The "best possible code"

Posted 1 October 2008 by PvM

A paper written by Knight et al in 2000 has created some confusion as to the nature of the genetic code, leading some design proponents to jump to the conclusion that these findings show evidence of 'design' when in fact, the findings, in proper context show strong support for an evolutionary thesis of the origin and evolution of the genetic code. Let me explain. The paper in question is: Early fixation of an optimal genetic code published in Molecular Biology and Evolution 17:511-518 (2000) and written by Knight, Freeland, Landweber and Hurst. The quote that caused much confusion is

If our definition of biosynthetic restrictions are a good approximation of the possible variation from which the canonical code emerged, then it appears at or very close to a global optimum for error minimization: the best of all possible codes.

which was quoted by ChunkDZ as (warning, many of ChunkDZ's responses include insults, invectives, follow the links at your own risk).

If our definition of biosynthetic restrictions are a good approximation of the possible variation from which the canonical code emerged, then it appears at or very close to a global optimum for error minimization: the best of all possible codes.
— ChunkDZ

Later abbreviated to (warning, many of ChunkDZ's responses include insults, invectives, follow the links at your own risk).

After all your lying, posturing, obfuscating, pretending, and doubletalk, several scientific discoveries remain unchanged. 1) The code is "at or very close to a global optimum for error minimization across plausible parameter space." 2) The code is "the best of all possible codes".
— ChunkDZ

However, the abstract itself could have been a hint as to the nature of the claim

Finally, other analyses have shown that significantly better code structures are possible. Here, we show that if theoretically possible code structures are limited to reflect plausible biological constraints, and amino acid similarity is quantified using empirical data of substitution frequencies, the canonical code is at or very close to a global optimum for error minimization across plausible parameter space.

or from the actual paper

Estimates based on PAM data for the restricted set of codes indicate that the canonical code achieves between 96% and 100% optimization relative to the best possible code configuration (fig. 2c).

So what went wrong in ChunkDZ's analysis of the quote? Note that ChunkDZ argued that the paper showed that the code was globally optimal, which indeed could be seen as evidence against evolution and in favor of design since evolution seldomly optimizes globally but rather finds a local optimum given the initial conditions which are guided by historical contingencies and other constraints. However, a 'designer' has no limitations to how the optimization is performed and thus could, if it pleased her, optimize in a truly global fashion. When you read the paper, the authors also looked at the unrestricted code performance and as expected, the standard code fared much worse placing its performance at between "76% and 97%" of optimal value. ChunkDZ realizes his problems when he states

It's globally optimal within all plausible biological constraints.
— ChunkDZ

but fails to recognize that these are not biological constraints, since any code could function as the genetic code. However it is the historical constraint based on the prevailing hypothesis of the origin and evolution of the genetic code which proposes that pre-biotic chemistry determined the link between the code and the amino acid assignment (this concept is called stereochemistry) and that subsequent optimization further shaped the code to some 'optimum' (also called selection). Under this hypothesis, the analysis shows that indeed, given the hypothetical pre-biotic linkage, the code is indeed optimal in the sense that no or few codes which similarly reflect pre-biotic conditions exist which do better (the 96 to 100% claim). In other words, the code is only globally optimal in a constrained fashion, as expected from evolutionary theory, and not as expected from a 'design' perspective unless one restricts the designer to be constrained by the similar pre-biotic chemistry. In fact, the global nature of the optimization was an essential argument in ChunkDZ's claim that the research supported 'design' and now that it has been shown that in fact the opposite is true, one comes to understand how ChunkDZ may have missed the important limitation of the claim. ChunkDZ's claim is further clarified by the following comment (warning, many of ChunkDZ's responses include insults, invectives, follow the links at your own risk).

My point was, and remains, that you moron critics love to point out that nature is expected to make kludgy hodge-podges. Then when confronted with evidence that the basis for every single biological system is a non-hodge-podged, sophisticated, elegantly designed, optimal "best of all possible codes", you monkeys simply wallow in your own feces, ignore the research, and complain about the evils of Big Bad Billy Dembski. What a predictable bunch of pansies you are. Anyhow, here's another research paper that shows that the code is also optimal for parallel coding. http://genome.cshlp.org/cgi/content[...]act/17/4/405
— ChunkDZ

Note the 'best of all codes', as opposed to a historically constrained optimum, which suggests to ChunkDZ not only that evolutionary theory seems flawed, even though it was an evolutionary prediction that suggested that the code originated from a linkage with pre-biotic chemistry and was then optimized 'locally' and not the best of all codes in the sense of an unconstrained optimum, which as I explained would have been a problem for evolution and add some relevance to the concept of 'design', assuming that 'designers' are not constrained by pre-biotic chemistry and are interested more in a truly global optimum. In fact, and this is worth repeating, there are no biological reasons why the code has to reflect the pre-biotic chemistry, in fact, the code could very well have been one which was totally unrelated to said chemistry and still function biologically. Note also how ChunkDZ in the above quote refers to another paper which he believes claims 'optimality'. Let me quote from the actual title of the paper "The genetic code is nearly optimal for allowing additional information within protein-coding sequences". Note the word nearly, in front of 'optimal'. Furthermore, the conclusions again do not show a global but rather local optimum, but it does require one to read the paper. And finally, the coup de grace, so to speak. Knight was one of the reviewers of a more recent paper which looked at the global optimality of the genetic code, where the code was obviously not constrained by pre-biotic chemistry to show that the code was far from a truly global optimum, and Knight observed that

They recapture the uncontroversial result that the genetic code is much better at minimizing errors than a random genetic code (as has been shown by many authors), but is at neither a local nor global optimum (as has also been shown previously).

What more needs to be said but... 'priceless' Except of course, ChunkDZ seems to be unconstrained and argued that Compare the design hypothesis according to ChunkDZ

the designers (far from being constrained) chose the ones that they used for their own reasons.

versus the scientific hypothesis

The origin of the genetic code was constrained by pre-biotic chemistry (stereochemistry hypothesis) followed by a period of selection

Now which one do you think is the better hypothesis and why? Oh and about this more recent paper? Artem S Novozhilov, Yuri I Wolf, and Eugene V Koonin Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape, Biol Direct. 2007; 2: 24. Instead of analyzing just the restricted code set, they analyzed the full code set and found some interesting results

1. The code fitness landscape is extremely rugged such that almost any random initial point (code) tends to its own local optimum (fitness peak). 2. The standard genetic code shows a level of optimization for robustness to errors of translation that can be achieved easily and exceeded by minimization procedure starting from almost any random code. 3. On average, optimization of random codes yielded evolutionary trajectories that converged at the same level of robustness as the optimization path of the standard code; however, the standard code required considerably fewer steps to reach that level than an average random code. 4. When evolutionary trajectories start from random codes whose fitness is comparable to the fitness of the standard code, they typically reach much higher level of optimization than that achieved by optimization of the standard code as an initial condition, and the same holds true for the minimization percentage. Thus, the standard code is much closer to its local minimum (fitness peak) than most of the random codes with similar levels of robustness (Fig. 9).

2. is the clincher which shows that a genetic code from almost any initial condition could evolve to reach an optimum as good or better than the standard code. So much for 'best of all possible codes' Now you know "the rest of the story", and you have been reminded once again why ID is a scientifically vacuous position.

57 Comments

tresmal · 2 October 2008

Now what ever could have inspired you to write this post?

PvM · 2 October 2008

To clarify my thoughts and the arguments and because I must be a moron

djlactin · 2 October 2008

This entire argument (both sides) seems to overlook a possibility. The idea that one code originated, then climbed a local adaptive peak, is too simplistic. Competition among direct ancestors of extant life may only have been part of the process of (near) optimization of the code.

The "Last universal common ancestor" (LUCA) of all extant organisms was not necessarily the only life form present at the time. Numerous other life forms may have (probably?) existed* contemporaneously with LUCA, and there is no reason to assume that they had the same genetic codes as LUCA or each other. (Indeed, they could even have used different genetic materials and amino acids). Each experiment in genetic coding would have climbed its own adaptive peak, and then the set of them would have been set competing against each other. LUCA is just the winner of the tournament among these forms. So I postulate a 2-level competitive elimination among the set of possible universal ancestors: within-group hill-climbing and among-group 'war'.

At first, any coding system that performed better than random would have been 'good enough', but the war would have eliminated all but the systems closest to optimal (subject to a few randomizing factors).

* I do not necessarily mean that life originated independently more than once (not impossible), but that after an origin, several "experimental" coding systems arose by elaboration of the first one.

PvM · 2 October 2008

Very Woese words :-)

Yes, those early days of the genetic code may have been full of surprises, with different 'species' relying on differing codes. However, if the codes wer all constrained by prebiotic chemistry, they would eventually evolve under selection to code very similar. So I am not sure, how to interpret your proposal. Not to dismiss it because I love these kinds of discussions to explore the limits of our creative thoughts to explore ways to look at events that happened hundred of millions or perhaps billions of years ago.

Imagine that by looking at today's code assignments we can still track its early origin and evolution...

Dale Husband · 2 October 2008

Well, at least you did what I had asked chunkdz to do and thus blew him away, PvM. I'll just move my earlier comment from that thread chunkdz pooped on to here:

Dale Husband said: Right. There is the question of whether DNA is the best possible carrier of genetic information. There is also the question of whether amino acids are the best agents to translate that genetic information into structual forms. Finally, we have to agree on what "best" is. It should be noted that if there was such a system of life that allowed for no copying errors (mutations), evolution would not occur. THEN intelligent design would have had to create any complex forms of life made up from that coding system. Not bad for a moronic monkey brain flinging poo, eh?

Dale Husband · 2 October 2008

Check out this article from the December 2007 issue of Scientific American: http://www.sciam.com/article.cfm?id=are-aliens-among-us It mentions alternative ways of life forms arising via other forms of chemistry. http://www.sciam.com/article.cfm?id=are-aliens-among-us&page=4

The chance of confusing a separate tree of life with an undiscovered branch of our own tree is diminished if one considers more radical alternatives to known biochemistry. Astrobiologists have speculated about forms of life in which some other solvent (such as ethane or methane) replaces water, although it is hard to identify environments on Earth that would support any of the suggested substances. (Ethane and methane are liquid only in very cold places such as the surface of Titan, Saturn’s largest moon.) Another popular conjecture concerns the basic chemical elements that make up the vital parts of known organisms: carbon, hydrogen, oxygen, nitrogen and phosphorus. Would life be possible if a different element were substituted for one of these five? Phosphorus is problematic for life in some ways. It is relatively rare and would not have existed in abundance in readily accessible, soluble form under the conditions that prevailed during the early history of Earth. Felisa Wolfe-Simon, formerly at Arizona State University and now at Harvard University, has hypothesized that arsenic can successfully fill the role of phosphorus for living organisms and would have offered distinct chemical advantages in ancient environments. For example, in addition to doing all the things that phosphorus can do in the way of structural bonding and energy storage, arsenic could provide a source of energy to drive metabolism. (Arsenic is a poison for regular life precisely because it mimics phosphorus so well. Similarly, phosphorus would be poisonous to an arsenic-based organism.) Could it be that arseno-life still lingers in phosphorus-poor and arsenic-rich pockets, such as ocean vents and hot springs?

DaveH · 2 October 2008

As hypothesised above: http://www.sciencemag.org/cgi/content/abstract/321/5891/967

Bobby · 2 October 2008

Who is ChunkDZ, and why should we care?

David Stanton · 2 October 2008

Thanks PvM.

PT is still a place where people can learn some real science, despite the disruptive efforts of trolls.

wad of id · 2 October 2008

In the other thread, I posted additional reasons why this code is suboptimal... problems that took me, a mere unSupernatural designer to figure out schemes around in 15 minutes:

http://pandasthumb.org/archives/2008/09/mark-pallen-on.html#comment-168890

djlactin · 2 October 2008

The answer to all your questions is ‘co-option’.

This means that genetic structures change function over time, as a result of variation and natural selection. For example, the genes ‘for’ fingers and toes were used to build bone structures in the fins of fish ancestral to tetrapods. yes. bones in their fins: these were lobe-finned fishes and not at all like your familiar trout.

A man who knows a little is the smartest man he knows.

djlactin · 2 October 2008

PvM said: Very Woese words :-) Yes, those early days of the genetic code may have been full of surprises, with different 'species' relying on differing codes. However, if the codes wer all constrained by prebiotic chemistry, they would eventually evolve under selection to code very similar. So I am not sure, how to interpret your proposal. Not to dismiss it because I love these kinds of discussions to explore the limits of our creative thoughts to explore ways to look at events that happened hundred of millions or perhaps billions of years ago. Imagine that by looking at today's code assignments we can still track its early origin and evolution...

All I meant was that the adaptive landscape metaphor is incomplete if it considers only one initial group, which then climbs the nearest peak and attains (most likely) a local maximum, where it becomes stranded. My idea is that if the process begins using several such groups, each at a different starting point, each will reach a separate local max and that subsequent competition among these could result in survival of only the group on (one of) the highest local max. It's a concept that gets around the stranding problem.

David Stanton · 2 October 2008

Who is your creator wrote:

"If evolution predicts that genetic complexity is gained slowly and ‘as needed,’ how is it that ..."

I don't know of a single scientist who would claim that things evolve "as needed". You are confusing evolution with creationism. Variation arises by random mutations and is selected on by natural selection. This process does not know when something is needed. There is no foresight or planning involved and no evidence that any exists.

Preadaptation and exaptation are features of successful lineages, not evidence of planning. "Overly complex" features are simply not selected against in some circumstances and can later give rise to adaptive features. This is a far better explanation than some intelligent disigner who anticipates the needs of future organisms and provides for those needs millions of years in advance.

There is no such thing as a "Universal Genome". Try again. This time, try to comment on the topic of the thread.

eric · 2 October 2008

who is your creator said: If evolution predicts that genetic complexity is gained slowly and ‘as needed,’ how is it that coding for specific features has appeared “long before” or has become “latent” in organisms that supposedly evolved millions of years earlier?

1. You cite evidence of genomic complexity to support a claim that 'coding for specific features appeared long before [the feature].' The former does not imply the latter. 2. You also make the the common mistake of expecting (e.g.) sea urchins to have a less complex genome because they are somehow, in your mind, simpler than humans. However this concept of evolution as having direction or being a ladder is wrong. Discovering that the sea urchin genome is complex is evidence against your faulty idea, not evidence against evolution. 3. Evolution via exaptation predicts that genes used for the development of (e.g.) the eye may be present in eyeless species, because evolution works through small changes in present genes. Exaptation can be demonstrated by the fact that these genes in almost all cases serve other functions in organisms without eyes. 4. Philosophical web pages are not convincing references for a scientific claim that you have discovered some "latent" gene. Its about as useful as someone claiming to have disproven QM on their blog. If you want us to pay attention, publish your findings in peer reviewed scientific journals. I would also suggest you seriously consider the theological implications of your claim (that the coding for complex features was built in to primitive organisms, who then evolve). It implies no need for 'kinds'and no need for special creation. It implies a designer perfectly okay with natural selection ("nature, red in tooth and claw"). It implies the original creation was imperfect, i.e. not realized to its full extent. It implies evolution can trigger genes to turn on and add function, i.e. create information. Now personally, I'm okay with all of these implications, but I wonder if someone with the online identity "who is your creator" really is.

Paul Burnett · 2 October 2008

PvM said: according to ChunkDZ:
...the designers (far from being constrained) chose the ones that they used for their own reasons.

Waitaminute! "...the designers...chose the ones that they used for their own reasons." A plurality of designers? Not One Creator God? That's the Manichaean Heresy! ChunkDZ is a heretic, and should be burned at the stake by his fellow intelligent design creationists.

Bobby · 2 October 2008

Dale Husband said: And the same goes for you, Bobby! You may also be chunkdz!

No, I'm the sane Bobby, an infrequent poster, former frequent poster on talk.origins. I think there's a creationist kook who posts as 'bobby' sometimes.

Henry J · 2 October 2008

In fact, and this is worth repeating, there are no biological reasons why the code has to reflect the pre-biotic chemistry, in fact, the code could very well have been one which was totally unrelated to said chemistry and still function biologically.

With the provision that the organisms would have to be able to make what they need from the edible chemicals in their environment. Henry Btw, the blog's spell checker seems to be down.

Henry J · 2 October 2008

No, I’m the sane Bobby, an infrequent poster, former frequent poster on talk.origins. I think there’s a creationist kook who posts as ‘bobby’ sometimes.

Is that evidence that English is not the best of all codes? :p

Saddlebred · 2 October 2008

Bobby said: No, I'm the sane Bobby, an infrequent poster, former frequent poster on talk.origins. I think there's a creationist kook who posts as 'bobby' sometimes.

You might want to consider a new handle. =)

Dale Husband · 2 October 2008

who is your creator said: Thank you all for the enlightening responses. While they may make perfect sense to you, it's great material for us! This one is by far the best!!! "2. You also make the the common mistake of expecting (e.g.) sea urchins to have a less complex genome because they are somehow, in your mind, simpler than humans. However this concept of evolution as having direction or being a ladder is wrong. Discovering that the sea urchin genome is complex is evidence against your faulty idea, not evidence against evolution. 3. Evolution via exaptation predicts that genes used for the development of (e.g.) the eye may be present in eyeless species, because evolution works through small changes in present genes. Exaptation can be demonstrated by the fact that these genes in almost all cases serve other functions in organisms without eyes.

It's only great material for you if you understood it, which clearly you didn't. Indeed, it seems you have no understanding of reality itself if you think for one moment that the issue you raised even makes a dent in the case for evolution. Quite the opposite, actually. So, who is your creator? No one I know! Pun intended!

PvM · 2 October 2008

clean up cycle finished

iml8 · 2 October 2008

DaveH said: As hypothesised above: http://www.sciencemag.org/cgi/content/abstract/321/5891/967

I'd seen references to that article in the pop science press but it was a bit puzzling. The organisms need arsenic in metabolic chain -- but are they clear on what it does? Is is just an important trace element in the process, or is it a primary component in the process -- like CO2 and water are for plant photosynthesis? White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

a lurker · 2 October 2008

I pointed out that Google did not reveal the source of the unlinked to creationist. This resulted in a personal attack for no apparent reason from Dale Husband who also attacked without reason Bobby:

You only needed to look here, dumbass: http://pandasthumb.org/archives/2008/09/mark-pallen-on.html It's not PvM's fault that you haven't been paying attention these past few days! That's why you are a "lurker" and not an active participant, unless you ARE chunkdz trying to cover your @$$. And the same goes for you, Bobby! You may also be chunkdz!

I am NOT a creationist. Indeed the NCSE charges my credit card every month, I write letters to the editors of publications local to me in favor of evolution, write to elected officials, etc. 1) Is it the policy of the Panda's Thumb that everyone must read every post and every comment? I read that post in question, but I did not read through 12 screens worth of comments. Google and PT's own search function did not reveal the comment's location. 2) It is PvM's fault not to have linked to the comment in question. As it is was in the Panda's Thumb itself there is certainly no reason to fear increasing the traffic to one of the bad guy's web sites. (Though I do fault PvM on that point, otherwise his post was excellent.) 3) If someone is to be quoted or referred to, a proper reference or link should always be included. Historically improper citation has been a creationist tactic: helpful to keep people from debunking them. The trend as of late has been pro-science people to use the tactic as well on the dubious hypothesis that merely linking to them grants them some sort of validity. It does not. And with proper web attributes, it does not even help them with Google.

PvM · 2 October 2008

good points, however please understand that both Bobby/Jobby and Chunkdz have been quite busy spamming the site with nonsense. And yes, unlike some of the other moderators, I do enforce a level of discourse. I will add the relevant links, I apologize for the oversight.

a lurker said: I pointed out that Google did not reveal the source of the unlinked to creationist. This resulted in a personal attack for no apparent reason from Dale Husband who also attacked without reason Bobby:
You only needed to look here, dumbass: http://pandasthumb.org/archives/2008/09/mark-pallen-on.html It's not PvM's fault that you haven't been paying attention these past few days! That's why you are a "lurker" and not an active participant, unless you ARE chunkdz trying to cover your @$$. And the same goes for you, Bobby! You may also be chunkdz!
I am NOT a creationist. Indeed the NCSE charges my credit card every month, I write letters to the editors of publications local to me in favor of evolution, write to elected officials, etc. 1) Is it the policy of the Panda's Thumb that everyone must read every post and every comment? I read that post in question, but I did not read through 12 screens worth of comments. Google and PT's own search function did not reveal the comment's location. 2) It is PvM's fault not to have linked to the comment in question. As it is was in the Panda's Thumb itself there is certainly no reason to fear increasing the traffic to one of the bad guy's web sites. (Though I do fault PvM on that point, otherwise his post was excellent.) 3) If someone is to be quoted or referred to, a proper reference or link should always be included. Historically improper citation has been a creationist tactic: helpful to keep people from debunking them. The trend as of late has been pro-science people to use the tactic as well on the dubious hypothesis that merely linking to them grants them some sort of validity. It does not. And with proper web attributes, it does not even help them with Google.

Bobby · 2 October 2008

Please do not delete my posts. You'll start looking like a creationist site.

iml8 · 2 October 2008

Bobby said: Please do not delete my posts. You'll start looking like a creationist site.

PvM's clearly a little testy today -- cut him some slack, if you saw the, uh, "discourse" with the unpleasant visitors in other rooms it would be clear why. He'll be back to level in a day or so. I think's also been experimenting with site security and it might be having some unpredictable effects. White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

PvM · 2 October 2008

Then stay on focus, I have moved quite a few off topic posting to avoid the thread from derailing. Check the bathroom wall

Bobby said: Please do not delete my posts. You'll start looking like a creationist site.

PvM · 2 October 2008

Just trying to keep the discussion on topic, discussions about particular participants can be had at After the Bar Closes or the Bathroom wall. Since, as I explain, the originators of the thread control them, I can only enforce a level of civility and on topicness (what a word...) on these threads. People are welcome to contribute and whether pro or con, no off topic or foul language postings will be allowed. If you do not like my standards, then there are sufficient other threads open for disruption.

iml8 said:
Bobby said: Please do not delete my posts. You'll start looking like a creationist site.
PvM's clearly a little testy today -- cut him some slack, if you saw the, uh, "discourse" with the unpleasant visitors in other rooms it would be clear why. He'll be back to level in a day or so. I think's also been experimenting with site security and it might be having some unpredictable effects. White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

iml8 · 2 October 2008

PvM said: People are welcome to contribute and whether pro or con, no off topic or foul language postings will be allowed.

ACHTUNG! DAS OFFENTOPIK IST VERBOTEN! KEEPEN ZE HANDS UN POCKETS UN VATCHEN DAS BLINKEN LITES! White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

PvM · 2 October 2008

Okay funny although it should be illegal to do this to any language...

iml8 said:
PvM said: People are welcome to contribute and whether pro or con, no off topic or foul language postings will be allowed.
ACHTUNG! DAS OFFENTOPIK IST VERBOTEN! KEEPEN ZE HANDS UN POCKETS UN VATCHEN DAS BLINKEN LITES! White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

iml8 · 2 October 2008

PvM said: Okay funny although it should be illegal to do this to any language...

You seem like a sensible person. You might want to sleep on things a bit ... White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

Bobby · 2 October 2008

PvM said: If you do not like my standards, then there are sufficient other threads open for disruption.

If you can't set higher standards than UD, then no, I *don't* like them. Is this your site now?

iml8 · 2 October 2008

Bobby said: Is this your site now?

Chill please. The point's been made, if he's NOT agitated after his activities elsewhere, I'd be astounded. Let him sleep on it. White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

Bill Gascoyne · 2 October 2008

PvM said: If you do not like my standards, then there are sufficient other threads open for disruption.

"Those are my principles. If you don't like them, I have others."
Groucho Marx ;-)

Dale Husband · 2 October 2008

I guess I should apologize for assuming a lurker was looking to cause trouble, but after seeing so much crap around here, I was like a wasp ready to sting the next troll. Sorry, PvM!

a lurker said: I pointed out that Google did not reveal the source of the unlinked to creationist. This resulted in a personal attack for no apparent reason from Dale Husband who also attacked without reason Bobby:
You only needed to look here, dumbass: http://pandasthumb.org/archives/2008/09/mark-pallen-on.html It's not PvM's fault that you haven't been paying attention these past few days! That's why you are a "lurker" and not an active participant, unless you ARE chunkdz trying to cover your @$$. And the same goes for you, Bobby! You may also be chunkdz!

PvM · 2 October 2008

Nope but it is my thread. Feel free to spam any other

Bobby said:
PvM said: If you do not like my standards, then there are sufficient other threads open for disruption.
If you can't set higher standards than UD, then no, I *don't* like them. Is this your site now?

mharri · 2 October 2008

Now, I have a personal policy of giving plenty of leeway for what people might have meant, and I try to be understanding of the ignorant, even the stubbornly so. (Even I can grow as a person.) But what got me was ChunkDZ's line
"the designers (far from being constrained) chose the ones that they used for their own reasons."
So, now any procedure we had for prediction is thrown up to a whim of the designers. So that now we have no method for prediction. So that any argument ChunkDZ might have had for scientific evidence of ID is out the window. Is this the gist of it?

Henry J · 2 October 2008

Regarding the conclusion in the paper that sometimes some of the codes for a particular amino acid would change to use different but chemically similar amino acid: that was interesting. I had been wondering how a code assignment could change from one amino acid to another without breaking all the genes that currently used that particular code. But if the change is to something chemically similar, I guess it might on rare occasions manage to occur without breaking something critical that used to use the old "meaning" of that code.

Henry

David Stanton · 2 October 2008

Henry,

That is exactly why most of the variation in the "universal" genetic code occurs in the mitochondria. Animal mitochondrial DNA only encodes thirteen proteins. Of course they are important for central metabolic processes, but obviously they did indeed tolerate some minor alterations in the genetic code.

There are many publications on this topic. I don't have access to them right now, but I can try to look them up later if you or anyone else is really interested.

DaveH · 3 October 2008

Sorry, don't have access to the paper either, but it does appear to be AsO3 is the source of electrons, replacing water. http://www.rsc.org/chemistryworld/News/2008/August/15080802.asp

iml8 said: I'd seen references to that article in the pop science press but it was a bit puzzling. The organisms need arsenic in metabolic chain -- but are they clear on what it does? Is is just an important trace element in the process, or is it a primary component in the process -- like CO2 and water are for plant photosynthesis? White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

Robin · 3 October 2008

who is your creator.com said: Please explain to us how the 'best possible code' created the genetic material for specific features LONG before they arose?

The code didn't crate genetic material for specific features long before the features arose. The code had SOME genes that would have allowed the expression of limbs and other complex features IF the other genetic material (code for limb development) had also existed. What is so remarkable about the discovery is that this demonstrates that genetic development is NOT purposeful, but rather haphazard. Genes can develop that could be used to express complex features when there is no material for the features. For most organims, these genes will be wasted efforts and many will go extinct NEVER having used those genes. But SHOULD such a group of organisms live to see a day when environmental changes place pressures on the group to rapidly reproduce in in other ways affect their population dynamics, then such groups will produce changes quicker and will likely have an adaptive advantage since they will have a foundational set of change expressing genetic material in place.

If evolution predicts that genetic complexity is gained slowly and ‘as needed,’ how is it that coding for specific features has appeared “long before” or has become “latent” in organisms that supposedly evolved millions of years earlier? Did organisms "evolve" them millions of years BEFORE they were needed in pure speculation that one day they might need them?:

...and this pretty much explains the error in your understanding. Evolution doesn't predict that genetic complexity is gained necessarily slowly and specifically 'as needed'; evolutionary theory explains that how environmental and population conditions can affect the rate of genetic change. Further, it specifically notes that neither the process (evolution) nor the hereditary mechanism (genes) "know" anything and cannot "anticipate" or "work toward" any specific goal. So, your premise is false - evolution doesn't work towards complexity (or any other change) 'as needed'. Rather it creates change (of which complexity is a by-product) and if the changes are beneficial in the specific conditions at that specific time, those changes will likely give an organism a competitive advantage and thus spread through a population as a fitness adaptation.

PvM · 3 October 2008

Who is Your Creator had a good question but I do not want to distract from the topic. The answer is co-option, in other words, the genes for limbs have to come from somewhere and evolution does not rely on a miraculous 'poof' that when they are needed, the mutations somehow happen. Instead evolution builds slowly on pre-existing structures and genes to reshape them.

PvM · 3 October 2008

Perhaps a common confusion is that evolution creates mutations which then are selected for when needed, rather than evolution relying on a reservoir of variation and which slowly evolves when the environmental pressures change. And rather than reinventing the wheel, it uses what is available. This co-option is what one expects, although it may give the impression that certain features pre-evolved.
A common confusion.

Larry Boy · 3 October 2008

An open letter to internet trolls:

Dear Mr. Troll.

Being unable to understand the clear and unambiguous statements of intelligent individuals because the content of these statements differs from your own opinions is not a sign of intelligence or clear thinking, as you no doubt suppose, but actually a good indicator of past emotional trauma and psychological instability. I primarily advise you to make peace in your own heart, and I fear that persistence in anti-social behaviors will at best distract you from the troubles in your own life.

I cannot speculate what has caused you to divorce yourself from intelectual activities; however, if you can recover from your misanthropy and anti-intellectualism, I would happily aid you in understanding the complexities of material world. Understanding reality is immensely personally rewarding, and, if you are not obdurate in your ignorance, I believe you will discover those rewards dwarf the cheep emotional thrill of trolling.

-A concerned scientist.

Larry Boy · 3 October 2008

slightly OT: But "whoisyourcreator.com" is clearly written by some one who has no understanding of biology:

"During meiosis, male and female chromosomes combine to create an offspring that has a ‘blend’ of the two difference sets of homologous (same DNA structure) alleles."

I don't think I could say it worse if I tried.

Inoculated Mind · 3 October 2008

Good post. I've debated the optimization of the genetic code with some creationists, notably Fuz Rana of RTB. He is fond of selectively quoting the research to say that the genetic code is 'one in a million'... leaving out the fact that billions upon billions of codes are possible. PvM, have you read the paper by Wu et al (2004), called "Evolution of the Genetic Triplet Code via Two Types of Doublet Codons"? Fantastic stuff.

Scott · 4 October 2008

Does the paper talk about how one evaluates whether one "code structure" is more "optimal" than another? What criteria does one use? I'm approaching this from the perspective of a computer language designer. A "code structure" sounds like a "language" used to store or express certain concepts or information. By optimality are we talking about the relative efficiency and sufficiency of the "code structure"?

tresmal · 4 October 2008

Scott said: Does the paper talk about how one evaluates whether one "code structure" is more "optimal" than another? What criteria does one use? I'm approaching this from the perspective of a computer language designer. A "code structure" sounds like a "language" used to store or express certain concepts or information. By optimality are we talking about the relative efficiency and sufficiency of the "code structure"?

The paper describes the code as being optimal for error minimization. This means that the code is structured in such a way that most point mutations result in the same amino acid or a functionally similar aa being coded for. The point did come up once or twice on another thread where this paper was discussed.

PvM · 4 October 2008

A code refers to the mapping of a sequence of nucleotides, and the final expression of proteins.

Scott said: Does the paper talk about how one evaluates whether one "code structure" is more "optimal" than another? What criteria does one use? I'm approaching this from the perspective of a computer language designer. A "code structure" sounds like a "language" used to store or express certain concepts or information. By optimality are we talking about the relative efficiency and sufficiency of the "code structure"?

RBH · 5 October 2008

Paul Burnett said:
PvM said: according to ChunkDZ:
...the designers (far from being constrained) chose the ones that they used for their own reasons.

Waitaminute! "...the designers...chose the ones that they used for their own reasons." A plurality of designers? Not One Creator God? That's the Manichaean Heresy! ChunkDZ is a heretic, and should be burned at the stake by his fellow intelligent design creationists.

Well of course there are/were multiple designers!

chuck · 7 October 2008

RBH said:
Paul Burnett said:
PvM said: according to ChunkDZ:
...the designers (far from being constrained) chose the ones that they used for their own reasons.

Waitaminute! "...the designers...chose the ones that they used for their own reasons." A plurality of designers? Not One Creator God? That's the Manichaean Heresy! ChunkDZ is a heretic, and should be burned at the stake by his fellow intelligent design creationists.
Well of course there are/were multiple designers!

Multiple designers? Or just multiple Noodly Appendages?

gregwrld · 7 October 2008

I would have that if the code is so damn well-designed then most of the species that have appeared on this planet would not have gone extinct...

thisisfunny · 8 October 2008

Has the code reached a global optima?
Spectacular convergence into a reasonably universal optimal code?
Why isn't it improving or getting more complex?
Is it a global or local optima with regards to fitness. Seems to have been static (reached a global optima) for a few billion years with regards to fitness (few off shoots here and there, nothing major).

I mean, there are millions of other possibilities, yet life got stuck with one that is reasonably optimized for a variety of processes.

Are those other possibilities really so bad with regards to fitness that they just did not get selected?
Or was it a case of self-organization into a reasonably optimal code that dominated over all other possibilities? Just curious why just a single code (with a few off shoots) emerged.
And why do self-replicating entities need a code to replicate?

Abiogenesis research (and virtual simulators) should be able to determine whether self-replicating entities can self-replicate to ever greater complexity (like we observe in the evolution of life and not in virtual simulators) with or without a code.

Henry J · 8 October 2008

As for why the code ceased changing, I'd think that changing the amino acid produced for a particular code value would run the risk of breaking the function of any proteins that use that code.

What surprised me on reading this stuff is that the code could change at all after it was in use, for the reason I just mentioned. But I guess early on, there might be codes that weren't yet critical to the species, so those might (on very rare occasions) shift to a chemically similar amino acid.

Of course, codes that happen to not be used by a species, could be changed without hurting that species. Or if the only use is in parts of the protein that don't affect it's folded shape or its chemical properties after folding.

Also, if the change is to a chemically similar amino acid, that's less likely to break something important than a shift to a quite dissimilar one.

Self replicating without a code of some sort strikes me as highly unlikely; such a creature would have to measure and analyze itself in order to build the offspring, whereas with a code, it just copies the code sequence, then the offspring in effect builds itself from provided raw materials.

Henry

fnxtr · 8 October 2008

(safire)

optimum - singular
optima - plural

(/safire)

Joe G · 9 October 2008

Is there any data, evidence or observation(s) that would demonstrate nature, operating freely, can create a coding system?

We do have direct observations of designing agents doing that very thing.

And what happens once we discover that the biological information cannot be traced back to the sequence? IOW what happens once we determine that it is not just the sequence that is the code?

Once we discover that the biological information rides on the DNA, just as computer data rides on its various mediums, then ID would be a given.

And it looks like someone has started to figure that out:

“Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype. The emerging picture made it increasingly difficult to see genes in Weismann’s “unambiguous bearers of information” or to view them as the sole source of the durability and stability of organic form. It is true that genes influence every aspect of development, but influencing something is not the same as determining it. Only a very small fraction of all known genes, such as developmental fate switching genes, can be imputed to have any sort of directing or controlling influence on form generation. From being “isolated directors” of a one-way game of life, genes are now considered to be interactive players in a dynamic two-way dance of almost unfathomable complexity, as described by Keller in The Century of The Gene.”
Michael John Denton page 172 of [i]Uncommon Dissent[/i]

iml8 · 9 October 2008

Joe G said: Is there any data, evidence or observation(s) that would demonstrate nature, operating freely, can create a coding system?

Yes, INDEED! It's called "natural selection" AKA The Grim Reaper. It is an intelligence that makes a very definite and clear decision between SURVIVAL and EXTINCTION. This is an ON or OFF, YES or NO decision that sorts out genomes with bad bits (zeroes if you like) from those with good bits (ones if you like). Sigh, yet another variation on the (AHEM) "Law Of Conservation Of Information (LCI)". If indeed "intelligence is required to create [genetic] information" then the Grim Reaper is smart enough to do the job. Incidentally, there is no entry for the LCI on Wikipedia. Considering that I can easily find entries on the least celebrities, TV shows that ran ten episodes, and was even to my surprise able to figure out things like "LEET / 1337" and "Maschinen Krieger" ... that gives the status of the LCI accordingly. I keep saying: I don't care about Darwin one way or another, any way Nature actually works is fine by me. But I buy Darwin because the evidence tells me that's the way Nature works. I also buy it because if there was a hundredth as much wrong with evo science as the Darwin-bashers claim there is, they'd be able to come up with arguments that didn't sound like such hokum. White Rabbit (Greg Goebel) / http://www.vectorsite.net/gblog.html