Let's Discuss - Is it Time to Shut Down NHGRI?

Professor Ken Weiss once proposed that the money allocated for NHGRI, the human genome research division of NIH, should be given to NSF and be spent on basic research on genomes. I think that is a very good idea, because there is nothing unusual in human genome that is not found in other genomes. Some parts of the human genome (information processing blocks) are conserved all the way to bacterial genomes. Some other parts came in after the origin of eukaryotes. Many developmental genes are conserved in almost all multicellular eukaryotes and definitely vertebrates. Ciliary genes are conserved all the way to chlamy.

Moreover, spending money to study only the human genome has the bad effect of making worthless ‘discoveries’ not consistent with evolutionary principles. In the ENCODE fiasco, a large group of researchers got large amount of money from NHGRI to show that human genome was unusual and they ended up ‘proving’ 80% functionality of human genome !!

On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE

A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 - 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as “affirming the consequent,” by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivity over specificity, and by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass- media hype, and public relations may well have to be rewritten.

Not that NHGRI learned anything from that exercise, because it appears to find new ways to waste money. Here they are on to a ‘new’ problem solved decades ago. From the recent NIH press release -

NIH grants aim to decipher the language of gene regulation

The National Institutes of Health has awarded grants of more than $28 million aimed at deciphering the language of how and when genes are turned on and off. These awards emanate from the recently launched Genomics of Gene Regulation (GGR) program of the National Human Genome Research Institute (NHGRI), part of NIH.

The GGR program aims to develop new ways for understanding how the genes and switches in the genome fit together as networks.

There is a growing realization that the ways genes are regulated to work together can be important for understanding disease, said Mike Pazin, Ph.D., a program director in the Functional Analysis Program in NHGRIs Division of Genome Sciences.

You gotta be kidding !!

Yes, there is network involved, but it is a different kind of network. Who is Mike Pazin?

pazinm

From the NIH website -

Dr. Pazin joined the National Human Genome Research Institute’s NHGRI’s Extramural Research Program in 2011. Mike is part of the NHGRI team overseeing the ENCODE project, generating an Encyclopedia of DNA Elements from the human genome, and the modENCODE project, identifying functional elements in the fly and worm genomes. He manages a portfolio of grants in functional genomics. He is also a member of the NHGRI Data Access Committee.

He is an ENCODE guy.

…and who does he give money to? Surprise, surprise - ENCODE leader Mike Snyder, who was the main author of their discredited paper, gets the biggest award to ‘decipher the language of gene regulation’.

Snyder_Michael

Stanford University, Stanford, California, $7.1 million

Principal Investigator: Michael Snyder, Ph.D.

Dr. Snyder and his team will study the development of one type of skin cell (keratinocyte) as it develops from an early stage skin cell into a mature cell. To do this, they will examine the network of genes and pathways that control this developmental change. The results may ultimately have implications for better understanding skin biology and hundreds of skin disorders.

At this point, shutting down NHGRI and transferring funds to NSF will be the only way to end this endless waste of taxpayers’ money.

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Also check -

Eric Green, Funding, Authorship, Integrity, and an Answer to @phylogenomics

Eric Green is the Director of the National Human Genome Research Institute at NIH.

The National Human Genome Research Institute and other institutes at NIH provide the bulk of the hundreds of millions of dollars for the ENCODE Project and other Big Science obscenities, such as modENCODE.

Eric Green is an author on many ENCODE papers, including the 2012 idiotic article in Nature, and of the many press releases which proclaimed that junk DNA does not exist.

Dan Graur has publicly described Eric Green and his ilk as badly trained technicians.

Dan Graurs previous main source of research money was NIH.

It isnt anymore.

NIH Director Francis Collins ridiculous We would have had an Ebola vaccine if the NIH were fully funded meme

But what really bothers me the most about this is that, rather than trying to exploit the current hysteria about Ebola by offering a quid-pro-quo Give me more money and Ill deliver and Ebola vaccine, Collins should be out there pointing out that the reason were even in a position to develop an Ebola vaccine is because of our long-standing investment in basic research, and that the real threat we face is not Ebola, but the fact that, by having slashed the NIH budget and made it increasingly difficult to have a stable career in science, were making it less and less likely that well be equipped to handle all of the future challenges to public health that were going to be face in the future.

Dont get me wrong. I get what Collins is trying to do. I just think its a huge mistake. Every time I see testimony from NIH officials to Congress, they are engaged in this kind of pandering talking about how concerned they are about [insert pet disease of person asking question] or that and how, if only they could get more money, wed be able to take make amazing progress. But guess what? It hasnt worked. The NIH budget is still being slashed. Its time for the people who run the biomedical research enterprise in this country to make basic research the center of their pitch for funding. Collins had a huge opportunity to do that here, but he blew it.

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2016 update

A New Yorker article by Sid Mukherjee on epigenetics got widespread criticisms from well-known scientists.

Epigenetics Debacle - Do You Feel Sad for Sid Mukherjee?

The condemnations are indirect criticisms of NHGRI given that the topics discussed in Mukherjee’s article came from bad science sponsored and promoted by the same government agency


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Written by M. //