Register | Sign In


Understanding through Discussion


EvC Forum active members: 65 (9162 total)
4 online now:
Newest Member: popoi
Post Volume: Total: 915,817 Year: 3,074/9,624 Month: 919/1,588 Week: 102/223 Day: 0/13 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   The origin of new genes
AdminModulous
Administrator
Posts: 897
Joined: 03-02-2006


Message 31 of 164 (351587)
09-23-2006 12:47 PM
Reply to: Message 30 by macnietspingal
09-23-2006 12:36 PM


Topic?
This doesn't seem terribly on topic. We try and keep even subthreads related to the topic in the first post. Might I ask for a bit more focus when you post? Thanks.

New Members should start HERE to get an understanding of what makes great posts.
Comments on moderation procedures (or wish to respond to admin messages)? - Go to:
General discussion of moderation procedures
Thread Reopen Requests
Considerations of topic promotions from the "Proposed New Topics" forum
Other useful links:
Forum Guidelines, Observations about Evolution and This could be interesting....

This message is a reply to:
 Message 30 by macnietspingal, posted 09-23-2006 12:36 PM macnietspingal has replied

Replies to this message:
 Message 33 by macnietspingal, posted 09-23-2006 3:59 PM AdminModulous has replied

  
bernd
Member (Idle past 3981 days)
Posts: 95
From: Munich,Germany
Joined: 07-10-2005


Message 32 of 164 (351591)
09-23-2006 12:56 PM
Reply to: Message 23 by Faith
09-23-2006 12:30 AM


Hello Faith,
You wrote:
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
We obviously have a different understanding of the tems like gene, allele and locus. I propose the following definitions
Gen: Structurally, a basic unit of hereditary material; an ordered sequence of nucleotide bases that encodes a product (this product could be just RNA like rRNA or finally coding for a protein). The gene includes, however, regions preceding and following the coding region (5' UTR and 3' UTR) as well as (in eukaryotes) intervening sequences (introns) between individual coding segments (exons).
Allele: Alternative form of a gene. One of the different forms of a gene that can exist at a single locus
Gen locus: The specific place on a chromosome where a gene is located.
The topic of this thread is the origin of genes, not of alleles.
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.
In the case of GLUD2 we can reconstruct the evolutionary history of the gene by analysing its sequence differences in primates. Here are the results:
  • GLUD1 is an intron carrying gene, present in all primates
  • GLUD2 is only present in apes and humans, but not in Old World Monkeys
  • GLUD2 is a intronless copy of GLUD1 on a different chromosome, suggesting retrotransposition of a spliced mRNA derived from GLUD1
  • GLUD1 hasn’t accumulated amino acid substitutions (suggesting strong purifying selection)
  • GLUD2 in human has accumulated 15 amino acid substitutions compared to GLUD1. Two of this substitutions are shared by apes and humans. This two have been shown to be essential for the brain specific function of GLUD2
  • Analysis of Ka/Ks ratio suggests strong positive selection for certain sites of GLUD2
  • The phylogenetic tree based on GLUD2 sequences reflects the nested hierachy of Great World Apes, apes and humans obtained by a cladistic analysis.
The results support that GLUD2 is a young primate retrogene created by retroduplication of GLUD1 with subsequent evolution of its brain specific function.
How do you know it's a mutation as opposed to a normally occurring alternative allele?
In the case of GLUD2 we know that it is not simply an allele because its linked to a different chromosome (GLUD1 is linked to chromosome 10, GLUD2 is X linked).
If it's a mutation, how sure are you that it is not contributing something the organism would be better off without?
Because decreased activity of GLUD2 leads to neurodegenerative disorders.
-Bernd

This message is a reply to:
 Message 23 by Faith, posted 09-23-2006 12:30 AM Faith has not replied

  
macnietspingal
Inactive Member


Message 33 of 164 (351623)
09-23-2006 3:59 PM
Reply to: Message 31 by AdminModulous
09-23-2006 12:47 PM


Re: Topic?
Well I don't think it's scientific to discuss diseases either with respect to gene's. Especially cancer. I don't think any one knows what they are talking about. The whole pharmaceutical scene has been politicised with false information. If you stick strictly to the mathematics of gene's then it's on focus. Once you mention cancer, you are way off base. It's been this false information given to doctors that caused my cancer. I waited 15 years before I took HRT and when I did, it caused cancer. I thought 15 years was sufficient to be safe using others as guinea pigs.
But obviously it wasn't.

This message is a reply to:
 Message 31 by AdminModulous, posted 09-23-2006 12:47 PM AdminModulous has replied

Replies to this message:
 Message 42 by AdminModulous, posted 09-24-2006 2:03 PM macnietspingal has not replied

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


Message 34 of 164 (351690)
09-23-2006 10:23 PM
Reply to: Message 25 by Hawks
09-23-2006 4:53 AM


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.

This message is a reply to:
 Message 25 by Hawks, posted 09-23-2006 4:53 AM Hawks has replied

Replies to this message:
 Message 47 by Hawks, posted 09-26-2006 8:41 PM Faith has not replied
 Message 48 by Dr Adequate, posted 09-26-2006 8:55 PM Faith has not replied

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


Message 35 of 164 (351695)
09-23-2006 10:30 PM
Reply to: Message 26 by Dr Adequate
09-23-2006 7:20 AM


Reciting this does not make it true
Recitation doesn't make anything true, but thinking it through ought to show that this really is just circumstantial speculative reasoning with no actual facts involved:
Dr. A writes:
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.
Because this form occurs within a certain group is not evidence for your claim. You are assuming descent from one to another, but this is not proved, merely assumed. Similarity of design accounts just as well for the facts. Morphology and genetics and the fossil record are equally well accounted for by this other explanation. You are arguing from theory through association and comparison. There is no actual proof here. Mere analogizing.

This message is a reply to:
 Message 26 by Dr Adequate, posted 09-23-2006 7:20 AM Dr Adequate has replied

Replies to this message:
 Message 37 by Dr Adequate, posted 09-23-2006 10:45 PM Faith has replied

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


Message 36 of 164 (351697)
09-23-2006 10:44 PM
Reply to: Message 27 by jerker77
09-23-2006 7:41 AM


Re: New Genes?
... 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.
OK, this sounds like a topic I may want to take to the mutation discussion threads eventually.
It IS a different question, yes, but WHAT the DNA "says" has to be the most important thing.
A gene is a very very long string of these amino acids, right? That codes for a specific protein, right? 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?
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. 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.

This message is a reply to:
 Message 27 by jerker77, posted 09-23-2006 7:41 AM jerker77 has replied

Replies to this message:
 Message 38 by Dr Adequate, posted 09-23-2006 10:57 PM Faith has not replied
 Message 46 by jerker77, posted 09-26-2006 5:08 PM Faith has not replied
 Message 56 by Equinox, posted 09-28-2006 12:17 PM Faith has replied

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


(1)
Message 37 of 164 (351698)
09-23-2006 10:45 PM
Reply to: Message 35 by Faith
09-23-2006 10:30 PM


Recitation doesn't make anything true, but thinking it through ought to show that this really is just circumstantial speculative reasoning with no actual facts involved:
Merely reciting this will not make it true.
Where is the bit where you "think it through"?
Because this form occurs within a certain group is not evidence for your claim. You are assuming descent from one to another.
No. Do not tell me falsehoods about what I think, as this is neither polite, accurate, nor moral.
, but this is not proved, merely assumed.
No, don't be silly.
Similarity of design accounts just as well for the facts. Morphology and genetics and the fossil record are equally well accounted for by this other explanation.
No: which is why you cannot account for them in this way.
You are arguing from theory through association and comparison. There is no actual proof here. Mere analogizing.
No. Do not tell me falsehoods about how I am arguing, as this is neither polite, accurate, nor moral.
Edited by Dr Adequate, : No reason given.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 35 by Faith, posted 09-23-2006 10:30 PM Faith has replied

Replies to this message:
 Message 39 by Faith, posted 09-23-2006 11:04 PM Dr Adequate has replied

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


Message 38 of 164 (351701)
09-23-2006 10:57 PM
Reply to: Message 36 by Faith
09-23-2006 10:44 PM


And this one example, or maybe there are two or three by now,
"Or maybe there are two or three right now"?
Sheesh.
that is brought out as supposedly typical of mutation...
No it isn't.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 36 by Faith, posted 09-23-2006 10:44 PM Faith has not replied

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


Message 39 of 164 (351705)
09-23-2006 11:04 PM
Reply to: Message 37 by Dr Adequate
09-23-2006 10:45 PM


Seems to me what I said is a fair representation of the implications of what you said, but if I'm wrong you need to show how, not just keep saying it over and over. As you yourself said, merely reciting something doesn't make it true.

This message is a reply to:
 Message 37 by Dr Adequate, posted 09-23-2006 10:45 PM Dr Adequate has replied

Replies to this message:
 Message 40 by Dr Adequate, posted 09-23-2006 11:24 PM Faith has not replied

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


(1)
Message 40 of 164 (351708)
09-23-2006 11:24 PM
Reply to: Message 39 by Faith
09-23-2006 11:04 PM


Seems to me what I said is a fair representation of the implications of what you said but if I'm wrong you need to show how ...
Wow, you're asking me to substantiate my statements about what my opinions are.
I mean ... what? Sheesh.
(1) I said nothing of the sort. Where did I say that my statements were "not proved, merely assumed"? I didn't. Did I say that my statements were "mere analogizing"? No, I did not.
(2) I have explicitly told you that these are not my opinions.
This is how you know that the opinions which you have attributed to me are not mine.
Could anything be clearer?
, not just keep saying it over and over. As you yourself said, merely reciting something doesn't make it true?
What have I repeated? Ah yes, my advice to you not to tell me falsehoods about my opinions.
Let me repeat that sentiment once more.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 39 by Faith, posted 09-23-2006 11:04 PM Faith has not replied

  
mick
Member (Idle past 4986 days)
Posts: 913
Joined: 02-17-2005


Message 41 of 164 (351736)
09-24-2006 4:50 AM
Reply to: Message 20 by Faith
09-23-2006 12:15 AM


mutations give rise to new genes, and do not just disrupt old ones
faith writes:
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.
Hi Faith,
An article recently published in Genomics gives evidence of the mutational origin of new alleles coding for completely novel proteins in human beings. The article is Frequent appearance of novel protein-coding sequences by frameshift translation by Okamura et al.
The authors concern themselves with two types of mutation: first, gene duplication (in which a gene coded once in parental DNA is copied incorrectly such that it appears twice or more in offspring DNA); second, frame-shift mutation. I'm sure you know what a frame-shift mutation is, Faith, but I'll explain it for the benefit of others.
The nucleotides which make up the sequence for a gene are converted into a protein by the ribosomes, which "read" nucleotides three at a time. Each consecutive triplet of nucleotides corresponds to a single amino acid in the protein. So, a string of 300 nucleotides would result in a protein consisting of 100 amino acids. For example, below is a random string of fifteen nucleotides followed by a string of five amino acids. Like nucleotides which are represented by A,C,G and T, amino acids are also represented by single letter codes:

nucleotides: ATACGATTCTTACTT
protein: A R F L L
A frame-shift mutation involves the deletion or insertion of nucleotides such that the triplets are thrown out of sync with the "correct" protein. For example, if the first nucleotide of the sequence above were to be deleted by a mutation, the translated protein would be completely different because instead of "ATA" being the first triplet, "CGA" being the second, etc, the first triplet would be "TAC", the second would be "GAT", etc. See below:

nucleotides: TACGATTCTTACTT
protein: Y D S Y X
It's easy to imagine that if duplication of a gene is followed by a frame-shift mutation in one of the copies, that copy would end up producing a completely different protein to that produced by the original version of the gene. According to you, these novel proteins would be deleterious and removed from the genome by selection.
The authors of the paper decided to identify the existence of functional proteins arising from duplication and frame-shift mutation in human beings. They searched the databases for known protein-coding nucleotide sequences. For each sequence they generated five possible frame-shifted versions (1: deleting the first nucleotide; 2: deleting the first two nucleotides; 3: reading the sequence backwards; 4: deleting the first nucleotide and reading the sequence backwards; 5: deleting the first two nucleotides and reading the sequence backwards). They then worked out what amino acids these "mutated" sequences would code for in the human body and searched for the existence of such proteins in the DNA databases.
They found 470 proteins that appear to have arise by duplication and frame-shift from preexisting genes in the human genome. These proteins are functional in the human body, in that they create proteins that actually do useful stuff inside the cell. But the proteins are completely different to the original version of the gene in terms of their amino acid sequences so they are truly "novel" proteins.
The authors generated their simulated mutated sequences from a database of 23000 curated proteins. This means that around 2% of all functional human proteins arose from duplication and frame-shift. That's just from one single type of mutation!
If you are unwilling to accept that mutation can generate novel and functional proteins, then you need to explain these results. It seems to me that either spontaneous random mutations do indeed account for the origin of new genes; or, God uses mutations to create new genes. Either way, mutations DO create new, functional genes.
I think it is important to point out that the authors of the paper considered the possibility that 470 matches might have occurred simply by chance. They tested this possibility by generating 23000 completely random nucleotide sequences and repeating the experiment. They found zero matches. I would be interested to know how you would explain these results if you persist in believing that mutation does not contribute to the formation of new functional genes.
Mick
Edited by mick, : Added final paragraph and challenge
Edited by mick, : edited thread title

This message is a reply to:
 Message 20 by Faith, posted 09-23-2006 12:15 AM Faith has not replied

Replies to this message:
 Message 43 by Maxwell's Demon, posted 09-25-2006 3:52 PM mick has not replied
 Message 95 by Jazzns, posted 10-30-2006 2:36 PM mick has not replied

  
AdminModulous
Administrator
Posts: 897
Joined: 03-02-2006


Message 42 of 164 (351810)
09-24-2006 2:03 PM
Reply to: Message 33 by macnietspingal
09-23-2006 3:59 PM


Re: Topic?
I appreciate that you wanted to mention that you think cancer isn't necessarily related to mutations in the genome. That it is not scientific to suggest it is caused by mutagens acting at a genetic level to cause cells to erroneously replicate or what have you. That alone would have sufficed as a response to sidelined (and hopefully he would suggest the issue be resolved in a new topic where it can be the focus of discussion), however your Message 30 did not just state this.
Message 30 talked about smoking, dermal absorption of chemicals, menstruation, orgasms, gorillas and free availability of genomes for all humans. This is why you were pulled up for not focussing and being off topic.
If you wish to continue your discussions regarding cancer then propose a new topic (by clicking here) on the causes of cancer. Any further discussion in this thread will be off topic and will warrant a suspension. Do not respond to this post, but instead take any comments about this moderator decision to the appropriate thread linked to in the blue box in my signature below.
Thank you for your consideration.
Edited by AdminModulous, : dicsussion sounds *too* rude not to correct.

New Members should start HERE to get an understanding of what makes great posts.
Comments on moderation procedures (or wish to respond to admin messages)? - Go to:
General discussion of moderation procedures
Thread Reopen Requests
Considerations of topic promotions from the "Proposed New Topics" forum
Other useful links:
Forum Guidelines, Observations about Evolution and This could be interesting....

This message is a reply to:
 Message 33 by macnietspingal, posted 09-23-2006 3:59 PM macnietspingal has not replied

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


Message 43 of 164 (352171)
09-25-2006 3:52 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
The results of the article you referenced are interesting, but I'm a bit disappointed in the part where the authors considers chance as a possibility. I mean... they only do it for one set of sequences (the sequences being the elements of the set)?
Without knowing the total ammount of possible sets, and the ammount of those wherein you'd get no "hits", it's really hard to know if that test has any significance. I mean... maybe the ratio of sets with no "hits" to the ammount of total possible sets is somewhere like... I dunno... 0.25. Then it's not a very impressive test at all, at least not when only performed once (since 1 out of 4 tests would come out with no hits by chance alone).
Based purely on my knowledge about how these sort of calculations usually pan out, I do think that this ratio is fantastically small, and so the result would have significance, but I don't know that...
If these sorts of calculations were possible however, I would much prefer a calculation of the ratio of the ammount of sets with 470 "hits" or more, to the total ammount of possible sets. This would give us the probability that the actual experiment got a result of the level it did by chance alone.
Maybe these sorts of calculations are impossible with todays computer power (considering the sizes of the numbers involved), but in the very least there should be some kind of approximate method, to show that a given ratio is lesser than, or larger than a certain upper or lower bound (depending on which of the previously mentioned numbers one wants to check, "no hits" or "470 or more hits"), that might give you an idea of what kind of numbers we're talking about...
With some kind of numbers involved here (and if those numbers pointed in the right direction) I'd consider this yet another overwhelming piece of evidence for evolution... but without them... I dunno...
Maybe I'm missing something (maybe these numbers (or something similar) are in the article... I could only read the abstract without paying up a bunch of money I'm not willing to pay)?
EDIT: Looking over what I've written, some of it doesn't make sense. For instance, my whole part on the probability of no "hits" is just stupid. Obviously, you'd want the percentage of no "hits" to total ammount of sets to be large... that means that the result of the actual experiment, with 470 hits is unlikely if evolution did not take place.
The point I was trying to make stands though... that is, we have no real numbers to tell us how likely any of this is. Yes, performing the test gives us some kind of probability that no "hits" probably is a high percentage of the sets... but it's not very precise.
Edited by Maxwell's Demon, : Edited because I realised a large part of my text made little sense, and I wanted to clarify.

This message is a reply to:
 Message 41 by mick, posted 09-24-2006 4:50 AM mick has not replied

Replies to this message:
 Message 44 by Dr Adequate, posted 09-26-2006 12:35 PM Maxwell's Demon has replied

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


Message 44 of 164 (352392)
09-26-2006 12:35 PM
Reply to: Message 43 by Maxwell's Demon
09-25-2006 3:52 PM


It would be difficult to put an exact figure on the improbability; however, if mick can tell us the range of lengths of the nucleotides involved, it should be possible to figure out a conservative estimate for improbability: i.e. to say "it is at least n to 1 against this occuring by chance."
However, I think the empirical approach of the researchers is OK. You say that they used only one set --- yes, but it had 23000 members, and so over two hundred million opportunities for a match by chance. They found none. In fact, using more sets would not be the way to go if you wanted more data: it would be more efficient to use a set with more members.

This message is a reply to:
 Message 43 by Maxwell's Demon, posted 09-25-2006 3:52 PM Maxwell's Demon has replied

Replies to this message:
 Message 45 by Maxwell's Demon, posted 09-26-2006 3:20 PM Dr Adequate has replied

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


Message 45 of 164 (352418)
09-26-2006 3:20 PM
Reply to: Message 44 by Dr Adequate
09-26-2006 12:35 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, just as humans will sometimes do with their designs. Such a "prediction" however, cannot give us any numbers. It's just an either/or deal. But it would explain why a randomly generated set of sequences wouldn't find any "hits". God doesn't generate randomly.
Evos would (more obviously) have the upper hand in this case, if some kind of numbers could be produced to quantify the results (which is impossible in the creo "prediction" I suggested).
EDIT:
Maybe I'm talking out of my backside here, but that's the way it seems to me. Without numbers all we have is "Evolutionary theory predicts we'd see *some* ammount of hits", and we do. Which would be no better than "Designer likes to reuse designs sometimes predicts we'd see *some* ammount of hits". But since I know there are numbers there... the TOE should be able to easily trump the latter example.
Edited by Maxwell's Demon, : Added some stuff after the "EDIT:".

This message is a reply to:
 Message 44 by Dr Adequate, posted 09-26-2006 12:35 PM Dr Adequate has replied

Replies to this message:
 Message 49 by Dr Adequate, posted 09-26-2006 9:26 PM Maxwell's Demon has replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024