BARACK Obama's anti-Israel jihad is one of the most irresponsible policy lurches by any modern American president. It rightly earns Obama the epithet of the US president least sympathetic to Israel in Israel's history. Jimmy Carter became a great hater of Israel, but only after he left office.
Obama's dangerous new lurch into anti-Israel populism changes global politics in extremely dangerous ways, and poses a challenge for Kevin Rudd.
Perhaps Obama's most distinctive contribution to the foreign policy debate in the lead-up to the US presidential election was his avowed determination to talk to and engage the US's enemies if he became president. He was happy in principle to talk to Iran's Mahmoud Ahmadinejad, but did not know for sure that the Iranian president wielded real power. But he sent all manner of felicitations and greetings to Iran and its government. When that government stole an election on Ahmadinejad's behalf and viciously brutalised its citizens, Obama refrained from speaking too much or too forcefully, as, he said, he didn't want to be seen to be interfering in Iranian internal affairs.
When Obama met the king of Saudi Arabia, a nation in which no one votes, women are subject to severe and demeaning restrictions and it is against the law to have a Christian church, Obama bowed in deep respect.
When Obama ran into Venezuela's murderous despot, Hugo Chavez, at a summit, there was a friendly greeting observed by all.
But there is one leader whom Obama draws the line at. He will not be seen in public with Israel's Prime Minister, Benjamin Netanyahu. Astonishingly, when Netanyahu saw Obama at the White House this week, all photographers and all TV cameras were banned, a level of humiliation almost completely unique in modern White House practice.
You might even conclude that Obama is trying to interfere in internal Israeli politics and bring down a government. This is something post-colonial, post-multicultural Obama would never do with Iran, but with Israel, the US's longstanding ally, it's fine.
And what was Netanyahu's crime, this act of infamy that Obama's senior staff described as an "affront" to America? It was that the relevant housing authority passed another stage of approval for 1600 Israeli housing units to be built in East Jerusalem in about three years' time. It was very foolish that the Israelis allowed this announcement to take place while US Vice-President Joe Biden was in Israel. But they apologised to Biden at the time, Biden kissed and made up with the Israelis and was back to delivering fulsome pro-Israel speeches before he left.
After that point, though, the US reaction went into overdrive. Impeccable American sources tell me this reaction was driven by Obama, and to a lesser extent the Chicago mafia around him.
We must ask why this is so, but first let's get Netanyahu's infamous crime into perspective.
Last November Netanyahu announced a 10-month moratorium on all building activity in Jewish settlements in the West Bank. Israel has already promised not to take any more land for settlements but there is the question of renovating existing buildings and constructing new ones in existing settlements.
As Hillary Clinton acknowledged in her speech this week to the American Israel Public Affairs Committee, East Jerusalem was never part of this agreement. The two main peace offers Israel has made to the Palestinians in recent years were the Camp David/Taba proposals and the accompanying Clinton parameters in 2000, and Ehud Olmert's offer to Palestinian president Mahmoud Abbas in 2008. Both plans offered essentially the same formula. The Palestinians get all of the Gaza Strip, about 95 per cent of the West Bank and a compensating parcel of territory from Israel proper to make up for the small amount of territory in the West Bank that Israel would keep which houses the main Jewish population blocks. The Palestinians also get some parts of East Jerusalem as their capital. This principle of territorial swaps was accepted by Yasser Arafat and Abbas.
East Jerusalem has always had a different status from the West Bank and some Israelis certainly don't want to give any of it to a new Palestinian state. But everyone accepts that some Jewish neighbourhoods would remain part of Israel. These are mostly neighbourhoods, as Netanyahu pointed out this week, which are five minutes from the Knesset and a couple of blocks beyond the 1949 armistice line. The administration of George W. Bush had formally agreed with the Israelis that these areas would be permanently part of Israel. Bill Clinton had negotiated an offer to the Palestinians in 2000 which accepted this.
It would be a radical change of policy for an Israeli government to decree that no building would ever take place in Jewish areas of Jerusalem. It would also be a change of American policy.
Moreover, no serious analyst could believe that such building is a roadblock to peace. Peace negotiations have gone on with such building taking place in the past. And all the things that truly make peace impossible - Arab and Palestinian refusal to accept the legitimacy of any Jewish state, Palestinian insistence on certain deal breakers such as the right of return of all Palestinian refugees and their descendants to Israel proper, the insistent and violent anti-Semitism of Palestinian and Arab propaganda and the regional ambitions of players such as Iran and Syria - will be completely unaffected by any decision to build apartments in a Jewish neighbourhood in East Jerusalem in three years time. So why has Obama gone into full jihad mode against Israel? Three explanations suggest themselves. Obama has had a terrible year in foreign policy. He has achieved nothing on Iran or China or anything else of consequence. He is too smart to believe this intimidation of Israel will advance peace, but it might get peace talks going again. The Palestinians only made settlements a roadblock after Obama did. They are refusing to join Israel in peace talks, which Netanyahu would be happy to participate in. They have said they might engage in proximity talks - which means not talking to the Israelis directly but to mediators who will shuttle back and forth carrying messages between them and the Israelis. This is primitive and ridiculous stuff, but if such talks get going Obama could claim some kind of victory, or at least progress.
And Obama is showing that his personal popularity, not America's standing, still less matters of substance such as Iran's nuclear program, is what motivates him.
This leads to the second explanation of his behaviour, and that is to make himself personally popular in the Muslim world. Beating up on Israel is the cheapest trick in the book on that score and it can earn him easy, worthless and no doubt temporary plaudits in some parts of the Muslim world.
And thirdly, Obama is the first post-multicultural president of America. In his autobiography he talks of seeking out the most radical political theorists he could at university. For these people Israel is an exercise in Western neo-imperialism. Obama makes their hearts sing with this anti-Israel jihad.
Accompanying Obama's own actions has been some of the most dangerous rhetoric ever to come out of a US administration, to the effect that Israeli intransigence endangers US troops by inflaming extremists in the Islamic world. No serious analyst anywhere believes that Israel is an important source of the conflicts in Afghanistan or Iraq. Using this type of argument comes dangerously close to the administration licensing a mutant strain of anti-Semitism - it's all the Jews' fault. Why is all this a challenge for Rudd?
The anti-Israel hysteria is totally disproportionate and wildly over the top. The British decision to expel an Israeli diplomat because Israel is alleged to have used forged British passports in a Mossad operation is a case in point.
The British precedent pressures Rudd to do the same. Rudd should resist this pressure, as Opposition leader Tony Abbott has urged him to. 2010 is a critical year for the Middle East. Israel's friends now should rally round it, or the spectre of wild and hysterical anti-Israel sentiment will be unleashed with all manner of destructive consequences.
Now is the time for anyone who cares about Middle East peace, or who claims as Rudd does to care about Israel, to stick close to Jerusalem. The Australian Federal Police inquiry will not be conclusive about whether Israel used Australian passports or not. Obama wants to be popular. Gordon Brown wants Muslim votes and to distract attention from the latest scandals of his government. Rudd could be tempted to bash Israel as a way of courting Arab League votes at the UN. But the path of statesmanship here does not lie in apeing these foolish American and British moves.
There would also be a gruesome comparison in the way Australia responds to big as to small nations. China imprisons one of our citizens, denies consular access to most of the trial and treats Canberra with contempt. In return Rudd changes policy and declines to see the Dalai Lama and similarly declines to send an Australian minister to Taiwan in the entire course of the government's parliamentary term.
Yet Israel, our close friend, is alleged to misuse a passport and then gets the very big diplomatic penalty of having a diplomat expelled. It would be disproportionate and foolish and cowardly.
The Americans and Brits don't always get things right. There are times when Canberra should definitely not follow their lead.
http://www.nature.com/nature/journal/v431/n7011/full/nature03022.html
From the abstract, no mention of ultraconserved elements being deleted, which is far as I can get before hitting a paywall.
If I understand the "conserved between humans and rodents" part correctly, these are noncoding sequences from the human/mouse common ancestor which are still 70% identical.
It's only the main paper and the editorials that really feature those statements (and if you know what is meant by "function" there, they would not sound nearly as alarming), the companion papers are mostly focused and often very useful functional genomic studies that do not touch on this subject.
The text description of the region from the paper is,
"We selected two regions for deletion, a 1,817 kilobase (kb) gene desert mapping to mouse chromosome 3, and a second region, 983 kb in length, mapping to mouse chromosome 19 (Fig. 1). Orthologous gene deserts of about the same size are present on human chromosomes 1p31 and 10q23, respectively. No striking sequence signatures such as repeat content or nucleotide composition distinguish these two selected gene deserts from other regions of the genome, except for their lack of annotated genes and lack of evidence of transcription (see Supplementary Information). Together, the two selected regions contain 1,243 human–mouse conserved non-coding elements (more than 100 base pairs (bp), 70% identity), also similar to genome averages, whereas no ultra-conserved elements9 or sequences conserved to fish (more than 100 bp, 70% identity) are present."
ch19:35033162-35878431
ch3:151157238-152668920
But the was for build October 2003 assembly in UCSC. This is no longer available, so I do not know if the co-ordinates are now accurate.
One of the papers listed on that website has a breakdown of where UCEs occur in the human genome, exons being in the minority. I think the short answer is that we don't really know much about UCEs at this point. They're getting noticed in phylogenetics though. We've recently been working with a set of UCEs that will (hopefully) be informative across tetrapods.
I'm not sure why you want my grinning mug on your posts, but if you must, could you please credit the photographer, Jason Varney http://www.varneyphoto.com/. He's a wonderful guy from Philly, who gave me permission to use it some time ago. I've tried to credit him in platforms that allow it, but perhaps it got lost. It wouldn't be a bad idea to ask him for permission, either. He's a nice guy and will likely say, yes.
I know Nature's editorial structure is opaque, but I was not the lead editor on the ENCODE story. I work on the news team, and although there is an obvious relationship with the back half editors, we are in practice separated by literal and figurative walls to allow (and even encourage) us on the news team to be tough and dispassionate about the research in our journal and others. I can only do my best to be as objective as possible. I'll continue to follow your blog as I continue to report on whether this behemoth project has worth the time and investment.
Also, I noticed a point mutation has crept into my name. It's Brendan with an 'a'.
Cheers!
Thank-you for correcting my spelling and for letting me know that your photograph was taken by a professional named Jason Varney.
It's true that Nature's editorial structure is "opaque." That wasn't true when John Maddox was editor. I spent 10 minutes on the Nature and NPG websites trying to find the names of editors. I couldn't even find YOUR name!
Nature is under attack for irresponsible journalism. You were the one who responded to the initial criticism of ENCODE back in September but the editors have been silent since then—correct me if I'm worng.
If you weren't involved in writing the recent editorial then who was? And why did they choose to be anonymous? Do they hold senior positions in the Nature hierarchy? Were they involved in the decisions to publish the ENCODE papers or are they covering up for underlings who made mistakes?
Why didn't they tell us what kind of review the papers were subjected to before publication? After all, as you yourself said, the discussions went on for months.
What is your personal opinion on the controversy now that you've had a chance to see both sides of the issue? Do you think that most of our genome is junk or do you think that most of it consists of thousands of biologically functional elements that control gene expression?
If you had it to do over again would you still write what you wrote last September? Let me remind you what you said ...
The consortium has assigned some sort of function to roughly 80% of the genome, including more than 70,000 ‘promoter’ regions — the sites, just upstream of genes, where proteins bind to control gene expression — and nearly 400,000 ‘enhancer’ regions that regulate expression of distant genes.
There's nothing in your original article of Sept. 5th that even hints at a controversy or how the ENCODE Consortium deals with the problem of noisy binding and spurious transcripts. Why?
You mention the 2007 pilot project in your review but were you aware of the controversy that followed publication of those results? Do you know why the ENCODE authors failed to address those criticisms?
As you know, other science journalists announced that ENCODE refutes junk DNA. This theme was prominent in most articles written for the general public ("Junk DNA Is Dead!"). There even an article by Joseph Ecker in the Sept.5th issue of Nature where he says ...
One of the most remarkable findings ... is that 80% of the genome contains elements linked to biochemical functions, dispatching the widely held view that the human genome is mostly 'junk DNA.'
Did you or any other Nature editors write to these other journalists and scientists to point out that they had misinterpreted the Nature papers? Did any of the ENCODE authors complain about this misrepresentation as far as you know?
I apologize for my crack about Nature. I have cooled down a little.
But, do you at least agree that these questions are relevant?
Brendan,
I understand that you are not responsible for everything written at Nature. I understand you may not have written the editorial we're discussing here.
However, we get little response from Nature and Science regarding their "Death of Junk DNA" hoax, so I was hoping you could answer me a simple question.
According to the myth of Func DNA, supposedly 3 billion nucleotides in the human genome are now regulatory elements or "switches" as John Stamatoyannopoulis told us, regulating ~25,000 genes including RNA genes. So each gene including RNA genes is regulated by on average 120,000 nucleotides, or "switches" as John Stamatoyonnopoulis blurted hysterically. That's the average.
Name one, just one, well-studied gene known experimentally to be regulated by 120,000 nucleotides. Just one.
If there were one such gene, it wouldn't prove that most of the genome can suffer deleterious mutations (meaning, non-junk)-- you would need to show that the AVERAGE gene, over 25,000 genes total, is regulated by 120,000 nucleotides.
Admittedly, it might take longer for scientists to show that the AVERAGE gene, over 25,000 genes total, is regulated by 120,000 nucleotides, on average.
But can you name just one such gene, right now?
If you can't name even one gene, that is known experimentally to be regulated by 120,000 nucleotides, then how many publication cycles will you go through before before we expect to find one?
And then the other 24,999 after that?
Simple question. Do you agree the question is relevant?
If it's relevant, how come the editors at Nature never asked it?
Oh come on, he's Irish. He ought to have a sense of humor.
;)
With the completion of the current ENCODE project junk DNA effectively disappeared because there's no useless DNA in the genomes no more [sic].
Oy vey.
So there's still some hope that the damage hasn't (and won't) spread too much, at least as far as textbooks go.
I noticed the symposium on "Where Did The Junk Go?" and it almost tempted me to go to the meeting.
Do you think there will be participants who defend junk DNA or do you think most attendees are adaptationists who dislike the idea of junk?
One of the invited speakers is Dan Graur, and assuming all the invited speakers have accepted the invitation, he won't be shy about venting his outrage at the premature dismissal of the notion of junk DNA.
Here is the description, and list of speakers, from Wojciech Makalowski's announcement which was posted on the evoldir mailing list"
As a part of the is year SMBE meeting, I'm happy to announce the symposium "Where did the junk go"? We are currently accepting abstracts for contributed talks (15min). Abstract submissions are open until March 18th, and travel awards are available to support graduate and post-doc travel to the conference. Please check the meeting web site http://www.smbe2013.org/ for additional information and registration. For any inquires related to the symposium please contact Wojciech Makalowski at wojmak [at] uni-muenster.de. I expect very exciting discussion on this hot topic.
Sincerely,
Wojciech Makalowski, Ph.D.
Professor and Director
Institute of Bioinformatics
University of Muenster
Niels Stensen Strasse 14
48149 Muenster, Germany
On sabbatical at the Department of Medical Genome Sciences University of Tokyo
Where did "junk" go?
Late Susumu Ohno once said "So much junk DNA in our genome" and the phrase junk DNA was born. For a long time mainstream scientists avoided these parts of the genomes. However, over the years the picture slowly started to appear suggesting that the junk DNA hides a genomic treasure. With the completion of the current ENCODE project junk DNA effectively disappeared because there's no useless DNA in the genomes no more. This symposium will discuss the current understanding of these not so far ago obscure areas of the genomes with the special attention to transposable elements activities and their evolutionary consequences. The integral part of the symposium will be general discussion of Ohno's idea and its place in todays biology.
Invited speakers include:
1. Josefa Gonzalez (Institut de Biologia Evolutiva, Barcelona, Spain)
2. Valer Gotea (National Human Genome Institute, Bethesda, USA)
3. Dan Graur (University of Houston, Houston, USA)
4. Dixie Mager (University of British Columbia, Canada)
5. Masumi Nozawa (National Genetic Institute, Mishima, Japan)
Too bad they didn't invite Jonathan Wells. He could have given them a summary of "The Myth of Junk DNA."
I don't know any of those people except Dan Graur. A quick Google search suggests that none of them are going to defend junk DNA.
Why do you suppose that Wojciech Makalowski thinks that "junk DNA effectively disappeared because there's no useless DNA in the genomes no more." According to ENCODE leaders, they said no such thing! They were only identifying "biochemical functions" and those didn't refute junk DNA. It's amazing how many "experts" in the field misinterpreted the ENCODE results, isn't it?
Simple question: supposedly 3 billion nucleotides are now regulatory elements regulating ~25,000 genes including RNA genes. So each gene incl. RNA genes is regulated by on average 120,000 nucleotides. That's the average.
Name one, just one, well-studied gene known experimentally to be regulated by 120,000 nucleotides. Name just one, Makalowski.
Yes, Malakowski is the genius who write "Not Junk After All" declaring Junk DNA dead back in 2003. Then it was dead again in 2007 and again in 2012.
I am sure after this ENCODE stuff blows over, Malakowski will declare Junk DNA dead again in 2016, then again in 2022, etc. Some memes are immortal.
With the completion of the current ENCODE project junk DNA effectively disappeared because there's no useless DNA in the genomes no more.
Oy vey indeed. Genomes, plural. I guess he includes the marbled lungfish, onions, amoeba genomes etc. Nope, no junk in the genomeS no more.
That should be Casey Luskin's signature. Well, if I'd known earlier I'd've written an abstract for submission, but if the deadline's the 18th...
"Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus, on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function."
http://www.mendelspod.com/podcast/debating-encode-with-dan-graur-and-michael-eisen
I laughed at the part where Graur says, chewing gum sticks to my shoe. But it is not the function of my shoe to collect chewing gum.
Reading an article posted by JAMA yesterday. http://jama.jamanetwork.com/article.aspx?articleid=1666972#ref-jvp130033-5
Crossing the Omic Chasm
A Time for Omic Ancillary Systems
4th paragraph states,
"Omic data are different. An individual's germline genetic sequence changes little over a lifetime, but understanding of that sequence is changing rapidly. For years the DNA between coding regions was called “junk,” but it is now known that this DNA plays an important role in gene regulation.5- 6 The 1000 Genomes project has identified tens of millions of different genomic variants; the clinical significance of these variants is mostly unknown, but current understanding is rapidly changing. Unlike serum sodium levels, the clinical implications of NGS obtained today will keep changing for years as knowledge evolves."
smh
You said,
The truth is that while this is not arguing over semantics, debunking junk DNA was never the goal of the ENCODE consortium, the goal was to find "functional elements" (which, unfortunately, has turned not to be nearly as straightforward as initially hoped for).
It's true that debunking junk DNA was not a well-defined goal of the consortium. Their goal was to attribute function to as much of the genome as possible. You are correct when you say that this turned out to be difficult—especially in light of abundant evidence for junk.
In your opinion, what's the best paper that discusses this difficulty and addresses the problems of noise and spurious transcripts? There should be at least one paper that tries to distinguish between real biological function and accidental elements, right?
It's only the main paper and the editorials that really feature those statements (and if you know what is meant by "function" there, they would not sound nearly as alarming), the companion papers are mostly focused and often very useful functional genomic studies that do not touch on this subject.
With all due respect, this is nonsense. In light of the 2007 criticism of the pilot project, every single paper should have been aware of the problem of distinguishing between real biological function and nonfunctional effects. In the absence of that critical analysis of their own data, I can only conclude that they meant to convey the idea of real biological function associated with most of their elements.
There were six different articles written by ENCODE Consortium leaders who summarized their results. Every single one of them emphasized the biological importance of their elements and none of them even mentioned junk DNA or the possibility that they could be looking at artifacts.
Do you think they were completely unaware of the criticism that was about to be leveled at their interpretation of their own data? Isn't it more likely that they actually believed that they were annotating true biological function and debunking junk DNA? Some of the leaders have actually said this in interviews.
That's not correct either - the goal is to find the functional elements that drive gene regulation and to annotate the transcriptome as fully as possible. That's not the same as attributing function to as much of the genome as possible. Now, "function", whatever definition of it you want to adopt, has turned out to be more of a continuously distributed rather than a discrete, binary characteristic of genomic features, and then we start having the old argument over where you draw the threshold or whether there can even be a threshold, and that's where the difficulty arises.
What I said regarding the companion papers is still true. I clearly said the main paper and the editorials are what the debate is over, most of the companion papers (which, BTW, are not limited to the 30+ papers in GR, GB, and other journals from September, many more papers came out before or after that and many are still to come out) are just focused on different aspects of genome biology and/or functional genomic technology development and do not say anything on the subject of junk DNA, because they don't have to. It is simply not correct to attack them on the same grounds as the main paper and the editorials.
P.S. The problems with experimental artifacts and uncertainty in the interpretation of data are explicitly mentioned in what I have personally written and published (and there is a lot I have not published as a result of those topics featuring too prominently). They feature in other consortium papers too. Should discussion of them have a much more prominent place in papers - I agree wholeheartedly, but the facts of life are that the days of the papers that explicitly discussed at length what's wrong with the data are gone. It has always amazed me how often old papers, say from the 70s, would indulge in such discussions, and how such a thing is a non-starter in today's publishing climate. It's not a perfect situation but it is not easy to change it.
You said,
That's not correct either - the goal is to find the functional elements that drive gene regulation and to annotate the transcriptome as fully as possible. That's not the same as attributing function to as much of the genome as possible.
I know that ENCODE characterized pseudogenes and that over 90% of them are not transcribed. They also looked at chromatin interacting regions—I don't know if this includes SARs but I don't think they are transcribed. Some of the groups studied evolution and sequence comparisons to find conserved stretches of DNA. Some studied SNPs and their association with other features of the genome.
Are you saying that the ENCODE Consortium deliberately excluded origins of replication, centromeres, and telomeres in their attempt to annotate the genome? Why would they do that?
You said,
The problems with experimental artifacts and uncertainty in the interpretation of data are explicitly mentioned in what I have personally written and published ...
Here's one of the papers with your name on it: Landscape of transcription in human cells. I don't know if you think of it as one of the companion papers.
Here's part of the abstract ...
Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.
Now, if your results are so good that we have to redefine a gene then I expect a detailed discussion of possible artifacts and errors in the interpretation of your data. I didn't find that anywhere in the paper. No mention of spurious transcription and no references to the papers that discuss this possibility and criticize the earlier ENCODE results. Why is that?
I also expected a discussion about aberrant splicing and possible artifacts. There should have been some mention of the possibility that what you were detecting was due to splicing errors. This directly impacts your re-definition of a gene. Did I miss this in your paper?
I stand by my claim that most of the ENCODE papers focus on establishing the functionality of their discoveries with scant attention to any other possibility. This is not good science and it's inexcusable given the controversies that arose when the pilot project was published.
Good scientists will go out of their way to address criticism and ways in which their hypotheses and interpretations can be falsified.
Do you agree?
Origins of replication were studied by the pilot phase and by modENCODE. For some reason, there wasn't a specific project on this in ENCODE2, though there was RepliSeq data generated for a lot of cell lines.
Centromers and telomeres cannot really be studied with current functional genomics tools because the read lengths are too short and/or they're not even present in the genome assembly, plus we mostly already know what they do and what their chromatin state
You say,
Should discussion of [problems] have a much more prominent place in papers - I agree wholeheartedly, but the facts of life are that the days of the papers that explicitly discussed at length what's wrong with the data are gone. It has always amazed me how often old papers, say from the 70s, would indulge in such discussions, and how such a thing is a non-starter in today's publishing climate. It's not a perfect situation but it is not easy to change it.
We all understand what's going on here. The ENCODE Consortium didn't really do anything that's not done routinely by lots of other labs. They are only getting criticized because their lack of attention to the "problems" was so blatant that we can't ignore it. They were given a chance to write a series of papers that explained their results and how they fit in with the abundant evidence for junk DNA. They blew it even when presented with this opportunity.
It would be nice if they would just admit, as you did, that they made a mistake.
Moreover, the press releases are the real problem here, not so much the papers.
I don't agree with Larry's thesis that all authors of all papers should have known this would happen.
The 2007 kerfuffle was in the blogosphere, and how many scientists follow blogs? Most don't. I myself would not have heard about if I didn't argue with creationists.
How could the average scientist of these 400 have known that Birney would pull a trick like that, or Stamatoyannopoulis? How could they see that coming? Most scientists tend to trust each other.
They didn't all get together in a big room and vote on that!
Anyway, if 10 nucleotides of an intron are found to be functional, you can't generalize to all nucleotides of all introns.
Likewise, if 3-4 scientists out of 400 twisted the facts, you can't generalize to all 400. Larry here is pulling a Casey Luskin-style overgeneralization.
The most important paper was Kevin Struhl's Nature paper: Transcriptional noise and the fidelity of initiation by RNA polymerase II. Here's the abstract ...
Eukaryotes transcribe much of their genomes, but little is known about the fidelity of transcriptional initiation by RNA polymerase II in vivo. I suggest that approx90% of Pol II initiation events in yeast represent transcriptional noise, and that the specificity of initiation is comparable to that of DNA-binding proteins and other biological processes. This emphasizes the need to develop criteria that distinguish transcriptional noise from transcription with a biological function.
You can't tell me that the ENCODE scientists and all the members of their labs were completely unaware of this problem. Do you mean to imply that this never came up in any of their group meetings or journal clubs?
I'm not saying any such thing. However, it would be nice to find at least one ENCODE paper that gets it right. Do you know of any?
(All 400+ scientists put their names on several of the papers that made outlandish claims. I can understand why some of them didn't want to challenge their bosses but would you have done that?)
The most important paper was Kevin Struhl's Nature paper: Transcriptional noise and the fidelity of initiation by RNA polymerase II.
Eh, OK I concede that point.
First, why are you assuming that a paper with a large number of authors has been written collectively by all of those? Such a paper would never get published - it's hard enough to get all collaborators to respond in timely manner even on small paper that have just a few authors, for something with many dozens or hundreds of authors, it would be practically impossible to get it done in any sort of reasonable time, it would take years to finalize the text. Which itself would not be possible for the reason that if all authors had an equal say in the content, with such a large number of them, there will be tons of statements and phrases that someone would not agree with. These things get written by a small number of people while the rest of the authors are included because they contributed data, developed the analysis methodology, did some analysis, or didn't do anything but were associated with the project and got on the paper because in the shuffle nobody realized they did nothing. It's the nature of big consortium science.
Now, if your results are so good that we have to redefine a gene then I expect a detailed discussion of possible artifacts and errors in the interpretation of your data. I didn't find that anywhere in the paper. No mention of spurious transcription and no references to the papers that discuss this possibility and criticize the earlier ENCODE results. Why is that?
I also expected a discussion about aberrant splicing and possible artifacts. There should have been some mention of the possibility that what you were detecting was due to splicing errors. This directly impacts your re-definition of a gene. Did I miss this in your paper?
Actually, the statement that the gene needs redefining is correct - the paper talks about later how the basic unit should be the transcript and not necessarily the gene. That's not that controversial, especially if we're talking about alternative promoters. Of course, a lot of the different isoforms that get expressed from the complex genes are most likely garbage, and that's not that controversial either. BTW, my paper on the subject is not that one - I was leading a separate analysis of a similar nature where I did discuss the issues of noise and artifacts at length, but that paper was never submitted for reasons I don't want to go into.
Good scientists will go out of their way to address criticism and ways in which their hypotheses and interpretations can be falsified.
Do you agree?
There probably will be an official response to criticism at some point.
Kevin Struhl is one of those 400+ scientists on the main papers...
"First, why are you assuming that a paper with a large number of authors has been written collectively by all of those?"
Why is it unreasonable to assume (or even conclude) that the people listed as "authors" actually authored (wrote) the paper?
"Such a paper would never get published - it's hard enough to get all collaborators to respond in timely manner even on small paper that have just a few authors, for something with many dozens or hundreds of authors, it would be practically impossible to get it done in any sort of reasonable time, it would take years to finalize the text. Which itself would not be possible for the reason that if all authors had an equal say in the content, with such a large number of them, there will be tons of statements and phrases that someone would not agree with."
If that's the case the collaborators should write their own individual papers, and include any disagreements they have with anyone else. Either that or not allow themselves to be listed as "authors".
"These things get written by a small number of people while the rest of the authors are included because they contributed data, developed the analysis methodology, did some analysis, or didn't do anything but were associated with the project and got on the paper because in the shuffle nobody realized they did nothing."
Then the non-authors should be listed as collaborators, developers, analyzers, contributors, or whatever label actually fits along what they actually did, and if they did nothing they shouldn't be listed at all. Is the janitor who cleans the building the paper is written in listed as an author because he/she 'contributed'?
"It's the nature of big consortium science."
That's a cop out and it certainly doesn't make false lists of so-called "authors" acceptable. Giving people credit for something they didn't do, especially if they did nothing, and especially if the false credit is in any way meant to inflate the 'authority' of the paper, just plays into the hands of the science bashing religion pushers, and it damages trust in science by the public.
Trust must be earned and science needs the trust of all the scientists within it, and the public. Accepting responsibility engenders trust and anyone who is listed as an author should accept responsibility as an author.
It's apparently past time for scientific papers to have a different, mandatory format. Think of the way that multiple-judge courts do their thing. The judges all read the briefs, hear the case, ask questions and/or make statements, research previous cases and precedents, collaborate/contribute/discuss/argue or whatever, mull it over for awhile, and then state their decisions ('opinions') in writing. Their individual 'opinions', including disagreements, are available to other courts and to the public. When multiple people are listed as "authors" of a scientific paper, the discussion section of the paper should include any disagreements between the listed "authors".
or whatever label actually fits along with what they actually did
"There probably will be an official response to criticism at some point."
If so, who exactly will author it, and will all of the collaborators, developers, contributors, analyzers, or "didn't do anything" associates originally listed as "authors", who disagree with the 'official' claims/position, be allowed to speak in the probable "official response" too?
I must say that your statement above sounds just like one that would typically come from a politician or their spokesperson.
That's true, but Marinov cannot presume to speak for the consortium when nobody anointed him as spokesperson. It would be presumptuous for him to talk like he's the representative of the consortium.
Are you eligible for a retirement yet Larry?
If junk-DNA hasn't collapsed in 5 years, you will send money to Larry Moran(or me, I'll gladly take your money). How much are you willing to part with?
For example, according to your understanding, what function did the ENCODE project discover? Be specific.
I'd ask what evidence you cite for that, but I know ID pussies never answer questions relevant to the assertions they themselves make. They never answer, because Intelligent Design is a fraud.
Simple question, Dominic: supposedly 3 billion nucleotides are now regulatory elements regulating ~25,000 genes including RNA genes. So each gene incl. RNA genes is regulated by on average 120,000 nucleotides. That's the average.
Name one, just one, well-studied gene known experimentally to be regulated by 120,000 nucleotides. Name just one, Dominic.
Dominic will not answer, because Intelligent Design is a fraud.
Would you care to make a bet, Dominic? I bet you $2,000 that within a year and a half of the publication of the ENCODE papers, there will not be a single gene, not one gene, in the human genome known experimentally to be regulated by 120,000 nucleotides.
Even if I lost that bet (I'd win), it wouldn't prove most of the genome can suffer deleterious mutations-- you need to show that the AVERAGE gene, over 25,000 genes total, is regulated by 120,000 nucleotides.
Admittedly, it might take longer for evolutionists to show (only evolutionists make scientific discoveries nowadays) that the AVERAGE gene, over 25,000 genes total, is regulated by 120,000 nucleotides.
But, if we're going in the right direction, surely within a year and a half of the publication of the ENCODE papers, there will be a single gene, just one gene, out of 25,000 in the human genome known experimentally to be regulated by 120,000 nucleotides. One out of 25,000-- any gene, any function-- you pick! You pick, pussy! YOU PICK, YOU PUSSY!
So are you willing to bet $2,000 that will happen? Put your money where your mouth is, witch doctor creationist.
Oh no! I'm sure we would have all preferred to be much more circumspect if we'd only known that we were posting to a publicly accessible blog on the internet! Now what shall we do?!
If you're really taking screen caps, even though it's completely daft, then you can add my message to your little archive.
Larry has a handy page on this site called "What's in Your Genome?". Perhaps you'd be kind enough to look it over and tell us which genomic elements identified as "junk" actually have selectable, organism-level functions and what they are.
Thoughts?
I can say the same thing but I've never been involved in a mega project with dozens of authors.
I can see Georgi's point. On many of these papers he's just a cog in a big machine and it's really not possible for him to take the kind of stand that you and I would take.
But let's talk about "groups." Most of the papers are the work of several groups and each one is under some PI. In Georgi's case, the PI is Barbara Wold at CalTech. I assume that her group discusses genomes and junk DNA from time to time and I assume that the PI has a view on whether most of the genome is functional or not.
PI's could speak out if their views are being misrepresented in a paper. The fact that none of them have spoken out suggests to me that they all share the opinion of the ENCODE leaders; namely, that all that "function" they've discovered is actually real biological function.
That's the sad part. This isn't really a debate about the definitions of function—it's a debate about the existence of junk DNA and the fact that many prominent biochemists and molecular biologists dismiss it out of hand without ever bothering to learn about the issue.
I'm going to Los Angeles in June, maybe I'll visit CalTech and give them my "Junk DNA" talk to bring them up to speed. :-)