Talk:ENCODE

massive change needed

This page needs a massive overhaul given that ENCODE is in fourth phase with each phase bigger than the one before. There is a long discussion of ENCODE 1 here that no one pruned. — Preceding unsigned comment added by 134.174.140.132 (talk) 14:16, 13 November 2018 (UTC)

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)

Yes, as you say, many people have thought about these issues - however, this includes molecular biologists and population geneticists. It is one thing to conclude that the number of functional non-coding RNAs is much greater than we once thought, and another thing to conclude that 80% of the human genome is "functional". The idea that much of the genome is required for human physiology is incompatible with the measured mutation rate in humans (estimate to be 50-150 mutations per generation) and considerations of genetic load. In particular work from Herman Muller and others indicate that an organism can only tolerate a maximum of about 5 mutations per generation in functional sequence (here functional = necessary for the physiology of the organism) before the genome experiences an irreversible meltdown. Another important concept that has been developed over the past 50 years is the nearly neutral theory of molecular evolution, especially the work of Motoo Kimura, Tomoko Ohta and Michael Lynch ( see this post by evolutionary biologist Michael Eisen). Lynch in particular has studied how these forces have shaped genomic architecture. Unfortunately much of this work has been ignored by the ENCODE project leaders, science journalists and much of the scientific community, likely through ignorance rather than maliciousness. Please consult the following:

• Lynch et al., The repatterning of eukaryotic genomes by random genetic drift.
• Lynch, The Origins of Genome Architecture]
• Koonin et al., Constraints and plasticity in genome and molecular-phenome evolution.
• Gregory, Synergy between sequence and size in large-scale genomics.
• Palazzo et al., Nuclear export as a key arbiter of "mRNA identity" in eukaryotes.

Microtubules (talk) 01:08, 19 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)

Alas it was NOT due to the press reports, but rather the authors themselves and their big name publisher. [1] [2]. 86.121.137.227 (talk) 14:58, 16 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. [3][4] Right now it reads like another PR piece. 86.121.137.227 (talk) 14:22, 16 September 2012 (UTC)

Also, how it inadvertently fueled the ID machine. [5] 86.121.137.227 (talk) 14:28, 16 September 2012 (UTC)

Indeed, it would be pretty silly not to rewrite the article in light of Graur et al. (2013), "On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE" [6]. As it stands, the article still reads like a PR piece. — Preceding unsigned comment added by Skadefryd (talk • contribs)

I don't believe that article accurately reflects the consensus of opinion in the field. It might be worth citing as the harshest criticism that has appeared, but I believe a more common view is that the project produced extremely important results but that their meaning was stretched beyond what the evidence could fully justify. Looie496 (talk) 16:48, 25 February 2013 (UTC)

Both the initial PR hype that surrounded the ENCODE project and Graur's reaction to it represent extreme view points and the truth probably lies somewhere in between. I think the present version of the article is a fair description of the project and what it has accomplished and does not overly hype it. Boghog (talk) 22:22, 25 February 2013 (UTC)

Controversy section

A controversy section was added in these edits. While I think adding a controversy section would be useful, the version that was recently inserted was way over the top and does not conform to WP:NPOV. Therefore I have reverted it. Boghog (talk) 10:15, 15 August 2013 (UTC)

Has ENCODE oversold the significance of the project results? Absolutely. Are the results of the project useless? Absolutely not. In support of the later statement, the ENCODE results have been invaluable in determining how non-coding region of DNA contribute to disease (PMID 22955986). Boghog (talk) 13:19, 15 August 2013 (UTC)

I agree with both of your main points: (a) a controversy section could be useful; (b) the material that was added is not neutrally worded. IP editor, please enter the discussion here rather than edit-warring. Looie496 (talk) 14:25, 15 August 2013 (UTC)

Instead of removing entire section according to your bias, would you please restore it and fix any error?

(a) The article as it stands is biased, one-sided and misleading. It does not point out that ENCODE's Nature paper claimed to have shown that '80% of the human genome was functional'. The abstract of a scientific paper is the place to report the most important findings of the project. So, the wiki page must truthfully report that. That is even without going into the 'controversies'. 50.47.87.195 (talk) 14:54, 15 August 2013 (UTC) 50.47.87.195

(b) It is important to include a controversy section highlighting what came out since the publication of ENCODE. It is ok not to include various blog discussions, but I do not see why the peer-reviewed publications cannot be included here.

(c) Graur and Mike Eisen discussed about ENCODE's cost in a radio show. They are both respectable scientists. Even if you want to call Graur 'biased', I would like to see Eisen's points being included about ENCODE's cost and relative lack of merit of its data. 50.47.87.195 (talk) 14:54, 15 August 2013 (UTC) 50.47.87.195

(d) Mike White showed in a PNAS paper that random DNA mimics ENCODE like transcriptional behavior. That is important to note and possibly outside 'controversy' in a separate section on scientific merits of ENCODE. Your comment 'the ENCODE results have been invaluable in determining how non-coding region of DNA contribute to disease' may be false, if random DNA and ENCODE are indistinguishable. — Preceding unsigned comment added by 50.47.87.195 (talk) 14:58, 15 August 2013 (UTC)

To reiterate, I agree that the article should have a controversy section, however the are some serious problems in how the current section is worded. One problem is that it contains synthesis (conclusions that are not directly support by the sources). For example:

• ENCODE project has been widely criticized – The source supplied document that Dan Graur and Michel Eisen have been critical. What we need is a secondary source to document the wide spread criticism.
• or very high costs (400 million dollars) – supplied source does not mention cost.
• overselling of science ≠ biggest splash possible
• supports the above account of intent to mislead the public – pure synthesis, we need a secondary source that directly states the intent
• valuable data resource' claim of ENCODE is false – source only indirectly supports the claim that the raw data in one of the ENCODE papers has not been used for serious research and then extrapolates this observation to the entire ENCODE project. This is far from proof.
• wasteful public funding of ENCODE – the source only state the funding has been extended five years and does not support that the funding has been wasteful. The spending may very well have been wasteful, but we need a source to directly support that statement.

A second problem is that it does not maintain a neutral point of view (not all significant view points are presented). For example Michel Eisen admits that the data is useful in some sense (he admits that he himself has used the data) while at the same time he didn't think the results of the project justified the costs. Hence there are a spectrum of opinions. One significant view point holds that while the project has been overhyped, it has generated some useful data. Boghog (talk) 15:14, 16 August 2013 (UTC)