On Tuesday, June 19, 2007 [sic]I posted an article on this blog which I titled The ENCODE project: beyond the genome project. In it I revealed that the transcription into RNA of the raw DNA material more often than not involved the addition of and/or portions of many other genes besides the principal one, as well as sequences from those regions in the DNA molecule once thought to be "junk DNA" but now known to play a significant role in the process of protein synthesis. It is evident based on this information that the process of interfering with nature by altering a genetic sequence in plants that are part of the food chain to benefit the agricultural industry might have some serious detrimental effects.
The Scientific American web site invited reader comment on its member blog on the subject of genetically altered crops. One informed and concerned reader links to a website representing Physicians and Scientists for Responsible Application of Science and Technology (PSRAST). The website makes reference to the ENCODE study and raises concern over the risk assessment of genetically engineered foods, especially with respect to the concept of "substantial equivalence", which in the legal definition is the limit to which analysis of trans genetic products are compared to the pre-trans genetic parent. This comparison does not cover the subtleties of all the components involved in an affected gene's transcription process during a plant's normal metabolic growth. It is suspected that in at least one serious case a trans genetic product acquired a highly toxic characteristic which caused 37 fatalities and rendered 1500 victims permanently disabled. In other words, genetic engineering is evidently unpredictable.
In light of what we now know about RNA transcription and the possible risks involved in creating biologically engineered foods, it is imperative that a moratorium be held on the practice while the process of risk assessment is overhauled. This requires a substantial investment in time and research. In order to effectively bring a genetically engineered food to the marketplace, the entire process of transcription of not just the principal gene in question but involving all the sub units of DNA must be first analysed to determine that any resulting protein products that derive from normal plant growth do not present risk.
The ramifications do not end there. In an article published by the International Herald Tribune on July 3, 2007 it was pointed out that "..many diseases are caused not by the action of single genes, but by the interplay among multiple genes," and, "..one of the most virulent forms of Malaria.. may involve interactions among as many as 500 genes." Obviously, the concept of gene therapy involving the alteration of a single gene to address the issue of a genetically inherited mutant gene is inherently short-sighted if the procedure does not address all of the DNA components involved in transcribing the defective protein. This might for the time being present an almost insurmountable obstacle to providing effective gene therapies to eliminate genetically based diseases. The challenges are far more complex than previously thought, in light of the ENCODE study.
Monday, January 21, 2008
Rethinking genetic engineering
The ENCODE project: beyond the genome project
"The human genome is an elegant but cryptic store of information."
In 2001 the project to catalog the human genome was completed. Embedded in the DNA molecule are genes and what were once believed to be "junk DNA", noncoding portions of the DNA that represented fully 98.8% of the entire genome. It has been found that some of these noncoding portions are shared among mammals. This suggests that they play some crucial role as yet undetermined. Information contained herein is partially derived from a June 13, 2007 Scientific American article.
In 2003 a new project involving 35 research groups was undertaken to create the encyclopedia of DNA elements (ENCODE). The pilot phase of the project targeted 1% of the human genome (roughly 30Mb of data).
All species have been found to transcribe large portions of "noncoding" DNA for some unapparent reason, and in addition to the role that RNA plays in protein synthesis, some RNA's play roles by themselves.
The ENCODE consortium selected 44 separate sections of the genome for study of which 3% make up genes, yet 93% of the material was transcribed and extensive overlapping in the noncoding portions was discovered when transcription was compared with any of the 399 ENCODE genes. 65% of the gene transcription process also involved selected portions of other genes as well as pieces of DNA far outside of the target genes [distal regions]. ENCODE findings confirm reports from other sources that often a protein is synthesized from exons (cleaved gene portions) of different genes.
23% of mammals share 5% of the studied sequence. Of these 5% approximately 60% show evidence of function. Evaluation from a purely scientific point of view would suggest that evolution has preserved these DNA portions as species have diverged. Yet it is not untoward to suggest that they would exist even from separate evolutionary beginnings based on the premise that there is a very distinct progression that the evolution of life takes when it does manifest - an intelligent design principle based on the natural anthropocentric process. Either suggestion is speculative, although I personally believe the latter one.
What is known is that we are just analysing the tip of the iceberg with respect to the full extent of the knowledge that we require to fully understand the code that DNA represents and the processes which interpret that code to produce life. But we are already far ahead of that day in 2001 when it was announced that the complete human genome had been sequenced.
Genome biologist George Weinstock of the Baylor College of Medicine in Houston says, "this study shows us how far we are from a comprehensive understanding of the human genome."
