009 9:28 AM Kaichos Man has responded
 Message 4 by Dr Jack, posted 10-20-2009 9:33 AM Kaichos Man has responded
 Message 10 by Phage0070, posted 10-21-2009 2:42 AM Kaichos Man has responded
 Message 25 by Blzebub, posted 10-21-2009 4:31 PM Kaichos Man has responded
 Message 50 by Briterican, posted 10-22-2009 5:53 PM Kaichos Man has responded

    
Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 5 of 280 (531988)
10-20-2009 7:06 PM
Reply to: Message 3 by Wounded King
10-20-2009 9:28 AM


You seem to be saying that there are mutations which can cause phenotypic variation which can be acted upon by natural selection but which do not constitute changes in information

Which do not constitute a nett increase in information. I think I made that clear.

Heritable variation with a phenotypic effect causing a difference in reproductive success

That's right. But in order for the nett information to increase (as opposed to merely "change")that variation has to be additional to all the other information on the genome. Modifying the function of existing information might give you the effect, but there's no nett increase in information.

at whatever level that variation is generated

Precisely my question. What is the minimum level of new information -not modified existing information- that can cause a phenotypic effect visible to natural selection? A new protein? A new enzyme? A new gene?


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
 Message 3 by Wounded King, posted 10-20-2009 9:28 AM Wounded King has not yet responded

Replies to this message:
 Message 7 by Coyote, posted 10-20-2009 9:28 PM Kaichos Man has responded

    
Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 6 of 280 (531992)
10-20-2009 7:24 PM
Reply to: Message 4 by Dr Jack
10-20-2009 9:33 AM


First you must define information. Really for your argument to mean anything at all you must do this; otherwise you're just playing humpty-dumpty

DNA that has, or contributes to, an effect on phenotypic form or function.

That's nice. What about the ones that aren't "generally"? Like the mutation that produced chloroquine resistance in Plasmodium (the malaria parasite).

Are you suggesting that it is this form of mutation that has caused the functional, non-redundant genome to grow 7.8 fold every billion years?

I don't understand what you mean here? Could you elaborate?

The supposedly observed increase in the size of the genome requires the addition of new information. That new information must be created from non-functional DNA (otherwise it is simply modifying existing information). What is the minimal genetic structure that can be randomly assembled from non-functioning DNA that will be visible to natural selection?

Edited by Kaichos Man, : No reason given.


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
 Message 4 by Dr Jack, posted 10-20-2009 9:33 AM Dr Jack has responded

Replies to this message:
 Message 11 by Dr Jack, posted 10-21-2009 6:47 AM Kaichos Man has responded

    
Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 8 of 280 (532039)
10-20-2009 11:22 PM
Reply to: Message 7 by Coyote
10-20-2009 9:28 PM


Re: No new information indeed...
You do realize that this "no new information" is a talking point derived from a fundamentalist religious belief in "the fall" don't you?

From where it is derived is irrelevant. It should be easy to falsify with scientific data.

Unfortunately, this belief in "the fall" is not supported by science, nor is the absolute mandate that there can be no new information in the genome.

Again, if you have the scientific data to support this, the debate is over. Let's see it.

Those unsupported religious beliefs would perhaps be more appropriate for one of the Religion Forums rather than the Science Forum.

Were they unsupported, you would undoubtedly be right.


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
 Message 7 by Coyote, posted 10-20-2009 9:28 PM Coyote has responded

Replies to this message:
 Message 9 by Coyote, posted 10-21-2009 12:04 AM Kaichos Man has responded

    
Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 13 of 280 (532061)
10-21-2009 6:57 AM
Reply to: Message 9 by Coyote
10-21-2009 12:04 AM


Re: No new information indeed...
Then the debate is over. Scientists have only to convince other scientists, relying on empirical evidence. That has long since been done.

Empirical evidence! I can't wait- let's see it.


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
 Message 9 by Coyote, posted 10-21-2009 12:04 AM Coyote has not yet responded

    
Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 14 of 280 (532065)
10-21-2009 7:07 AM
Reply to: Message 10 by Phage0070
10-21-2009 2:42 AM


Mutations that reduce complexity and increase survivability are going to be preserved through natural selection just as much as those that increase complexity and increase survivability.

No-one's disputing this.

Behold, natural selection is preserving a lot of completely non-functional DNA, yet increasing "complexity" by your measurement.

I made my definition of complexity quite clear. An addition of non-functioning DNA is not an increase in complexity. The DNA needs to be functional to the point that it is "seen" by natural selection, and -most importantly- additional to all the original functioning DNA.

The question is pointless, nearly meaningless, and completely irrelevant to the issue.

The question is the issue. I started this thread, remember?


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
 Message 10 by Phage0070, posted 10-21-2009 2:42 AM Phage0070 has responded

Replies to this message:
 Message 21 by Phage0070, posted 10-21-2009 11:35 AM Kaichos Man has responded

    
Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 15 of 280 (532066)
10-21-2009 7:18 AM
Reply to: Message 11 by Dr Jack
10-21-2009 6:47 AM


So, you're saying that a section of DNA contains information if and only if it has an effect on phenotypic form or function. Okay. How is that to be quantified? Do we simply count genes that have "an effect"? Or is there a more subtle measure here? One, that would, for example, take notice of a change to DNA that improves or changes it's function?

Improving or changing it's function may get a gene "seen" by natural selection, but it isn't going to get you the many-fold increase in coding DNA.

With other forms of mutational events, yes, it accounts for all increase in gene function, however meaningfully measured

It's the "other forms of mutational events" I'm interested in, given that point mutations are not going to generate huge increases in the amount of functional DNA.

According to you, if a gene is copied, and the one of those copies mutates adopting a new function is that an increase in information?

Yes.


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
 Message 11 by Dr Jack, posted 10-21-2009 6:47 AM Dr Jack has responded

Replies to this message:
 Message 16 by Dr Jack, posted 10-21-2009 7:27 AM Kaichos Man has responded

    
Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 17 of 280 (532081)
10-21-2009 8:23 AM
Reply to: Message 16 by Dr Jack
10-21-2009 7:27 AM


The vast majority in increase in gene function is produced by gene copying followed by modification of one of those copies or the resplicing of exons from one or more genes. We know this because of the patterns formed by similarities in the genes of living organisms.

Mr Jack,

First of all thank you and congratulations on having the courage to offer a straight answer.

Now then, these "patterns formed by similarities in the genes", can you give me a reference to that?


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
 Message 16 by Dr Jack, posted 10-21-2009 7:27 AM Dr Jack has responded

Replies to this message:
 Message 18 by Percy, posted 10-21-2009 8:59 AM Kaichos Man has responded
 Message 20 by Dr Adequate, posted 10-21-2009 11:11 AM Kaichos Man has responded
 Message 22 by Dr Jack, posted 10-21-2009 1:12 PM Kaichos Man has responded

    
Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 28 of 280 (532194)
10-21-2009 10:20 PM
Reply to: Message 20 by Dr Adequate
10-21-2009 11:11 AM


your hopeless foggy stew of shifty evasion

How can the person first posing the question be guilty of evasion?


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
 Message 20 by Dr Adequate, posted 10-21-2009 11:11 AM Dr Adequate has responded

Replies to this message:
 Message 37 by Dr Adequate, posted 10-22-2009 3:16 AM Kaichos Man has not yet responded

    
Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 29 of 280 (532195)
10-21-2009 10:21 PM
Reply to: Message 18 by Percy
10-21-2009 8:59 AM


Thank you, Percy.


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
 Message 18 by Percy, posted 10-21-2009 8:59 AM Percy has acknowledged this reply

    
Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 30 of 280 (532196)
10-21-2009 10:46 PM
Reply to: Message 22 by Dr Jack
10-21-2009 1:12 PM


Thanks, Mr Jack.

The problem with gene duplication as a path to increased genomic complexity is that in some ways the phenomenum is its own worst enemy. When a gene duplicates its susceptibility to natural selection is (roughly) halved. A deleterious mutation to one copy is compensated for by the other copy, rather than being selected out. This results in rapid "subfunctionalisation", with two damaged genes doing the work of the undamaged original.

This means that the two subfunctionalised copies are actually constrained to their tasks (assuming the original gene was a vital one) and neither of them actually have the luxury of evolving into something novel.

This is probably why Zhang writes (under the heading of "Outstanding questions"):

How does an entirely new function originate after gene
duplication? More detailed molecular studies of model gene
families are needed to look into the emergence of novel
gene function.


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
 Message 22 by Dr Jack, posted 10-21-2009 1:12 PM Dr Jack has responded

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Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 31 of 280 (532197)
10-21-2009 10:53 PM
Reply to: Message 21 by Phage0070
10-21-2009 11:35 AM


DNA does not need to be "functional" to be selected for, so your question is irrelevant.

Okay, to return to the question. How do you see the functional, non-redundant genome growing over time?

Edited by Kaichos Man, : No reason given.


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
 Message 21 by Phage0070, posted 10-21-2009 11:35 AM Phage0070 has responded

Replies to this message:
 Message 34 by Phage0070, posted 10-21-2009 11:36 PM Kaichos Man has responded

    
Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 32 of 280 (532198)
10-21-2009 11:30 PM
Reply to: Message 25 by Blzebub
10-21-2009 4:31 PM


the bacterium has evolved the ability to survive flucloxacillin therapy, by acquiring a new gene (extra "information")

This is horizontal gene transfer (HGT), popular among microbes but rare among eukaryotes. It certainly isn't going to multiply the functional genome by nearly 8 fold per billion years, is it?

A valid answer, nonetheless.

Edited by Kaichos Man, : typo


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
 Message 25 by Blzebub, posted 10-21-2009 4:31 PM Blzebub has not yet responded

Replies to this message:
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Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 35 of 280 (532203)
10-21-2009 11:48 PM
Reply to: Message 34 by Phage0070
10-21-2009 11:36 PM


Perhaps you could be more specific with your question?

According to one researcher (and I don't know if he's right or wrong, but the maths is pretty simple so he's probably right) the size of the functional, non-reduntant genome has increased by 7.8 fold every billion years. Concentrating on the "functional, non-redundant" part, I'd like to know by which process(es) this was achieved.


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
 Message 34 by Phage0070, posted 10-21-2009 11:36 PM Phage0070 has not yet responded

Replies to this message:
 Message 36 by Dr Adequate, posted 10-22-2009 3:13 AM Kaichos Man has not yet responded

    
Kaichos Man
Member (Idle past 2654 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


(1)
Message 42 of 280 (532236)
10-22-2009 7:44 AM
Reply to: Message 40 by Dr Jack
10-22-2009 5:55 AM


Hi Mr jack.

Still reading up on lysozymes, and fascinating stuff it is. Came across this pearler and thought I'd share it with youo:

"The challenge was that evolution of lactation was not feasible, because a neonate could not obtain a survival benefit from consuming the chance secretion of a rudimentary cutaneous gland. In response, Darwin hypothesized that mammary glands evolved from cutaneous glands that were contained within the brood pouches in which some fish and other marine species keep their eggs, and provided nourishment and thus a survival advantage to eggs of ancestral species. Two hundred years after Darwin's birth, the theory of evolution by natural selection remains a cornerstone of biology, as it has withstood this and other challenges."

Doesn't it sound triumphant? Can't you see Charlie standing there, jut-jawed and resolute, beating back the hordes of bleating Creationists?

Unfortunately, the paragraph finishes:

However, it is now clear that the mammary gland did not evolve from a brood pouch [1].

Laugh!


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin
This message is a reply to:
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