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Author Topic:   Adding information to the genome.
Kaichos Man
Member (Idle past 4488 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 121 of 280 (533831)
11-03-2009 5:42 AM
Reply to: Message 119 by Huntard
11-03-2009 4:44 AM


Re: False Logic again: the ear development is sequential
And as longs as that isn't too severe, it does not impede the organism and will thuis be given to its offspring. Who can then have a mutation that makes it all nice and straight again.
As you well know, the rule with stepwise mutations is that each must confer a survival advantage (in order to become fixed in the population). An overbite or underbite, severe or not, is never going to be a survival advantage.
What you're suggesting is reminiscent of Kimura's "survival of the luckiest". Though this particular cynodont would have to be extra lucky to a) survive being selected out with a misshapen jaw, and b) have progeny that possess a compensatory mutation.

"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 119 by Huntard, posted 11-03-2009 4:44 AM Huntard has replied

Replies to this message:
 Message 122 by Huntard, posted 11-03-2009 7:12 AM Kaichos Man has not replied
 Message 125 by lyx2no, posted 11-03-2009 3:27 PM Kaichos Man has not replied
 Message 128 by Parasomnium, posted 11-04-2009 2:51 AM Kaichos Man has replied

  
Huntard
Member (Idle past 2295 days)
Posts: 2870
From: Limburg, The Netherlands
Joined: 09-02-2008


(1)
Message 122 of 280 (533845)
11-03-2009 7:12 AM
Reply to: Message 121 by Kaichos Man
11-03-2009 5:42 AM


Re: False Logic again: the ear development is sequential
Kaichos Man writes:
As you well know, the rule with stepwise mutations is that each must confer a survival advantage (in order to become fixed in the population). An overbite or underbite, severe or not, is never going to be a survival advantage.
But if it is "neutral" (not disadvantageous or advantageous), then it will still be passed on to the offspring. If they then have a mutation that makes it beneficial, you've got what you want.
What you're suggesting is reminiscent of Kimura's "survival of the luckiest".
No it isn't. Luck has nothing to do with it.
Though this particular cynodont would have to be extra lucky to a) survive being selected out with a misshapen jaw...
There's no selection at all, if it isn't impeding it, it's passed along.
...b) have progeny that possess a compensatory mutation.
Yes, the offspring would have have a mutation that makes it right again, tthis doesn't have to be the immediate descendant though, as long as there's nothing to impede the creature, it will hapily pass along the "crooked" jaw.

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This message is a reply to:
 Message 121 by Kaichos Man, posted 11-03-2009 5:42 AM Kaichos Man has not replied

  
Percy
Member
Posts: 22393
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 123 of 280 (533850)
11-03-2009 8:01 AM
Reply to: Message 116 by Kaichos Man
11-03-2009 4:24 AM


Re: Lactose added to genome is added information
Kaichos Man writes:
So the shrinkage of the malleus and incus and their migration back into the inner ear didn't happen through gene expression?
This is a public thread, not a private chat room with just you and me. Everyone can read what everyone says, and so, for example, I saw what you said in response to NosyNed's recipe analogy: "Yes, that seems to be what Percy's getting at."
Clearly you played dumb with me, but then you forgot to maintain the ruse in reply to NosyNed. So given that you really did understand what I meant in Message 114, why don't you try again?
--Percy

This message is a reply to:
 Message 116 by Kaichos Man, posted 11-03-2009 4:24 AM Kaichos Man has replied

Replies to this message:
 Message 129 by Kaichos Man, posted 11-04-2009 6:29 AM Percy has replied

  
Percy
Member
Posts: 22393
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 124 of 280 (533851)
11-03-2009 8:07 AM
Reply to: Message 118 by Kaichos Man
11-03-2009 4:38 AM


Re: Parameter specification
Kaichos Man writes:
Yes, that seems to be what Percy's getting at. However, we are learning more and more about DNA every year. It was only about five years ago that scientists were suggesting only 2% of the human genome codes for anything. Now, with the discovery of regulatory pathways etc. the figure seems to have grown to around 10%.
So I wouldn't be surprised if the "blueprint" does exist, and we just haven't worked out how to read it yet.
Ignoring your errors concerning the history of genetics, your argument seems to be that future discoveries will prove you right, a sort of, "I am too right and someday you'll see," type of argument.
Is there any evidence currently in hand supporting what you believe? Or do you reach all your conclusions using information you don't have?
--Percy

This message is a reply to:
 Message 118 by Kaichos Man, posted 11-03-2009 4:38 AM Kaichos Man has replied

Replies to this message:
 Message 130 by Kaichos Man, posted 11-04-2009 7:00 AM Percy has seen this message but not replied

  
lyx2no
Member (Idle past 4716 days)
Posts: 1277
From: A vast, undifferentiated plane.
Joined: 02-28-2008


(2)
Message 125 of 280 (533930)
11-03-2009 3:27 PM
Reply to: Message 121 by Kaichos Man
11-03-2009 5:42 AM


Re: False Logic again: the ear development is sequential
An overbite or underbite, severe or not, is never going to be a survival advantage.
Okay, if you say so.
Edited by lyx2no, : Add Mr. Gomphotheres
Edited by lyx2no, : Stack-um like Pringles.

It's not the man that knows the most that has the most to say.
Anon

This message is a reply to:
 Message 121 by Kaichos Man, posted 11-03-2009 5:42 AM Kaichos Man has not replied

Replies to this message:
 Message 126 by RAZD, posted 11-03-2009 9:32 PM lyx2no has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 126 of 280 (533955)
11-03-2009 9:32 PM
Reply to: Message 125 by lyx2no
11-03-2009 3:27 PM


under over - where's the right side?
Hi lyx2no2, how are you doing these days?
An overbite or underbite, severe or not, is never going to be a survival advantage.
Okay, if you say so.
One can also compare the variation within a population to show that they could seesaw back and forth as one grew and then another shrank. These minor variations would be seen at the population\species level, while the overall trend is visible in the tree of descent.
We also have the evolution of the teeth going on at about the same time, so this may be what drives the change in the jaw bones - making room for the new kinds of teeth that are more fit for consumption.
Enjoy.
ps - could you (or a mod) reduce the picture sizes or stack them? I can't see the right side of the page.

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by our ability to understand
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This message is a reply to:
 Message 125 by lyx2no, posted 11-03-2009 3:27 PM lyx2no has replied

Replies to this message:
 Message 127 by lyx2no, posted 11-03-2009 10:28 PM RAZD has seen this message but not replied

  
lyx2no
Member (Idle past 4716 days)
Posts: 1277
From: A vast, undifferentiated plane.
Joined: 02-28-2008


(2)
Message 127 of 280 (533956)
11-03-2009 10:28 PM
Reply to: Message 126 by RAZD
11-03-2009 9:32 PM


Re: under over - where's the right side?
Hi lyx2no2, how are you doing these days?
Well, my stupid, theivin', pot smoking cousin is destroying his family and I keep getting dragged off to Baltimore in my mum's vain attempt to help her sister survive the situation. I've never missed a day of school in my life until now, and now I'm missing so many I won't likely be getting the top grades I've always been brought up to understand are the most important thing I can do for the future. I was thinking that for my upcoming birthday a smallish comet could take out Baltimore; however, upon reflection, in my new-found maturity, I've come to believe that that may be a tad self-centered. Or maybe it's some of your strength rubbing off on me, thanks. And though I don't have a god to beseech or belief that blessings have any magic value, bless you.

One can also compare the variation within a population to show that they could seesaw back and forth as one grew and then another shrank. These minor variations would be seen at the population\species level, while the overall trend is visible in the tree of descent.
That is basically how I see it: little mutations happening here and there throughout the population. None of them having much of an effect. This one changing the timing of this; that one changing the timing of that. The mixing and matching widening the bell curve of some parameter or another; i.e., instead of budgies weighing between 22.254 grams and 37.886 grams, now they weight between 21.969 grams and 38.112 grams. Then in one part of their territory a new, predator lizard makes the scene and likes wee budgies better then hefty ones; while in another part of their territory there's a prolonged drought where only the wee budgies can find enough to eat. And blah, blah, blah No need for coordinated genetic mutations. A random lot of mutations with selection of the ones that suit the situation best will do.

And I took care of that picture thingy too.
Edited by lyx2no, : Typo.
Edited by lyx2no, : My poor education catching up with me.

It's not the man that knows the most that has the most to say.
Anon

This message is a reply to:
 Message 126 by RAZD, posted 11-03-2009 9:32 PM RAZD has seen this message but not replied

  
Parasomnium
Member
Posts: 2224
Joined: 07-15-2003


(1)
Message 128 of 280 (533962)
11-04-2009 2:51 AM
Reply to: Message 121 by Kaichos Man
11-03-2009 5:42 AM


Re: False Logic again: the ear development is sequential
An overbite or underbite, severe or not, is never going to be a survival advantage.
I wouldn't be too sure of that. Hypothetically, if all else fails - which it doesn't, as lyx2no's pictures show - an overbite could be subject to sexual selection.
Usually, when you have to resort to an argument from incredulity, there's something you have overlooked.

"Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.

This message is a reply to:
 Message 121 by Kaichos Man, posted 11-03-2009 5:42 AM Kaichos Man has replied

Replies to this message:
 Message 131 by Kaichos Man, posted 11-04-2009 7:05 AM Parasomnium has not replied

  
Kaichos Man
Member (Idle past 4488 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 129 of 280 (533981)
11-04-2009 6:29 AM
Reply to: Message 123 by Percy
11-03-2009 8:01 AM


Re: Lactose added to genome is added information
Clearly you played dumb with me, but then you forgot to maintain the ruse in reply to NosyNed.
Anyone who knows me will assure you that I don't have to play dumb
So given that you really did understand what I meant in Message 114, why don't you try again?
The fact that I understood it doesn't mean that I considered it an adequate answer. The "recipe" doesn't specify shape, size or orientation- so I pressed you to say what does.

"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 123 by Percy, posted 11-03-2009 8:01 AM Percy has replied

Replies to this message:
 Message 133 by Percy, posted 11-04-2009 9:14 AM Kaichos Man has replied

  
Kaichos Man
Member (Idle past 4488 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 130 of 280 (533985)
11-04-2009 7:00 AM
Reply to: Message 124 by Percy
11-03-2009 8:07 AM


Re: Parameter specification
Is there any evidence currently in hand supporting what you believe? Or do you reach all your conclusions using information you don't have?
Well it's funny you should ask that, Percy. For better or worse, I'm about to radically change my position. (Takes a deep breath).
What if the development of the mammalian jaw, far from being too complex for evolutionary processes, is actually too simple to require them? What if the pattern for the mammalian jaw is already in the genome, and requires very few mutations to be activated?
"Is he mad?", I hear you ask. Consider this:
"Therefore, the `Dlx codes' appear to regionalize the jaw primordium such that Dlx1/2 regulate upper jaw development, while Dlx5/6 confer the lower jaw fate. Towards identifying the genetic pathways downstream of Dlx5/6, we compared the gene expression profiles of the wild-type and Dlx5/6-/- mouse mandibular arch (prospective lower jaw). We identified 20 previously unrecognized Dlx5/6-downstream genes, of which 12 were downregulated and 8 upregulated in the mutant.
The full paper is available here:
Dlx genes pattern mammalian jaw primordium by regulating both lower jaw-specific and upper jaw-specific genetic programs | Development | The Company of Biologists
Okay, what do we have here? It appears two genes, Dlx5 and Dlx6 are largely responsible for lower jaw development in mammals. Fascinatingly, when both are inactivated, we see a marked downstream effect on no fewer than 20 genes, and of those genes 12 are downregulated and 8 upregulated. Now, I am obviously not saying that the downregulation and upregulation applies directly to the shrinking of the malleus and incus and the growth of the dentary, but it does suggest that such a twofold effect is possible. It certainly shows that widespread effects on jaw development are possible with very few mutations, and that the "compensatory" effect needed may actually be built in.
So where does that leave us? It suggests that the development of the mammalian jaw may rely on simple loss-of-function mutations to existing control genes. Which makes the whole process so simple that one might expect it to have occurred more than once. And that appears to be the case:
"We report a Cretaceous trechnotherian mammal with an ossified Meckel’;s cartilage in the adult, showing that homoplastic evolution of the DMME occurred in derived therian mammals, besides the known cases of eutriconodonts. The mandible with ossified Meckel’;s cartilage appears to be paedomorphic. Reabsorption of embryonic Meckel’;s cartilage to disconnect the ear ossicles from the mandible is patterned by a network of genes and signaling pathways. This fossil suggests that developmental heterochrony and gene patterning are major mechanisms in homoplastic evolution of the DMME."
(Luo et al 2007)
DMME refers to the mammalian middle ear. Homoplasy, or convergence, is mentioned often in connection to mammalian middle ear and jaw development. Exactly what you would expect if the information for the organs was already in the genome, waiting for the very few mutations needed for activation.

"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 124 by Percy, posted 11-03-2009 8:07 AM Percy has seen this message but not replied

Replies to this message:
 Message 132 by Wounded King, posted 11-04-2009 8:52 AM Kaichos Man has replied

  
Kaichos Man
Member (Idle past 4488 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 131 of 280 (533987)
11-04-2009 7:05 AM
Reply to: Message 128 by Parasomnium
11-04-2009 2:51 AM


Re: False Logic again: the ear development is sequential
an overbite could be subject to sexual selection.
That is a most disturbing notion, given your avatar

"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

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 Message 128 by Parasomnium, posted 11-04-2009 2:51 AM Parasomnium has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(1)
Message 132 of 280 (533998)
11-04-2009 8:52 AM
Reply to: Message 130 by Kaichos Man
11-04-2009 7:00 AM


Gene networks in development
It suggests that the development of the mammalian jaw may rely on simple loss-of-function mutations to existing control genes.
No it doesn't. How does a double knockout of Dlx5 and 6 suggest that loss-of-function mutations are what are responsible? If you think that what the double-knockout produces resembles an ancestral phenotype then you are arguing for a chain of gain-of-function mutations. If not then where do the genes whose function was lost exist? Have they been expunged from the genetic record when they lost their function? Should we expect to see them in animals with jaw structures considered more ancestral?
It certainly shows that widespread effects on jaw development are possible with very few mutations, and that the "compensatory" effect needed may actually be built in.
I agree with you here, I just think that what has 'built in' the compenstory elements is the duplicative evolutionary origin of the Dlx network, neither the DLx5 or Dlx6 knockout has as severe a phenotype as the double mutant. indeed the single mutant knockouts show a great deal of reduncdancy with them both regulating similar sets of downstream gene required for mandibular development in branchial arch 1.
I would also point out that while null mutants, the naturally occuring equivalent of a knockout mouse, can be the result of single mutations they are one of the more radical levels, and certainly a study across species and phyla using phylogenetics does not show a pattern of progressive gene loss in most cases. Rather what we see are generally small scale nucleotide level changes, a few larger effect indels and some rare but very large effect chromosomal genomic level mutations. What you seem to want to ignore is that small single nucleotide level changes can also have widespread developmental effects which need not be detrimental in the way that the double knockouts, and indeed pretty much all the single knockouts were, i.e. causing the mice to die before or soon after birth.
DMME refers to the mammalian middle ear. Homoplasy, or convergence, is mentioned often in connection to mammalian middle ear and jaw development. Exactly what you would expect if the information for the organs was already in the genome, waiting for the very few mutations needed for activation.
Except there is no evidence for such pre-existing information. It is well worth noting that morphological convergence is a very distinct thing from genetic convergence. A marsupial and a placental may appear to share a gross morphology but genetic analysis will tend to show that the placental more closely resembles other placentals genetically. Similarly some elements of the development of the independent middle ear are thought to have arisen more than once, but there is no evidence that the same mutations gave rise to them.
I'm also not clear how such 'activation' is consistent with your previous loss-of-function characterisation of the process. Do you see activation as the result of the removal of repressive genes or driven by front-loaded mutation causing a new gene/function to be expressed. These would seem to predict different patterns in the guided genetic evolution of the DNA. Or do you think it may be an inconsistent mixture of multiple different mechanisms?
TTFN,
WK
Edited by Wounded King, : No reason given.

This message is a reply to:
 Message 130 by Kaichos Man, posted 11-04-2009 7:00 AM Kaichos Man has replied

Replies to this message:
 Message 135 by Kaichos Man, posted 11-05-2009 6:41 AM Wounded King has replied

  
Percy
Member
Posts: 22393
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 133 of 280 (534003)
11-04-2009 9:14 AM
Reply to: Message 129 by Kaichos Man
11-04-2009 6:29 AM


Re: Lactose added to genome is added information
Kaichos Man writes:
The fact that I understood it doesn't mean that I considered it an adequate answer. The "recipe" doesn't specify shape, size or orientation- so I pressed you to say what does.
Normally I don't demur on requests like this, but I've explained this several times in this very thread, and so have others. I think you've convinced me that this isn't an act.
--Percy

This message is a reply to:
 Message 129 by Kaichos Man, posted 11-04-2009 6:29 AM Kaichos Man has replied

Replies to this message:
 Message 134 by Kaichos Man, posted 11-05-2009 6:10 AM Percy has replied

  
Kaichos Man
Member (Idle past 4488 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 134 of 280 (534130)
11-05-2009 6:10 AM
Reply to: Message 133 by Percy
11-04-2009 9:14 AM


Re: Lactose added to genome is added information
Normally I don't demur on requests like this
Percy, it's not a request, it's an explanation. You accused me of "playing dumb", and subsequently revealing myself in an exchange with NosyNed. I pointed out that I was not playing dumb, I understood your answer perfectly, and I felt that Ned's suggestion of a "recipe" rather than a "blueprint" pretty well summed up what you were saying.
Understanding an explanation does not imply its acceptance. The fact remains that your answer(s) pertain more to what genes don't do, leaving the question of specification of the size, shape and orientation of the jaw bones unanswered.
I think you've convinced me that this isn't an act
It never was.

"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 133 by Percy, posted 11-04-2009 9:14 AM Percy has replied

Replies to this message:
 Message 137 by Percy, posted 11-05-2009 9:53 AM Kaichos Man has replied
 Message 144 by Dr Adequate, posted 11-05-2009 4:54 PM Kaichos Man has not replied

  
Kaichos Man
Member (Idle past 4488 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 135 of 280 (534132)
11-05-2009 6:41 AM
Reply to: Message 132 by Wounded King
11-04-2009 8:52 AM


Re: Gene networks in development
How does a double knockout of Dlx5 and 6 suggest that loss-of-function mutations are what are responsible?
Actually, given that homeobox genes are being discussed here, loss-of-function was a bad choice of terms. Modification-of-function would be more appropriate.
Except there is no evidence for such pre-existing information
I don't mean "pre-existing" in the sense that the phenotype has existed before. I mean that the phenotype already exists in the form of a possible permutation of the downstream genes, just waiting for the appropriate modification of Dlx5 and/or 6.
I agree with you here, I just think that what has 'built in' the compenstory elements is the duplicative evolutionary origin of the Dlx network, neither the DLx5 or Dlx6 knockout has as severe a phenotype as the double mutant.
I was talking more about the "compensatory effect" needed for simultaneously growing the dentary while shrinking the malleus and incus. The fact that modification of Dlx5/6 resulted in upregulation of some genes and downregulation of others suggests that this is possible.
Or do you think it may be an inconsistent mixture of multiple different mechanisms?
I'm suggesting that the mammalian jaw may be the result of mutational modification of Dlx5 and Dlx6

"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 132 by Wounded King, posted 11-04-2009 8:52 AM Wounded King has replied

Replies to this message:
 Message 136 by Wounded King, posted 11-05-2009 7:12 AM Kaichos Man has replied

  
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