Always finish what you start…

by Guts

[poll id="4"]

This entry was posted on Thursday, December 11th, 2008 at 12:53 am and is filed under Biology. You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed.

37 Responses to “Always finish what you start…”

Alan Fox Says:
December 11th, 2008 at 5:05 am
You missed out an option. We don't know. Or are you attaching that caveat to your three choices as a given? Would the EF help?

My guess:

Frozen accident, if you mean was it the result of serendipitous mutations* becoming fixed by natural selection. It would have been a mistake if all descendants of the gene pool acquiring this modification went extinct.

*In the broadest sense, to include HGT, symbiogenesis, etc.

Comment by Alan Fox — December 11, 2008 @ 5:05 am

Zachriel Says:
December 11th, 2008 at 10:19 am
Guts: Methionine is nearly universal as a start amino acid when it comes to protein synthesis

Methionine is considered a late addition to the genetic code. It's assignment may have been "tacked" onto the underutilized start codon AUG. This allows methionine to be used for protein synthesis, but it is typically stripped off the initial position.

Comment by Zachriel — December 11, 2008 @ 10:19 am

GringoRoyale Says:
December 11th, 2008 at 11:13 am
Alan:

Frozen accident, if you mean was it the result of serendipitous mutations* becoming fixed by natural selection. It would have been a mistake if all descendants of the gene pool acquiring this modification went extinct.

Zach:

It's assignment may have been "tacked" onto the underutilized start codon AUG.

If it's post-translational and not inherent to AUG, simply "tacked on" after the fact. How does it become fixed? Like post-translational mutations in snake venom that have right handed amino acids in the peptide chains. The can't become fixed/inherent to the actual DNA that specifies the venom…. since it's a post-translational event.

Comment by GringoRoyale — December 11, 2008 @ 11:13 am

Zachriel Says:
December 11th, 2008 at 11:34 am
GringoRoyale: If it's post-translational and not inherent to AUG, simply "tacked on" after the fact.

It's not post-translational. It's posited as a modification of the primitive genetic code.

GringoRoyale: How does it become fixed?

There is no complete history of the origin of the genetic code, but presumably it became fixed the usual way. Stability became more important than continued evolution of the code as other aspects of cellular metabolism became increasingly dependent on the code. Further changes only served to disrupt the evolution of these other adaptations.

Comment by Zachriel — December 11, 2008 @ 11:34 am

Alan Fox Says:
December 11th, 2008 at 11:38 am
Curious about (R)-amino acids in snake venom, I tried googling various combinations of key words, but I can't find anything apparently relevant. Would you have a link, Gringo?

Comment by Alan Fox — December 11, 2008 @ 11:38 am

GringoRoyale Says:
December 11th, 2008 at 1:53 pm
Alan, let me get back to you with that.
For awhile I was studying up on the presence of d-aa in polypeptide chains, with these peptides being produced biotically.
I came across some studies were certain bacteria had incorporated d-aa's in their surface proteins as well as snake venom that had d-aa's.

Comment by GringoRoyale — December 11, 2008 @ 1:53 pm

GringoRoyale Says:
December 11th, 2008 at 1:53 pm
Hi Zach,

I misunderstood, my bad.
I took your "tacked" comment alittle too loosely.

Comment by GringoRoyale — December 11, 2008 @ 1:53 pm

GringoRoyale Says:
December 11th, 2008 at 1:59 pm
Alan,

Here's an abstract I have saved:

D-amino acids have been detected in a variety of peptides synthesized by animal cells. These include opiate and antimicrobial peptides from amphibian skin, neuropeptides from snail ganglia, a hormone from crustaceans, and a constituent of a spider venom. cDNA cloning has shown that at those positions where a d-amino acid is found in the end-product, a normal codon for the corresponding l-amino acid is present. This implies that the d-residues are formed from l-amino acids by a posttranslational reaction. A prototype enzyme catalyzing such a reaction has recently been isolated from the venom of the funnel web spider.

But I can't remember the source. If you google any portion of it the study should come up.

Comment by GringoRoyale — December 11, 2008 @ 1:59 pm

GringoRoyale Says:
December 11th, 2008 at 2:02 pm
One of the advantages that a bacterial cell would have with a d-aa would be that it would increase the bacteriums chance at surviving the the immune system of the host. But again, the selective advantage would end there and be exempt from being passed on to progeny.

Comment by GringoRoyale — December 11, 2008 @ 2:02 pm

Alan Fox Says:
December 11th, 2008 at 2:14 pm
If you google…

Got it! Funnel web spider not snake! And it's only available on subscription. '97 so there must be some follow up somewhere… *googles*

Comment by Alan Fox — December 11, 2008 @ 2:14 pm

Alan Fox Says:
December 11th, 2008 at 2:26 pm
But again, the selective advantage would end there and be exempt from being passed on to progeny.

Why? If the process of making D-ala and D-glu is carried out by enzymes that are coded for in the genome, the trait will be heritable, and if advantageous it will become fixed.

BTW, for me, chirality is much the strongest evidence for common descent, especially when considered with all the basic biochemical structures and processes that are almost universal, with their rare and fascinating exceptions.

Comment by Alan Fox — December 11, 2008 @ 2:26 pm

GringoRoyale Says:
December 11th, 2008 at 3:17 pm
Why? If the process of making D-ala and D-glu is carried out by enzymes that are coded for in the genome, the trait will be heritable, and if advantageous it will become fixed.

Everywhere I read about it said that any incorporation of d-aa was post-translational. Charging aa's to tRNA is stereospecific as well. So it would be quite the trick to just randomly start incorporating d-aas to be coded from the DNA.

BTW, for me, chirality is much the strongest evidence for common descent, especially when considered with all the basic biochemical structures and processes that are almost universal, with their rare and fascinating exceptions.

I have never argued against common descent. But, chirality makes the problem quite relevant for abiogenesis. Since random samples from natural and artificial (Urey-Miller) have racemic yields.

Comment by GringoRoyale — December 11, 2008 @ 3:17 pm

Bradford Says:
December 11th, 2008 at 3:41 pm
Don't people believe in voting anymore?

Comment by Bradford — December 11, 2008 @ 3:41 pm

don provan Says:
December 11th, 2008 at 4:26 pm
Don't people believe in voting anymore?

I find it interesting and a little disturbing that anyone considers this a matter that it makes sense to vote on.

Comment by don provan — December 11, 2008 @ 4:26 pm

Bradford Says:
December 11th, 2008 at 4:34 pm
I find it interesting and a little disturbing that anyone considers this a matter that it makes sense to vote on.

Lighten up Don.

Comment by Bradford — December 11, 2008 @ 4:34 pm

GringoRoyale Says:
December 11th, 2008 at 5:00 pm
I find it interesting and a little disturbing that anyone considers this a matter that it makes sense to vote on.

Disturbing? Odd choice of words.

Most things don't make sense to vote on.

Comment by GringoRoyale — December 11, 2008 @ 5:00 pm

Zachriel Says:
December 11th, 2008 at 5:20 pm
don provan: I find it interesting and a little disturbing that anyone considers this a matter that it makes sense to vote on.

If a majority think that methionine was a frozen accident, then it was obviously a frozen accident. So far, logical reasoning is winning. That would be a huge electoral upset.

Comment by Zachriel — December 11, 2008 @ 5:20 pm

Alan Fox Says:
December 11th, 2008 at 5:35 pm
Don't people believe in voting anymore?

Absolutely. I voted for "none of the above". There's no option for don't knows.

Comment by Alan Fox — December 11, 2008 @ 5:35 pm

Joy Says:
December 11th, 2008 at 7:24 pm
Zach:

If a majority think that methionine was a frozen accident, then it was obviously a frozen accident.

That's snark, right?

Comment by Joy — December 11, 2008 @ 7:24 pm

don provan Says:
December 11th, 2008 at 8:27 pm
Disturbing? Odd choice of words.

Most things don't make sense to vote on.

We vote on things that are a matter of opinion. It's disturbing to see people calling for a vote on what appears to be a matter of fact. One wonders what will happen if the vote doesn't agree with the actual fact.

Notice that this hinges on the verb "vote". Really, this is a poll, not a vote, and I think everyone agrees that was the intent. But I was making light of the fact that the action in this blog is labeled "vote" which, by some (but not all) definitions, implies an actual decision is being made: in this case, to act as if the winning answer was fact.

Ha-ha. (That's per Bradford's request to lighten up.)

Comment by don provan — December 11, 2008 @ 8:27 pm

GringoRoyale Says:
December 12th, 2008 at 11:06 am
We vote on things that are a matter of opinion.

Not necessarily. Certainly not simply a matter of an opinion for most of those who would go out of their way to vote on something (whatever that might be).

It's disturbing to see people calling for a vote on what appears to be a matter of fact.

A fact that may be forever obscured from our eyes.
Also, this is simply polling. Person A may currently think the 1st option is most plausible… Person B may think the 3rd. It's not necessarily a indicator of personal certitude. And if you were to ask, "do you really think your 'vote' will change what actually happened?", I would venture to guess that most would reply, "what an odd thing to ask for a poll. Of course polls regarding views on historical matters don't actually impact the events in question."

One wonders what will happen if the vote doesn't agree with the actual fact.

Nothing will happen. At least in regard to the truth regarding that actual fact. The actual historical fact will be in no more risk changing any more than the actual intentions of Guts' poll taking will risk changing because someone is hypersensative to a poll.

Notice that this hinges on the verb "vote". Really, this is a poll, not a vote, and I think everyone agrees that was the intent.

Voting is the action on the part of the respondent, polling is the action on the part of the solicitor.

Comment by GringoRoyale — December 12, 2008 @ 11:06 am

GringoRoyale Says:
December 12th, 2008 at 12:00 pm
AUG is the start codon on mRNA.
Is TAC a start signal on DNA for the polymerase that constucts the mRNA?
Or is it simply based off of where ever the promoter region is relative to the gene to be transcribed?
Or, is the promoter region always preceding TAC?

Comment by GringoRoyale — December 12, 2008 @ 12:00 pm

don provan Says:
December 12th, 2008 at 12:57 pm
A matter of opinion remains a matter of opinion no matter how important the question, how earnestly people go to the polls, or how convinced someone is that there's only one correct answer.

Pollsters ask questions which are answered, not "voted on". Of course, casually we speak of this as voting, but I was ignoring this casual misuse for comedic effect, as I pointed out.

There's an important point around here somewhere, but it's hard to talk about when you pointlessly try to trip me up on my command of English without actually considering what I'm saying.

Comment by don provan — December 12, 2008 @ 12:57 pm

GringoRoyale Says:
December 12th, 2008 at 1:36 pm
There's an important point around here somewhere, but it's hard to talk about when you pointlessly try to trip me up on my command of English without actually considering what I'm saying.

Pointlessly? Just following your lead, Don.

Comment by GringoRoyale — December 12, 2008 @ 1:36 pm

don provan Says:
December 12th, 2008 at 1:58 pm
Pointlessly? Just following your lead, Don.

No. you're really not. You're acting as if I'm not making sense rather than following my lead and trying to work out what I'm saying or why you're not understanding me. But now that I've explained what you misunderstood about the term "voting", will you try to see what the point was? Or will you just continue debating the meanings of uncontroversial terms?

Comment by don provan — December 12, 2008 @ 1:58 pm

GringoRoyale Says:
December 12th, 2008 at 2:10 pm
Don you were turning some simple thing into such a big deal. Playing with terms "voting" and "polling". And seemingly making something out of nothing.
Yeah, I found it pointless.
You think I was trying to trip you up on your words. Wasn't the case at all. It's a pattern: you read too much into the point of this all thread and you read too much into me saying a distinction between "voting" and "polling".

You're acting as if I'm not making sense rather than following my lead and trying to work out what I'm saying or why you're not understanding me.

There's nothing worth working out.
You want to get worked up and pull out the Columbo routine over something like this? Then do it.

I find it interesting and a little disturbing that anyone considers this a matter that it makes sense to vote on.

Comment by GringoRoyale — December 12, 2008 @ 2:10 pm

don provan Says:
December 12th, 2008 at 3:10 pm
Don you were turning some simple thing into such a big deal.

Well, no, I just made a joke because Bradford was complaining about no one voting on a matter of fact. Bradford apparently missed the humor since he reacted to my joke by telling me to lighten up, and you're the one pretending it was a big deal. In this case, the seriousness only surfaced when you seemed to fail to understand why voting on matters of fact should seem disturbing.

But it's interesting that you say I read too much into the points of threads. I find that bloggers here typically read too little into their own points: if their point really is valid, the implications are much larger than they're considering. I'm sorry that bothers you, but I find it to be the biggest blindspot ID advocates have. Take as an example the discussion I'm having with Bradford on another thread: ID advocates are perfectly willing to rule out all manner of explanations based on "likelihood" or on epistemology, but they never seems to follow those thoughts through to see that the ID explanation is beyond even the ability to calculate "likelihood" and is at least as easy to ruled out based on questioning reality.

Comment by don provan — December 12, 2008 @ 3:10 pm

GringoRoyale Says:
December 12th, 2008 at 3:19 pm
If you meant it more jokingly. Then I apologize.
I guess I was the one reading too much into other things.
Maybe some projection on my part

Comment by GringoRoyale — December 12, 2008 @ 3:19 pm

chunkdz Says:
December 12th, 2008 at 3:49 pm
Provan: I find it interesting and a little disturbing that anyone considers this a matter that it makes sense to vote on.

LOL!

Comment by chunkdz — December 12, 2008 @ 3:49 pm

Guts Says:
December 12th, 2008 at 10:21 pm
Don wrote:

We vote on things that are a matter of opinion. It's disturbing to see people calling for a vote on what appears to be a matter of fact. One wonders what will happen if the vote doesn't agree with the actual fact.

Really? What is the fact? I was asking for people's opinions on a matter for which the answer is not currently known.

Comment by Guts — December 12, 2008 @ 10:21 pm

Allen_MacNeill Says:
December 14th, 2008 at 12:51 am
In intro bio (which I took almost forty years ago) we were told that the reason that methionine is the universal "start" amino acid (among prokaryotes) is that it can be modified in such a way (by the addition of an aldehyde functional group, yielding N-formylmethionine) as to set the direction of polymerization by limiting the addition of new amino acids to one end of the growing polypeptide chain. This greatly reduces errors in polypeptide chain elongation, and is therefore highly favored by natural selection. Having been the "start" amino acid in prokaryotes, it would therefore retain this position among their eukaryote descendants, at least for a while (assuming that one believes, like Michael Behe does, in evolutionary homology). See:
http://en.wikipedia.org/wiki/N-Formylmethionine

Ergo, this "poll" is simply testing whether the respondents know anything about the biochemistry of protein synthesis in prokaryotes. That is, it is asking for respondents to verify a "fact", as several commentators have pointed out.

Comment by Allen_MacNeill — December 14, 2008 @ 12:51 am

don provan Says:
December 14th, 2008 at 4:27 am
Really? What is the fact? I was asking for people's opinions on a matter for which the answer is not currently known.

Dang. You blew your cover. When you didn't chime in for so long, I was sure you were making a joke the whole time. Now you blunder in and admit it was just a poll.

Comment by don provan — December 14, 2008 @ 4:27 am

Zachriel Says:
December 14th, 2008 at 9:57 am
Allen MacNeill: Having been the "start" amino acid in prokaryotes, it would therefore retain this position among their eukaryote descendants, at least for a while

N-formyl-methionine is still used in the mitochondria (which is a direct descendant of prokaryotic symbiotes). In the nucleus, unmodified methionine is used as the start residue.

Comment by Zachriel — December 14, 2008 @ 9:57 am

Zachriel Says:
December 14th, 2008 at 10:38 am
Should read "in nuclear-directed protein synthesis". (Nucleic protein synthesis actually occurs in cytoplasmic ribosomes.)

Comment by Zachriel — December 14, 2008 @ 10:38 am

Guts Says:
December 15th, 2008 at 1:46 am
Don:

Dang. You blew your cover. When you didn't chime in for so long, I was sure you were making a joke the whole time. Now you blunder in and admit it was just a poll.

Huh? I have no idea what you mean. Are you going to answer my question?

Comment by Guts — December 15, 2008 @ 1:46 am

Guts Says:
December 15th, 2008 at 1:55 am
Allen wrote:

Ergo, this "poll" is simply testing whether the respondents know anything about the biochemistry of protein synthesis in prokaryotes. That is, it is asking for respondents to verify a "fact", as several commentators have pointed out.

Well no, I was asking people's opinions on why methionine is a nearly universal start codon. None of the reasons mentioned have been established such that one could call it a "fact". I also just learned that methionine is resistant to cytosine deamination, and it sets the reading frame.

Comment by Guts — December 15, 2008 @ 1:55 am

don provan Says:
December 15th, 2008 at 3:38 pm
Are you going to answer my question?

No, I'm not.

Comment by don provan — December 15, 2008 @ 3:38 pm

Always finish what you start…

37 Responses to “Always finish what you start…”

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