codeblog code is freedom — patching my itch

9/22/2005

decompiling myself

Filed under: Health,Reverse Engineering — kees @ 9:01 pm

Figured I should try to decompile myself. The first step would be get a full dump of my DNA base pairs as letters. Looks like that’s not going to be easy though. Even a DNA stain takes a lot of steps (and I’ll probably never be allowed to do the radioactive steps myself). The real goal here is that with current US law, I should copyright myself (I’m the first performance of the specific base pair “idea”) and possibly patent myself (my methods are a unique variation of other methods).

Obviously this doesn’t take into account my immune system or my memories, but I figure it’s a good start. At like just under 10 billion base pairs, that’s a 10GB program. I think Inkscape is only 45M or so, and that’s not even counting shared libraries.

Since I don’t really want to share my DNA with a company (I’ve got to be the first to copyright it), I wanted to find out what it would take to sequence at home. Since a sequencer is in the $100k price range, that’s not really going to happen. Talking to my NIH-employed friend techne23, she suggested a possible “cheap” way to do it would be in pieces, doing PCRs on specific SNPs, and send those out for sequencing to get back base pair letters. For example, on a gene, the red ones here are considered “interesting”. The PCR machines can be had for cheap, too.

So, in summary:

  • need all the standard lab stuff (centifuge, gloves, tips, pipets, tubes, autoclave, glassware, etc)
  • need chemicals to isolate my DNA
  • need a little space in my freezer to store my DNA
  • need to buy PCR reagents, about $100 for 50-100 reactions
  • need two base pair-specific primers at $40 total for up to 500 base pairs per PCR
  • need thermal cycler to do the PCR in
  • need electrophoresis equipment to see if the PCR worked (maybe reuse my UV EPROM wiper?)
  • need toxic (careful!) reagents for the electrophoresis
  • need a sequencing company that is willing to work with a non-University
  • need FedEx account to ship PCR to sequencers :)

Or I can spend crazy money doing thousands of SNPs at once in microarrays. (Or wait until they’re in every doctor’s office.)

© 2005, Kees Cook. This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License.
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2 Comments »

  1. This is interesting, but remember that currently documented SNPs only represent “likely” places for humans’ DNA sequences to be different. Even if you checked every known one in existence, well, you’d probably miss some important differences that are unique to you and not represented in the population at large.

    Also, 10GB? I dunno… The DOE HGP says the genome is 3.2 gb long. DNA bases are not 8-bit like text… They really only need 2 bits for each base since there are only 4 nitrogenous bases releavant to DNA. Even if you want to include methylation status, 3 bits ought to be more than enough.

    So 1.2 GB, tops. Also, our genomes are 25-50% highly repetitive sequences, which would make for an eminently compressible dataset. So tarball it, and you’re down to the kind of sizes you could fit it on a CD and sell people for exorbitant license fees. Also be sure to lock down the proprietary file format you use.

    That was a fun excercise.

    -Random NIH employed Inkscaper
    -Other NIH guy

    Comment by Yashka — 9/26/2005 @ 8:17 am

  2. This is a noble, wise yet foolhardy venture. Here is my take:
    1. Legally the proposal is great, but you do not have to make it all or nothing. I presume that you *are* doing this to safeguard your genecode from insurance companies or the likes. So, start with the possible areas for breach: most expensive healthcare procedures cross with your family history; cogenes related to mental health, etc. I don’t think their is an evil conspiracy yet, just an economical desire to increase profits. But seriously, it would not serve your goal as the data will have to be characterized for copyright or patent. If the data is public, anyone can access it. It can only sorta safeguard (if you have the funds to sue) someone else with your genotype and phenotype to state that they are you (this legal person). We are many tens of decades from such a possibility. (*Please note: Copyright 2007, this author. Safeguards are made.)

    2. Biologically: If you have the funds for this ad-venture, you probably would not mention it here. Paying for reagents, equipment, radioactive or florescenct labels, electricity, clean lab-space, reference data, local and federal approval, and, man-hours (a lot of it) may be heafty. You would probably achieve some of your goals by working in some cytogentics or molecular biology capacity for a company and spending a few hours after work for your experiements (and that’s if they will allow it).

    You could just extract your genetic material (dna & rna) and deep freeze. Do a gross analysis, i.e. forensic dna fingerprinting, plus, and patent the intact dna with the gross data. Just don’t get into any criminal trouble as the authorities have ready access to you profile.

    Another thing, the genotypic you is constantly changing: how would you count for that. I think the legal defination of a human entity is only grossly phenotypic with traceable provenance and base competence.

    Comment by JackPots — 2/22/2007 @ 5:17 pm

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