SI
SI
discoversearch

We've detected that you're using an ad content blocking browser plug-in or feature. Ads provide a critical source of revenue to the continued operation of Silicon Investor.  We ask that you disable ad blocking while on Silicon Investor in the best interests of our community.  If you are not using an ad blocker but are still receiving this message, make sure your browser's tracking protection is set to the 'standard' level.
Politics : Evolution -- Ignore unavailable to you. Want to Upgrade?


To: TigerPaw who wrote (51509)4/1/2014 7:50:33 PM
From: Brumar89  Read Replies (1) | Respond to of 69300
 
It's not haphazard ... it's designed intelligently to minimize errors.



To: TigerPaw who wrote (51509)4/1/2014 7:54:06 PM
From: Brumar89  Read Replies (3) | Respond to of 69300
 
The Genetic Code Is One in a Million
Stephen J. Freeland, Laurence D. Hurst … show all 2 hide


Abstract.
Statistical and biochemical studies of the genetic code have found evidence of nonrandom patterns in the distribution of codon assignments. It has, for example, been shown that the code minimizes the effects of point mutation or mistranslation: erroneous codons are either synonymous or code for an amino acid with chemical properties very similar to those of the one that would have been present had the error not occurred. This work has suggested that the second base of codons is less efficient in this respect, by about three orders of magnitude, than the first and third bases. These results are based on the assumption that all forms of error at all bases are equally likely. We extend this work to investigate (1) the effect of weighting transition errors differently from transversion errors and (2) the effect of weighting each base differently, depending on reported mistranslation biases. We find that if the bias affects all codon positions equally, as might be expected were the code adapted to a mutational environment with transition/transversion bias, then any reasonable transition/transversion bias increases the relative efficiency of the second base by an order of magnitude. In addition, if we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.

link.springer.com



To: TigerPaw who wrote (51509)4/1/2014 7:56:02 PM
From: Brumar89  Respond to of 69300
 
In summary, we found that the genetic code is nearly optimal for encoding additional information in parallel to its main function of encoding for the amino acid sequence of proteins. This optimality is related to the identity of the stop codons in the universal code: when frame shifted, the stop codons overlap with codons of abundant amino acids. We showed that this optimality is strongly tied to a second useful property—minimization of the effect of translational frame-shift errors.

Robustness to frame-shift errors may be a reasonable inherent constraint on the early genetic code. One may therefore propose that the ability to carry parallel codes may have emerged as a side effect that was later exploited to allow genes and mRNA molecules to support a wide range of signals to regulate and modify biological processes in cells ( Kirschner et al. 2005). Alternatively, the ability to include arbitrary parallel sequences within coding regions may have contributed to the selection of the early genetic code. For example, early RNA molecules that had the ability to both specify peptides and to include sequences that conferred useful RNA structure may have had an advantage over RNAs that were less effective at simultaneously fulfilling both objectives.

Whereas many of the currently known regulatory codes reside in nontranslated regions of the genome ( Robison et al. 1998; Lieb et al. 2001), the present findings support the view that protein-coding regions can carry abundant parallel codes. It would be interesting to use information-theoretical approaches ( Gusev et al. 1999; Wan and Wootton 2000; Troyanskaya et al. 2002) to search for such codes in genomes.

genome.cshlp.org



To: TigerPaw who wrote (51509)4/1/2014 11:44:22 PM
From: Solon  Respond to of 69300
 
"No author would have made such haphazard code, for one thing."

Compare it to the first light bulbs which lasted seconds. They were horrible. But the designers
kept improving and they will keep improving.

Why did this designer begin an idiot and never grow??



To: TigerPaw who wrote (51509)4/2/2014 5:39:46 AM
From: 2MAR$  Read Replies (2) | Respond to of 69300
 
DNA is Not a Code ( As usual, this argument comes down to using words improperly)
livinglifewithoutanet.com

There’s been a rather tired argument making its way around the theist blogosphere of late, arguing that DNA is a code, and codes are designed things. The very fact of it being a code proves that there must have been someone who designed the code.


A code, by the strictest definition, is in fact something designed by intelligent beings. It is a system of symbols that either arbitrarily or by some system represent various things. The alphabet I’m using to write this blog is a code. There’s nothing about the individual letters that have any inherent meaning. They don’t do anything in and of themselves. By agreement between multiple humans, we have a legend, or a key, which most of us learned in grammar school. By using this legend, we can look at anything in the code “English” and through substitution, come to the knowledge of the concepts sybolized by the various letters.

This is the traditional idea of a code, and it is what theists think they mean when they argue that DNA is a code. The thing is, DNA is not that kind of a code. DNA is a a polymer, which is composed of individual chemical units called nucleotides. There are four types of these nucleotides, and we humans have decided to call them adenine, guanine, cytosine, and thymine. These names are not entirely arbitrary, but in the end, there’s nothing magical about them. We could call them Blob, Clob, Dob, and Emu, and they’d still be the same. Our language — the code we humans use to communicate — is just a way for us to give each other information and keep things separate in our own minds.

The nucleotides in DNA are often said to be the “blueprints” or “code” which define a sequence of messenger RNA which in turn defines at least one protein. In a sense, these proteins are the building blocks of life, and DNA is the “code” which determines the qualities of the life that will be built.

The problem with the theist argument, however, is that the DNA code is not arbitrary, and it does not rely at all on the agreement of sentient beings. In fact, it is exactly the same in nature as any other dynamic chemical process. When you see an explosion on TV, you’re watching a chemical reaction that was controlled by the same kind of “code.” Crystals grow based on such a code. Stars give off light and energy from the same kind of code.

All DNA is, to the chagrin of creationists, is a very, very complicated organic molecule that can react in a staggeringly large number of ways with other organic molecules. Unlike an explosion or a crystal, which can be described mathematically with a few simple formulas, the process of building a living thing is several orders of magnitude more complicated. It takes perhaps 10 billion bits to convey all the necessary information needed to build a human, and the process is never really finished until the human dies, so we’re talking about a very, very long process by comparison with an explosion, and billions more unique steps than the formation of a crystal.

Yet, it’s the same process. This molecule, when in the presence of that molecule, will bond and make this new molecule. It’s just chemistry.

The thing is, we humans recognize the complexity of the chemical process we call life, and we notice that it is not completely dissimilar from the process by which we build a skyscraper or a watch. We have a set of instructions, and we refer back to them throughout the whole process of putting materials together in very specific ways, until we have a finished product. We like to argue that messenger RNA is “referring to the instructions” to figure out which protein to build in the same way, but it’s not. Neither DNA nor RNA is sentient. They are both just doing what chemicals do. DNA is more akin to a catalyst than a set of instructions. That is, the DNA stays essentially the same throughout the building process, but it is facilitating chemical reactions the whole time it is part of a living thing.

So, here is the ultimate problem with this particular theist argument. DNA is not an arbitrary set of symbols that “stand for” something else that will be interpreted through some kind of a legend. It is a set of chemicals which are nonthinking, and have no choice but to do what they do, in the same way that a crystal has no choice but to grow when in the presence of the appropriate aqueous solution. DNA is just a very, very, very complicated molecule that happens to be capable of facilitating incredibly complex sets of chemical reactions.

Sure, it seems magical that something as simple as four little nucleotides could be responsible for all the diverse life on the planet, but our sense of wonder at the versatility of carbon shouldn’t woo us into the false belief that incredible versatility is equivalent to design. DNA is not a “code” in the normal sense of the word. We call it a code because doing so gives us an easy way to think of the process by which a strand of DNA is responsible for the building of a living thing.