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Author Topic:   Evolving New Information
pandion
Member (Idle past 1322 days)
Posts: 166
From: Houston
Joined: 04-06-2009


Message 136 of 458 (519200)
08-12-2009 10:35 AM
Reply to: Message 135 by Wounded King
08-12-2009 4:56 AM


Re: Condons
WoundedKing writes:

I think you failed to appreciate the rather abstract nature of Percy's example.


Actually, it is you who has failed to understand that the example was not abstract but grossly incorrect, and when you use that example and try to ask a question, your question is basically gibberish. Again you demonstrate that you lack the integrity to at least read where all of this was previously explained (in this thread) and thus at least speak from some sort of basic knowledge rather than complete ignorance. None of the discussion so far has exceeded what I ever learned in the first college course I ever took on genetics.

This message is a reply to:
 Message 135 by Wounded King, posted 08-12-2009 4:56 AM Wounded King has responded

Replies to this message:
 Message 137 by Wounded King, posted 08-12-2009 11:11 AM pandion has not yet responded
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Wounded King
Member (Idle past 2416 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 137 of 458 (519207)
08-12-2009 11:11 AM
Reply to: Message 136 by pandion
08-12-2009 10:35 AM


Point collection failure
Exsqueeze me?!

Percy's example was about increasing numbers of allelic variants leading to an increase in information in the genome. The allelic variant sequences were essentially arbitrary, they don't represent real sequences in any extant organism. This is why I say it is abstract, Percy is positing a hypothetical organism with a hypothetical gene with three then four allelic variants producing different eye colours. If this isn't abstract then can you tell me what organism it was Percy was talking about and whose biology he had so grossly incorrect?

The actual sequence is irrelevant, it isn't taken into consideration in Percy's calculations except in as much as it represents a distinct message. To criticise the biology of the sequence choice is to miss the point of the whole exercise.

Again, if it isn't abstract then what organism do you think Percy was failing to describe?

I can think of a situation where Percy's example need not be entirely biologically messed up. Suppose that the 'gene' Percy is discussing is not a protein coding gene but in fact a regulatory region upstream of a traditional protein coding gene. This protein coding gene encodes a rate limiting element of the melanin biosynthesis pathway. Let us suppose that the different eye colour phenotypes are caused by differential binding affinities to a transcription factor as a result of the small nucleotide polymorphisms at the binding site for the transcription factor, these polymorphisms would be Percy's allelic variants. This change in transcription levels of the melanin biosynthesis pathway element leads in turn to differential levels of melanin deposition in the iris.

Of course since the biology is actually irrelevant to Percy's example there is no need to do so, just as there is no need to complain about his choice of sequence.

TTFN,

WK

Edited by Wounded King, : No reason given.

Edited by Wounded King, : Cleaned up pointless example.

Edited by Wounded King, : and again


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traderdrew
Member (Idle past 3475 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 138 of 458 (519213)
08-12-2009 11:54 AM
Reply to: Message 132 by Theodoric
08-11-2009 12:53 PM


Re: Off Topic Theodoric
Many times. As a matter of fact, you have pulled out of a few threads when things were not going your way.

I will state this one time here because it is off topic. There have been many times when I just stopped the debate when it turns in to an argument. I really think it starts to become childish when people carry on with arguments on these threads. Other times I pull out when the person who is debating me is/or employing the use of various types of equivocations, strawman agruments, off topic, or just doesn't get my point for whatever reason. Sometimes I hold off hammering my points because part of me doesn't want to disturb some of you. Also, just because I don't answer doesn't necessarily mean that I am stuck. I know about five ID websites where I go for researching some of topics on posts around here.

Go back through the threads. I know I am looking for a response on at least a couple.

OK I will go back to the Expelled forum to see what you said. What do you think of my post #390?


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traderdrew
Member (Idle past 3475 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 139 of 458 (519221)
08-12-2009 12:34 PM
Reply to: Message 134 by pandion
08-11-2009 6:30 PM


Re: Codons
Don't know what you are asking. ACG encodes threonine, UCG encodes serine, and AAG encodes lysine. The changes may or may not change the function of the protein.

You partly answered it here:

A point mutation of one of the bases in either the first or second position, and only sometimes in the third position will produce a different amino acid in the protein sequence.

For example: ACG becoming UCG instead of ACG becoming AAG

The ACG becoming UGC was a change in the first postition and ACG becoming AAG was change in the second position. It seemed to me the differences in eye color were from variations in the first positions. But as you stated, it is more complicated than that.

Thank You

Edited by traderdrew, : No reason given.


This message is a reply to:
 Message 134 by pandion, posted 08-11-2009 6:30 PM pandion has not yet responded

  
cavediver
Member (Idle past 1964 days)
Posts: 4129
From: UK
Joined: 06-16-2005


Message 140 of 458 (519222)
08-12-2009 12:39 PM
Reply to: Message 136 by pandion
08-12-2009 10:35 AM


Re: Condons
Actually, it is you who has failed to understand...

Hmmm, Pandion, good idea to check to whom you are replying, and to whom they in turn were replying. Saves a good bit of egg on your face. Just saying...


This message is a reply to:
 Message 136 by pandion, posted 08-12-2009 10:35 AM pandion has responded

Replies to this message:
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pandion
Member (Idle past 1322 days)
Posts: 166
From: Houston
Joined: 04-06-2009


Message 141 of 458 (519240)
08-12-2009 2:53 PM
Reply to: Message 140 by cavediver
08-12-2009 12:39 PM


Re: Condons
cavediver writes:

Hmmm, Pandion, good idea to check to whom you are replying, and to whom they in turn were replying. Saves a good bit of egg on your face. Just saying...


Well, I see you are correct there. I responded to traderdrew and assumed that the ignorant response that I received was from him. I owe drew an apology. But that makes WoundedKing's comments even more unintelligible. He then tries to dig himself out of his hole of ignorance by explaining why a question about incorrect data is somehow meaningful. traderdrew asked, essentially that if a mutation from ACG to ACA can produce a different eye color, wouldn't a mutation to UCG or produce a larger mutation? My answer was to explain it correctly. WoundedKing apparently lacks the knowledge to understand that.

This message is a reply to:
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Replies to this message:
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Huntard
Member (Idle past 616 days)
Posts: 2870
From: Limburg, The Netherlands
Joined: 09-02-2008


Message 142 of 458 (519243)
08-12-2009 2:57 PM
Reply to: Message 141 by pandion
08-12-2009 2:53 PM


Re: Condons
Woundedking wasn't talking about Drew's example. He was talking about Percy's example first given here: Message 1

So, uhm, I think you owe someone an apology.


I hunt for the truth

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Percy
Member
Posts: 18996
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.4


Message 143 of 458 (519244)
08-12-2009 3:13 PM


A Clarification
In case it helps, my example in Message 1 was concocted solely to illustrate how a point mutation can increase the amount of information in a genome by adding to the number of alleles for a gene. I didn't go to the trouble of actually making sure my codons were valid because it wasn't relevant from an information standpoint.

Would it be helpful to edit Message 1 to remedy this problem? I could include an explanation at the top that such an edit was performed, and I could include the entire original message in a hide section.

--Percy


  
cavediver
Member (Idle past 1964 days)
Posts: 4129
From: UK
Joined: 06-16-2005


Message 144 of 458 (519248)
08-12-2009 3:44 PM
Reply to: Message 141 by pandion
08-12-2009 2:53 PM


Re: Condons
WoundedKing apparently lacks the knowledge to understand that.

I've always said that once you've started digging yourslef a hole, you may as well see how deep you can get it

As a hint, WK is actually our resident professional geneticist, microbiologist, biochemist, or whatever... I'm unclear as to whether he's merely a post-doc, or a long-tenured HoD with far too much time on his hands, but either way he talks the talk and certainly does not suffer from a lack of knowledge in this area


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Wounded King
Member (Idle past 2416 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 145 of 458 (519250)
08-12-2009 4:30 PM
Reply to: Message 144 by cavediver
08-12-2009 3:44 PM


Re: Codons
As ever qualifications are supremely irrelevant. If Pandion has an actual specific criticism of what I wrote, other than that he didn't understand it, I have yet to make out what it is. If he just didn't understand it I'm happy to explain in greater detail.

Although I should think Percy saying what his intentions were should be sufficient to demonstrate the utter irrelevance of Drew and Pandion's discussion.

TTFN,

WK


This message is a reply to:
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Replies to this message:
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pandion
Member (Idle past 1322 days)
Posts: 166
From: Houston
Joined: 04-06-2009


Message 146 of 458 (519293)
08-12-2009 11:39 PM
Reply to: Message 145 by Wounded King
08-12-2009 4:30 PM


Re: Codons
WoundedKing writes:

As ever qualifications are supremely irrelevant. If Pandion has an actual specific criticism of what I wrote, other than that he didn't understand it, I have yet to make out what it is. If he just didn't understand it I'm happy to explain in greater detail.


Well, that would be just great. Why don't you explain to me what you're talking about. I not only read this thread, I was instrumental in hashing out the errors in the first place. So WoundedKing has a degree. Whoopee! That makes him an expert. So I also have degrees, in biology. I have degrees from St. Mary's College of California, Montana State U, El Instituto de Estudios Superiores de Monterrey, and the University of Montana. Along the way I studied genetics far beyond the level of this discussion.

So after the errors that lead this discussion off track in the first place were corrected early on in this thread, now the thread has been lead off track again because of an unwillingness to actually read the thread. The genetic coding wasn't ever the main point anyway. So, now along comes our resident geneticist, who actually thinks that this is somehow subtle rather than just wrong. How irrelevant can anyone person be. And the rest of you just tumble to an argument because you think that someone is a doc candidate or a post doc or something? You all are so dazzled that you miss the point.

Why on earth would anyone ever imagine that I was responding to Percy since that was ironed out at the beginning of the thread? Jeeze! WoundedKing, can you even find a hat to fit?


This message is a reply to:
 Message 145 by Wounded King, posted 08-12-2009 4:30 PM Wounded King has responded

Replies to this message:
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Wounded King
Member (Idle past 2416 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 147 of 458 (519303)
08-13-2009 4:17 AM
Reply to: Message 146 by pandion
08-12-2009 11:39 PM


As Percy confirms below, this is all off topic.

TTFN,

WK

Edited by Wounded King, : Original post off topic


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Admin
Director
Posts: 12647
From: EvC Forum
Joined: 06-14-2002
Member Rating: 2.4


Message 148 of 458 (519320)
08-13-2009 7:53 AM


Moderator Reminder
I'm of course not going to moderate my own thread, but I would like to remind participants to keep their focus on the discussion and not on the discussion's participants.

Touching briefly on WK's claim that credentials are irrelevant, I feel much the same way. In debate what should matter most is the quality of the arguments one can marshal around evidence.

Of course, if one is seeking rather than arguing about answers, a credentialed expert is best.


--Percy
EvC Forum Director

  
Wounded King
Member (Idle past 2416 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 149 of 458 (519339)
08-13-2009 10:06 AM


Some questions about genetic information
So what, if any, useful measures of information can we go by for measuring information in the genome? As Percy and Pandion show the Shannon information measure that Percy is using is essentially useless. The information content of any sequence we are studying can change at any moment unbeknownst to us as somewhere out in the wild a mutation occurs increasing the genetic diversity of that sequence within the population. The calculable information content will obviously also vary depending on the sampling I am using for my population, am I looking at all the variants in a particular species? across species? across phyla?

How do we extend this to larger scales than a single gene sequence? In a human population would every unique genome generated increase the information content in all genomes? And aren't almost all genomes unique to some small extent?

Can we ever hope to actually measure the information outside of a very specific population? Surely our incomplete knowledge would preclude us doing so?

Obviously the ID camp will never accept a concept of information where it is so trivially easy to show the widespread and continuous increase of information, even if we can't actually measure it except in controlled experimental settings.

What metrics can we use for studying a single sequence or genome? Shannon entropy? Kolmogorov complexity? Can we even make a useful measurement of information in a single gene/genome?

Is there a method for taking a pre and post mutation sequence and measuring their relative information contents?

It is interesting to me that the IDists Smooth Operator has been promoting here recently seem to be relying on sequence alignment comparisons as the basis for their information metrics rather than actual analysis of a specific sequence in isolation. Maybe isolated sequences simply aren't usable in this context.

TTFN,

WK

Edited by Wounded King, : No reason given.


  
greyseal
Member (Idle past 2183 days)
Posts: 464
Joined: 08-11-2009


Message 150 of 458 (519475)
08-14-2009 2:45 AM


so, WK has pointed out that Percy's example is just that - an example with no actual genetic code behind it.

The point is, that this abstract example is still useful to explain an increase in information in the genetic code as it gives a direct example.

So, anyone complaining that Percy's example wasn't abstract is a moron who didn't bother reading the thread. Glad that's over.

Now for the kicker - do IDiots actually define what they mean by "an increase in information"? My opinion (with no examples here, because I cannot prove a negative) is that they don't know themselves, and it was just some buzzword they latched onto, like "genetic code" and "alelles" and "mutation" from skimming the real science as lightly as possible lest their quaint notions get knocked out of joint.

somebody who sincerely believes what they say and holds this viewpoint, what exactly do you mean by "an increase in information"?


Replies to this message:
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