your 3)

yes- the ATG (start codon for protein synthesis) is never the start position for RNA synthesis. Since where you start is messy, and turning things on and off everywhere can make things even messier.

1) take 1% of the human genome and identify every regulatory element … within that 1% using as many different techniques as labs could invent.

Wow, there’s actually a really interesting sounding project buried under the awful description in that article.

I suppose I shouldn’t be surprised by anything that happens in science journalism, but, however it happened (i.e. whether the problems derive from the regulatory proteins, the RNA, or the DNA the editor, the reporter, or some sloppy press release) this seems to go beyond the usual muddiness to the point of being actively misleading.

2) My understanding was that biotech patents are often more sweeping than attaching single functions to single genes. For example, I thought that some process, probably the cloning process used for Dolly the sheep, had led to a patent that covered a substantial portion of the mammalian reproductive system. Unfortunately I can’t figure out where I heard this and how much I should trust the impression.

I’m curious as to what everyone thinks might be problematic with biotech patents, or, conversely, if the concerns over biotech intellectual property are overhyped.

3) most DNA in the cell is expressed as RNA at some point

It is? Even the “junk” DNA? Is there a mechanism which is capable of expressing fairly arbitrary chunks of DNA with no proper starting point? Or am I reading too much into your statement?

4) Given what UC and fish have said about patents, what is behind the statements by Prof. Heinemann in the article that “regulators may be unaware of the potential impacts arising from these network effects” and that “companies and regulators alike … ‘blind themselves to network effects’”?

5) and fish, no, I don’t think traveling with your own generator is worth it.

I suppose for some gene therapy groups that are trying to get genes expressed under entirely endogenous gene control, some of the ENCODE findings may pose new challenges, but I’m not really aware of gene therapy people that are concerned that whatever patents they may have will be challenged or challengeable by these results.

I’m somewhat surprised at the hype that came about from the ENCODE project, because I thought it was something that was far more geared toward the attention-to-detail kind of scientist and not of any concern to the general public. It’s really not going to change how science is taught at the high school or maybe even undergraduate level. I suppose the enormous amount of public funds that went into supporting the project means that the scientists are now accountable to the public to justify the cost. It’s just a hard set of findings to hype.

That Nature article was I think the longest I have ever read, and it was more a summary of all the genome research articles in a way. Anyhow, another aspect that was surprising to some, not myself, is that most DNA in the cell is expressed as RNA at some point and in very complicated patterns. It is not necessarily clear whether this all of this RNA is made into protein, however some of the RNA may be made into many different versions of a particular protein, so it becomes even more complicated about what an actual “gene” is.

Forget I just said that- to follow Clif’s lead:

Like I said, Fish, do NOT watch a TV that is perched on the edge of a bathtub.

2) I can probably add some informed commentary here as I reside in the belly of this particular beast.

Plover, you are correct. Every biologist that has taken 3 seconds to think about the nature of gene regulation has known that gene expression is a highly networked and interdependent system. The project that was recently published (one article in Nature [doubleplusgood journal] and 32(!) in Genome Research [plusgood journal]) is labeled ENCODE, and its purpose was to take 1% of the human genome and identify every regulatory element (this is the DNA that does not code for proteins but is important for controlling the expression of the proteins) within that 1% using as many different techniques as labs could invent. This effort was/is both impressive and unprecedented.

The problem here is that the press release info was converted into layperson speak and either the release misrepresented the work or it was misinterpreted. The writer of the piece is confusing the function of the gene which is to code a protein (the central dogma that he alludes to) and as far as we know, that is all it does, with the regulation of the genes and/or the functions of the proteins which are the products of the genes. Biotechs are claiming rights to genes because it is the underlying mechanism for production of their product. Proteins can have multiple functions, but in the current biotech model, it doesn’t matter. The company has to find ONE use or function to lay legal claim. If there are other functions it is value added bonus for the company, but irrelvent for the patenting process.

This is a combination of the scientific hype machine leading writers and phiosophers down roads of overgeneralization and false understanding (see global warming and stem cell topics for extended examples).