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Author Topic:   Problems with evolution? Submit your questions.
Wounded King
Member (Idle past 2327 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 214 of 752 (577682)
08-30-2010 2:47 AM
Reply to: Message 212 by Blue Jay
08-30-2010 12:05 AM


Shocking lack of amino acids in DNA
amino acid sequences in nucleotides

What is it with creationists/IDists and this nonsense. This is something like the third one we have had turning up here talking about amino acids in DNA. Is there some sort of handbook about how to show you know nothing about genetics/molecular biology that they are all following?

TTFN,

WK


This message is a reply to:
 Message 212 by Blue Jay, posted 08-30-2010 12:05 AM Blue Jay has responded

Replies to this message:
 Message 215 by bluegenes, posted 08-30-2010 6:24 AM Wounded King has acknowledged this reply
 Message 216 by Blue Jay, posted 08-30-2010 10:04 AM Wounded King has acknowledged this reply
 Message 220 by dennis780, posted 08-31-2010 5:58 AM Wounded King has responded

  
Wounded King
Member (Idle past 2327 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 223 of 752 (577940)
08-31-2010 6:40 AM
Reply to: Message 221 by dennis780
08-31-2010 6:14 AM


Re: Shocking lack of amino acids in DNA
What was your point exactly? That you can produce a badly constructed google search? Or that you can't talk about molecular biology coherently?

The one result was from what you yourself posted, I hardly see that as being a result for ID. I could make a cross board spam attack putting "Evolution facts are found" all over the internet, would that suddenly mean evolutionary theory was winning?

Are you standing by the idea that there are amino acids in DNA/nucleotides? Or would you agree that what you wrote was at best badly phrased. Persumably what you meant was the amino acid sequences coded for by particular sequences of nucleotides.

TTFN,

WK

P.S. Do you use 'BAM' to denote when you have said something particularly stupidly?


This message is a reply to:
 Message 221 by dennis780, posted 08-31-2010 6:14 AM dennis780 has not yet responded

  
Wounded King
Member (Idle past 2327 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 242 of 752 (578210)
09-01-2010 5:00 AM
Reply to: Message 220 by dennis780
08-31-2010 5:58 AM


Re: Shocking lack of amino acids in DNA
I said the sequences are in the nucleotides. Which they are.

No they aren't.

Nucleotide arrangements code for amino acids.

Which is a different thing entirely. Plus anyone with the first clue about modern genetics would know that looking only at protein coding sequences misses a vast amount of genomic information using any coherent and rational metric.

I'm not sure that just whining and insulting everyone else when you write very bad descriptions of molecular biology is really a substitute for having an actual answer to the question of how to measure, as in actually measure not just say 'wow that looks pretty complex, I bet god did it', the informational content of a genome or sequence of DNA.

Were you adopted?

No. Why? Are adopted people particularly stupid? Is this some new brand of bigoted christian fascism we should look forward to hearing more of in the future? First they come for the jews, then the gays, then the adopted?

TTFN,

WK


This message is a reply to:
 Message 220 by dennis780, posted 08-31-2010 5:58 AM dennis780 has responded

Replies to this message:
 Message 247 by dennis780, posted 09-01-2010 5:48 AM Wounded King has responded

  
Wounded King
Member (Idle past 2327 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 256 of 752 (578246)
09-01-2010 8:11 AM
Reply to: Message 247 by dennis780
09-01-2010 5:48 AM


Re: Shocking lack of amino acids in DNA
Dummy this please, no idea what your point is....

By a rational metric I mean some actual formula or calculation that can be used to repeatably measure the information content of a genome/sequence such that 2 independent people could get the same result when performing an analysis of the same genome/sequence.

You never seem to finish sentences.

I did finish the sentence you just seem unfamiliar with the parenthetical use of the comma. Without my parenthetical interjection "as in actually measure not just say 'wow that looks pretty complex, I bet god did it'" the original phrase would be "an actual answer to the question of how to measure the informational content of a genome or sequence of DNA."

You still aren't providing any such measure and Michael Polanyi certainly didn't have one.

Nucleotide content, coding densities, total functional DNA sequences, and complexity of sequences.

None of these are suitable. Nucleotide content, which normally means the ratios of the different nucleotides so I'll assume that is what you meant, can tell you something about a stretch of DNA but it is by no means a measure of information in any standard sense.

Similarly 'coding densities' tell us something about the composition of the genome, but they don't tell us about its informational content, just how the coding sequences are distributed. It also ignores the fact that a lot of functional elements are well characterised which are not within protein coding sequences (Taft et al, 2007).

Total functional DNA sequences, seems reasonable as a starting point but is a damn hard thing to actually measure and you still have to decide how to use it for comparing genomes. Is the proportion of functional sequences the important thing, or the total number of nucleotides in a functional seuqence, or the number of critical functional nucleotides without which the sequence will lose its function? Is a 'functional density' measure perhaps a better approach?

As to 'complexity' that is almost as problematic to measure as information. Are we talking kolmogorov complexity or some other formalised mathematical approach?

Some of those things may serve as the basis for a useful informational metric, but just thrown out like that they are virtually useless.

Which is more complex: Human, or an amoeba? AND why

As I just said above, complexity is not itself a straightforward measure. Certainly in what might be termed 'morphological complexity', the organisation of a collection of cells as part of one organism a human with billions of cells is clearly more complex than an amoeba's one.

If we look at the genomic level then things get more complicated. Many amoebae have much larger genomes than humans, up to 100s of times as large (Ref). Humans have much more in terms of regulatory genetic mechanisms though with hundreds of transcription factors and extensive non-coding regulatory sequences.

So in terms of gentic complexity there is no one simple answer, depending on how one chooses to measure it the answer may be either, which is why specifying how you are choosing to measure either information or complexity is so important if we want to actually be talking about the same thing.

And you cannot use any of the answers I provided, since you called them all wrong

I don't believe I did, but certainly you haven't put them forward in a way that would actually tell anyone how they could be reliably used to measure information content in a genome/sequence.

Okay, then where do Amino acids come from?

From different sources. Some amino acids are taken from the external environment, in humans there are a number of such 'essential' amino acids. Some amino acids, the 'non-essential' ones, are synthesised within the cell from other compounds. Having been synthesised or extracted the amino acids stay in the cell cytoplasm until they are recruited by tRNA for protein synthesis.

...you are re-inventing science, right before my eyes

No, I'm just telling you what science has actually found.

While you continue to refuse to offer up some usable measure of genetic information/complexity it is virtually impossible to demonstrate an increase in same because what we think is a good example may not fit your own vague criteria.

TTFN,

WK


This message is a reply to:
 Message 247 by dennis780, posted 09-01-2010 5:48 AM dennis780 has not yet responded

  
Wounded King
Member (Idle past 2327 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 263 of 752 (578666)
09-02-2010 8:47 AM
Reply to: Message 262 by Dr Adequate
09-02-2010 6:21 AM


The original papers are freely available(here and here(PDFs)) as is the third one ...

Gene duplication as a mechanism of genetic adaptation in Saccharomyces cerevisiae.(PDF)
Hansche PE.
Genetics. 1975 Apr;79(4):661-74.

Its interesting to note that even though they say that the same mutations ocurred in the precis on the site you linked to the actual papers make it clear that they think the specific mutations are different although they give rise to similar, though not identical, traits.

TTFN,

WK


This message is a reply to:
 Message 262 by Dr Adequate, posted 09-02-2010 6:21 AM Dr Adequate has not yet responded

  
Wounded King
Member (Idle past 2327 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 357 of 752 (580449)
09-09-2010 6:08 AM
Reply to: Message 344 by dennis780
09-08-2010 11:17 PM


Re: What's the problem?
I'll make you a deal. If you find me 15 examples of genetic mutation of new functional DNA (coding for any protien, trait, or physical attribute that was not present in past organisms of the species)

No problem, you just give me the exhaustive data of all proteins traits or physical attributes for all past organisms for some nice quickly reproducing species/organism with well understood genetics and I'll get right on it. I'd suggest E. coli or Drosophila as good candidates.

Is this just another way of ignoring the wealth of experimental data where we know that novel functional mutations have arisen in an originally clonal culture?

By asking for eivdence that such a trait has never existed before in the entire history of the species you are just tagging on a totally unreasonable and irrelevant rider. We can know that the ancestral genome of a clonal culture didn't have the trait, how is it relevant if the trait evolved separately in another bacterium 50 years ago?

quote:
Incorrect - you've failed to understand what "random" means.

Oh? I'm thinking of a number between 1 and 3 million. Guess what it is. I'll give you one hundred tries. If you are correct, within 100 tries, you should get the same result as me. GO!

If you think people guessing or choosing numbers is random then you are just demonstrating that Caffeine is correct.

TTFN,

WK


This message is a reply to:
 Message 344 by dennis780, posted 09-08-2010 11:17 PM dennis780 has not yet responded

  
Wounded King
Member (Idle past 2327 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 662 of 752 (607161)
03-02-2011 10:37 AM
Reply to: Message 657 by havoc
03-02-2011 10:18 AM


Recurrent informational mess
Most of the cases I'm aware of for cave fish involve outcrossing between different populations. So the necessary information for eye development is split between the 2 lineages although neither has it in isolation. By mixing the 2 lineages a complete eye developmental pathway can be reconstituted (Borowsky, 2008).

If a cell once had the ability to regulate say the production of a certain protein and now it doesn’t this is loss of information

I'd echo Dr. A here, does this mean you would consider the gain of a regulatory mechanism for a gene to be a gain of information?

TTFN,

WK


This message is a reply to:
 Message 657 by havoc, posted 03-02-2011 10:18 AM havoc has not yet responded

  
Wounded King
Member (Idle past 2327 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 664 of 752 (607164)
03-02-2011 10:59 AM
Reply to: Message 651 by havoc
03-02-2011 9:58 AM


Informational nonsense
Fluoroquinolones Loss of affinity to gyrase

There is probably a lot wrong with this list but this particular example is one that I covered in detail with Smooth operator in Message 185 on the thread What is an ID proponent's basis of comparison? (edited).

Fluoroquinolones are a synthetic antibiotic that binds to and interferes with Gyrases in bacteria. As an antibiotic resistance mechanism a strain of bacteria arose which had changed the epitope that Fluoroquinolones bound to so that they bound less well.

In what way is this a loss of information for the bacterial genome? The bacterium didn't evolve gyrase to bind this modern antibiotic, it didn't lose any biological function due to the mutation.

So what logical rationale is there to describe this as a loss of information for the bacterial genome?

TTFN,

WK


This message is a reply to:
 Message 651 by havoc, posted 03-02-2011 9:58 AM havoc has not yet responded

  
Wounded King
Member (Idle past 2327 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 708 of 752 (607339)
03-03-2011 9:12 AM
Reply to: Message 703 by havoc
03-03-2011 8:22 AM


Re: goalposts on the run.
Shannon would measure them the same.

This is not the case. A random set of data would have a higher Shannon entropy than a structured one like an instruction manual. The structure of the language and potentially of the manual's format would mean that it would require less information to optimally convey than would a totally random sequence.

Given that Shannon entropy is already used to identify genomic features in DNA (Stanley et al., 1999; Chen et al, 2005) it seems obtuse to pretend that it can't distinguish between random and structured strings.

TTFN,

WK


This message is a reply to:
 Message 703 by havoc, posted 03-03-2011 8:22 AM havoc has not yet responded

  
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