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Author Topic:   The origin of new genes
RAZD
Member (Idle past 644 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 91 of 164 (359779)
10-30-2006 7:56 AM
Reply to: Message 84 by Philip
10-27-2006 5:21 PM


Fallacious results of re-definitions
If I write the books I can redefine "beneficial mutation";

Please read Definitions, Daffynitions, Delusions, Logic and Critical Thinking.

Let me give you an example of how this works: I redefine "jesus" to mean "devil"

Then I say that because of this definition, all christians are praying to the devil.

This of course does not make it so, so what is wrong here?

I am using one definition for "jesus" and every christian is using a different definition, so what I am really doing by saying that all christians are praying to the devil is equivocating between my definition and that used by christians.

Equivocation is the logical fallacy of using two different definitions of words in different parts of the logical structure.

What you are doing in making up your own definition of mutation is (1) creating a straw man (a false definition) and then using that to (2) equivocate between your (false) meaning and the (real) meaning used by biologists.

This means your argument is invalid, because you are using two different definitions.

IF you want to discuss what biologists are talking about THEN you will use the definitions of the terms they use.

Otherwise you are talking about something else and PRETENDING that it is about what the biologists are talking about.

Enjoy.


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This message is a reply to:
 Message 84 by Philip, posted 10-27-2006 5:21 PM Philip has replied

Replies to this message:
 Message 92 by Philip, posted 10-30-2006 10:23 AM RAZD has seen this message

  
Philip
Member (Idle past 3962 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 92 of 164 (359819)
10-30-2006 10:23 AM
Reply to: Message 91 by RAZD
10-30-2006 7:56 AM


Re: *New* Genes ...
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)


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 91 by RAZD, posted 10-30-2006 7:56 AM RAZD has seen this message

  
Philip
Member (Idle past 3962 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 93 of 164 (359841)
10-30-2006 11:52 AM
Reply to: Message 88 by Dr Adequate
10-27-2006 7:08 PM


Re: "mutation" means a change in the genome
Dr Adequate writes:

admit that "mutation" means a change in the genome

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 (www.Answers.com):

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.


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.

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Wounded King
Member (Idle past 3334 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 94 of 164 (359862)
10-30-2006 12:40 PM
Reply to: Message 93 by Philip
10-30-2006 11:52 AM


Re: "mutation" means a change in the genome
What colour are your wife's eyes?

In what way are those definitions of genome 'diametrical', no.2 seem to encompass no.1 provided one is prepared to allow that viruses are organisms.

No.1 will allow one to discuss subsets of a full human genome such as the haploid genomes of sperm and egg cells.

If so, there seems to be no change (no mutation) at the gene pool level

This is by no means clear, we would have to know exactly what mutation was present in your child and whether or not it was already present in the gene pool. If it wasn't then you would have at least a novel genetic, if not phenotypic, allele.

TTFN,

WK


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Jazzns
Member (Idle past 3151 days)
Posts: 2657
From: A Better America
Joined: 07-23-2004


Message 95 of 164 (359884)
10-30-2006 2:36 PM
Reply to: Message 41 by mick
09-24-2006 4:50 AM


Re: mutations give rise to new genes, and do not just disrupt old ones
It is unfortunate that this post was ignored by Faith and others.

If you don't mind, I would like to copy the contents of this post for future reference the next time a creationist wants to bring up the "no new information" argument.

Thanks for you involvement in this forum mick. Even if you didn't get through to Faith and others, there are others who read, enjoy, and appreciate you sharing your expertise with us.


Of course, biblical creationists are committed to belief in God's written Word, the Bible, which forbids bearing false witness; --AIG (lest they forget)

This message is a reply to:
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Philip
Member (Idle past 3962 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 96 of 164 (359886)
10-30-2006 2:39 PM
Reply to: Message 90 by bernd
10-29-2006 12:02 PM


Re: no ‘new gene-data’
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 (www.Answers.com): “Any of a number of alternative forms of a gene.” ?#!

Bernd writes:

gene pools are somehow comparable to C programs

...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.


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.

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Replies to this message:
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crashfrog
Member (Idle past 706 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 97 of 164 (359928)
10-30-2006 4:41 PM
Reply to: Message 96 by Philip
10-30-2006 2:39 PM


Re: no ‘new gene-data’
In sum: Computer science and biology seem to me the same, essentially.

God forbid you be hired to do any programming. If you wrote software like genomes are structured, I'd flunk you out of any programming class.

I appreciate that, as a computer scientist, computer science is how you approach the world. As a fellow programmer, though, as well as a student of genetics, let me assure you that there's almost no similarity between genetics and programming. Computers are Turing automata, finite state machines; genes aren't. The cellular mechanisms of biology's so-called central dogma don't compute algorythms or model number theory; they catalyze the formation of proteins in response to environmental triggers.

I appreciate that your in-the-trenches familiarity with the fragility of software leads you to the conclusion that, if genetics are software, any little random change should break the whole thing - like when you inadvertently substitute assignment (=) for comparison (==) in programs, which I do a lot. (Although surely a computer programmer is aware of techniques in genetic programming and evolutionary algorhythms, which produce functional behaviors by exactly this mechanism of reiterative, small random changes to programming?)

But genetics isn't like programming. The purpose of an organism's genetic code is not to be an easily-readable, straightforward, verifiable implementation of an alogrhythm; it's to catalyze the formation of proteins in response to environmental triggers by storing amino acid sequences in an informational molecule. Genetics aren't software; it's more like the data you feed into software. And just like I can make a random change to one letter in my term paper without crashing Microsoft Word (because Word is a program designed to edit arbitrary text strings), I can make random changes to a genetic code, because the system is designed to synthesize arbitrary chains of amino acids.

Moreover - it's ludicrous to assert that there can be no new alleles, because we observe new alleles all the time. There's no intellectual future in an argument that asserts the impossibilty of something we observe all the time.


This message is a reply to:
 Message 96 by Philip, posted 10-30-2006 2:39 PM Philip has replied

Replies to this message:
 Message 101 by Philip, posted 12-06-2006 10:45 AM crashfrog has replied

  
RAZD
Member (Idle past 644 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 98 of 164 (360059)
10-31-2006 7:44 AM
Reply to: Message 93 by Philip
10-30-2006 11:52 AM


brown eyes green genes
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' ...

Green eyes are known in the human genome, so the question becomes did she inherit an existing green eye gene or acquire a new green eye gene mutation.

You have brown eyes, which are dominant, so you could carry a recessive gene for green eyes. We don't know your wife's eye color(s) so beyond this all we can say is that it is entirely possible for the child to inherit an existing gene.

Your daughter could also have a new green gene, but to determine that we would need to compare her green gene with other green genes in the genome, and see where the specific genetic changes agree or disagree.

Now if they were purple eyes we'd be pretty sure they were a new mutation.

Enjoy.


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ramoss
Member
Posts: 3225
Joined: 08-11-2004


Message 99 of 164 (360074)
10-31-2006 8:50 AM
Reply to: Message 98 by RAZD
10-31-2006 7:44 AM


Re: brown eyes green genes
Of course, if he had blue eyes, and his wife had blue eyes, and the child's eyes were brown, then one possible solution would be a new mutation for brown eyes.

This message is a reply to:
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Replies to this message:
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crashfrog
Member (Idle past 706 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 100 of 164 (360075)
10-31-2006 9:01 AM
Reply to: Message 99 by ramoss
10-31-2006 8:50 AM


Re: brown eyes green genes
Of course, if he had blue eyes, and his wife had blue eyes, and the child's eyes were brown, then one possible solution would be a new mutation for brown eyes.

I can think of a much more likely solution. If he has blue eyes and his wife has blue eyes, and "their" child has brown eyes, he should probably look around and see if his wife has any male friends with brown or green eyes.


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Philip
Member (Idle past 3962 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 101 of 164 (367937)
12-06-2006 10:45 AM
Reply to: Message 97 by crashfrog
10-30-2006 4:41 PM


Re: no ‘new gene-data’
Thank you for your thoughtful feedback: Please accept my belated response. I'll try to respond as it pertains to the "novel genes" misnomer.

CF writes:

...computer science is how you approach the world


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 writes:

...let me assure you that there's almost no similarity between genetics and programming


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)

CF writes:

... The purpose of an organism's genetic code is not to be an easily-readable, straightforward, verifiable implementation of an alogrhythm; it's to catalyze the formation of proteins in response to environmental triggers


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).

CF writes:

...Genetics aren't software; it's more like the data you feed into software.


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)

CF writes:

...because Word is a program DESIGNED to edit arbitrary text strings ... the SYSTEM IS DESIGNED to synthesize arbitrary chains of amino acids


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.


This message is a reply to:
 Message 97 by crashfrog, posted 10-30-2006 4:41 PM crashfrog has replied

Replies to this message:
 Message 102 by crashfrog, posted 12-06-2006 11:13 AM Philip has replied
 Message 105 by RAZD, posted 12-07-2006 8:53 PM Philip has replied

  
crashfrog
Member (Idle past 706 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 102 of 164 (367940)
12-06-2006 11:13 AM
Reply to: Message 101 by Philip
12-06-2006 10:45 AM


Re: no ‘new gene-data’
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.

Well, congratulations. I've been programming computers since I was 6 (working in HyperTalk and Pascal) and studied the field for several years before switching to English, flunking out, and then getting hired as a lab assistant by the USDA. (And also marrying a molecular phylogeneticist and entomologist.) I can program in C++, Java, and the LISP family; I can script in a couple of different languages like PHP (and probably Perl if I saw the need to.)

Like I said, if you wrote programs like genetics I'd flunk you out. Haphazard structure - control sequences in the middle of data strings - huge blocks of nonsense for no reason whatsoever. Infinite loops. Corrupted data. No comments whatsoever. If you brought that code to me on the job I'd have you replaced by two guys from New Delhi by the end of the day.

Let me assure you programs are programs, only the languages are different. (i.e., You might wish to retract the above statement)

I have no wish to retract anything. Your continued assertions that genes are programs are meaningless, since genes are not programs. They're genes.

I stated gene-pools are software programs, specifically.

Actually, no, you didn't. You wrote a bunch of malarky, redefining biological terms as you saw fit (and with no regard to physical reality) until you were able to simply claim genetics and computers to be the same thing, by fiat.

But that's nonsense. Any computer programmer can tell you - and this one is. You don't even program, by your own admission - you write scripts and markup documents for HTML. (You don't apparently even know enough about programming to know that scripting and markup languages aren't programming languages.)

And you've completely avoided any response to my argument. Here, I'll repeat it. I suggest you take another two months, and at the end of that, come back with something that actually speaks to my argument. Here it is again, for your edification:

quote:
But genetics isn't like programming. The purpose of an organism's genetic code is not to be an easily-readable, straightforward, verifiable implementation of an alogrhythm; it's to catalyze the formation of proteins in response to environmental triggers by storing amino acid sequences in an informational molecule. Genetics aren't software; it's more like the data you feed into software. And just like I can make a random change to one letter in my term paper without crashing Microsoft Word (because Word is a program designed to edit arbitrary text strings), I can make random changes to a genetic code, because the system is designed to synthesize arbitrary chains of amino acids.

Genes aren't programs. Genes are strings, if you prefer. The system of genetics allows for genes to be arbitrary and selected upon by the environment. Unlike a program, where little in the code can really be arbitrary.

As scientists we’re forced to concede that in all probability, there are no novel alleles in any given gene-pool program.

You're not a scientist, and scientists are forced to conclude the exact opposite, because of direct observation of new alleles in gene pools. If new alleles are impossible, according to a podiatrist, then where are all the new alleles coming from?


This message is a reply to:
 Message 101 by Philip, posted 12-06-2006 10:45 AM Philip has replied

Replies to this message:
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Philip
Member (Idle past 3962 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 103 of 164 (368305)
12-07-2006 7:58 PM
Reply to: Message 102 by crashfrog
12-06-2006 11:13 AM


Re: no ‘new gene-data’
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.


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:
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Replies to this message:
 Message 104 by Modulous, posted 12-07-2006 8:24 PM Philip has replied

  
Modulous
Member (Idle past 1343 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


Message 104 of 164 (368307)
12-07-2006 8:24 PM
Reply to: Message 103 by Philip
12-07-2006 7:58 PM


lying?
Lying about your programming at the age of 6

Why the incredulous attack on somebody's integrity? I started programming at the age of 6. My step-father bought me a Commodore-64 and showed me how to write BASIC. By the time I was 7 I had written my own (crappy) games and I was fluent in binary by the time I was 8 (I didn't know it was called binary at the time, but generating sprites required counting in binary for some insanely stupid reason).


This message is a reply to:
 Message 103 by Philip, posted 12-07-2006 7:58 PM Philip has replied

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RAZD
Member (Idle past 644 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 105 of 164 (368317)
12-07-2006 8:53 PM
Reply to: Message 101 by Philip
12-06-2006 10:45 AM


Re: no ‘new gene-data’
As scientists we’re forced to concede that in all probability, there are no novel alleles in any given gene-pool program.

Let's get back to the real world for a minute eh?

Perhaps you'd care to tell me how the "IC" system re-evolved in Hall's experiment without a new allele?

Irreducible Complexity, Information Loss and Barry Hall’s experiments

The original gene was deleted, and a new - different - system evolved to replace it.

Allele removed.

Allele replaced.

New.

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

RebelAAmericanOZen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.


This message is a reply to:
 Message 101 by Philip, posted 12-06-2006 10:45 AM Philip has replied

Replies to this message:
 Message 106 by Philip, posted 12-08-2006 11:19 PM RAZD has replied

  
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