March 2010 Genomics Update

Genetics news has been commonplace for many years, complete with premature promises of revolutionary new medical treatments. These inflated expectations are certain to disappoint the uninitiated. The unfolding science reveals more complexity and uncertainty with each discovery. New methods emerge quickly that empower scientists to discover more, faster and at lower cost, but there is no assurance that new discoveries will take us closer to practical applications, rather than farther away from affordable medical miracles.

In their description of the National Human Genome Research Institute’s Encyclopedia of DNA Elements (ENCODE) project, Guigó and Reese stated:  “Finding human genes is a complex task because of the peculiar anatomy of the eukaryotic genome. Eukaryotic genes lie within long stretches of intergenic DNA, and within the genes only a few short fragments—the exons—are spliced together, often in alternative configurations, to form the mRNAs. Sequence signals in the genome are degenerate, and computational programs using them are able to identify the exons and link them into genes with relative success. But only through the sequencing of the corresponding mRNA molecule can a gene be unequivocally identified. It is unclear, however, what fraction of genes can be ascertained through mRNA sequencing. In addition, genes are only one type of functional elements. It is likely that most of the functionality of the human genome sequence remains largely unexplored.”   The modest aim of the first phase of ENCODE was to identify all functional elements in about 1% of the genome sequence through the collaborative effort of computational and laboratory-based scientists. 

In time, the genomes of many species and many individuals within a species will be determined. Sophisticated comparative analyses of genomes will reveal more about the evolution of species. Computers with increasingly sophisticated software are essential to using genomic information in meaningful ways.  DNA sequencing, brilliant programming and digital computing are perfect matches.

Personal Genome

The idea that each person will have their entire genome sequenced and that someone, somehow can read the genome and predict the future is both intriguing and misleading. Sequencing technology is advancing rapidly toward cheap, fast, somewhat reliable genome analysis. However the brutal truth is that having access to 3 million base pairs in a sequence is having a surplus of mostly useless information. The intriguing aspect of having abundant genome information is that the doors open to a century of new research, new methods of computing large data sets and work for armies of researches who can  runs studies of populations of humans to find out what the genomic information really means. In other words genomes are just a beginning of a journey of discovery, not an endpoint.

George Church, a professor of genetics at Harvard Medical School, founded of the Personal Genome Project with intention of sequencing selected individuals who were willing to share their genomes and medical histories in a public database. PersonalGenomes.org is organizing a conference in Boston on April 27, 2010. Genomes, Environments, Traits, inviting prominent individuals who have already been sequenced to share their experiences. Personal Genomics stated that there are fewer than 25 individuals to-date with public genome sequences, we expect that in this decade, there may be 1 million or more individuals with complete genome sequences worldwide. Genome sequenced speakers include James Watson, Jay Flatley, Skip Gates, Esther Dyson, Stephen Quake, Misha Angrist, George Church, James Lupski, Dan Stoicescu, Seong-Jin Kim, Greg Lucier and Rosalynn Gill.

Medical Genetics Old Fashioned

In medical papers, old ideas of genes often prevail. Phrases such as genetic tendency, genetic component, and genes play a role in are typical of obsolete generalities that confuse rather than inform. The new appreciation that genes are not solid, real entities is difficult for physicians to understand. Part of the problem is that medical education pretends that humans are static entities and that diseases are discrete phenomena.

A dynamic, interactive systems model better accounts for what actually happens. Rather than solid, reliable genes, you can imagine segments of DNA as codes that are read differently depending on circumstances. Much of the coding deals with getting food, digesting it, distributing nutrients, and excreting waste products. Food intake to the body is a major player in determining gene expression.

Beyond the genome lies epigenetics - the study of how the expression of the DNA code is altered as dynamic processes that can change in minutes. The expression of DNA is balanced between stability mechanisms that preserve a longterm species memory in the genome and adaptive mechanisms that change the expression, depending on circumstances. It is the adaptive mechanisms and changing DNA expressions that making predictions based on genome analysis alone an act of faith rather a reliable expression of science.

Epigenetic began with the discovery that DNA nucleotides can be silenced by adding methyl groups. Somehow, somebody in cells or cell to cell communications adds or subtracts methyl code to change the expression of DNA. Methylation is just the beginning of discoveries that revealed  more and more mechanism that alter the expression of the genome.

Medical Care and Planet Ecology is produced by Alpha Education. These brief essays by Dr. Stephen Gislason are taken from his books and blogs.  His books are published in two series: Alpha Education Books and Persona Digital Books. Persona Digital publishes a series of books  that present important topics in psychology, neuroscience and philosophy.

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