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Author Topic:   The origin of new genes
crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 121 of 164 (369805)
12-14-2006 7:41 PM
Reply to: Message 120 by Wounded King
12-14-2006 5:59 PM


Re: Number Theory not in Genetics?
The former - there are functional theoretical proteins connecting all known proteins by single amino acid changes.

This message is a reply to:
 Message 120 by Wounded King, posted 12-14-2006 5:59 PM Wounded King has not replied

  
Philip
Member (Idle past 4722 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 122 of 164 (370544)
12-17-2006 11:24 PM
Reply to: Message 120 by Wounded King
12-14-2006 5:59 PM


Re: *Functional-fictitious molecules*
Shhh!
I was about to expose CF's evo-fallacy 2-fold:
1) Denying *respectable* P. Equilibria theory
2) Denying substantial mutation altogether (the foundation of the ToE) (chrom. duplic., splicing, etc.)

DISCLAIMER: No representation is made that the quality of scientific and metaphysical statements written is greater than the quality of those statements written by anyone else.

This message is a reply to:
 Message 120 by Wounded King, posted 12-14-2006 5:59 PM Wounded King has not replied

Replies to this message:
 Message 125 by crashfrog, posted 12-18-2006 12:35 AM Philip has not replied

  
Philip
Member (Idle past 4722 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 123 of 164 (370545)
12-17-2006 11:24 PM
Reply to: Message 119 by crashfrog
12-14-2006 4:50 PM


Re: Brand-Spanking-New Alleles (Again)
... there are functional theoretical proteins connecting all known proteins by single amino acid changes
Ah . another brand-spanking-new mutational gene mechanism!
Though *functional-fictitious molecules*, seem not as embarrassing as Quetzel's "all proteins are enzymes" blurp, you really need to validate (or clarify) what these functional-fictitious molecules really are (without jousting the physics math).
Recall that every amino acid has a tricky little *dynamic* electromagnetic force-vector when juxtaposed to any other molecule. A.k.a., the categorical fit of these molecules must be tested and proven to have existed, not theorized on paper.
Theoretical long-lived-mutations are all evo-trash until functional implementation is proven: Survival of the *new-molecules*, the organism, and its gene-pool must all be demonstrated to have increased (over time). To date, no such mutation has been proven.
Or to infer “single amino acid changes” --> (all?) brand-new enzyme-proteins: This can never allow for necessary raw-mutation(s) in a ToE. At least beg P. Equilibrium of latent substantial deleterious mutations *suddenly* combining into beneficial mutations, or something.
The key-word for novel genes is “substantial” mutation (gene splicing and dicing). Somehow “single amino acid changes” don’t seem to add up to substantial mutation . at all.
... Or, you may wish to rephrase (or recant) this (and that), your last two posts are a bit nonsensical.
Peradventure, someone else might come to Frog’s rescue to explain how “single amino acid changes” increment (one atom at a time) as they mutate into “brand-new alleles”!#?
Edited by Philip, : Grammar

DISCLAIMER: No representation is made that the quality of scientific and metaphysical statements written is greater than the quality of those statements written by anyone else.

This message is a reply to:
 Message 119 by crashfrog, posted 12-14-2006 4:50 PM crashfrog has replied

Replies to this message:
 Message 124 by crashfrog, posted 12-18-2006 12:30 AM Philip has replied

  
crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 124 of 164 (370573)
12-18-2006 12:30 AM
Reply to: Message 123 by Philip
12-17-2006 11:24 PM


Re: Brand-Spanking-New Alleles (Again)
Ah . another brand-spanking-new mutational gene mechanism!
Nothing new here. Just the same old mechanisms - random mutation and natural selection.
Recall that every amino acid has a tricky little *dynamic* electromagnetic force-vector when juxtaposed to any other molecule. A.k.a., the categorical fit of these molecules must be tested and proven to have existed, not theorized on paper.
Why? We know the "fit" is loose, not tight. Generally you can change up to 60% of a protein's primary structure with little to no effect on the function of its active site.
Your world, where molecules fit like keys into the locks of enzymes, is fictitious. It's make-believe. The world we actually live in is a lot fuzzier, as I've indicated.
To date, no such mutation has been proven.
What are you talking about? Hundreds of such cases exist in the literature.
.. Or, you may wish to rephrase (or recant) this (and that), your last two posts are a bit nonsensical.
No, actually, it's your posts that don't make any sense. Like this:
someone else might come to Frog’s rescue to explain how “single amino acid changes” increment (one atom at a time)
One atom at a time? Like, where do you get this stuff?
How is it that a podiatrist can be so utterly ignorant of even the most basic knowledge of biology?

This message is a reply to:
 Message 123 by Philip, posted 12-17-2006 11:24 PM Philip has replied

Replies to this message:
 Message 126 by Philip, posted 12-19-2006 7:52 PM crashfrog has replied

  
crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 125 of 164 (370575)
12-18-2006 12:35 AM
Reply to: Message 122 by Philip
12-17-2006 11:24 PM


Re: *Functional-fictitious molecules*
I haven't done either of those two things.
Is it really so hard to grapple with my points that you have to invent strawmen instead?

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 Message 122 by Philip, posted 12-17-2006 11:24 PM Philip has not replied

  
Philip
Member (Idle past 4722 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 126 of 164 (370999)
12-19-2006 7:52 PM
Reply to: Message 124 by crashfrog
12-18-2006 12:30 AM


Re: Brand-Spanking-New Alleles (Again)
How is it that a podiatrist can be so utterly ignorant of even the most basic knowledge of biology?
A.k.a. I'm an idiot? [qs] CF, your posts increasingly appear to me as fictitious ("60% of proteins"), nonsensical (like Quetzel's equating proteins with enzymes), off-topic (evading a beneficial mutation mechanism altogether), and overly derisive (above). Stop it.
Bernt's topic here is novel genes (essentially mutations that aren't deleterious). Peradventure discover a convincing *proof* of 'brand-new alleles' that have mutated. I searched the web and found about 20 (false) examples of mutation that were hyped as beneficial. (Off-topic: . Appalling and irresponsible for ”scientists’ teaching our children.)
That’s right, nothing but false examples of beneficial mutation are repeatedly hyped up by biologists as beneficial mutation! Computer scientists rightfully question the hype of “brand-new alleles” because they must debug, test, and prove their own brand-new alleles (if you will).
Do any of you really believe multiple repressed deleterious genes (in a gene pool) can become assimilated together (via NS) as a *punctuated* beneficial mutation in a gene pool. Can this *explain* 'Pre-Cambrian events' of fossil records?

DISCLAIMER: No representation is made that the quality of scientific and metaphysical statements written is greater than the quality of those statements written by anyone else.

This message is a reply to:
 Message 124 by crashfrog, posted 12-18-2006 12:30 AM crashfrog has replied

Replies to this message:
 Message 127 by crashfrog, posted 12-19-2006 11:59 PM Philip has not replied
 Message 128 by Fosdick, posted 12-20-2006 11:16 AM Philip has replied
 Message 139 by rockondon, posted 03-29-2010 4:01 PM Philip has not replied

  
crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 127 of 164 (371046)
12-19-2006 11:59 PM
Reply to: Message 126 by Philip
12-19-2006 7:52 PM


Re: Brand-Spanking-New Alleles (Again)
A.k.a. I'm an idiot?
Well, if you say so. Certainly explains it; thanks much.
CF, your posts increasingly appear to me as fictitious ("60% of proteins"), nonsensical (like Quetzel's equating proteins with enzymes), off-topic (evading a beneficial mutation mechanism altogether), and overly derisive (above). Stop it.
How can I stop what I haven't done?
Your "feeling" that my facts are wrong is not a rebuttal. Asserting that enzymes are proteins is not nonsensical, it's a fact. I've provided the "beneficial mutation mechanism" on several different occasions, but to repeat, the mechanism is random mutation - the source of all mutations.
And as for being "derisive" - I'm sorry, but I'm not prepared to accept accusations of being "derisive" from a man who, twice now, had directly accused me of being a liar but provided absolutely zero evidence to back that up.
Peradventure discover a convincing *proof* of 'brand-new alleles' that have mutated.
You're not using the word "peradventure" correctly, by the way.
I searched the web and found about 20 (false) examples of mutation that were hyped as beneficial.
We're just supposed to take your word that these were "false"?
False how? The scientists lied? They weren't actually beneficial?
Computer scientists rightfully question the hype of “brand-new alleles” because they must debug, test, and prove their own brand-new alleles (if you will).
Fascinating but irrelevant; genetics is nothing like programming computers.
As I proved several posts ago. I'm still waiting for you to address my proof. Instead you've chosen to completely evade the issue with off-topic smears against my character.
Do any of you really believe multiple repressed deleterious genes (in a gene pool) can become assimilated together (via NS) as a *punctuated* beneficial mutation in a gene pool. Can this *explain* 'Pre-Cambrian events' of fossil records?
Do you really believe that we don't know you're simply cramming words together without understanding what they mean?
I assure you, the opposite is true. Your ignorance is abundant for all to see. Are you prepared to deal with my arguments, or not?

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 Message 126 by Philip, posted 12-19-2006 7:52 PM Philip has not replied

  
Fosdick 
Suspended Member (Idle past 5499 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 128 of 164 (371124)
12-20-2006 11:16 AM
Reply to: Message 126 by Philip
12-19-2006 7:52 PM


Re: Brand-Spanking-New Alleles (Again)
Phillip, you asked:
Do any of you really believe multiple repressed deleterious genes (in a gene pool) can become assimilated together (via NS) as a *punctuated* beneficial mutation in a gene pool. Can this *explain* 'Pre-Cambrian events' of fossil records?
I'm unsure about what you mean here. Are you conflating genes with alleles, perhaps? Or, possibly, it's the notion of "deleterious genes" that confuse me, ones that "...can become assimilated together (via NS) as a 'puncuated' beneficial mutation..." What?
Without a firm grasp of your point, I would want instead to invoke S. J. Gould's argument for "exaptation" to explain how an ineffectual allele might be drawn into service by circumstantial changes that register in the gene pool. Exaptation can explain a lot, usefully displacing those grandiose notions of convergence and homoplasy.
”Hoot Mon

This message is a reply to:
 Message 126 by Philip, posted 12-19-2006 7:52 PM Philip has replied

Replies to this message:
 Message 129 by Philip, posted 02-20-2007 8:14 PM Fosdick has replied

  
Philip
Member (Idle past 4722 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 129 of 164 (386306)
02-20-2007 8:14 PM
Reply to: Message 128 by Fosdick
12-20-2006 11:16 AM


Re: New Alleles (novel genes)
Conflating alleles with genes?
--Guilty as charged?
This topic is *origin of new genes*. You 'dutifully' suggest exaptation and resurrect this thread (for me).
Exaptation is probably the only mega-ToE mechanism I could remotely consider (as a podiatrist and programmer).
The real problem with exaptation is that it seems "built in" to be viable:
1) Exaptation within 'extremely primitive' life forms seems statistically impossible (DNA codons, left-handed helixes, etc.)
2) If indeed exaptation has occurred (at all), it would have to take place in *modernish* organisms that have so many bio-systems built-in already.
3) The abused metaphor of a GPS auto-navigation NS-mutating into "driver-intelligence" is too metaphysical and religious for me to accept in my materialistic logic.
(Hopefully, we'll discuss more on this exaptation principle)

This message is a reply to:
 Message 128 by Fosdick, posted 12-20-2006 11:16 AM Fosdick has replied

Replies to this message:
 Message 130 by Fosdick, posted 02-21-2007 11:20 AM Philip has replied

  
Fosdick 
Suspended Member (Idle past 5499 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 130 of 164 (386374)
02-21-2007 11:20 AM
Reply to: Message 129 by Philip
02-20-2007 8:14 PM


Alleles and Exaptation
Conflating alleles with genes?
--Guilty as charged?
Well, of course alleles function as genes, but genes do not function as alleles. Try this:
allele : gene :: oak : tree.
Exaptation is probably the only mega-ToE mechanism I could remotely consider (as a podiatrist and programmer).
The real problem with exaptation is that it seems "built in" to be viable:
1) Exaptation within 'extremely primitive' life forms seems statistically impossible (DNA codons, left-handed helixes, etc.)
2) If indeed exaptation has occurred (at all), it would have to take place in *modernish* organisms that have so many bio-systems built-in already.
3) The abused metaphor of a GPS auto-navigation NS-mutating into "driver-intelligence" is too metaphysical and religious for me to accept in my materialistic logic.
(Hopefully, we'll discuss more on this exaptation principle)
Maybe someone put a Mickey my morning coffee, but I can't make any sense of this.
”HM

This message is a reply to:
 Message 129 by Philip, posted 02-20-2007 8:14 PM Philip has replied

Replies to this message:
 Message 131 by Philip, posted 02-21-2007 11:06 PM Fosdick has not replied
 Message 133 by RAZD, posted 02-22-2007 7:27 AM Fosdick has not replied

  
Philip
Member (Idle past 4722 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 131 of 164 (386468)
02-21-2007 11:06 PM
Reply to: Message 130 by Fosdick
02-21-2007 11:20 AM


Did the Pharyngeal Slits 'Burst-Mutate' into Gill Slits?
... Nor can I make sense of any of your caffeinated grammar, HM ...
'Straining knats' (alleles vs genes) is off topic anyway. (I'm not trying to intimidate you HM; I'm interested in your frank logic ... regardless of how loopy the grammar gets).
I'm interested in why you, Gould, or another person, buys into exaptation. Can it be validated with any statistical probability whatsoever?
You might wish to elaborate more on when the 'exapted' gene (or allele) is new or not.
Awesome! Did the complex pharyngeal slits really mutate into complex gill slits?
Sounds like a couple thousand repressed deleterious mutations expressing themselves together advantageously. Cool! Now what are the odds, really?

DISCLAIMER: No representation is made that the quality of scientific and metaphysical statements written is greater than the quality of those statements written by anyone else.

This message is a reply to:
 Message 130 by Fosdick, posted 02-21-2007 11:20 AM Fosdick has not replied

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


(1)
Message 132 of 164 (386499)
02-22-2007 6:01 AM
Reply to: Message 131 by Philip
02-21-2007 11:06 PM


Re: Did the Pharyngeal Slits 'Burst-Mutate' into Gill Slits?
Awesome! Did the complex pharyngeal slits really mutate into complex gill slits?
Um, no. Did anyone ever say they did? I think you'll find that as soon as pharyngeal slits appeared in proto-chordates they were gill slits. Over time some vertebrate phyla developed which no longer required the gill slits for respiration although they are still sometimes inaccurately referred to as gill slits or branchial slits, even though they aren't associated with gills anymore and are not necessarily ever true slits, many structures which develop from the surrounding pharyngeal arches were retained and modified.
Sounds like a couple thousand repressed deleterious mutations expressing themselves together advantageously. Cool! Now what are the odds, really?
The odds are probably higher than of you ever making a post which accurately represents any aspect of evolutionary biology. You still seem to have no idea what evolutionary theory posits, no wonder you think it is a fairy tale, the version of it you are familiar with is but it was one made up by creationists.
TTFN,
WK
P.S. How complex is a slit? Seriously. Some of the accessory structures may be complex but a slit itself is probably about as uncomplex a structure as you can come across.
Edited by Wounded King, : No reason given.

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 Message 131 by Philip, posted 02-21-2007 11:06 PM Philip has not replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 133 of 164 (386508)
02-22-2007 7:27 AM
Reply to: Message 130 by Fosdick
02-21-2007 11:20 AM


Re: Alleles and Exaptation
Well, of course alleles function as genes, but genes do not function as alleles. Try this:
allele : gene :: oak : tree.
You forgot one ...
phillip : troll

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This message is a reply to:
 Message 130 by Fosdick, posted 02-21-2007 11:20 AM Fosdick has not replied

  
xXGEARXx
Member (Idle past 5120 days)
Posts: 41
Joined: 08-17-2006


Message 134 of 164 (550384)
03-15-2010 10:55 AM
Reply to: Message 114 by jerker77
12-12-2006 8:19 PM


Re: New Genes?
As for creating matter of our own that is a minor problem with nuclear fission and designing life man have been doing all since she settled in the Indus valley.
I cetainly would not call creating matter a "minor" problem. I do think someday we will be creating our own matter. The designing life part doesn't make sense to me. The closest we come to designing life is robots. Someday, I think they will be self aware and run the show-if we allow it to happen-and we will.

This message is a reply to:
 Message 114 by jerker77, posted 12-12-2006 8:19 PM jerker77 has not replied

Replies to this message:
 Message 135 by Wounded King, posted 03-15-2010 11:12 AM xXGEARXx has replied

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


Message 135 of 164 (550390)
03-15-2010 11:12 AM
Reply to: Message 134 by xXGEARXx
03-15-2010 10:55 AM


Re: New Genes?
I can't imagine you are likely to get much of a response for a post from 4 years ago, but who knows, maybe in another 4 years jerker77 will come by and respond.
TTFN,
WK

This message is a reply to:
 Message 134 by xXGEARXx, posted 03-15-2010 10:55 AM xXGEARXx has replied

Replies to this message:
 Message 136 by xXGEARXx, posted 03-16-2010 7:24 PM Wounded King has not replied

  
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