Talk:ENCODE

1% (30mb) ??

The article said that 1% of the genome had been selected...and after the "1%" we had "(30mb)" - I checked the reference for that statement and it has "(30Mb)" - so I corrected it (mb==milli-bits! Mb==Megabits). However, I'm unsure whether we are really talking about "Megabits" - as in computer jargon - or is it perhaps "Mega-base-pairs" or something else? The referenced paper doesn't make it clear - presumably because geneticists can infer it from the context...but we have a more general readership - so we really should be more specific. SteveBaker (talk) 15:45, 6 September 2012 (UTC)

In genetics, Mb is mega-base-pairs. Looie496 (talk) 16:26, 6 September 2012 (UTC)

Thanks - I've written it out in full in the article. SteveBaker (talk) 19:19, 6 September 2012 (UTC)

We need a radical change

The 2012-09 results are a new and qualitatively different description of the genome. Human DNA chomosomes were formerly described as being "genes", interspersed with "junk DNA" ( 1% genes, 99% junk.) Now, chromosomes are a set of functional elements of several types. At least 80% of the genome is categorized into a functional type, and statistically the remainder of the genome will almost all be so categorized, leaving little or no junk DNA. How should we address this?-Arch dude (talk) 01:32, 7 September 2012 (UTC)

• I started just this discussion in the Human genome talk page. --Thorwald (talk) 02:31, 7 September 2012 (UTC)

I fundamentally disagree witnh this. ENCODE's best estimates are that 8% of the genome is influencing gene expression, and they beleive that possibly another 11% may also play a role. However, the vast majority of the rest of the genome is simply being transcribed into non-functional RNA. This was true in 2007, and it seems equaly valid in the 2012 data as well. Microtubules (talk) 16:18, 9 September 2012 (UTC)

It's not easy to get exactly the right wording for things like this. It would seem odd, for example, to describe transposons as nonfunctional, but there are likely to be very few cases where they enhance the evolutionary fitness of a species. Looie496 (talk) 18:19, 9 September 2012 (UTC)

The following articles I think do an excellent job of putting things in perspective:

• Most of what you read was wrong: how press releases rewrote scientific history
• Reports of Junk DNA's Demise Have Been Greatly Exaggerated
• Science Writes Eulogy for Junk DNA

In short, the results of the ENCODE project are important, but the importance has been wildly exaggerated. Boghog (talk) 19:20, 10 September 2012 (UTC)

I'm not a geneticist, just a neurobiologist watching in wonder from the sidelines, but I would put it a little differently. The fact is that lots of people have thought for a long time that the exome is where the all the important stuff happens. ENCODE is a big step toward mapping out the regulome and understanding how important it is. You could almost say that for a long time the central dogma in genetics was, evolution works primarily by altering the structure of proteins. We are increasingly moving toward a new dogma that evolution works primarily by altering the expression levels of proteins. That's really a fundamental change, but as with many such things, it is occurring gradually, which makes its importance hard to get across to a broad public. Any time such a change occurs, there are going to be people who say that they knew it all along -- and maybe they did -- but what is important is that the community as a whole did not know it all along. Looie496 (talk) 20:03, 10 September 2012 (UTC)

The results are remarkable, but the use of the 80% figure is unfortunate. It would be more accurate to say that 20% of the genome is functional while another 60% is transcribed with no known function. Boghog (talk) 20:29, 10 September 2012 (UTC)

I can agree with that. Looie496 (talk) 21:00, 10 September 2012 (UTC)

Section missing

I'm not familiar enough with the subject to write it myself, but I definitely think this article is missing a "Significance" section. What will this mean for the biological sciences? What are the practical possibilities that ENCODE makes possible? Etc. Leptictidium (mt) 16:55, 8 September 2012 (UTC)

ERV and pseudogene pages

Do the ERV and pseudogene pages on wiki need to be updated re ENCODE?, pseudgenes looks retardedly outdated....

Jinx69 (talk) 19:02, 9 September 2012 (UTC)

The pseudogene article already mentions that some pseudogenes may have function (see Pseudogene#Functional_pseudogenes.3F), so I don't think that article is terribly out of date. Boghog (talk) 19:19, 9 September 2012 (UTC)

Ah k thanks for the reply, im reading the ENCODE papers now and havnt come across anything about ERV's are they mentioned anywhere in there? Still reading them...

Jinx69 (talk) 20:34, 9 September 2012 (UTC)

This link might be useful

Just ran across this, and thought it might be good for the editors of this article to consider it: http://arstechnica.com/staff/2012/09/most-of-what-you-read-was-wrong-how-press-releases-rewrote-scientific-history/ • Jesse V.^(talk) 20:22, 10 September 2012 (UTC)

Yes! I'm not sure it would meet WP:MEDRS but it's dead-on in terms of the widespread misinformation being peddled. Thanks for that link. Anyone beating the "Junk DNA is Dead!" drum needs to read this piece and realize how devoid of highly-relevant nuance the press reports have been. — Scientizzle 21:16, 10 September 2012 (UTC)

See also above discussion. I have also revised the articles's text to replace the misleading "80% biologically active" figure with the more accurate "20% functional + 60% transcribed" estimate. Finally while this article has medical implications, I think WP:SCIRS not WP:MEDRS applies. Ars Technica is a fairly respectable publication and the author has a doctorate in Molecular and Cell Biology from Berkeley. I think this link qualifies as a reliable source. Boghog (talk) 02:06, 11 September 2012 (UTC)

Controversy

There should be discussion in this article about the controversy it caused by the way the results were presented and the delay. [1][2] Right now it reads like another PR piece. 86.121.137.227 (talk) 14:22, 16 September 2012 (UTC)