Evolution Diary

7 responses so far ↓

• Henry Brown // Jan 7, 2009 at 4:34 pm

  Could evolutiondiary create a SPORE add on library for Biology education? Students could use SPORE video game to learn molecular biology.

  Genetic Network Modeling – SPORE level design

  My son is using SPORE by Maxis. They use a cartoon approach to evolution.

  A set of libraries could be added to SPORE to use with students to show students molecular biology.

  This library could be open sourced for use in biology classrooms.

  http://en.wikipedia.org/wiki/Spore_(game)

  In addition, some user-created content will be highlighted by Maxis at the official Spore site, and earn badges of recognition for their work.[27]

  Cell

  The Cell phase. The monstrously large creatures in the background will come to the foreground as the player’s organism slowly grows and evolves.

  The cell phase (sometimes referred to as the tide pool, cellular, or microbial phase) is the first phase in the game, and begins with a cinematic demonstrating the scientific concept of panspermia, with a meteor crashing into the ocean of a planet, which breaks, revealing a single-celled organism

  Code Swarm is a tool for modeling software development.

  Many open source software projects can now be mapped using code swarm. Donations of code can be tracked and contributors noted.

  http://vis.cs.ucdavis.edu/~ogawa/codeswarm/

  Could genes be mapped moving into genomes in a similar fashion using Code Swarm / SPORE to visualize genome code like open source code?

  Could Ocean microbes be caught in the act of generating genes that are then imported into larger genomes? Rotifers and insects do this.

  http://www.sciencemag.org/cgi/content/abstract/320/5880/1210

  Code Swarm models lateral transfer in genomes as software?

  Use Code Swarm as a tool for comparative genomics to watch evolution?

  Does Vanderbilt have any experience with these tools?

  Genetic networks have been created over time as genes are added and turned on. The p53 gene has grown to dominate human immune systems.

  This is similar to the development of software.

  Elements of software are shared and connected.

  Movable Elements (transposons) in genomes have been shown to be laterally transferred by viruses. http://www.sciencedaily.com/releases/2007/11/071114121359.htm

  Valence is a new language visualization tool built under processing tool.

  http://processing.org/exhibition/works/001/index_link.html

  Code swarm models software design and the history of that development.

  http://vis.cs.ucdavis.edu/~ogawa/codeswarm/

  Tools like Valence/Code Swarm are open source.

  I would like to visualize the transfer of genes into genomes and watch them dominate the domains they enter.

  Could historical maps of gene transfers in prokaryotes be created?

  Processing is a java interface used in bioinformatics.

  http://acg.media.mit.edu/people/fry/

  http://benfry.com/valence/applet/

  Could this cell phone microscope be adapted to metagenomic chips or field sampling of prokaryotes?

  Cell phone adapted for blood analysis:

  http://www.wired.com/science/discoveries/multimedia/2008/12/gallery_microscope_phone

  http://science.slashdot.org/article.pl?sid=08%2F12%2F20%2F2012230&from=rss

  Could Greene chip be adapted to cell phone microscope? Other microarrays?

  http://www.wired.com/science/discoveries/multimedia/2008/12/gallery_microscope_phone

  I worked at Los Alamos on HIV and Human genome. I also worked in Peace Corps in rural areas with HIV and child health. This blood analysis tool should be connected to a MYCIN expert system. My thesis used a MYCIN like AI to reassemble genomes. MYCIN blood analysis allows doctors to diagnose disease cooperatively. MYCIN was the combination of thousands of doctor’s diagnosis. Eventually a second step would be to use microarrays to analyze the DNA and proteins in the sample. How would microarrays be analyzed via cell phone? A cute SciFi book “Galapagos” by Kurt Vonnegut describes an AI like this. A Dwave Quantum supercomputer could use Grover’s Algorithm to analyze all past blood samples to make a match. The phone based health care system could then be used world wide to diagnose disease. Costs for health care would drop quickly as diagnosis became cheap.

  We also used genetic algorithms to reassemble contigs at Los Alamos. The MYCIN model was used to allow scientists to collaborate on rule sets for DNA assembly.

  At the time many said it was contamination of samples. It was instead contamination of all eukaryote genomes by retroelements/transposons. I still have the thesis if you are interested I could send it to you. Transposable elements (TEs) make up a significant proportion of many eukaryotic genomes, totaling almost 45% for human [1], . They play important evolutionary roles

  My son and I created gene machine cartoons for kids that covers the basics.

  http://scratch.mit.edu/projects/GeneMachine/20917

  http://scratch.mit.edu/projects/GeneMachine/51835

  http://scratch.mit.edu/projects/GeneMachine/293704

  http://scratch.mit.edu/projects/GeneMachine/235527

  However the field of genetic analysis has forged ahead. Craig Venters work with shotgun cloning has largely eclipsed my work. His use of fifteen redundant sequence coverages and computer reassembly of the redundant DNA strings allowed Celera corporation to beat the US Human Genome project. It also made him rich. See how he is now rewriting evolutionary theory by scanning the oceans of the world for genes.

  http://collections.plos.org/plosbiology/gos-2007.php

  http://www.pacificbiosciences.com/index.php (view 4 min SMRT Tech video) $100 genomes

  Add a quantum computer http://www.dwavesys.com/index.php?page=bioinformatics and Grover’s algorithm http://en.wikipedia.org/wiki/Grover’s_algorithm and we could reach diagnose disease using the gene universe.

  Could prokaryote genome databases be searched exhaustively using Grover’s Algorithm?

  Could the output be visualized using processing? Code Swarm?

  Could kids learn genomics and LGT using SPORE?

  Henry Brown

  hbrown@sisna.com

  henry.brown@state.nm.us

  505 795-3680

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