The origin of new genes

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. 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 ?
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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?
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2Th 2:11 And for this cause God shall send them strong delusion, that they should believe a lie and be damned

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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!

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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)

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.)

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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

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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?

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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)

... 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?

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