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Theory of Intelligent Design, the best explanation of Origins » Intelligent Design » Information Theory, Coded Information in the cell » The different genetic codes

The different genetic codes

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1 The different genetic codes on Tue Jan 19, 2016 4:43 pm


The different genetic codes

the National Center for Biotechnology Information (NCBI), currently acknowledges nineteen different coding languages for DNA

Bye bye common ancestry !! 

The basic process by which proteins are made in a cell. (click for credit)
I am still reading Shadow of Oz by Dr. Wayne Rossiter, and I definitely plan to post a review of it when I am finished. However, I wanted to write a separate blog post about one point that he makes in Chapter 6, which is entitled “Biological Evolution.” [url="To+date,+the+National+Center+for+Biotechnology+Information+%28NCBI%29,+which+houses+all+published+DNA+sequences"&source=bl&ots=y3djhymXWq&sig=SSjcioRSaQEZcuSGiztSRGYrJIw&hl=en&sa=X&ved=0ahUKEwjelt-frrPKAhWISCYKHSuJD9UQ6AEIHjAA#v=onepage&q="To date%2C the National Center for Biotechnology Information %28NCBI%29%2C which houses all published DNA]He says[/url]:

To date, the National Center for Biotechnology Information (NCBI), which houses all published DNA sequences (as well as RNA and protein sequences), currently acknowledges nineteen different coding languages for DNA…

He then references this page from the NCBI website.
This was a shock to me. As an impressionable young student at the University of Rochester, I was taught quite definitively that there is only one code for DNA, and it is universal. This, of course, is often cited as evidence for evolution. Consider, for example, this statement from The Biology Encyclopedia:

For almost all organisms tested, including humans, flies, yeast, and bacteria, the same codons are used to code for the same amino acids. Therefore, the genetic code is said to be universal. The universality of the genetic code strongly implies a common evolutionary origin to all organisms, even those in which the small differences have evolved. These include a few bacteria and protozoa that have a few variations, usually involving stop codons.

Dr. Rossiter points out that this isn’t anywhere close to correct, and it presents serious problems for the idea that all life descended from a single, common ancestor.
To understand the importance of Dr. Rossiter’s point, you need to know how a cell makes proteins. The basic steps of the process are illustrated in the image at the top of this post. The “recipe” for each protein is stored in DNA, and it is coded by four different nucleotide bases (abbreviated A, T, G, and C). That “recipe” is copied to a different molecule, RNA, in a process called transcription. During that process, the nucleotide base “U” is used instead of “T,” so the copy has A, U, G, and C as its four nucleotide bases. The copy then goes to the place where the proteins are actually made, which is called the ribosome. The ribosome reads the recipe in units called codons. Each codon, which consists of three nucleotide bases, specifies a particular amino acid. When the amino acids are strung together in the order given by the codons, the proper protein is made.
The genetic code tells the cell which codon specifies which amino acid. Look, for example, at the illustration at the top of the page. The first codon in the RNA “recipe” is AUG. According to the supposedly universal genetic code, those three nucleotide bases in that order are supposed to code for one specific amino acid:methionine (abbreviated as “Met” in the illustration). The next codon (CCG) is supposed to code for the amino acid proline (abbreviated as Pro). Each possible three-letter sequence (each possible codon) codes for a specific amino acid, and the collection of all those possible codons and what they code for is often called the genetic code.

Now, once again, according to The Biology Encyclopedia (and many, many other sources), the genetic code is nearly universal. Aside from a few minor exceptions, all organisms use the same genetic code, and that points strongly to the idea that all organisms evolved from a common ancestor. However, according to the NCBI, that isn’t even close to correct. There are all sorts of exceptions to this “universal” genetic code, and I would think that some of them result in serious problems for the hypothesis of evolution.
Consider, for example, the vertebrate mitochondrial code and the invertebrate mitochondrial code. In case you didn’t know, many cells actually have two sources of DNA. The main source of DNA is in the cell’s nucleus, so it is called nuclear DNA. However, the kinds of cells that make up vertebrates (animals with backbones) and invertebrates (animals without backbones) also have DNA in their mitochondria, small structures that are responsible for making most of the energy the cell uses to survive. The DNA found in mitochondria is called mitochondrial DNA.

Now, according to the hypothesis of evolution, the kinds of cells that make up vertebrates and invertebrates (called eukaryotic cells) were not the first to evolve. Instead, the kinds of cells found in bacteria (called prokaryotic cells) supposedly evolved first. Then, at a later time, one prokaryotic cell supposedly engulfed another, but the engulfed cell managed to survive. Over generations, these two cells somehow managed to start working together, and the engulfed cell became the mitochondrion for the cell that engulfed it. This is the hypothesis of endosymbiosis, and despite its many, many problems, it is the standard tale of how prokaryotic cells became eukaryotic cells.
However, if the mitochondria in invertebrates use a different genetic code from the mitochondria in vertebrates, and both of those codes are different from the “universal” genetic code, what does that tell us? It means that the eukaryotic cells that eventually evolved into invertebrates must have formed when a cell that used the “universal” code engulfed a cell that used a different code. However, the eukaryotic cells that eventually evolved into vertebrates must have formed when a cell that used the “universal” code engulfed a cell that used yet another different code. As a result, invertebrates must have evolved from one line of eukaryotic cells, while vertebrates must have evolved from a completely separate line of eukaryotic cells. But this isn’t possible, since evolution depends on vertebrates evolving from invertebrates.
Now, of course, this serious problem can be solved by assuming that while invertebrates evolved into vertebrates, their mitochondria also evolved to use a different genetic code. However, I am not really sure how that would be possible. After all, the invertebrates spent millions of years evolving, and through all those years, their mitochondrial DNA was set up based on one code. How could the code change without destroying the function of the mitochondria? At minimum, this adds another task to the long, long list of unfinished tasks necessary to explain how evolution could possibly work. Along with explaining how nuclear DNA can evolve to produce the new structures needed to change invertebrates into vertebrates, proponents of evolution must also explain how, at the same time, mitochondria can evolve to use a different genetic code!
In the end, it seems to me that this wide variation in the genetic code deals a serious blow to the entire hypothesis of common ancestry, at least the way it is currently constructed. Perhaps that’s why I hadn’t heard about it until reading Dr. Rossiter’s excellent book.

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Codon reassignment and amino acid composition in hemichordate mitochondria 1

The genetic code, once thought to be “universal,” is now known to vary among several groups of organisms (1). There exist two hypotheses that attempt to explain how changes in the code come about. First, according to the “codon capture hypothesis” (1–4), it would be deleterious for an organism if a codon was assigned to two amino acids (or an amino acid and polypeptide chain termination) simultaneously. Thus, the first step in the change of the genetic code is assumed to be the complete disappearance of a codon from a genome. Subsequently, the tRNA (or release factor) assigned to this codon loses its capacity to recognize it, so that the codon becomes unassigned, and another tRNA acquires this capacity, allowing the codon to reappear at new positions in protein-coding genes. Second, in contrast, the “ambiguous intermediate hypothesis” (5, 6) proposes that the reassignment of a codon takes place via an intermediate stage during which the codon is recognized by two tRNAs assigned to different amino acids (or a tRNA and a release factor). This leads to heterogeneity in the encoded proteins that, according to this hypothesis and experimental results (7, 8), can be tolerated by an organism. Because a change in the assignment of a codon must occur over relatively long evolutionary periods, it should in principle be possible to find organisms that represent intermediate stages in this process and thus to differentiate between the codon capture and ambiguous intermediate hypotheses. Indeed, unassigned codons have been observed in bacterial and mitochondrial genomes (911). Most of these cases are associated with a bias in the base composition. However, none of the codons effected are known to change their amino acid assignment in related evolutionary lineages (1).


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3 Re: The different genetic codes on Wed Jan 18, 2017 10:36 am


The following genetic codes are described here:

1. The Standard Code
2. The Vertebrate Mitochondrial Code
3. The Yeast Mitochondrial Code
4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
5. The Invertebrate Mitochondrial Code
6. The Ciliate, Dasycladacean and Hexamita Nuclear Code
9. The Echinoderm and Flatworm Mitochondrial Code
10. The Euplotid Nuclear Code
11. The Bacterial, Archaeal and Plant Plastid Code
12. The Alternative Yeast Nuclear Code
13. The Ascidian Mitochondrial Code
14. The Alternative Flatworm Mitochondrial Code
16. Chlorophycean Mitochondrial Code
21. Trematode Mitochondrial Code
22. Scenedesmus obliquus Mitochondrial Code
23. Thraustochytrium Mitochondrial Code
24. Pterobranchia Mitochondrial Code
25. Candidate Division SR1 and Gracilibacteria Code
26. Pachysolen tannophilus Nuclear Code
27. Karyorelict Nuclear
28. Condylostoma Nuclear
29. Mesodinium Nuclear
30. Peritrich Nuclear
31. Blastocrithidia Nuclear

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