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Author Topic:   The origin of new genes
Philip
Member (Idle past 4723 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 106 of 164 (368586)
12-08-2006 11:19 PM
Reply to: Message 105 by RAZD
12-07-2006 8:53 PM


Re: no ”new gene-data’
Without going *too deep* into your oversimplified 'brand-new allele' magic (... and, especially after CF's spastic IDist *awakening*),
...Am I to read that 3 page post with all its references, assimilate all that verbage, defend Behe, and then concede to you that statistical impossibility (A.K.A. improbability) that 'advantageous mutation' has somehow been violated in Miller's 2 experiments?
Consider that the motive of this topic is really:
"New Alleles == Advantageous Mutation for the Gene-Pool" (though you're probably in denial on this point)
Now, if the *master* Gene-Pool (program) of Miller's bacteria-populaton is coded to allow variants of alleles being removed and replaced like sentences in MS-Word (comparable to junk-DNA), thats just NS and nothing new.
So what if lactase (or galactosidase) selection *appears* as "adaptive mutation", as a scientist you should suspect that raw sporadic advantageous mutation is impossible in the robust alleles of the *master* Gene-Pool program.
Many Bacterial genomes have always had pre-built sophisticated adaptive mechanisms of robust alleles mastering mutable alleles (junk DNA, hot spots, etc.)
Again, I see nothing new here (at all).
Edited by Philip, : Typos and disclaimer

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 105 by RAZD, posted 12-07-2006 8:53 PM RAZD has replied

Replies to this message:
 Message 107 by RAZD, posted 12-09-2006 12:02 AM Philip has replied

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


Message 107 of 164 (368595)
12-09-2006 12:02 AM
Reply to: Message 106 by Philip
12-08-2006 11:19 PM


Re: no ”new gene-data’
......Am I to read that 3 page post with all its references, assimilate all that verbage, ...
Yes, if you want to debate in good faith.
Again, I see nothing new here (at all).
Denial of evidence that contradicts your opinion is not faith, it is
quote:
delusion” -noun
1. an act or instance of deluding.
2. the state of being deluded.
3. a false belief or opinion: delusions of grandeur.
4. Psychiatry. a fixed false belief that is resistant to reason or confrontation with actual fact: a paranoid delusion.
Enjoy.

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This message is a reply to:
 Message 106 by Philip, posted 12-08-2006 11:19 PM Philip has replied

Replies to this message:
 Message 109 by Philip, posted 12-09-2006 1:56 AM RAZD has replied

  
Philip
Member (Idle past 4723 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 108 of 164 (368604)
12-09-2006 12:49 AM
Reply to: Message 104 by Modulous
12-07-2006 8:24 PM


Re: "Truly Lying About Brand New Alleles"
Please bear my unpoliteness considering his curious slanders against me ("You're not a scientist", etc). I'm a 50 y/o podiatrist (chiropodist in the UK). I highly respect CF's persistence, intelligence, and thoughtful-feedback (before God and man). I'll gladly label myself a "stupid liar" if it'll please CF.
You I believe. Basic (more than Paschal and Fortran) seemed more popular language for game creation on Commodores in the early 80's.
Also, your posts have always seemed a tad bit more brilliant, modest, and interceding for others (e.g., for CF). If I offended CF, consider this a formal apology for him, that I stand corrected and must now concede mega-points in this debate. I'm a bold-faced blatant liar. There it is.
Our contention stems from my unfortunate hypothesis that each gene-pool is an extremely robust *software*, a master-program to be sure:
1) Robust genes exist until their robust portions mutate into *new (crappy) alleles*. Then robustness breaks down, if reproduced and radiated into the gene-pool, extinction results
2) Non-robust alleles (junk-DNA, mutation hot-spots, plasmids, etc.) with all the recombinant mechanisms mentioned (e.g., by Berndt in post 1) are never to be regarded as 'new alleles' proper. (As new sentences in MS-Word are never considered new bytes of info within that App)

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 104 by Modulous, posted 12-07-2006 8:24 PM Modulous has not replied

Replies to this message:
 Message 111 by crashfrog, posted 12-10-2006 6:07 PM Philip has replied

  
Philip
Member (Idle past 4723 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 109 of 164 (368609)
12-09-2006 1:56 AM
Reply to: Message 107 by RAZD
12-09-2006 12:02 AM


Ah, that new allele notion again...
Beneficial Mutations, advantageous mutants, novel-genes, freak-codons, hopeful-monsters, molecules-to-man. They just don't stop transforming the world around us, do they now?
I ("in good faith") read what I read (in my paranoiac transformation as you've accused me) and repeat the fallacies that I perceived on that seemingly gross yet pointless thread. You’re welcome to refute these specifically or bash me as totally deluded.
Philip writes:
. lactase (or galactosidase) selection *appears* as "adaptive mutation", as a scientist you should suspect that raw sporadic advantageous mutation is impossible in the robust alleles of the *master* Gene-Pool program.
Many Bacterial genomes have always had pre-built sophisticated adaptive mechanisms of robust alleles mastering mutable alleles (junk DNA, hot spots, etc.)
Again, I see nothing new here (at all).
The key words are: “pre-built”, “always”, and “robust alleles”. Which of these do you wish to falsify as newly begotten genes or beneficial mutations ?
------------------------------------------------------------------
Btw: Are you still preaching at me that alleles are new and ever-transforming; ... still searching for that ubiquitous *new allele*, that advantageous mutation that somehow constitutes a *missing link*?
Good luck on your quest; despite the improbability of finding one, it seems that this somehow means a lot to you. Why are you chasing the wind?
------------------------------------------------------------------
2Th 2:11 And for this cause God shall send them strong delusion, that they should believe a lie and be damned

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 107 by RAZD, posted 12-09-2006 12:02 AM RAZD has replied

Replies to this message:
 Message 110 by RAZD, posted 12-09-2006 8:02 AM Philip has not replied

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


Message 110 of 164 (368621)
12-09-2006 8:02 AM
Reply to: Message 109 by Philip
12-09-2006 1:56 AM


Re: Ah, that new allele notion again...
First off I find statements like:
Message 108
Please bear my unpoliteness considering his curious slanders against me ("You're not a scientist", etc). I'm a 50 y/o podiatrist (chiropodist in the UK). I highly respect CF's persistence, intelligence, and thoughtful-feedback (before God and man).
To be totally irrelevant. First off they are an argument from authority, except here it isn't substantiated except by your say-so.
And it's a way of saying "look who I am, my argument must be good" ... or trying to anyway.
What you are on these forums is what you post and nothing more.
I ("in good faith") read what I read (in my paranoiac transformation as you've accused me)
I said "Denial of evidence that contradicts your opinion is not faith, it is delusion" -- you are free to choose the definition you think suits you best, if you wish to wear those shoes. I've only pointed out the consequences of continued denial.
... and repeat the fallacies that I perceived on that seemingly gross yet pointless thread. You’re welcome to refute these specifically or bash me as totally deluded.
The key words are: “pre-built”, “always”, and “robust alleles”. Which of these do you wish to falsify as newly begotten genes or beneficial mutations ?
The issue is that a gene was deleted. The function of the gene ceased. There was no “pre-built” response that just started up into operation to replace the function: why? it did not exist in the form necessary to do so.
It was not a copy section of the previous gene that mutated either, so it was not a matter of “robust alleles” hiding in wait for such an opportunity.
The section of another gene that mutated filled one of the two functions necessary to replace the system disrupted by the deletion of the gene in question.
It did not happen right away, because it had to change.
Neither does “always” apply, as not all of the bacteria in the study evolved the new gene, mostly they died.
After the first mutation there was a second that replaced another part of the original system to metabolize lactose, thus regaining the original ability with a different system than existed before.
Now you can hand wave, and label things with new terms of your making, but the fact remains: a gene mutated, it was different than it was before mutation, it increased the ability of the bacteria to survive.
More to the point, it replaced information that had been removed.
Therefore it added information.
In order to show that information was not added, you have to now show that it was not lost in the experiment: that all the bacteria survived on lactose even with the destroyed gene.
Good luck on your quest; despite the improbability of finding one, it seems that this somehow means a lot to you. Why are you chasing a phantom?
Enjoy.
ps - calling a post "that seemingly gross yet pointless thread" while not making any attempt to show that this is the case, or in any way addressing a single point on the post to even show you read it is intellectual dishonesty.
Edited by RAZD, : added ps

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This message is a reply to:
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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 111 of 164 (368855)
12-10-2006 6:07 PM
Reply to: Message 108 by Philip
12-09-2006 12:49 AM


Re: "Truly Lying About Brand New Alleles"
You I believe. Basic (more than Paschal and Fortran) seemed more popular language for game creation on Commodores in the early 80's.
I guess I don't understand. You don't think I could have had my hands on a Pascal development environment when I was 6? You don't think I could have figured out how to write simple programs with it?
It's just not clear to me from what basis you're calling me a liar - other than a complete and total inability, apparently, to grapple with my actual points. And as much as you'd like to present yourself as the aggrieved party in all of this, you'll find absolutely no post by myself where I accused you of not being a podiatrist or something.
If you're done with your little meltdown, could you return to my post and actually address it's points? You've done nothing but repeat the exact same contentions that I obliterated several posts ago. If there was something you didn't understand, could you quote that part and ask for explanation? Because at this point I simply can't see how there's any room for disagreement except for willing ignorance on your part.

This message is a reply to:
 Message 108 by Philip, posted 12-09-2006 12:49 AM Philip has replied

Replies to this message:
 Message 113 by AnswersInGenitals, posted 12-12-2006 7:51 PM crashfrog has not replied
 Message 115 by Philip, posted 12-13-2006 12:13 AM crashfrog has replied

  
xXGEARXx
Member (Idle past 5121 days)
Posts: 41
Joined: 08-17-2006


Message 112 of 164 (369372)
12-12-2006 6:11 PM
Reply to: Message 46 by jerker77
09-26-2006 5:08 PM


Re: New Genes?
Nature also lack foresight as the phenomenon of extinction well shows and the same would be true of a designer. I can see no comfort in believing in a creator that either is a pathologic sadist or a complete moron.
So true. What a joke. I mean I know you could form your own elements and create life arranging everything in just the right order.

This message is a reply to:
 Message 46 by jerker77, posted 09-26-2006 5:08 PM jerker77 has replied

Replies to this message:
 Message 114 by jerker77, posted 12-12-2006 8:19 PM xXGEARXx has replied

  
AnswersInGenitals
Member (Idle past 151 days)
Posts: 673
Joined: 07-20-2006


Message 113 of 164 (369392)
12-12-2006 7:51 PM
Reply to: Message 111 by crashfrog
12-10-2006 6:07 PM


Put-on?
Come on guys! Can't you tell when your leg is being pulled? Didn't Phillip's advanced degree, an MSBS give you a hint? And from Barry University no less (named in honor of Barry Hall?) Or that at age 50 he has been a podiatrist for 15 years. Like it would take anyone 'til age 35 to learn how to diagnose feet. I think you guys invented this 'Phillip' because you miss Faith so much.

This message is a reply to:
 Message 111 by crashfrog, posted 12-10-2006 6:07 PM crashfrog has not replied

Replies to this message:
 Message 117 by RAZD, posted 12-14-2006 1:32 AM AnswersInGenitals has not replied

  
jerker77
Inactive Member


Message 114 of 164 (369398)
12-12-2006 8:19 PM
Reply to: Message 112 by xXGEARXx
12-12-2006 6:11 PM


Re: New Genes?
I was not referring to particle physics but to the process that has given us all the diversity of life. Natural selection is a poor designer and this nature bear ample proof of, but a designer it is none the less. Mindless and blind but with a logic of its own, if it can proliferate and procreate let it dominate!
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.

This message is a reply to:
 Message 112 by xXGEARXx, posted 12-12-2006 6:11 PM xXGEARXx has replied

Replies to this message:
 Message 134 by xXGEARXx, posted 03-15-2010 10:55 AM jerker77 has not replied

  
Philip
Member (Idle past 4723 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 115 of 164 (369437)
12-13-2006 12:13 AM
Reply to: Message 111 by crashfrog
12-10-2006 6:07 PM


Re: More Bold-Face Lies: Brand New Alleles
Alright CF, I verily denounce the lying part (about your Pascal programming at the age of 6, we all believe you) and appreciate your patience with me. I stand corrected. Profuse apologies are rendered. Also note my disclaimer.
Btw, I was banned from posting privileges on all EvC science forums for being "nonsensical" against some very sensitive geologists ... for about a year (ouch). So I’d better watch my step.
This is primarily an evo-centric forum. The discovery of advantageous *raw mutation* (if there be such a thing) is pivotal to the ToE and is guised here on Berndt’s thread: as the “origin of new genes”. RASD, on the other hand, is so entangled by mutational systems, that he recently *created* another unreadable mega-post (http://EvC Forum: Irreducible Complexity, Information Loss and Barry Hall's experiments -->EvC Forum: Irreducible Complexity, Information Loss and Barry Hall's experiments) extolling the usual evo-trash that one novel enzymatic genome (a.k.a. “galactosidase system” *precursors*) really mutated.
RASD demands sweet “intellectual rigor” to generalize his scheme . that to prove one novel enzymatic precursor (via a novel gene) somehow advances the ToE into a palatable science.
CF, I thought I addressed most of your points verbatim (http://EvC Forum: The origin of new genes -->EvC Forum: The origin of new genes)! You can say I “hand-waved” this or that. If so, please re-specify, and I’ll try to address that point in greater detail. Seriously, the YEC-IDologist terms you employed reminded me of Billy Graham’s unpleasant worship of wafers and popes as vicars. (Please excuse the avatar; I’m trying to fend off the growing stench of trollic activity lurking in the last 3 posts . )
*Honestly*, it seems to me research biologists must become entrenched in low-level programming languages to realize what they’re dealing with in chromosomal libraries:
They are: Non-mutable robustly-designed low-level programs whose highest level implementations alone are mutable.
Bullet proof apps like MS-Word require robustly compiled unchangeable alleles (or bytes if you prefer) of codon-information (commands, functions, expressions). The only *mutation-hot spots* in MS-Word would be the high-level user-portion: Mutational grammar checker, spelling checker, style sheets, etc.
Biological apps would seem more unchangeable in their robustly compiled alleles. Furthermore, repair-DNA-ase processes hinder mutation (+ and -) in many organisms. For that matter, who in their right mind would deduce that DNA-polymerase with its 100,000 (or so) precisely joined atoms somehow *slipped into* transcriptional systems without any designer intersession whatsoever!

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 111 by crashfrog, posted 12-10-2006 6:07 PM crashfrog has replied

Replies to this message:
 Message 116 by crashfrog, posted 12-13-2006 12:56 AM Philip has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 116 of 164 (369454)
12-13-2006 12:56 AM
Reply to: Message 115 by Philip
12-13-2006 12:13 AM


Re: More Bold-Face Lies: Brand New Alleles
CF, I thought I addressed most of your points verbatim
You didn't address anything, as far as I can tell.
If so, please re-specify, and I’ll try to address that point in greater detail.
Just address the post. Programs implement algorhythms by modeling number theory. Is it your contention that genetics do the same thing?
No? Then comparisons to computer science are specious, and clearly misleading, at best. Genetics is not a programming language.
Bullet proof apps like MS-Word
Are you just nuts, or what? When was the last time you used a Microsoft product that could be called "bulletproof"?
Biological apps would seem more unchangeable in their robustly compiled alleles.
That's great that you think so. Of course, that's radically at odds with what we observe.
It's a simple question, Phil, that I've asked you several times already. If there are no new alleles, then where do all the new alleles come from?
Just answer the questions. Try to do so without impugning my honesty.

This message is a reply to:
 Message 115 by Philip, posted 12-13-2006 12:13 AM Philip has replied

Replies to this message:
 Message 118 by Philip, posted 12-14-2006 4:32 PM crashfrog has replied

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


Message 117 of 164 (369689)
12-14-2006 1:32 AM
Reply to: Message 113 by AnswersInGenitals
12-12-2006 7:51 PM


Re: Put-on?
Can't you tell when your leg is being pulled?
Another possibility is "trolling"
Internet troll - Wikipedia
Always a possibility with any post. One can only deal with the position as presented however -- no matter how ludicrous it is.
One can't help wondering however who the joke is really on eh? The one's who take his words as being ridiculous and rebut the nonesense, or the ones who take his words as truth and support him against the evils of evolution ...
... named in honor of Barry Hall? ...
Or Dave Barry
Dave Barry, humor columnist and author of Insane City
Enjoy.

Join the effort to unravel {AIDS/HIV} {Protenes} and {Cancer} with Team EvC! (click)

we are limited in our ability to understand
by our ability to understand
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to share.

This message is a reply to:
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Philip
Member (Idle past 4723 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 118 of 164 (369773)
12-14-2006 4:32 PM
Reply to: Message 116 by crashfrog
12-13-2006 12:56 AM


Re: Number Theory not in Genetics?
CF writes:
Programs implement algorhythms by modeling number theory. Is it your contention that genetics do the same thing?
Yes, and more so.
Number theory (Answers - The Most Trusted Place for Answering Life's Questions)
The study of the properties and relations of the integers.
All designed (modeled) programs that implement algorhythms must accord with number theory, else their algorhythms are no algorhythms.
Consider sequences of atoms in *nucleic-acid* programs, enzyme-systems, harmonal programs, physiological and/or neurological processes (programs), etc. that seem so modeled on advanced physics math:
Fortunately, biochemical force-vectors of genetic molecules are a lot more sophisticated in their physics math than synthetic transistors in microchips. Peradventure, this is another reason why beneficial mutations and novel genes are exceedingly improbable.
You or I might contend there is wasted redundancy in genetic algorhythms. For example, 23 identically paired chromosomes might be found in most cell-types within a particular genome. As a software programmer I'm certainly tempted to question such redundancy. But I've discovered that my own apps are more bug-free and robust ('bulletproof') when I model upon this genetic design.
(E.g. Now, I create 'wasted-redundant' foundational classes and subclass them in my project-apps)

This message is a reply to:
 Message 116 by crashfrog, posted 12-13-2006 12:56 AM crashfrog has replied

Replies to this message:
 Message 119 by crashfrog, posted 12-14-2006 4:50 PM Philip has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 119 of 164 (369774)
12-14-2006 4:50 PM
Reply to: Message 118 by Philip
12-14-2006 4:32 PM


Re: Number Theory not in Genetics?
Consider sequences of atoms in *nucleic-acid* programs, enzyme-systems, harmonal programs, physiological and/or neurological processes (programs), etc. that seem so modeled on advanced physics math:
Fortunately, biochemical force-vectors of genetic molecules are a lot more sophisticated in their physics math than synthetic transistors in microchips. Peradventure, this is another reason why beneficial mutations and novel genes are exceedingly improbable.
Is it simply your hope that you'll be able to baffle me with bullshit?
I assure you, this is not the case; you don't grow up studying programming languages since the age of six without learning to recognize nonsense faux-computerese. ("physics math"? "peradventure"? Who talks like that?)
Your argument has boiled down to nothing more than "genetics is a prgramming language because I say it is." Can you understand why I wouldn't find that compelling?
Your contention is 100% false. The complexity of the genetic content of our chromosomes does not make novel genes improbable; in fact, it makes them all the more likely. H. P. Yockey's theoretical work shows that, due to the high proportion of functional proteins among all possible amino acid sequences, all known functional proteins are connected by single amino acid changes.
That's proof both that beneficial mutations are sufficiently likely and that common decent by mutation and selection is mathematically possible, as well as the most parsimonious explanation. Known functional proteins, which occupy such a limited space of the set of all possible functional proteins, are too closely clustered to simply be chance or design; the only reasonable explanation is the evolutionary model of decent by modification through random mutation and natural selection.

This message is a reply to:
 Message 118 by Philip, posted 12-14-2006 4:32 PM Philip has replied

Replies to this message:
 Message 120 by Wounded King, posted 12-14-2006 5:59 PM crashfrog has replied
 Message 123 by Philip, posted 12-17-2006 11:24 PM crashfrog has replied

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


Message 120 of 164 (369785)
12-14-2006 5:59 PM
Reply to: Message 119 by crashfrog
12-14-2006 4:50 PM


Re: Number Theory not in Genetics?
all known functional proteins are connected by single amino acid changes.
Are you saying that there are theoretical functional intermediate variants of 1 amino acid change steps between all functional proteins or that there are actual extant functional proteins which all differ by only 1 amino acid?
I assume you mean the former, but it wasn't entirely clear.
TTFN,
WK

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

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