The evolution of the genetic code

| 19 Comments

Scientists from the Weizmann Institute of Science report the exiting findings of Parallel Codes In Genes

These findings are exciting since they can help further unravel the origins and evolution of the genetic code

“Our findings open the possibility that genes can carry additional, currently unknown codes,” explains Dr. Uri Alon, principal investigator on the project. “These findings point at possible selection forces that may have shaped the universal genetic code.”

These findings provide for potential answers to our ignorance, further driving back Intelligent Design, forcing it to hide it the shadows of our ignorance.

Shalev Itzkovitz and Uri Alon The genetic code is nearly optimal for allowing additional information within protein-coding sequences Genome Res. Published February 9, 2007

Abstract: DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These “parallel codes” include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.

I wonder how ID proponents will spin these results. Nothing in ID predicts nor explain these findings. But I am sure that some will spin this, despite ID being nothing more than ‘science cannot explain X’ and does not provide for any framework to make scientifically relevant predictions.

19 Comments

I wonder how ID proponents will spin these results.

That’s an easy one - they’ll argue that this is proof of design. It’s really insipid, isn’t it, how ID proponents will take any new and surprising finding and play it off as though it’s obviously evidence of some higher power.

… when you’re convinced that God exists, everything is proof of God.

Re “The evolution of the genetic code

PvM posted Entry 2893 on February 10, 2007 04:15 PM. Trackback URL: http://degas.fdisk.net/cgi-bin/mt/mt-tb.fcgi/2883

Scientists from the Weizmann Institute of Science report the exiting findings of Parallel Codes In Genes”

exiting findings? Or exciting?

Henry

Pim wondered

I wonder how ID proponents will spin these results.

I fully expect Sal to start blathering about steganographic images concealed in alternative codes.

I wonder how ID proponents will spin these results.

Louie: Alright everybody, I’m Louie Anderson and welcome back to The Feud. Story family, are you ready?

Steve: Ready Louie!

Louie: Okay. The question is, a team of evolutionists make a new scientific discovery. The creationists read a news story about it. After the fact, what…will the creationists…say?

Steve: Uh…ugh…that they predicted it!

Louie: Show Me ‘They Predicted It’!

DING!

You mean you haven’t seen this yet?

http://www.uncommondescent.com/archives/2055

Is this yet another Biblical Code?

Don’t these findings imply that beneficial mutations are even more unlikely than previously believed? Not only do gene mutations need to improve the protein design, but also the parallel regulatory code.

I fully expect Sal to start blathering about steganographic images concealed in alternative codes.

DaveScot was faster. I may be wrong but I always had the impression that Sal and WD don’t post on Sundays but rather leave the field to their professed agnostic Dave.

Oh dear. Over at UD, they seem to think that this finding of a “parallel code” is actually another gene, with talk about the probability of it having “evolved” multiple times…

However, if one looks at the research, what they are saying is that the genetic code is very efficient at coding information for folding, regulation, splicing etc in parallel to the genes that actually code for proteins… It’s a feature of ALL DNA, and hence evolved way back at the start of life on the planet.

The researchers believe that the efficiency of the code to perform multiple tasks is a hallmark that the genetic code itself evolved early on in the history of life.

A couple of points:

1) If it’s true that this capability to be highly efficient evolved, that implies that we have metagenes (genes that describe genes) stashed away somewhere in our DNA. Finding this stuff would give us a great insight into what LUCA was like

2) Genetic algorithms are indeed well-known for using the same part of a “genome” to perform multiple tasks in a “phenome”. I worked with evolving circuits on PLA chips back in my undergrad days (a follow on from work done by Adrian Thomson), and we found for example that an evolved circuit would use a loop, both to generate an RF signal that critically affected the behaviour of another part of the chip, but also at the same time to introduce a delay into another signal. At least, we think that’s what the circuit was doing :-) Anyway, the point being that seeing this type of parallel use is what I would consider to be the very hallmark of a genetic algorithm, as opposed to an intelligent designer. There are very few examples in human history where we have designed a part of a machine that performs two tasks at once. Can anyone think of an example? It’s horrendously difficult to do - think on two levels of conflicting abstraction at once.

Maybe someone with a valid logon over at UD should point this out to the IDists… :-)

Wade,

The short answer is - no.

The long answer is that if the mutation doesn’t obey the rules needed for the genetic code to be respected, the mutation simply dies - the cell where the mutation occured doesn’t survive to pass the mutation on. Why doesn’t this make things harder to evolve? Simply because the rate of these “bad” mutations is probably many orders of magnitude higher than the rate of mutation that we generally talk about.

The reason your confusion arises is because you have used two different meanings of the word “mutation” in your question. Most of the time, when we talk about “mutation”, we are talking about viable mutations - where viable means that the cell where the mutation occured is still able to reproduce, even if ultimately the organism dies. This was the sense of the word that you used when talking about a “beneficial mutation”.

The second meaning of mutation is any error in the copying process of a cell’s DNA. Most of the time, these errors produce DNA that is not capable of reproducing. The mutation dies and disappears.

This mechanism can be more usefully thought of as an error correction mechanism. If an error occurs during cell reproduction that is so wrong that a viable offspring cell can’t be produced, the offspring cell is simply never created - saving energy for the organism… There are other studies around that show that we do infact have a fairly high failure rate when copying DNA during cell reproduction, but with the parallel code acting as a kind of checksum, our organism can automatically remove these types of errors. It’s very neat :-)

I can tell you what evolution deniers will say.

Evolution is based on RANDOM, ACCIDENTAL mutations culled by NATURAL SELECTION.

Everytime you find MORE COMPLEXITY the mathematical and REALISTIC CHANCE that what we have become is ACCIDENTAL continues to EVAPORATE!!!

It was already ludicrous when we hit our first basic understandings of genetics. Now that we are finding that the actual complexity are orders of magnitude above what we THOUGHT it was it is ABSOLUTELY LUDICROUS TO THINK IT HAS BEEN AN ACCIDENT THAT JUST HAPPENED WITHIN EVEN 4.5 BILLION YEARS!!!

There are more mutations required per year than you have years!!!

HAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHA

Yup, I LOVE to hear about the INCREASING COMPLEXITY that implies TRILLIONS of negative mutations that FAILED!!

Oh, and you can argue Evolution v ID all you want. I simply can’t believe the STUP!D!TY of arguing so hard for a THEORY you DON’T have FACTS to support!!

Just because you think your THEORY is the only reasonable one DOES NOT MEAN IT IS WORTH A SECOND GUESS!!

Maybe it is time to be looking for a MECHANISM that is FEASIBLE in REALITY??

HAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHA

I still have difficulties to imagine how the genetic code could evolve since any change in it should be lethal. Yet it did.

Are there reseach articles about the evolution of the genetic code? It seems that this one doesn’t discuss it, just the optimality of the “end product”.

Thanks.

I still have difficulties to imagine how the genetic code could evolve since any change in it should be lethal. Yet it did.

Are there research articles about the evolution of the genetic code? It seems that this one doesn’t discuss it, just the optimality of the “end product”.

Thanks.

That does appear to be an interesting puzzle. If I were to guess I’d guess that evolution of the code occurred while it was a secondary system in species that used something else for the primary inheritance method. If that makes sense.

Henry

jerry at UD: “What are the odds that such a sophisticated mechanism evolved in the short time before the Cambrian.”

Uhhh, ouch. Considering that the first life appeared 4 billion years ago, and the Cambrian started 543 million years ago, “the short time before the Cambrian” is actually 86% of the entire history of life on earth. But then, no one every accused the IDists of knowing their information.

It’s really hard to read the ignorance in some of those responses.

jeannot Wrote:

Are there reseach articles about the evolution of the genetic code?

Apparently there’s a Wiki about it, with a hefty reference library.

Wow! The comment of KuhnKat demonstrates once more the sophisticated level of ID science.

I have to say that one is one of my all-time favourites.

…especially the “HAHAH..” part. Imagine a scientific argument where one side actually behaves like that.

The article is (apparently) available without subscription at http://www.genome.org/cgi/reprint/gr.5987307v1 in the preprint (not yet published) section of the journal.

I downloaded the report and read all 9 pages of it. After reading it, I haven’t satisfied with the experiment result, because:

1. The genetic change that could illustrate the evolution theory must not only add information to organism’s genome, it must also add new information to the biocosm. The experiment didn’t show that.

2.Read this table of ‘Significance of the genetic code in representing arbitrary sequences’ carefully:

n-mer size P-value average P-value 20% log-probabilities

5 0.110 0.054 6 0.097 0.045 7 0.083 0.028 8 0.049 0.031 9 0.043 0.010 12 0.028 0.004 15 0.016 0.004 18 0.012 0.006 20 0.026 0.006 22 0.021 0.004 25 0.029 0.009 (Source: Shalev Itzkovitz and Uri Alon, “The genetic code is nearly optimal for allowing additional information within protein-coding sequences”, page. 5). The table showed that the probabilities of allowing additional information within protein-coding sequences is actually zero a.k.a nil. It means: Not a chance!

3. The report said that additional information within protein-coding sequences is useful. If it is, so, amazingly, the researchers had figured out of how amino acid could turn into protein, If they had, so, they were able to built a new kind of protein that never existed in the world before. If they were, so, they had ability to construct a mechanism of universal genetic code evolution. But unfortunately, the report didn’t tell all about that. Why? Because this experiment was based on mutation. Israeli biophysicist Lee Spetner said: “Evolution cannot be built by accumulating mutations that only degrade specificity”, (Dr. Lee Spetner, “Lee Spetner/Edward Max Dialogue: Continuing an exchange with Dr. Edward E. Max,” 2001, http://www.trueorigin.org/spetner2.asp )

4. The title of that report is: the genetic code is NEARLY optimal for allowing additional information within protein-coding sequences. In another words: the genetic code is ALMOST optimal for allowing additional information within protein-coding sequences. It means that genetic code is not yet optimal for it. So, we can not yet accept this experiment as an evidence of genetic code evolution.

Inal my thoughts exactly. Funny how your comment is the most recent and last one ;)

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This page contains a single entry by PvM published on February 10, 2007 4:15 PM.

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