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Author Topic:   Are mutations truly random or are they guided?
Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


Message 76 of 134 (548900)
03-02-2010 10:38 AM
Reply to: Message 74 by Bolder-dash
03-02-2010 10:22 AM


Re: carping creationists
How many more chances do you think your side should get? You claim it takes time...I don't know how much longer we can wait.
Oh, don't wait around for us. You go on and do your own research and see what you get. Who knows, you might just come up with something.
Your side does do research, doesn't it?

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.

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slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 77 of 134 (548916)
03-02-2010 1:20 PM
Reply to: Message 67 by Percy
03-02-2010 8:33 AM


Re: Neutral mutations
I'll start a topic on this later on this week about all this. The reason being that I don't have the references I need to support what my memory seems to remember (mutation rates, deleterious ratios, etc.)
But I will give a brief answer to your beetle example, even though the explanation will be similar to the ones coyote gave.
A beetle changing color isn't a near-neutral mutation, precisely because it gives a noticeable advantage to the beetle in a given environment. The mutation caused a change that has a sufficient enough impact on the phenotype for this (it changed color).
But as I said, I'll come back on this. I don't have Dr. Sanford's book with me right now.
PS On a final note, only 3% of the human genome codes for genes. But of course, what the ENCODE project is showing us is that more then 100% of it is being transcripted (because sometimes in both directions). This does not prove that it all serves a function of course, but it is very indicative of that in my opinion. Why would the cell spend so much energy and ressources transcripting what it doesn't even use ? It would make no sense in my opinion. I could make the prediction that eventually, science will find a function for all of the genome and that therefore, no mutation is actually effectively neutral.

This message is a reply to:
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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.6


Message 78 of 134 (548921)
03-02-2010 1:37 PM
Reply to: Message 77 by slevesque
03-02-2010 1:20 PM


Re: Neutral mutations
But of course, what the ENCODE project is showing us is that more then 100% of it is being transcripted (because sometimes in both directions). This does not prove that it all serves a function of course, but it is very indicative of that in my opinion.
Given the low number of actual transcripts it seems to be indicative of leaky RNA transcriptase activity, IMHO. No enzyme I know of has 100% substrate specificity, and I don't see why RNA trascriptase would be any different.

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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 79 of 134 (548923)
03-02-2010 2:04 PM
Reply to: Message 78 by Taq
03-02-2010 1:37 PM


Re: Neutral mutations
I think I understand what you are saying, but, could you please translate this to laymanese for us?

This message is a reply to:
 Message 78 by Taq, posted 03-02-2010 1:37 PM Taq has replied

Replies to this message:
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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.6


Message 80 of 134 (548925)
03-02-2010 2:47 PM
Reply to: Message 79 by AZPaul3
03-02-2010 2:04 PM


Re: Neutral mutations
If you compare the number of RNA molecules (i.e. trascripts) from a "traditionally" non-functional section of DNA with the number or RNA molecules from a functional section of DNA you will find that there are many more copies of RNA from traditionally functional DNA than non-functional DNA. The classic gene has RNA polymerase binding sites upstream of the actual coding portion allowing for transcription of the gene. By "leaky" trascriptase activity I am suggesting that RNA polymerase will bind to non-specific binding sites on occasion. When molecular biologists talk of "leaky" activity they are usually referring to non-specific activity.
Just as an example, endonucleases (enzymes that cut DNA at specific DNA sequences) are famous for this type of activity. It is called "star activity". When conditions aren't perfect or the endonuclease concentration is high enough the enzyme will cut at non-specific sites.

This message is a reply to:
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Replies to this message:
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slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 81 of 134 (548926)
03-02-2010 2:47 PM
Reply to: Message 79 by AZPaul3
03-02-2010 2:04 PM


Re: Neutral mutations
He is saying that the entire genome is being coded because the RNA transcriptases aren't specific enough to the gene-coding regions, and so mistakenly transcript other regions which they shouldn't.
Which as good a guess as any, but I prefer thinking that maybe the genome is even more complex then we thought
Edited by slevesque, : No reason given.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 82 of 134 (548927)
03-02-2010 2:53 PM
Reply to: Message 79 by AZPaul3
03-02-2010 2:04 PM


Re: Neutral mutations
What Taq is saying is that RNA polymerases, the proteins which bind to DNA and make mRNA from the DNA template, have specific patterns of DNA which they recognise and bind to when transcription is initiated. These proteins don't have a 100% perfect ability to bind only to those exact sequences so they may well bind to sequences which happen to be similar in other non biologically functional regions of the genome and transcribe that sequence into mRNA, even though the resulting mRNA serves no purpose.
This seems reasonable, but I would also add another factor which is that many transcription factor binding motifs are comparatively simple, like the common TATA box with the sequence TATAAA. So rather than the potentially non functional transcripts being the result of non-specific binding they are rather the result of binding to specific sequences which simply occur by chance in the genome in some cases.
TTFN,
WK

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.6


Message 83 of 134 (548928)
03-02-2010 3:03 PM
Reply to: Message 81 by slevesque
03-02-2010 2:47 PM


Re: Neutral mutations
Which as good a guess as any, but I prefer thinking that maybe the genome is even more complex then we thought . . .
Perhaps even overly complex as shown by the ability to delete large chunks of the mouse genome without producing a noticeable effect.
There is also the possibility that evolution has favored leaky RNA polymerase activity as a way of promoting variation. As a corrolary, the study below suggests that the binding site of DNA polymerases is "looser" than it could be allowing for mutations to occur indicating an evolutionary advantage compared to complete fidelity.
quote:
Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15803-8. Epub 2005 Oct 25.
Probing the active site tightness of DNA polymerase in subangstrom increments.
Kim TW, Delaney JC, Essigmann JM, Kool ET.
Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.
We describe the use of a series of gradually expanded thymine nucleobase analogs in probing steric effects in DNA polymerase efficiency and fidelity. In these nonpolar compounds, the base size was increased incrementally over a 1.0-A range by use of variably sized atoms (H, F, Cl, Br, and I) to replace the oxygen molecules of thymine. Kinetics studies with DNA Pol I (Klenow fragment, exonuclease-deficient) in vitro showed that replication efficiency opposite adenine increased through the series, reaching a peak at the chlorinated compound. Efficiency then dropped markedly as a steric tightness limit was apparently reached. Importantly, fidelity also followed this trend, with the fidelity maximum at dichlorotoluene, the largest compound that fits without apparent repulsion. The fidelity at this point approached that of wild-type thymine. Surprisingly, the maximum fidelity and efficiency was found at a base pair size significantly larger than the natural size. Parallel bypass and mutagenesis experiments were then carried out in vivo with a bacterial assay for replication. The cellular results were virtually the same as those seen in solution. The results provide direct evidence for the importance of a tight steric fit on DNA replication fidelity. In addition, the results suggest that even high-fidelity replicative enzymes have more steric room than necessary, possibly to allow for an evolutionarily advantageous mutation rate.

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.6


Message 84 of 134 (548929)
03-02-2010 3:12 PM
Reply to: Message 82 by Wounded King
03-02-2010 2:53 PM


Re: Neutral mutations
This seems reasonable, but I would also add another factor which is that many transcription factor binding motifs are comparatively simple, like the common TATA box with the sequence TATAAA. So rather than the potentially non functional transcripts being the result of non-specific binding they are rather the result of binding to specific sequences which simply occur by chance in the genome in some cases.
Not only that, but TATA boxes make up just a portion of the possible eukaryotic promoter sequences. There are also e-boxes with the sequence CACGTG. Add to that promoter regions from ERV's and their SINE and LINE derivatives, pseudogenes, promoters from recombination events involving one or both, and numts. Perhaps the best way to describe the transcriptome is "noisy".

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


Message 85 of 134 (548936)
03-02-2010 4:05 PM
Reply to: Message 68 by Bolder-dash
03-02-2010 8:45 AM


Re: unreal expectations based on false information
This is a good expalantion for why your side gets beat up so bad in live debates (see Meyer/Sternberg vs. Shermer/Prothero).
There is a good explanation of why creationists manage to swindle dupes like you into thinking that they're good debaters, which is that none of their statements are constrained by reality.
You have little to say to defend your own theory, and rely on the tired old saw of claiming a monopoly on knowledge, and go read a biology book. Man what a bore your (Taz, Dr. A, Percy, ad infinitum...) answers are.
If you find it boring to have your biological illiteracy pointed out, then there are two solutions, both in your own hands. One is to acquire a little basic biological literacy, the other is to stop talking about biology.
It is YOUR side that says these random mutations are so numerous as to be able to explain the existence of all of life's complexities-yet you can show none.
We can show you lots of random mutations, like all of them.
Can you show me one instance of God poofing organisms out of nothing by magic?
You make the erroneous claim, over and over btw, that I am seeking some magical point mutation of a completed new system. Absolutely not; but since your side claims all of these complex systems start with some mutation-a mutation big enough to cause a reproductive advantage-surely you should at least be able to show a few starting points right?
First, please tell us how we can determine a beneficial mutation which is a "starting point" from one which isn't. Thank you.
Percy of course tried to squirm out this dilemma by mentioning bacteria, but even then he couldn't give any examples of anything. The fact is that when you talk about bacteria your sides argument gets even weaker-we have witnessed in our lifetimes billions and billions of generations of bacteria ...
Speak for yourself. I for one am not older than Young Earth Creationists are prepared to admit that the Earth is, and if I was I wouldn't have spent my whole life looking at bacteria.
... -and not a single new complex system has seen to have been formed ...
But this is not actually true. See Barry Hall's experiments, for example.
There isn't enough time in all of history times 10 to make even one very very simple new system for life, if we go by the rate at which bacteria changes!
Show your working. Oh, wait, you haven't done any, have you? You've just made stuff up.
Which brings me back to my first point in this post. Creationists have lots of debating points which would be excellent if only they had any connection to reality or logic or math or the facts. The reason creationists can swindle people is that they address their balderdash to an audience too pig-ignorant of biology to notice that they base their case securely on stuff that they've made up in their heads.

This message is a reply to:
 Message 68 by Bolder-dash, posted 03-02-2010 8:45 AM Bolder-dash has replied

Replies to this message:
 Message 88 by Bolder-dash, posted 03-02-2010 9:26 PM Dr Adequate has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 86 of 134 (548956)
03-02-2010 6:52 PM
Reply to: Message 68 by Bolder-dash
03-02-2010 8:45 AM


Re: unreal expectations based on false information
Hi Bader-dash
This is a good expalantion for why your side gets beat up so bad in live debates (see Meyer/Sternberg vs. Shermer/Prothero).
And also why your side got creamed at the Dover trial - we stick to facts rather than fantasy. Facts may seem boring, but the tend to be more substantial than fantasy in the long run. Interestingly, whenever the judgment on who "wins" is based on the relation to reality, science wins over fantasy every time.
It's also why your side cannot get traction on the concept that ID is science ... except among people who are ignorant of science.
It is YOUR side that says these random mutations are so numerous as to be able to explain the existence of all of life's complexities-yet you can show none.
This has been answered by others, but I'll bet you won't understand. The reason you are different from every other human on the planet is due to mutations.
So, the only hopeful monster in the room seems to be your theory, claiming for all its worth, a divine exclusivity on the facts-while providing no evidence whatsoever.
And yet, somehow, whenever an experiment is done to test the theory (the real one used by scientists), they end up with results that show that indeed evolution occurs and documents precisely the effects of evolution on the results.
Meanwhile the results based on creationism are ... still missing.
... we have witnessed in our lifetimes billions and billions of generations of bacteria-and not a single new complex system has seen to have been formed-nothing leading down the path of greater complex organisms.
Curiously, the real theory of evolution explains why simple prokaryotic bacteria still exist, including cyanobacteria very similar to the fossils of the first know life, from 3.5 billion years ago.
It explains it because complexity is not a goal of evolution.
Enjoy.

we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 68 by Bolder-dash, posted 03-02-2010 8:45 AM Bolder-dash has replied

Replies to this message:
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AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 87 of 134 (548958)
03-02-2010 6:58 PM
Reply to: Message 80 by Taq
03-02-2010 2:47 PM


Re: Neutral mutations
Excellent. Thank you, Taq.

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Bolder-dash
Member (Idle past 3630 days)
Posts: 983
From: China
Joined: 11-14-2009


(1)
Message 88 of 134 (548971)
03-02-2010 9:26 PM
Reply to: Message 85 by Dr Adequate
03-02-2010 4:05 PM


Re: unreal expectations based on false information
Whoohoo, read a biology book! Good one! Strong reply!
Man you got me good with that one! How long did it take you to think of that devastating rebuttal?
And then you back it up with even stronger rhetoric-"show me where God poofed out a magic organisms"! Powerful stuff, A! I think the media has got it all wrong, Dawkins isn't Darwin's Rottweiler, instead you are his rabies infested laughing hyena, chewing out the opposition's bloody spleens with your gnarly yellow fangs. Awesome! Who can argue with you there?
But it gets better-with your biting wit, you declare-"we can show you lots of random mutations, all of them" So there!
And then your canines cut even deeper--"Please tell me how you can tell a beneficial mutation which is a starting point from one which isn't." Wow, I hadn't thought of that! Gee I don't know how one can tell-because I have never seen one. I assumed you could tell, because you are the one that has the theory that they exist-the basis for all of life in fact. I was so naive to think that since they are the foundation of your theory, you knew what they looked like. Touche, Docteur A! Morsure extraordinaire!
Well, how about some beneficial random mutations that COULD be starting points? Surely you at least can name a few of those right? Because they possess such useful reproductive advantages, obviously you can demonstrate lots of these, right?
Or am I just leaving myself open for more cuts of your intellectual incisors?
Go read a biology book! Ouch, I am bleeding!!
Edited by Bolder-dash, : No reason given.

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Bolder-dash
Member (Idle past 3630 days)
Posts: 983
From: China
Joined: 11-14-2009


Message 89 of 134 (548972)
03-02-2010 9:34 PM
Reply to: Message 86 by RAZD
03-02-2010 6:52 PM


Re: unreal expectations based on false information
And yet, somehow, whenever an experiment is done to test the theory (the real one used by scientists), they end up with results that show that indeed evolution occurs and documents precisely the effects of evolution on the results.
Hmm, they show evolution, by random mutations (you do mean evolution by random mutations, correct? Because certainly YOU would never post something off topic) occurring? Interesting.
I believe I had seen here before where posters are cautioned by the moderator that if they are going to make wild claims, they must back them up with evidence or be punished.
.....Oh, wait, no sorry I am wrong, I have only seen where 'creationists' are cautioned on this website for making claims without reference, I have never seen an evolutionist cautioned for anything of the sort.
My mistake.

This message is a reply to:
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Replies to this message:
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Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


Message 90 of 134 (548974)
03-02-2010 10:15 PM
Reply to: Message 89 by Bolder-dash
03-02-2010 9:34 PM


Re: unreal expectations based on false information
Hmm, they show evolution, by random mutations (you do mean evolution by random mutations, correct? Because certainly YOU would never post something off topic) occurring? Interesting.
I believe I had seen here before where posters are cautioned by the moderator that if they are going to make wild claims, they must back them up with evidence or be punished.
No wild claims, and evidence abounds. It is just that creationists have their fingers stuck in their ears up to the metacarpals and refuse to either acknowledge or even try to understand that evidence.
But I'll give it a try, realizing that it is probably futile. Give this site a try:
Welcome to the E. coli Long-term Experimental Evolution Project Site
Now, I'm not going to try to spoon feed this to you. You will have to look at the website, and the individual papers yourself. That is the way research and science are done.
These studies directly contradict your contention that evolution does not occur by random mutations, and they also provide the evidence to back up the not-so-wild claims.
Until you have taken a good look at these studies, don't bother to get back to me.

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.

This message is a reply to:
 Message 89 by Bolder-dash, posted 03-02-2010 9:34 PM Bolder-dash has replied

Replies to this message:
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