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I Ching Genomics

It will all make sense.
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We now have an unimaginably huge amount of information about the human genome: a pretty good sequence, annotated with features that include genes, regulatory elements, variant sequences and much much more (see link for example).

Interpreting it, however, is much harder. It's a huge mass of information, and most the interesting stuff is very subtle and hard to spot. A typical example is trying to find which particular genomic variations may predispose you toward depression, or make it more likely that your children will have big ears.

As the analyses get ever more complex and subtle, we are slowly getting bogged down.

I therefore propose that we add I Ching annotations to the genome. There are 64 codons (DNA "words" - each made of three DNA letters), from AAA through to TTT. By an odd coincidence, there are 64 hexagrams in the I Ching, each with its own meaning. It is a simple matter, therefore, to map the one onto the other.

To take a very simplistic example, the gene coding for normal beta globin (part of haemoglobin) contains the following sequence "..CTG ACT CCT GAG GAG..." (coding for amino acids leucine, threonine, proline, glutamic acid, glutamic acid, as part of the protein). According to the I Ching, and numbering the codons AAA through TTT as 1-64 respectively, this becomes:

..Conjoining-Grouping-Returning- Prospering-Prospering...

Clearly this is a good protein to have. The beta globin molecules join together (the protein is tetrameric - two betas and two alphas), and blood circulates freely (returning to the heart after passing through the fine capillaries of the lungs or tissues), enabling the person to prosper.

The most common mutation causing sickle-cell anaemia is a change of an "A" to a "T", so the sequence runs: "..CTG ACT CCT GTG GAG...". As a consequence, the first of the two glutamates becomes a valine. With the I Ching at hand, though, we can see that the first "Prospering" (hexagram 35, GAG) has been transmutated into "Ascending" (hexagram 46, GTG). Clearly, ascending is not something you want your blood to do.

Of course, more rigorous rules need to be worked out to establish a logical mapping between the I Ching and DNA sequence. For example, regulatory sequences in the genome don't come in three-letter "words", so their I Ching meaning will be harder to establish.

However, once this is done by a concerted effort amongst bioinformaticians, we will find the genome much more amenable to interpretation. Complex polygenic traits might suddenly become easier to spot amongst the mass of A,C,G and T. Perhaps your predisposition to obesity is because you've got alleles which give you Great Accumulating in one protein in a key metabolic pathway, and a Great Exceeding in a second enzyme in the same pathway.

MaxwellBuchanan, Sep 21 2007

A small piece of your genome http://www.ensembl....4;h=ensg00000188170
Shows some of the information on one small part of the human genome. The Ensembl genome broswer is already configured to display many different types of annotation to the sequence. I Ching would be easy to add. [MaxwellBuchanan, Sep 21 2007]

[link]






       Sorry, but making sequence data four times longer isn't going to help me.   

       What does help me is making little word sounds out of the segment I am searching for, and repeating that in my head while I look: Cat tuh tuh Gaaat tuh Kag (CATTTGAATTCAG)
GutPunchLullabies, Sep 21 2007
  

       PS what you call a coincidence I call four to the third power.
GutPunchLullabies, Sep 21 2007
  

       Trust me, Cat tuh tuh Gaaat tuh Kag breaks down over a megabase. And the I Ching will do as good a job of throwing up candidate genes as most of the current association studies are doing.
MaxwellBuchanan, Sep 21 2007
  

       Well, a three-times-longer system breaks down three times faster. I was trying in my head to come up with a more useful system than the current one, and all I could come up with was renaming the amino acids. The current names are hard to remember and only slightly descriptive.   

       Maybe call them by their side group, followed by "aminoacid".   

       So Hydrogenaminoacid, Methanaminoacid, isobutanaminoacid, phenylmethanaminoacid, etcetera.
GutPunchLullabies, Sep 21 2007
  

       Way too sensible. Shirley much more inspiring, for example, to have the genome decorated with annotations such as "SNP 23998: minor allele freq 0.3; Centre confirming -> Small exceeding."
MaxwellBuchanan, Sep 21 2007
  

       could I just read your palm before I try to make sense of this?
po, Sep 21 2007
  

       By all means.
MaxwellBuchanan, Sep 21 2007
  

       you have 16 children? did you know?   

       does the name Fred mean anything to you? she is standing behind you - waving rubber gloves, saying "latex, honey?"
po, Sep 21 2007
  

       I think you may be confused by the fact that my palm was recently re-potted. I believe that can affect the interpretation.
MaxwellBuchanan, Sep 21 2007
  

       I prefer an iPAQ over a palm, as it comes with its own built-in reader. It's bulk in my pocket though has been known to cause some i-tching.
RayfordSteele, Sep 26 2007
  

       Buchanan: Don't give up on this I Ching, genome thing - that's what spreadsheets and terabytes are for!
Macdaddyx1, Feb 05 2008
  

       There may be 64 codons, but there's only 20 amino acids in the standard translation [1]. If you also count 'stop', thats 21. Changing which of the several codons encodes an amino acid usually has little effect.   

       [1]other amino-acids can be inserted in a template-directed manner under certain very rare conditions. See - selenocysteine, pyrolysine.
Loris, Feb 06 2008
  

       //Changing which of the several codons encodes an amino acid usually has little effect.// (a) not necessarily true and (b) not necessarily relevant.   

       (a) Most organisms have a strong codon bias, preferring only one or two of the possible codons for a given amino acid. This strongly affects translation rates.   

       (b) there are many instances where you want to represent the DNA sequence, not just the amino acid sequence. For example, any time you want to manipulate DNA (restriction digest, PCR, probes, arrays..) you need the sequence.
MaxwellBuchanan, Feb 06 2008
  

       "...Conjoining- Grouping- Returning- Prospering- Prospering..." actually makes a neat little cult chant when your read it out loud.
notmarkflynn, Feb 06 2008
  

       Exactly. And patients will be so much more at ease if, instead of saying "You've got an A/T substitution in codon 4 of your beta globin", you can calmly say "We believe that your problem is due to an Ascending where you should be Prospering".   

       Genetic diseases could likewise be renamed in more comfortable terms. You haven't got DMD, you've got Sprouting disease. No longer will you suffer from Huntingdon's disease, you'll just have too many Great Possessings.   

       Bioinformaticians will suddenly become calm, wise people - for the first time.
MaxwellBuchanan, Feb 07 2008
  
      
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