I’ll be making a presentation at AM-NAT 2016, and Dan Graur will be the poster boy of impractical naturalism. Below are some things I collected from his websites, some of which I view as highly anti-science. The aim of my presentation isn’t to settle the question of God or no God or ultimate questions of whether godless naturalism is the best description of reality. The goal is to suggest there are some unspoken naturalistic creeds that often take priority over experiments and observations. In a manner of speaking, there are some interpretations of naturalism that actually go against dispassionate examination of how the natural world actually operates.
More than a decade after the French Academy of Sciences awarded a prize to Loius Pasteur for his work disproving spontaneous generation, Haeckel objected to Pasteur’s claims on philosophical (not scientific) grounds. From the abstract of my AM-NAT 2016,
The success of NIH initiatives and various other projects has drawn a bizarre reaction from [some] Methodological Naturalists in a way somewhat reminiscent of Haeckel who said in 1876: “If we do not accept the hypothesis of spontaneous generation, then at this one point in the history of evolution we must have recourse to the miracle of a supernatural creation.” The demise of the theory of spontaneous generation led to substantial advancement of practical scientific and medical knowledge as symbolized by the Pasteurization process. In the end, the metaphysical implications of the spontaneous generation debate were peripheral to direct experiment and observation necessary to settle scientific questions.
Because of the falsification of spontaneous generation, the germ theory of disease moved forward and so did medical science as a result. The philosophy of Haeckel didn’t prevail and medical science moved forward, even though, by Haeckel’s own admission, the falsification of spontaneous generation raises the specter of a highly improbable and atypical set of circumstances that led to the emergence of life. Years later, these sets of events were deemed so unlikely that they were said to be “almost a miracle” (to quote Francis Crick).
In the present day, the possibility of large amounts of biochemical function in the genome is drawing a reaction reminiscent of Haeckel’s words. This possibility has been most prominently associated with the work of the NIH ENCDOE project and its follow-on projects RoadmapEpigenomics and possibly E4 (Enabling Exploration of the Eukaryotic Epitranscriptome). From publicly available sources, I estimate the sum investment by the NIH could approach almost 800 million dollars, and there could easily be follow on projects.
But Dan Graur protested, “If ENCODE is right, evolution is wrong.”
No one knows the figure of what percentage of the genome is actually functional. Even if the genome is not as functional as some ENCODE researchers suggest, until we actually know which parts are and which parts aren’t functional, as a working hypothesis, much like searching for a missing person, we have to assume any place we look could bring us closer to finding what we seek. So even if ENCODE’s promoters are ultimately wrong, how can it be damaging to science at this stage of the game if we assume high functionality as a possibility? As a matter of investigative procedure, a medical researcher has to at least assume the stretch of DNA he may be studying may have significance until proven otherwise or until we heal every disease on the planet.
Some argue, “well all that ENCDOE money could be spent elsewhere.” Like where? Cancer researchers and researchers of autoimmune disease want to have data on biochemical activity in cells — even if the activity is not immediately indicative of function, it may be a good diagnostic. That data is provided in painstaking detail by ENCODE and RoadmapEpigenomics. Here is a sample of data cancer researchers use from ENCODE:
This quote from the above University of California website must get under Graur’s skin 🙂
The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.
The parts list is not completely known. ENCODE data provides hints which researchers can pursue and then contribute to defining the parts list. Want to know how researchers use ENCODE data? How about watching some video from this 3 day conference in 2015. The links to the videos are below. You’ll see medical researcher after medical researcher detailing how ENCODE, Roadmap and GWAS data are helping to develop understanding and treatments for various conditions:
https://www.encodeproject.org/tutorials/encode-users-meeting-2015/
One tally of the ENCODE consortium indicated there were 442 researchers spread out in 32 research centers around the world including top names like Harvard, Yale, MIT, Stanford….you get the picture. Yet it didn’t stop Graur from calling them “ignoramuses”.
My point of contention with Graur? He’s being presumptuous, he could be wrong, and he’s advocating an approach that is not helpful to advancing medical science. Not to mention his style is more becoming of a professional troll than a serious researcher.
I provide some quotes in his own words. And disturbing to me personally is that his anti-ENCODE crusade (not at all based on biochemical experiments) didn’t stop him from getting elected as a fellow of the AAAS recently.
And now, as promised, quotes from Gruar himself.
Ewan Birney, the person most responsible for the ENCODE fiasco
…
he became the scientific equivalent of Saddam Hussein.http://judgestarling.tumblr.com/page/56
http://judgestarling.tumblr.com/page/38
and
the evolution-free philosophy of ENCODE has not started in 2012. The only difference is that Friedrich Vogel was an honest scientist in a world in which disciplines were rigidly compartmentalized. In comparison, no such excuses exist for ENCODE. My only explanation for their continuing existence is that the wannabe ignoramuses, self-promoting bureaucrats, and ol’ fashion crooks of ENCODE are protected from criticism and penalties for cheating by the person who gives them the money. Thus, they can continue to take as much money from the public as their pockets would hold, and in return they will continue to produce large piles of excrement that are hungrily consumed by gullible journalists who double as Science editors.
http://judgestarling.tumblr.com/page/64
I visit the NIH once or twice a week to learn and report about what is going on there. Many of the researchers of non-coding RNA care deeply about their work in alleviating human suffering. I mingled with a lot of ENOCDE researchers in 2015 at the conference. The medical doctors and medical researchers among them especially care deeply about their work, some working at hospitals for decades. I take offense at Graur calling them “wannabe ignoramuses” and “old fashioned crooks”.
Graur at a talk at the Society for Molecular Biology and Evolution did this:
Toward the end of the presentation, he [Graur] showed a photograph of dollar bills taped together in the shape of a toilet paper roll—his view of what ENCODE had achieved with the $288 million spent on the project so far.
http://www.bio.davidson.edu/genomics/309redesigned/papers_current/ethics_2/2014ENCODE_critic.pdf
On his website he has a photo of his granddaughter with an extended middle finger and the caption:
My granddaughter, Lilla Keshet Graur, gives ENCODE the finger (2013)
http://nsmn1.uh.edu/dgraur/Encode.html
and of an MIT researcher
When Exactly Did @ManolisKellis Become a Crook? …. By late 2012, however, Manolis Kellis was unquestionably one of the main propagandist for that insidious pseudo-science project called ENCODE.
http://judgestarling.tumblr.com/page/79
and finally
I am sick and tired of all the ENCODEites, their apologists, their hired guns, their propagandists, and all the other badly trained technicians who claim that their favorite piece of DNA does not abide by the rules of evolutionary biology.
… If you cannot come with an evolutionary explanation for the evolutionary functionality of your pet molecule, shut up!
To prove that your sequence is functional in a meaningful evolutionary manner, you have show that the sequence is either maintained by purifying selection or by positive selection (or some other type of selection). You cannot base your claims of functionality on performance of a certain biochemical reaction.
http://judgestarling.tumblr.com/page/115
So how does one prove functionality via evidence of natural selection? Suppose one is dealing with an Orphan Gene, or Taxonimically Restricted Gene (TRG) or feature, an autapomorphy or whatever you call it, etc.? In such cases it’s kind of hard to apply evolutionary conservation to infer selection.
Since when should an evolutionary narrative take priority over lab-derived experimental analyses of biochemical activity? Shouldn’t evolutionary theory be constrained by biochemical analysis rather than the reverse? Dan Graur is a poster child for an impractical brand of naturalism that is more driven by ideological prejudice than empirical methods. So what “if ENCODE is right and evolution is wrong”? Is there a problem with that?
Petrushka asked:
my response:
The citation was:
http://www.bio.davidson.edu/genomics/309redesigned/papers_current/ethics_2/2014ENCODE_critic.pdf
How would you prefer I characterize Gruar’s antics?
Would you say that a photo of dollar bills taped to a toilet roll is evidence of Graur’s enthusiasm for how the money was spent? 🙂
My original abstract for AM-NAT 2016. It requires some revision, because the half-billion dollar figure has since been revised thanks to my revisiting the issue at TSZ — the figure is now around 793 million.
Graur undoubtedly thinks the money could have been better spent. Can we say for sure it couldn’t?
stcordova,
You misspelled Paley fyi. Any case, I don’t think there is anything ‘Rube Goldbergesque’ uncovered by ENCODE. There does not appear to be much interaction or complexity in the assays.
Sure, because if you didn’t say exactly that, using exactly those words, you didn’t say it at all, right? Unlike Rumraket, I’m willing to believe that you don’t know you’re doing it, but neither quote below makes sense unless that’s what you meant. You are equating “non-coding” with “stuff Dan Graur and Larry Moran think is junk”.
and
I would say that Graur is pissed that so much money resulted in a badly worded press release that will cause trouble for biology teachers for decades to come. I will take endless hours of otherwise unnecessary time to undo what appears to be a self serving press release.
Your claim that without this incredibly distorted view of genomics, children will die, is beyond ludicrous. It is insane.
Thanks for the correction Allan.
Actually the 5C and ChiA-PET assays and Histone’s related to enhancers imho are indicative of Rube Goldbergesque design because they are related to enhancer activity. Enhancers for one gene located on another gene are very Rube Goldbergesque.
Super enhancers that act between chromosomes are even more amazing.
Thanks though for that criticism. I take your comments in consideration more than from others.
ROFLMAO
Your comment, Sal, stated:
Anyone reading this paragraph is forced, per site rules, to conclude that the author does not understand what GWAS show.
The fact that you used the term in your OP does not demonstrate that you understand GWAS. All of your posting here indicates that you do not.
If you wish to maintain that you do, in fact, understand GWAS, then we should continue this conversation on Noyau.
😉
stcordova,
Yes, but I don’t think ENCODE uncovered anything unknown in the way of regulatory mechanism. It targeted sites for further investigation. Something novel might come out of it (probably will) but I don’t think it has yet.
I don’t. Where do I “seem” to do this?
My answer to the OOL question is “I don’t know how life originated”. There does not exist a statement by me in contradiction to this anywhere, because I have never expressed or held a different view.
I’m not the one with a dilemma.
This is straight up ridiculous. The entire genome has to be wrapped up to protect it whether it is mostly junk or not. You can’t have large swathes of the genome unwrapped just because it might not contain actual functional sequence, because then it’d be highly vulnerable to becoming damaged, it might even break apart, and then you run into a huge problem come cell-division time.
Think Sal, THINK.
Where are “all those” detractors anyway? So far the only one implicated in such a view is Dan Graur.
There’s a curious bait-and-switch at work here. You somehow want to implicate the entire evolutionary biology community with the hyperbolic blatherings of Dan Graur.
As if that one man and his blog represents a giant monolithic community of ENCODE-despising biologists who are purportedly actively trying to have it shut down.
I think Dan has a habit of saying outrageous and exaggerated things. Here’s more fodder for your pea-shooter Sal:
I don’t know about you, but I actually don’t believe Dan is really advocating executions. I could be wrong. How about you Sal, do you believe Dan Graur really wants to gun-murder authors that get the definition of junk-DNA wrong? If so I think you should contact the FBI.
I think everybody who uses hyperbole should be horsewhipped. Then dragged through the streets by the dragoons. I mean it. Literally. I am not a man to be trifled with.
Hyperbole will be the end of the world. It is the greatest evil one can even imagine.
Really?
I mentioned in July 2015:
So I even spelled out in 2015 what the acronym GWAS stands for and related it to the ENCODE 2015 conference.
Compare what I said:
Gee, GWAS helps find genetic variation that contribute to disease! Lots of the genetic variation is in the non-coding regions.
DNA_jock is just grasping at straws.
Yeah, I’m used to usual litany “Sal doesn’t understand.” But I know that’s just mostly a reflexive assertion whether true or not, and I know DNA_jock is just making this up because I’m making the grade at NIH grad school. So if researchers at NIH say I make the grade on a topic, then I understand.
Large segments of the genome may be subject to sequence constraint in order to make them more pliable to wrap around nucleosomes.
There is a chance that a larger fraction of the genome is under constraint than what Muller’s limit (1 mutation per individual per gnerations) would allow.
But even beyond that, if we accept Larry Moran’s 10% genome functional figure, that would imply on the order of 10 mutations per individual that creates a mutation load, a figure 10 times more than the limits articulated by Muller, Graur and even Moran himself!
Don’t you guys see even by their own criteria (much less ENCODE’s figures), they’ve falsified their own claims.
One could say,
“If Moran is right (10% functional), then evolution is wrong.”
Didn’t any one catch that Moran’s own estimate would also be beyond what Graur says is tolerable?
For around 10 mutations per generation
U = 10
therefore each couple needs to bear on the order of
1 out of 22,000 kids just to have one that is mutation free.
See the formula at the bottom:
Graur using similar calculation with ENCODE’s data:
Granted the result using Moran’s figure is smaller than the 7 buzzilion that would result from ENCODE’s figure, but 22,000 kids per couple is still pretty big.
Anyway, regarding the necessity of constraint a large fraction of the genome DNA sequences:
and
stcordova,
It seems unlikely to me that this periodicity has much to do with nucleosome formation, since the same paper says that E. coli shows the same periodicity, and that the effect in vivo largely disappears. Thoughts?
stcordova,
Can you give an example of a ‘pliable sequence’ and a ‘stiff sequence’, and an estimate of the respective distributions of these two categories in the genome?
stcordova,
So you’re saying Moran should revise his estimate downwards …
TBH though, naive mutation load calculations are not very conclusive IMO. One needs an assessment of mutation rate per selection coefficient (dividing the continuum into bins), and some account of the effect of selection against, which is of course proportional to that selection coefficient.
As far as histones keeping DNA safe and happy, it’s not just to provide a place for the DNA to wind, the histone modifications help coordinate DNA repair when it is damaged. What was that I said again about histones providing RAM? The RAM helps keep track of things during a repair cycle (which can take a few hours). There are papers also out there that indicate histone modifications help recruit the repair machinery!
And there is another thing. Given that chromatin remodelling seems essential for DNA repair for DNA that is wrapped around histones, how could DNA repair be effected without the histone modification coding and machinery in place when a prokaryote (or some eukaryotic ancestor lacking histones) came to be?
As I said, Universal Common Ancestry theory says it doesn’t need miracles because we have all those phylogenies that supposedly prove no miracles are needed to make UCA true. But mechanical considerations like Chromatin Remodelling make a mockery of such lines of reasoning where “phylogeny resolves all mechanical problems in evolution of interdependent complex systems”.
So histones keep DNA safe and happy as Saddam Hussein, ahem, I mean, Ewan Birney said — but it does so in more ways than just winding the DNA around the histones. Those RAM modifications have a lot to do with it.
Did Larry even consider the metabolic load imposed by junk DNA that needs to be reparied when he was saying that gene duplication or repeats don’t have much metabolic cost?
Oh, by the way, regarding epigenetic memory, yet another citation:
http://www.ncbi.nlm.nih.gov/pubmed/17185323
The explanation of the diagram below comes from:
http://www.cell.com/trends/cell-biology/fulltext/S0962-8924%2814%2900120-2
http://www.cell.com/cms/attachment/2019722595/2039716301/gr2.jpg
And yet prokaryotes accomplish DNA repair without histones. Which, according to your logic, is obviously impossible.
So you’re telling us that bumblebees cannot, in fact, fly? Perhaps there’s something wrong with your premise?
BTW, your polycomb/trithorax example is another example of “memory preservation” through mitosis, not gametogenesis. Do you understand the difference?
No, I didn’t say that. As usual you’ll knock down an argument I didn’t make.
If there are histones and DNA wraps around them, there needs to be chromatin remodeling to facilitate DNA repair.
Gee, DNA_jock, grasping at straws again by making up arguments I didn’t make and then knocking the straws down.
I first encountered Sal many years ago on a now defunct discussion forum.
He was trying to make people believe that molecular phylogenetics is all wrong and cannot possibly provide any sort of support for evolution. He set out to prove his point by taking a series of 8 letters, allow 1 ‘mutation’ per iteration, and showing that after a mere 8 replications, all of the letters were different! Thus, molecular phylogenetics disproved! Thus evolution is a lie!
Ever since then, I take anything Cordova writes on any subject with a grain of salt and a dose of disdain, for he seems to employ that same sort of “logic” in everything he does.
On the positive side, Sal is the only creationist/IDist I’ve seen back away from an unsupportable claim.
At his current rate of learning, I figure he will accept evolution and Old Earth in about 600 years.
But that’s better and faster than anyone else in the ID movement.
Is accepting evolution anything like accepting Jesus?
Nothing at all.
So it won’t help make me more like keiths?
Can’t improve on identity.
Identity