The origin of new genes

The article curiously repeats "New Genes", "New Genes", "New Genes", "New Genes" as if trying to beat "beneficial mutation" into idiots.The problem still remains: Your term "mutation" is misnomer: mutable genes and beneficial mutations (if there truly be such a thing) could only occur in
(1) "Mutation-hot-spots" (or the like) ... a serious misnomer for the "adaptability" vs.
(2) "Hopeful monsters"... given the very mechanisms of post 1.Faith may presently buy into prokaryotes and fruit-flies somehow mutating "new genes" that enhance survival.But random mutation of genes that enhance survival never really occurs in any viral or prokaryote scenario either ... at all ... with any statistical validation. Any true "newness" must eventually cascade into extinction.Such incoherent stammering: "NEW GENES" ain't gonna change that.---------------------------------------
A.K.A. "Nothing new under the sun" (Song of Solomon)

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What sidelined calls "mutation" here is layman’s misnomer for "natural adaptation" (NA).Ah, "mutations", "mutations", "mutations" ... if I repeat the term enough you'll probably misuse it, too (like the word 'new' in that referenced article).One thing we've been trying to clarify, Dr, is what really constitutes a 'NEW' gene. NA produces nothing new within any given gene-pool. Mutation-products really are, incoherent genetic sentences . via mechanisms in post 1For something to be 'mutational-new', genetic code must randomly generate into coherent genetic sentences (genetic commands, functions, procedures, events, expressions, etc.) that harmoniously cascade within a gene pool software program (GPSP) in real time and . that don’t interfere with other genetic paragraphs (of genetic sentences),
. that don’t interfere with other genetic pages (of paragraphs (of genetic sentences),
. that don’t interfere with genetic chapters (of genetic pages (of paragraphs (of genetic sentences))
. that don’t interfere with genetic books (of genetic chapters (of genetic pages (of paragraphs (of genetic sentences)))
. and seamlessly integrate within the GPSP.When mutation (a.k.a. *a genetically incoherent change*) ”bugs’ any of the GPSP, I expect only damage to that GPSP. Extinction or N.S. repair of the GPSP evolves.Unfortunately, GPSP damage only worsens during any *required high mutational frequency* in, say, viruses and prokaryotes.Fortunately, for these ani-molecules, their GPSPs are extremely non-mutable and their GPSPs never actually mutate in real time.Edited by Philip, : sickening grammar

Sorry, the disclaimer (below) failed in the last post. I stand corrected. But instead of trolling against my "childish analogies" and "qualified meanings of words" in this science sector, please focus on "BRAND NEW GENES" as REALITY or MYTH. Then, convince those less-educated than ourselves here with whatever analogies you'd HONESTLY employ.1) Do you or do you not accept that GENE POOLS are in fact SOFTWARE PROGRAMS of alleles for any given population (...and not just the sum of alleles)?2) Are not GENE POOLS themselves "BIBLES" ("collections of books") for any given population of organisms?3) Have not us physicians and biologists SERIOUSLY abused the term MUTATION? We've defined it to mean "change" only (Mutation - Wikipedia)? That leaves *wiggle room* for more ToE fallacies to pollute science.4) Do you really concede BRAND NEW SURVIVABLE GENES are formed daily out of nonsensical mutations?5) Do you understand how tricky data-code manipulations are in less complex windows-software-programs? Brand-new-genes never form alleles (code-lines) in these programs. How can you possibly accept ANY brand-new-survivable-alleles in gene-pool bibles?Philip M. Traynor, DPM, MSBS

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I ALWAYS welcome sincere feedback by bios, docs, laymen and/or tactful trollers, as long as they stay on topic and cough-up some 'credible' motives and/or evidences for their position. Your abstract on duplicated genes is of belated interest (my apologies). Let's break it down a bit: "Poorly understood" ... is the bottom line.
Poorly understood speculations on mutation mechanisms? Of course they're poorly understood! Beneficial (advantageous) mutations don't ever occur (unless one unscrupulously perverts the defintion of mutation into mere "change", "NS", "adaptation", or the like fallacy) Of course ToE forces of mutation are unknown! Even if a serious genetic programmer (human or divine) altered a given gene pool program to make artifical mutation somehow beneficial for survival, he'd risk ultimate extinction for that organism. HOW MUCH MORE would random mutations seem to expedite extinction of any gene pool program. Admittedly, duplicated genes are the only real commencing mechanism of evolution, were beneficial (advantageous) mutations *hopefully* viable. Ah, those computational approaches to the gene-pool-enzyme mutation, and their *complete* genomic sequences (notwithstanding the cascading eukaryotic protein factors of this monkey's complex gene-pool-app) Whoa cowboy! Is this REALLY mutation? ... or is it merely natural adaptation (pre-built genome variability or such)? "relaxation of purifying selection" ...Ouch, that babbling effeminate ToE syntax, again. This supports nothing concerning 'brand new genes', 'advantageous gene-pool-mutations', etc. Just bad grammar. Ah! so it is merely "adaptive" selection after all; this is not evolution. The monkey's gene-pool program never changed via this code-duplication. (... Any more than my C++ program changed when it passes 2 [vs. 1] parameters into a sub-routine function).Obviously, there is much flexibility of adaptive codon-parameters passing (unscathed) in programs and functions throughout eukaryotic gene pool programs and apps. Again, this is not evolution proper, just program 'design' with finite flexible parameters of adaptation.... Or did the gene REALLY duplicate into some 'freak' new code-function for the monkey's gene-pool-program? NOT!In sum: These studies in no way support: random "brand-new advantageous mutations" of new genes, just "hot-spot mutations" and other fallacious misnomers of beneficial mutation (i.e., having been pre-coded into that gene-pool program)

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Ouch! "the changing of the structure" vs. "a rare change". Your contrary lexicon and biology dafinitions seem ridiculous. So which definition are you supporting anyway, as validating the origin of new genes.Why not support YOUR own dafinition of 'beneficial mutation' (without 'mutating' it). My cat can barf up better definitions than these.Hey doc, I’m a doc (podiatrist and programmer (Home)). Not everything I code or write here is sensible nor without bias (hence the disclaimer below).Seems (to me) the *Creo's definition* ("pre-built genetic variability") aptly replaces those ridiculous *beneficial mutation* definitions anyway.

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Hello Dr,If I write the books I can redefine "beneficial mutation"; why do you trust *authority* anyway?What about the paradigms of 'no absolutes', 'legal disclaimers', etc. that implicitly advise you to question authority. *Brand new alleles* are NO DIFFERENT.I suffered 4 belaborous science degrees; as a podiatrist, MSBS, EET, and Psych, with minors in art, philos, education, etc., a lot of CS programming experience (Home) and am 49 years old. With my broad (albeit biased) *science-expertise* I (peradventure) just invented/defined a (hypothetical) *brand new concept*:'Gene-Pool-Software-Programs' (GPSPs)... to attempt to denounce the radical concept of *brand-new-alleles*I've demonstrated (to myself at least) that GPSPs invalidate *beneficial mutation* as either (1) Misnomer for natural adaptation or (2) 'Hopeful monster' mutations.At any rate, I'd be interested in your thoughts on GPSPs as it relates (if at all) to 'brand new allelic functions'

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Bernd: What’s the difference? Evos use one to infer the other and call them the same (e.g., macro vs micro mutant-evolution)In fact they seem EXACTLY THE SAME when viewed from a gene-pool-software-program (GPSP) level: At least the 2 are exceedingly and equally improbable at the GPSP level.Sorry to drift somewhat from the analytic intent of your interesting and venerable thread. (For a while I stupidly perceived you to be a troll ... please accept my apologies)Also, I dissected one abstract of yours already. I’m in full accord that the 8 comprehensive *mutant* evo-processes you recapitulated are viable and delusive mechanisms of “fast adaption”. To wit:
” Exon shuffling
” Gene duplication
” Retroposition
” Mobile elements
” Lateral gene transfer
” Gene fusion/fision
” De novo origination
” Combined MechanismThe view I’m *purporting* is that no natural software program (GPSP) is able to create brand new allelic functions, let alone brand new genes” at the GPSP level. The ”gottcha’ fallacy remains ”benefical-mutation' vs. ”novel gene’. Our sin is to separate their definitions (now) and then (later) equate their definitions under the ToE.The sin, bernd: is to discriminate 'beneficial mutations' vs. 'novel genes' at the GPSP level. Is this is what you're requiring me to do?Bernd: “Novel gene formation” is a fallacious concept some Evo unscrupulously *invented*. I seriously propose you concede your benefical-mutation thread as (1) misnomer and/or (2) impossible at the GPSP level.

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Dr Adequate,Please get back on topic.We're debating mutant new genes and the credibility of *new genes* at the gene pool level, not dafinitions.

Ouch!If you really want to narrow down this thread topic to mere *new* genes I concede on that point. (...the strawman being "beneficial mutation" as *unrelated in part* to 'new alleles') Otherwise, I'd be interested in your *valid* definition of 'beneficial mutation' (but then you'd be caught up in this strawman)(I was supposing that this thread was equivocating *new genes* with *beneficial mutations* as post 1 (and the ToE) seemed to suggest to me ... another topic)

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Thank you for your patient thoughts.OK Dr Adequate, Now I'd like to hold you to your definition: "Change in the genome":So, if I have brown eyes and my child evolves green eyes, is there a mutation? Methinks YES and NO, by the definitions of 'genome' ... Behold 2 diametrical *broad-ass* definitions of genome (Answers - The Most Trusted Place for Answering Life's Questions):1) The total genetic content contained in a haploid set of chromosomes in eukaryotes, in a single chromosome in bacteria, or in the DNA or RNA of viruses.
2) An organism's genetic material.Seems my child might have mutated green eyes by definition #2. Of course it depends what 'genetic material' REALLY is.I think you'd concur that its really the human 'gene pool' that ultimately 'houses' much of 'my genetic code'. If so, there seems to be no change (no mutation) at the gene pool level (nor NS ... since eye-color seems arbitrary for survival)Admittedly most ho-hum biologists blindly *accept* this obscure (A.K.A. broad-ass) definition of mutation without considering genomic complexity, let alone the IC of any gene pool (speaking as a YEC and CS programmer).To please Bernd's topic, we'd probably do better to focus more on *new gene* validation and/or his RNA studies in post 1.

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Thank you for your patient response(s), Bernd:Forgive me, I'm not going to write futile pages dissecting your sources. You may give me an abstract again and I might find time for that (again). Concise one-page-responses Bernd are all losers like me can read or write on this forum. Plus, I'm tired of 'straining knats' on this whole 'new gene' fallacy to *discover* exceptions.ALLELE (*broad-ass*) definition (Answers - The Most Trusted Place for Answering Life's Questions): “Any of a number of alternative forms of a gene.” ?#! ...I meant comparable to venerable 'low-level' computer programs per se: within the gene-pool... (albeit, most gene pool programs seem to me far more irreducibly written than man-made programs at present).(As far as presenting this concept on a different thread, I already proposed a similar thread that was 'not of interest' to Admins at the time.)Bernd, I purport:Bits --> bytes (of information) == genes --> alleles (of information).As you know, data-manipulation is tricky. By equivocating these units of information, I’m invalidating your hypotheses of ”new genes’. I don’t really envision any survivable ”new data’, ”new genes’, ”new bytes’, ”new alleles’, ”new bits’, ”new code’, ”new codons’, or ”new anything’ spontaneously generating in any software-like system . without *sophisticated* designer intervention. (Hence my YECism)The only (insignificant) difference in question on the softwares seems to me to be synthetic vs. organic storage of data (semi-conductor-storage vs. gene-storage (e.g., on some of the objects you listed)) of bits or alleles of data.In sum: Computer science and biology seem to me the same, essentially. Only their software languages and storage containers seem different. Because data-manipulation is usually tricky and cascading, no ”new gene-data’ seems randomly created to me . at all.

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Thank you for your thoughtful feedback: Please accept my belated response. I'll try to respond as it pertains to the "novel genes" misnomer. True, I perceive CS is the cornerstone of science. Herein is everything reduced to black and white, .T. and .F., 0 and 1, garbage-in-garbage-out, etc. I see no black-boxes, metaphysics, faith-healings, spontanous generations, nor evolutions (nor advantageous mutations) in CS. As such, methinks all (true) science may be percieved as CS of sorts. Physics laws, the Periodic Table, Quantum excellencies, etc., seem as finite programs to me (though infinitely vast). CF: Perhaps I'm missing something here; I've been a podiatrist (with a coveted MSBS from Barry University, Miami) for 15 years. Also, I've programmed painstakingly for 16 years (80% VFP, but use mainstream computer languages, primarily for scripting in HTML and COM objects). While its true that I currently don't program much in genetics, C++, net.asp, gene-pool software, Cobol, genetic recombinance, assembly, and other languages; I must deal with such programs on a day-to-day basis.
Pertaining to this topic, though: I never treat human gene-pool samples as advantageous mutants, but rather as created-programs with persons attached ("north of the feet") (when I'm debriding toenails or whatever)
Let me assure you programs are programs, only the languages are different. (i.e., You might wish to retract the above statement) Actually this is just one of many "purposes" of your gene-pool software (... please CF, you're beginning to sound just like an IDist employing teological terms). Other implementations (a better CS term) include self-replication, self-repair, surviving the niche, feedback-loops, *self-development* (for my lack of a better word), *tissue-compilation* ... etc.,
... which seems to me far more fragile than mere aa formation in response to protein triggers.
Of course, the chief purpose(s) of genetic software are 'biomechanical excellencies' (for lack of a better term). I stated gene-pools are software programs, specifically. (One day I'll probably catch you copying my logic vs. refuting it.) The "data you feed are": environmental triggers, hormonal reflexes and feedback systems, etc., while 99% of those triggers seem triggered by metaphysical stimuli. (Oops, I'm getting off the mutant-gene topic) Design, design, design! Ouch, CF. You’ve just proclaimed (to all the world) that you’re nothing but a flat-earth-IDist (like the Pope’s billionaire cheerleader, Billy Graham)!CF: In sum, Mutant alleles really have no place in any IDist scheme (unless there’s psychotic pentecostal faith-healing or Voodoo occurring). Beneficial Mutation is best proven in the metaphysical realms (i.e., non-science forums) and has no place in biology.Though empirically speaking you’d be correct stating: “Random improbability (of novel alleles) does not equal impossibility” in the (“==”) sense. But statistically, such “random improbability equals impossibility” in the (“=”) sense. As scientists we’re forced to concede that in all probability, there are no novel alleles in any given gene-pool program.

When you're ready to concede that you've been caught red-handed (before real-world lurkers):
1) As an IDist playing atheist
2) Trolling from the topic of "novel genes" and/or beneficial mutations.
3) Lying about your programming at the age of 6
4) Slandering scientists and physicians as fakes
5) Cheerleading yourself like Billy Graham does the Pope
6) Probably indulging in country music and/or ELO after being explained the risks, benefits, and complicatons of these events.Then we might get back on track.

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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

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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 results2) 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)

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