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Author Topic:   The origin of new genes
jerker77
Inactive Member


Message 46 of 164 (352439)
09-26-2006 5:08 PM
Reply to: Message 36 by Faith
09-23-2006 10:44 PM


Re: New Genes?
It IS a different question, yes, but WHAT the DNA "says" has to be the most important thing.
That would depend on the question.
A gene is a very very long string of these amino acids, right?
No, a gene is a chain of ribonucleic acid. A chain of amino acid is a protein.
That codes for a specific protein, right?
That would depend for what purpose you would define “gene”. If your aim is to talk about the distribution of hereditary traits over time within a population (i.e. evolution) the definition would have to be something like a piece of DNA “that segregates and recombines with appreciable frequency”
The 20 amino acids do combine into triplets that say something quite definite, but when strung out along a gene into the hundreds and thousands, are you claiming there are that many coherent/articulate proteins?
It’s the nucleic acid that form triplets that the ribosome read in threes when they use them as blueprints for synthesising amino acids into long chains (proteins). I’m not sure what you mean by “coherent/articulate” but I assume you are talking about proteins that are bioactive (i.e. perform a biological function). Today we know about more than 50.000 functioning proteins coded by DNA and new are discovered as we are speaking.
But of course I think from the perspective of God's designing it all, and in that case all the codes MUST code for something beneficial to life -- regardless of environment. Sickle cell is beneficial with respect to malaria but in itself it is deadly in ALL environments.
If a human population are to thrive in a malaria infested environment they need the sickle cell anaemia mutation but a by product of this it that a part of the population will become homozygote and thus die by biochemical suffocation.
Life in itself is deadly my deer friend. Most of the processes that take place within and outside the organism are hazardous to its sustainability. The reason there are any organisms at all is that the right mixture of processes can sustain its end product (the organism) long enough to make copies of itself.
Nature lack moral as would any conceivable designer. 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.

/Jerker
*Religions most formidable opponent has always been reality therefore it strives to monopolize truth*

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Hawks
Member (Idle past 6146 days)
Posts: 41
Joined: 08-20-2006


Message 47 of 164 (352470)
09-26-2006 8:41 PM
Reply to: Message 34 by Faith
09-23-2006 10:23 PM


Oh yes, I certainly know that DISEASES are caused by mutations. Diseases and deformities and miseries galore are caused by mutations. This is one of the reasons why mutations hardly seem like an engine that could power life at all.
How can you know that for sure? How do you know that you not really seeing allelic shuffling or evidence of design? Seems to me like you are trying to eat your cake and have it.
Well, I know this because God wouldn't DESIGN in disease and death; It is the deterioration or disintegration of the design, the result of sin.
I've agreed that it's possible that beneficial mutations may play a part in the processes of life, but the evidence so far is not very convincing. Variations are merely CALLED mutations without any evidence whatever that they are in fact mutations. Whatever it would take to prove that they are truly novel, never existing before in the population, is what is needed.
Like I said. You're eating your cake and having it. Thanks for proving my point.

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 48 of 164 (352475)
09-26-2006 8:55 PM
Reply to: Message 34 by Faith
09-23-2006 10:23 PM


Variations are merely CALLED mutations without any evidence whatever that they are in fact mutations. Whatever it would take to prove that they are truly novel, never existing before in the population, is what is needed.
Very well. We prove it thus. Only two of each kind of unclean beast was taken onto the ark, one male, one female. mtDNA is passed down through the female line. Therefore, any variation of the mtDNA in an unclean baramin is evidence of a novel mutation. Such variation exists. QED.

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 49 of 164 (352486)
09-26-2006 9:26 PM
Reply to: Message 45 by Maxwell's Demon
09-26-2006 3:20 PM


Yeah well... see... the reason I'd want some sort of quantification, is creos could easily just claim that god sometimes likes to reuse his gene-designs with small modifications...
But by the nature of a frame shift, the protein coded for is completely different (apart from the length of the protein chain). The nearest analogy I can think of is if a human designer wrote a set of instructions for putting up a tent which, read backwards, were instructions for assembling a food blender; constraining the design of both items according to this requirement.

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Maxwell's Demon
Member (Idle past 6229 days)
Posts: 59
From: Stockholm, Sweden
Joined: 05-09-2004


Message 50 of 164 (352525)
09-27-2006 1:02 AM
Reply to: Message 49 by Dr Adequate
09-26-2006 9:26 PM


Hah! You're right of course. Good call.
Still would feel better with numbers though.

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Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 51 of 164 (352582)
09-27-2006 7:22 AM
Reply to: Message 46 by jerker77
09-26-2006 5:08 PM


Re: New Genes?
Now here is an interesting idea. You can say you read it first on EvC.
Can a "gene" be something "other" than a piece of DNA that 'segregates and recombines with appreciable frequency.'
Steven Jay Gould finally thought that "junk" DNA might be a proper appelation for the repeating parts of DNA that have been hypothesized to arise by various means.
What if the this repeating DNA DOES have a function so far unrecognized in biology that is the influence of highest levels DOWN to the genic level of molecular forces? Could the repetative elements be discourgements to the individual organism's embryogeny from its species' individuality??
How could such a thing happen???
Well, I have a "crazy" idea. What if the Guanosine that can attach to microtubules actually represents some aspects of all the "traditional" genes (those defined as you suggested) but is REDISTRIBUTED in the cell soma by the independent dynamics of microtubule motion and yet due to the Gibbs/Gladshev minimization
Human Thermodynamics :: History
quote:
3. Gladyshev established that, in the process of ontogenesis, as well as phylogenesis and evolution, the specific value of the Gibbs function of formation of supramolecular structures of the ith organism tends toward a minimum, as defined by the following integral limit:
INCREASES the mechanical junctions that cause reptative elements to be added to genomes?
The "gene" would then be codable by a second kind of "information" flow not strictly limited to the triplets of DNA but dependent on macromolecular interactions and extra-cell interactions which might be population rather than organism specific.
I know it is speculative but this is a bare bones framework for an alternative notion of the gene. I remeber well when Amy McCune asked a lunchen of population biologists at Cornell exactly what a gene was and they could not answer short of the "thing" they manipulated in equations. This is not what she was looking for and neither was it what I was listening for.
This defintion of a gene and how new genes might arise by consequence extends the "managament" capabilities of individual levels of organization beyond that contained by strict adherence to Crick's CENTRAL DOGMA of MOLECULAR BIOLOGY except that there may be a still a "one-directional" flow from the guanosine
Guanosine - Chemicals - Pharmacological Sciences
only to a split somewhere within the circuit I suggested. Gould thought that "junk" was an ok adjective but in this idea it is not. Evolvability would be parsed differently than he suggested was his preference.

This message is a reply to:
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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 52 of 164 (352590)
09-27-2006 8:12 AM
Reply to: Message 51 by Brad McFall
09-27-2006 7:22 AM


Re: New Genes?
Do you know the meaning of the term "word salad"?

This message is a reply to:
 Message 51 by Brad McFall, posted 09-27-2006 7:22 AM Brad McFall has replied

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Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 53 of 164 (352694)
09-27-2006 6:41 PM
Reply to: Message 52 by Dr Adequate
09-27-2006 8:12 AM


What part of the word "g'e'n'e" did you not understand?
Yes I do Dr. A. This post however is NOT one.
Yes it was sketchy and YES it was just an idea unlike most all of my other posts. I am sorry if you can not tell the difference.
In the early 90s I was working with Jim Parks in the Animal Science Lab at Cornell on the cause of the low ratio of re-implanation in vitro fertilizations. He was favoring the idea that collagen may reveal the cause of the low experimental ratios while I suggested that the "information" necessary to sustain what I labeled the "centriolar" cycle might be the OBJECTIVE marker that could be observed and tracked to give some "time line" that could indicate where in the history of reproduction the faliures were resulting.
In the process I was doing monoclonoal antibodies to tubulin and getting pretty color pictures of the insides of cells where tubulin was. I also did some simple stains of DNA at the metaphase plate and recovered 1 in 30 cells (after I artifically mixed the sperm and egg) that had perfect circular symmetry of the chromosomes.
A decade earlier I was stitting down the road at a evolution"" seminar with Amy McCune who was asking as a new faculty member(who arrived on the campus AFTER I was already there) (Will Provine tried subsequently in the mid 90s to use her work, (she asked me specifically where in New Jersey to look for fossil fish), to argue against the simple logic of Phil Johnson's presenation of the how cladistics etc was being presented) EXACTLY what a gene was. I was shocked. If I was an undergraduate and I was being tested on all kinds of things then the faculty MUST be able to answer this question. They did not.
What I suggested above is an answer to that question now another decade beyond not a word salad. Sorry for the appearence.
The components I needed were:
A) some parts of organisms that increase in molecular quantity - hence "junk" DNA
B) some way to get the current taught "information" in THE GENE (ACTG of DNA as modified by ideas of the difference of regulatory and stuctural genes etc) into the idea I presented.
(Here I was a little short on suggestions which might have had you think of word salad. I simple question than a doubt would have served me better if you really desired a positive response from me) During the metaphase plate I assume that somehow the Guanosine along the DNA is coordinated with microtubule elongation AWAY from the plate. Thus the microtubule may FURTHER encode only the G part of the protein-DNA codes. Now in the soma but within the "centriolar cycle" (obvious qualifications would have to be made in detail for differences of the presence of the centriole in different organisms etc) the microtubules INTERACT and perhaps the the "Protein" information as per the amino acids triplets directly interact with other cell chemicals including lipids etc (at any rate those chemicals that react with guanosine).
C)use for the temporal realites from a higher level of combined ontogeny and phylogeny of the Gibbs Gladyshev Law, as the FORCE, capable of creating the increase in molecular representation of the quantity through the 2nd law of thermodynamics.
Thus I speculated (and THIS is what makes the post "just an idea") the somatic RE-Distribution of previously concieved central dogma flows in through a 1/3 ratio of full semantic information transfer FROM the soma BACK to the DNA via Gladshev's contribution of minimzation.
Word salads never result in anything but diagnoses. This however can lead to a complete change in biology. Obviously I have to recieve replys like, please explain that a gain rather than duhh that was really as incomprehensible as Wright's adaptive landscape holds orthogenesis etc. Regardless I KNOW the idea would result in a Nobel for the person who shows it exists. Ideas have to start somewhere. Try not to be so despondant that you might have come across something new and interesting at first blush. I am not saying this is, with my usual confidence I post with on EvC, I just wanted to point out an idea that shows that "the gene" may not be what one is tested to say it is in college.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 54 of 164 (352721)
09-27-2006 9:57 PM
Reply to: Message 53 by Brad McFall
09-27-2006 6:41 PM


Side issue
Brad, sometimes you sound like you may have some creationist views or at least sympathies -- not in this post but I thought I'd ask. Do you?
Edited by Faith, : No reason given.

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Brad McFall
Member (Idle past 5032 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 55 of 164 (352760)
09-28-2006 6:53 AM
Reply to: Message 54 by Faith
09-27-2006 9:57 PM


Re: Side issue
Yes, I think the proper expansion of evolutionary theory PROVIDES room for Creationism rather than achieveing a hierarchy at its' expense. I find the social reality that supports discussion of creation and evolution to be LARGER than the secular constriction that predominates currently correct psychology on the event.
It was nice that this thread was opened to deal with the more technical aspects of gene changes. If my less than rigorous proposal in this thread is correct, the actual chemical attractions and repulsions that accompany retrotransposition would have to be deriveable from the integral of Gladyshev I linked to and be "decodable" from the G content of DNA.
I do not know if this is actually possible. THAT would have been good criticism of my post.

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Equinox
Member (Idle past 5141 days)
Posts: 329
From: Michigan
Joined: 08-18-2006


Message 56 of 164 (352816)
09-28-2006 12:17 PM
Reply to: Message 36 by Faith
09-23-2006 10:44 PM


Re: New Genes?
Faith wrote:
quote:
And this one example, or maybe there are two or three by now, that is brought out as supposedly typical of mutation, is just not a convincing argument.
OK, I have to throw an honesty flag on the play here.
Faith, are you saying that there is only one example, or "maybe two or three by now" of a mutation which adds a trait? You and I discussed over a dozen on a thread here just the other day - some included my beautiful buttocks, the Apo person, whale legs, babies with tails, copper tolerant monkey flowers, conquistador algae, and more. You aren't claiming you forgot, are you?
As we discussed, for most of them there are reasons to know that we aren't talking about reshuffled already-present alleles. For instance, the algae is asexual - so you don't reshuffle anything. Similar reasons hold for the others.
Edited by Equinox, : No reason given.

-Equinox
_ _ _ ___ _ _ _
You know, it's probably already answered at An Index to Creationist Claims...
(Equinox is a Naturalistic Pagan -  Naturalistic Paganism Home)

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 Message 36 by Faith, posted 09-23-2006 10:44 PM Faith has replied

Replies to this message:
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Philip
Member (Idle past 4722 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 57 of 164 (352832)
09-28-2006 1:00 PM
Reply to: Message 27 by jerker77
09-23-2006 7:41 AM


Re: New Genes?
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

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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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 58 of 164 (352833)
09-28-2006 1:00 PM
Reply to: Message 56 by Equinox
09-28-2006 12:17 PM


Re: New Genes?
Faith, are you saying that there is only one example, or "maybe two or three by now" of a mutation which adds a trait? You and I discussed over a dozen on a thread here just the other day - some included my beautiful buttocks, the Apo person, whale legs, babies with tails, copper tolerant monkey flowers, conquistador algae, and more. You aren't claiming you forgot, are you?
Yeah I forgot some of them. What's your point now, it's not two or three but six or seven? And what are they supposed to prove? I thought the tail example wasn't supposed to be a mutation. What would be the point in that case? Isn't it supposed to prove we're related to apes? A novel trait wouldn't prove that.
As we discussed, for most of them there are reasons to know that we aren't talking about reshuffled already-present alleles. For instance, the algae is asexual - so you don't reshuffle anything. Similar reasons hold for the others.
There are some mutations. I've acknowledged that. They're an odd bunch these you list. Pretty pathetic evidence that mutation could possibly account for all the variety of life.

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Equinox
Member (Idle past 5141 days)
Posts: 329
From: Michigan
Joined: 08-18-2006


Message 59 of 164 (352884)
09-28-2006 3:37 PM
Reply to: Message 58 by Faith
09-28-2006 1:00 PM


Re: New Genes?
Faith wrote:
quote:
Yeah I forgot some of them. What's your point now, it's not two or three but six or seven?
First, we had listed over a dozen, with more coming up in conversation. My point wasn’t that it was this or that number, but that it is much more than just one or two cases, and that you know that.
quote:
And what are they supposed to prove?
They show that it is quite plausible that the current diversity of life is accumulated traits such as these. The principle here is statistical sampling. For instance, if I test a mL of water from 1000 different places around the earth, and I find bacteria in 941 of them, then it’s reasonable to conclude that bacteria is common in water on earth. BUT HOLD ON - I’ve only tested a total of 1 liter out of the over 1,000,000,000,000,000,000,000 liters of water on earth. (yes I calculated that out). It’s reasonable due to statistical sampling, even though the percentage tested is tiny.
In our case, we’ve seen plenty of mutations, some beneficial, some harmful, most neutral, in the past couple hundred years, even though we only have looked at a tiny percentage of animals and humans. Thus, if we’ve seen plenty in such a short time, it’s quite reasonable to expect that we are seeing the typical rate. Of all the millions of animals born in the past few centuries, we’ve only watched a tiny percentage of them, less than 0.00000001%. And as far as time goes, 200/4 billion=0.00000005. Multiplying those numbers predicts that we’ve only seen a very small fraction of the mutations that have occurred. So it’s quite reasonable that there have been billions of beneficial mutations based on what we’ve seen and discussed here at EvC.
quote:
I thought the tail example wasn't supposed to be a mutation. What would be the point in that case? Isn't it supposed to prove we're related to apes? A novel trait wouldn't prove that.
First, in science one piece of evidence doesn’t “prove” something. Evidence from different lines of inquiry all support (or don’t) a given hypothesis.
The tails are what we’d expect if we are descended from earlier primates (not just apes, which don’t have tails anyway). For instance, if 8 million years ago a gene is something like
AATACGTGTTGTGAC, and it promotes tail growth, then a mutation, say to
AATACGTGTTGTGAT, may render it nonfunctional. That gene may then be selected for (since maybe women find a shorter tail sexy), and so later humans could all have the second version. Then, in a baby in Spain in the 20th century or some such, a mutation occurs that switches it back to a C, or to an equivalent nucleotide, since the system is redundant anyway:
AATACGTGTTGTGAC. So the baby has a tail due to the mutation, revealing our evolutionary past (since the rest of the genetic mechanism for making a tail is still there).
Now, for a creationist, this mutation must be a novel trait, since humans didn’t come from tailed primates. That’s why I listed it, because in the creationist worldview, it’s novel. Did I misunderstand the creationist view of tails in human babies?

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 Message 58 by Faith, posted 09-28-2006 1:00 PM Faith has replied

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 Message 60 by Faith, posted 09-28-2006 4:35 PM Equinox has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 60 of 164 (352908)
09-28-2006 4:35 PM
Reply to: Message 59 by Equinox
09-28-2006 3:37 PM


Re: New Genes?
First, we had listed over a dozen, with more coming up in conversation. My point wasn’t that it was this or that number, but that it is much more than just one or two cases, and that you know that.
It isn't MUCH more, and even if it were fifty that is a paltry number for the job asked of it, and the kinds of mutations you are talking about are mostly just weird, not the kind of stuff that could put together such marvelous unities as life exhibits.
Yeah, I know the probabilities and they are simply astronomically unconvincing. I really don't know how they convince you.
And if the mutation that brought about the tail is simply the recurrence of a formerly expressed allele, in my book that's not a mutation, but I understand that in your book it must be that because your book is the book of the ToE. Yes you are right that in my book the tail IS a mutation, and not the recurrence of a formerly expressed allele, just a bizarre anomaly (and they aren't much in the way of tails anyway, just a flaccid rope of skin. But why is that such a big deal? YOu act as if we deny mutations. We don't. We deny that they are capable of bringing about the design and diversity of life we see around us.
And as usual, in your post, as per the ToE, the facts are SO scanty and all the rest is hypothetical, not evidence of any sort. I understand that one is often driven to that, but then don't claim the ToE rests on firm foundations.

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