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Author Topic:   The origin of new genes
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 16 of 164 (351466)
09-22-2006 7:35 PM
Reply to: Message 11 by Faith
09-22-2006 3:31 PM


Thank you for describing as "speculative thinking" a paper you can't be bothered to read.
How do I know a mutation was involved? Because this form of three-color vision is confined within a group of animals known to be a clade. How do I know this, I hear you ask? By comparing the predictions of this theory to the data in morphology, genetics, and the fossil record, of course.

This message is a reply to:
 Message 11 by Faith, posted 09-22-2006 3:31 PM Faith has replied

Replies to this message:
 Message 21 by Faith, posted 09-23-2006 12:19 AM Dr Adequate has replied

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


Message 17 of 164 (351487)
09-22-2006 9:26 PM
Reply to: Message 12 by bernd
09-22-2006 4:28 PM


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)

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


Message 18 of 164 (351488)
09-22-2006 9:33 PM
Reply to: Message 17 by Philip
09-22-2006 9:26 PM


Re: New Genes?
Can you explain what you're trying to say and on what grounds you're saying it?
Thanks.

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 Message 17 by Philip, posted 09-22-2006 9:26 PM Philip has replied

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sidelined
Member (Idle past 5907 days)
Posts: 3435
From: Edmonton Alberta Canada
Joined: 08-30-2003


Message 19 of 164 (351497)
09-22-2006 10:39 PM
Reply to: Message 7 by Faith
09-22-2006 1:10 PM


Faith
Again, of course mutations OCCUR, the doubt is whether they could possibly do what the ToE requires them to do, and I have not seen any actual facts that demonstrate that they could or do, merely speculations and assumptions.
I do not understand what you assume TOE requires them to do. If you understand that mutations can occur that are detrimental to macroevolution why do you seem to misunderstand that it is to be expected that detrimental effects outway beneficial ones? Since a complex organization of cells {which is what animals are} requires conditions to be met it should be obvious that there are more ways in which things can go "wrong "in the development of living animals than there are ways for it to go "right".
You also seem to think that evolution in bactria is somehow not macroevolution at all. All functions within human beings occur at the cellular level. Now what are the sizes of the cells in the animal world? Here is a chart listing the variety of size.
0.1 nm (nanometer) diameter of a hydrogen atom
0.8 nm Amino Acid
2 nm Diameter of a DNA Alpha helix
4 nm Globular Protein
6 nm microfilaments
10 nm thickness cell membranes
11 nm Ribosome
25 nm Microtubule
50 nm Nuclear pore
100 nm Large Virus
150-250 nm small bacteria such as Mycoplasma
200 nm Centriole
200 nm (200 to 500 nm) Lysosomes
200 nm (200 to 500 nm) Peroxisomes
800 nm giant virus Mimivirus
1 m (micrometer)
(1 - 10 m) the general sizes for Prokaryotes
1 m Diameter of human nerve cell process
2 m E.coli - a bacterium
3 m Mitochondrion
5 m length of chloroplast
6 m (3 - 10 micrometers) the Nucleus
9 m Human red blood cell
10 m
(10 - 30 m) Most Eukaryotic animal cells
(10 - 100 m) Most Eukaryotic plant cells
90 m small Amoeba
100 m Human Egg
up to 160 m Megakaryocyte
up to 500 m giant bacterium Thiomargarita
up to 800 m large Amoeba
1 mm (1 millimeter, 1/10th cm)
1 mm Diameter of the squid giant nerve cell
120 mm Diameter of an ostrich egg (a dinosaur egg was much larger)
3 meters Length of a nerve cell of giraffe's neck
So since we can agree that mutations can occur in bacteria such as E.Coli and that E.Coli {2 miliionths of a meter, as recorded in list} is a thousand times larger that of a DNA helix {2billionths of a meter} and that a tiny change within the DNA can have profound effects upon subsequent animal development it would follow that mutation occurs in DNA as well.
So we go on to ask what effect this can have in the natural world. If the animal has an advantage provided by a mutation that produces , say, a longer stride capabilty in an animal that is prey for another, then it is obvious that this particular animal would be more likely to live and reproduce. If ,in turn, this advantage is great enough then we find that a greater stride length will become more prevalent since ,as a prey develops a greater ability to evade being eaten then it shall produce a greater number of offspring inhereiting these characteristics.In turn, the predator will either adapt through the natural selection process and thus allow the population as a whole to survive or the group will tend towards extinction.
Now ,since we can examine the animal genome and determine that,yes, certain genes express different characteristics such as stride length through longer leg bones that in turn are selected by the enviroment we can see that mutations such as this are indeed beneficial.
What exactly is it about TOE that fails to account for life as it is?
Edited by sidelined, : No reason given.

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 Message 7 by Faith, posted 09-22-2006 1:10 PM Faith has replied

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


Message 20 of 164 (351512)
09-23-2006 12:15 AM
Reply to: Message 19 by sidelined
09-22-2006 10:39 PM


I do not understand what you assume TOE requires them to do. If you understand that mutations can occur that are detrimental to macroevolution why do you seem to misunderstand that it is to be expected that detrimental effects outway beneficial ones? Since a complex organization of cells {which is what animals are} requires conditions to be met it should be obvious that there are more ways in which things can go "wrong "in the development of living animals than there are ways for it to go "right".
What you don't get is that this kind of thinking is nothing but ingenious rationalization. There isn't a fact in the whole thing.
If the animal has an advantage provided by a mutation that produces , say, a longer stride capabilty in an animal that is prey for another, then it is obvious that this particular animal would be more likely to live and reproduce.
If if if. That's all true except the part about mutation being the cause of the advantageous variation, which is purely speculation. Many advantageous variations are selected but their SOURCE is what is in doubt.
Now ,since we can examine the animal genome and determine that,yes, certain genes express different characteristics such as stride length through longer leg bones that in turn are selected by the enviroment we can see that mutations such as this are indeed beneficial.
BUT NOBODY IS DENYING THAT THIS SORT OF SELECTION OCCURS. It's the SOURCE of these variations we are questioning. You do not know that these are MUTATIONS as opposed to normally occurring alleles.
What exactly is it about TOE that fails to account for life as it is?
It's all theory, all speculative guesswork! Why don't you see that? You can't actually prove those are mutations, track those supposed mutations to their origin point that you credit with bringing about all this change, you are simply ASSUMING they do so. You don't know if they are mutations, something novel, or simply a normally occurring allele that got selected in the recombination lottery.
Edited by Faith, : No reason given.

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


Message 21 of 164 (351513)
09-23-2006 12:19 AM
Reply to: Message 16 by Dr Adequate
09-22-2006 7:35 PM


All circumstantial evidence, Dr. A, thickly stuffed with assumptions. No hard evidence.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 16 by Dr Adequate, posted 09-22-2006 7:35 PM Dr Adequate has replied

Replies to this message:
 Message 26 by Dr Adequate, posted 09-23-2006 7:20 AM Faith has replied
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Philip
Member (Idle past 4722 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 22 of 164 (351514)
09-23-2006 12:22 AM
Reply to: Message 18 by Dr Adequate
09-22-2006 9:33 PM


Re: New Genes?
Sidelined (above) erroneously writes:
a mutation that produces , say, a longer stride capabilty
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 1
For 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

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


Message 23 of 164 (351515)
09-23-2006 12:30 AM
Reply to: Message 12 by bernd
09-22-2006 4:28 PM


you seem to accept that new genes are formed by mutation in bacteria and drosophila, but you ask for evidence that the same holds true for mammals.
I don't know why it is so hard to get this across, but I DO NOT DENY THAT NEW ALLELES ARE FORMED BY MUTATION. I don't know about genes. Genes are specific loci as I understand it, which are occupied by whatever number of alleles are available for that locus in a given population. I'm not aware that actual new genes are said to be created by mutation, merely alleles for that function.
But the problem is that the evidence for a particular allele's being really the product of a mutation and yet also beneficial, truly novel and truly functional as well, is pretty scant. But of course I still can't read links so I may have missed THE evidence. Most of the new links I try cause my computer to freeze up.
Most mutations don't do anything good, right?
22 examples of novel genes within drosophila, primates, rodents, fish, plants and protozoa (each with references to the relevant primary literature). You’ll find 11 examples of mammalian genes, one - named FOXP2 - is a transcription factor which controls language and speech related functions in homo sapiens.
How do you know it's a mutation as opposed to a normally occurring alternative allele? If it's a mutation, how sure are you that it is not contributing something the organism would be better off without?
Another example of an "useful" mammalian gene would be GLUD2, a gene, which probably affects higher cognitive functions. It has been formed by retrotransposition from the household gene GLUD1 in the hominoid line about 23 million years BP. It is expressed in human nerve and testis tissue and seems to positively influence cognitive functions by enhancing the flux of a neurotransmiter.
How do you know it's a mutation as opposed to a normally occurring alternative allele? If it's a mutation, how sure are you that it is not contributing something the organism would be better off without?
Please quote whatever you want me to read from the links, please explain it in your own words, and please don't use technical jargon. Thank you.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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


Message 24 of 164 (351516)
09-23-2006 12:36 AM
Reply to: Message 17 by Philip
09-22-2006 9:26 PM


Re: New Genes?
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.
Well, digesting nylon and surviving antibiotics DO sound like survival-enhancing variations. I just don't feel like fighting this battle on the level of bacteria and fruit flies. But if you have a good argument or some evidence that it all cascades into extinction, that would certainly fit with my overall expectations.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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


Message 25 of 164 (351539)
09-23-2006 4:53 AM
Reply to: Message 7 by Faith
09-22-2006 1:10 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.

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 Message 7 by Faith, posted 09-22-2006 1:10 PM Faith has replied

Replies to this message:
 Message 34 by Faith, posted 09-23-2006 10:23 PM Hawks has replied

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


Message 26 of 164 (351547)
09-23-2006 7:20 AM
Reply to: Message 21 by Faith
09-23-2006 12:19 AM


Reciting this does not make it true.

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 Message 21 by Faith, posted 09-23-2006 12:19 AM Faith has replied

Replies to this message:
 Message 35 by Faith, posted 09-23-2006 10:30 PM Dr Adequate has replied

  
jerker77
Inactive Member


Message 27 of 164 (351551)
09-23-2006 7:41 AM
Reply to: Message 22 by Philip
09-23-2006 12:22 AM


Re: New Genes?
For 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.
I don’t know if it has escaped the good doctor but there is no such thing as nonsense DNA, in the qualified meaning of the word. All possible combinations within the triplet actually say something. Either it is any of the 20 something amino acids or start or stop. So any given combination will say something. If that something that is said is beneficial for the survivability and proliferation of the gene is a different question.
Further it might deserve a notion to point to the fact that any gene is interacting whit an environment that is ever changing, so that which in one environment is deleterious is in another beneficial, i.e. sickle sell anaemia.
Childish analogies with books and computer programs have their severe limitation when they are taken for descriptions of reality instead of figures of speech.

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

This message is a reply to:
 Message 22 by Philip, posted 09-23-2006 12:22 AM Philip has replied

Replies to this message:
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fallacycop
Member (Idle past 5520 days)
Posts: 692
From: Fortaleza-CE Brazil
Joined: 02-18-2006


Message 28 of 164 (351553)
09-23-2006 8:40 AM
Reply to: Message 21 by Faith
09-23-2006 12:19 AM


All circumstantial evidence, Dr. A, thickly stuffed with assumptions. No hard evidence.
Faith, why don't you tell us what would you take as acceptable evidence. Then we could tell whether your expectations are reasonable or not, and perhaps this thread will be a little more interesting then the last two where you just kept shutting down all evidence given to you as not being acceptable evidence.
But remember that requiring a complete allele count of an organism before and after some speciation event will be considered unreasonable expectation by most people

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jar
Member (Idle past 393 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


(1)
Message 29 of 164 (351570)
09-23-2006 10:59 AM
Reply to: Message 23 by Faith
09-23-2006 12:30 AM


I don't know why it is so hard to get this across, but I DO NOT DENY THAT NEW ALLELES ARE FORMED BY MUTATION. I don't know about genes. Genes are specific loci as I understand it, which are occupied by whatever number of alleles are available for that locus in a given population. I'm not aware that actual new genes are said to be created by mutation, merely alleles for that function.
Let's parse that paragraph.
You agree that NEW alleles are formed by mutation.
You agree that genes are made up of alleles.
Therefore a gene that contains new alleles was made through mutation.
Faith, there is NO other possible conclusion based on what you said in that paragraph. If you believe that is incorrect, then you need to present the model.

Aslan is not a Tame Lion

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macnietspingal
Inactive Member


Message 30 of 164 (351585)
09-23-2006 12:36 PM
Reply to: Message 6 by sidelined
09-22-2006 12:40 PM


cancer from genes
Personally I believe that I got breast cancer from Estrogen (formerly Hormone) Replacement Therapy. Also it may be that birth control pills produce weakness to cancer. Also maybe viagra. Now that Lance Armstrong admits he used steroids, maybe that called his cancer. I think chemistry causes cancer.
We don't really study the natural biology of menstuation and orgasm at all. All the "juices" that are involved. Even smoking anything may effect the health of all of us since we now know that medication can be provided dermally. Think about the saliva that lies all around the remains of the cigarettes on the ground and when you shake hands. I found out from my vet that all veterans and pediatricians can smell the tobacco on their patients.
The recent tv documentary about Neanderthal and Homo Sapiens and Cro-Magnon points out to me that if you trace your DNA program too far back you may be closer to a gorilla than those who trace back to a later evolution
First we have to understand our own bodies via sexual components and especially orgasms. No one does this. It's beyond me how a man can feel like a woman when women don't have Y dna. Nothing makes sense any more if you are a creationist or an evolutionist. You are all talking about someone else, and not observing your own self. If people started talking only about themselves after getting some knowledge of DNA, we'd all come to more observable scientific solutions that would benefit all of us. Just dealing with the math isn't enough. It's the combination of how we use the hormones inside us and obey them that is important.
Don't you think all humans should be given their DNA at birth on their birth certificate. Until that happens there is no scientific information. With Internet, it's all up to us now. Even the homeless can be made to participate. Nothing should be free. Every human should be responsible for being human.
Edited by macnietspingal, : thought I spelled veterinarians wrong

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