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Author Topic:   The origin of new genes
crashfrog
Member (Idle past 1467 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

  
crashfrog
Member (Idle past 1467 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.

This message is a reply to:
 Message 99 by ramoss, posted 10-31-2006 8:50 AM ramoss has not replied

  
crashfrog
Member (Idle past 1467 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:
 Message 103 by Philip, posted 12-07-2006 7:58 PM crashfrog has not replied

  
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

  
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

  
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

  
crashfrog
Member (Idle past 1467 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

  
crashfrog
Member (Idle past 1467 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 1467 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?

This message is a reply to:
 Message 122 by Philip, posted 12-17-2006 11:24 PM Philip has not replied

  
crashfrog
Member (Idle past 1467 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?

This message is a reply to:
 Message 126 by Philip, posted 12-19-2006 7:52 PM Philip has not replied

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


(1)
Message 162 of 164 (570747)
07-28-2010 3:37 PM
Reply to: Message 160 by barbara
07-28-2010 2:42 PM


Re: New Genes
Out of 500 billion mutations are actually in the germ line?
All of them. The figures you're referring to are to heritable germline mutations.
The figure for mutations throughout the human body is several orders of magnitude higher; approximately 1 per 3 billion base pairs replicated. In tissues where cells are replicating constantly - skin, intestinal lining, hair follicles - that results in hundreds of accrued mutations throughout one human body every day. (More if you're out in the sun.)
I don't see how it is possible for humans to be anything but humans in the future.
Humans will indeed always be humans, but the term "human" will come to refer to more species than just "Homo sapiens." Evolution is a bush, not a ladder.

This message is a reply to:
 Message 160 by barbara, posted 07-28-2010 2:42 PM barbara has replied

Replies to this message:
 Message 163 by barbara, posted 07-28-2010 4:41 PM crashfrog has replied

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


Message 164 of 164 (570756)
07-28-2010 4:51 PM
Reply to: Message 163 by barbara
07-28-2010 4:41 PM


Re: New Genes
I really have a desire to obtain as many facts as I can to come to my own conclusion. It is very difficult to do when the information is so conflicting from one website to another.
That's true; that's a problem.
Why not abandon websites altogether and begin with appropriate science texbooks on the subject? You know, like they use in college. Brock's "Biology of Microorganisms" has a lot of interesting material on evolution, in fairly simple examples of microbes. But it goes into the kind of depth you need to talk about the science intelligently.
For the person that enjoys insulting people's intelligence
As a rule I don't insult people's intelligence. But some people have the strange notion that they know as much about biology as people with PhD's in the subject, despite having no formal training in it whatsoever and getting almost everything they say about it wrong. They need to know that they have much learning to do, and I don't consider it an insult to tell someone that they need to learn more, and to point them to the resource they need to do so.

This message is a reply to:
 Message 163 by barbara, posted 07-28-2010 4:41 PM barbara has not replied

  
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