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Tuesday, February 17, 2009

Junk DNA Is "Dead as a doornail"?

I just received an email message from András Pellionisz informing me that in America the concept of junk DNA is "dead as a doornail." He "proves" his case in an article on his website [HoloGenomics].
A Eureka Moment concerning the fractal character of neurons led in turn to a novel picture of genomics where protein structures act back recursively upon their DNA code -- in outright contradiction to prevailing orthodoxy. A household name in neuroscience for his tensor network theory, Dr. András Pellionisz has recently had another far-reaching discovery borne out. This insight has now received striking confirmation in stunning results from the new field of epigenetics -- promising a whole raft of novel medical diagnoses and therapies.

Sunnyvale, Calif. (PRWEB) July 16, 2008 -- A landmark article on "The Principle of Recursive Genome Function" (received December 7, accepted December 18, 2007) by András J. Pellionisz appears online in Springer's e-Journal Cerebellum.

The paper marks the first anniversary of an historic event--the release of pilot results for ENCODE, the Encyclopedia of DNA Elements project. Building on the results of the Human Genome Project, the ENCODE effort revealed a far more complex DNA coding sequence than was ever previously imagined. "There's a lot more going on than we thought," said Collins, who was director of the National Human Genome Research Institute (NHGRI). Dr. Collins issued a mandate a year ago "the scientific community will need to rethink some long-held views".

A happy few did not need to rethink either the "central dogma of molecular biology" (Crick, 1956) or the misnomer of "junk" DNA (Ohno 1972), since they never believed them in the first place. The dictum claiming that a flow of information from proteins back to DNA "never happens" or the idea that 98.7% of the human genome should be disregarded as junk was never very believable.

Genomes & Junk DNA
There are some interesting scientific debates about the role of noncoding DNA in large genomes. Much of it is junk but there's lot of other functions that we've known about for decades. Many respectable scientists dispute the notion that most of our genome is junk.

Unfortunately, very little of that interesting scientific debate can be seen on András Pellionisz's website. Instead, I direct you to the site in order to see a classic example of a modern kook in action. The site has all of the characteristics of kookdom (see crank) and serves as a self-evident answer to the question Is András Pellionisz a Kook?.


  1. received December 7, accepted December 18, 2007

    That's some turnaround time!

  2. Yeah, Pellionisz is a crank, at least on this issue, who has been kicking around for a few years on various blogs. Unfortunately he's a crank who some people don't recognize as a crank maybe because they've heard so much fluff about how all this noncoding DNA is clearly functional, yadda yadda.

    ...aaaaaannnnnddd here's the guy's article in _Cerebellum_:
    Cerebellum. 2008;7(3):348-59.

    The principle of recursive genome function.

    Pellionisz AJ.

    HelixoMetry, HQ, 935 Rosette Court, Sunnyvale, CA 94086, USA.

    Responding to an open request, the principle of recursive genome function (PRGF) is put forward, effectively reversing two axioms of genomics as we used to know it, prior to the Encyclopedia of DNA Elements Project (ENCODE). The PRGF is based on the reversal of the interlocking but demonstrably invalid central dogma and "Junk DNA" conjectures that slowed down the advance of sound theory of genome function, as far as information science is concerned, for half a century. PRGF illustrates the utility of the class of recursive algorithms as the intrinsic mathematics of post-ENCODE genomics. A specific recursive algorithmic approach to PRGF governing the growth of the Purkinje neuron is sketched, building the structure in a hierarchical manner, starting from primary genomic information packets and in each recursion using auxiliary genomic information packets, cancelled upon perusal. The predictive power of the principle and its experimental support are indicated. It is argued that genomics is no longer an exceptional instance of the applicability of recursion throughout the sciences.

    Wow, the guy turned over the Central Dogma! Just by thinking about it!

    Have a look at his other articles on Pubmed: the recent ones are 2 in Cerebellum, 2 in Bioinformation; but apparently the latter have a whole pile of coauthors, with Pellionisz last; but when you look at them, there is a bunch more random junk about The Pellionisz Principle etc. -- I wonder if he mostly wrote these articles too.

    This follows a more general pattern I've noticed lately for getting really silly stuff published:

    1. Find a relatively unknown new journal, perhaps it is hard up for submissions

    2. Write about something barely related to the topic

    3. Write whatever you want and they will publish it if it has some complex terminology and references, even if it claims the overthrown of all biology or says that mitochondria are divine or whatever.

    I could probably pull up 20 cases from my files, maybe there should be article written exposing this pattern?

  3. That paper is incoherent, and Pellionisz seems to be little more than a self-promoter. It annoys the crap out of me how he simply engages in revisionist history regardign 'junkDNA' - I've emailed him citations in the past proving that function in 'junkDNA' was not only hypothesized and speculated about well before his business partner Simons 'dared' to publish a paper on it in 1989 (the earliest paper of Simons' that I could find that had anything to do with DNA at all), but functions had been IDENTIFIED as early as 1975! He replied by simply claiming that the truth hasd been suppressed blah blah blah.

    Yeah, he's a crank.
    But watch out - he might threaten legal action.

    That is what cranks do when their antics are exposed. I believe John Woodmorrappe pulled thew same 'threat' a few years ago.

    But I do wonder why he sent an email to Larry - he referred to him as 'that Canadian moron' on the CARM discussion board...

  4. Morons who make a virtue out of ignorance may inadvertently play useful roles. When filing for IP protection, a necessary condition is to document the non-obviousness of an invention. Even an obscure "Canadian professor" comes in very handy with his wow of disbelief - the more visibility he cranks up, the better. Nobody will ask about his scientific accomplishments, if any. Suffices for non-obviousness that a country still pays him a tenured salary by their taxpayers. Neglecting to keep up with the advancement of science (see below), of course, may help explain why the Canadian system is so close to pulling the plug on them.

    All it took was a simple friendly letter, and Larry's knee jerk kicked, widely disseminated a dated manifesto that he is full of junk (see his DNA). His cohorts help verify that, unfortunately for Canadian taxpayers, he is not a fabrication.

    Thank you all - who can be identified. Regretfully, entries from anonymous "Doppelgangers", emotionally troubled "bored housewives", are trashed unread. It speaks highly of another Canadian blogger, who perhaps looking further ahead into a possible (?) science career in Canada, already decided to rid his budding reputation of anonymous name-callers masquerading uncontrolled on his blog.

    In my few friendly words in a letter to Larry Moran, whose habits include misquoting sources, I pointed out that these days in the USA (not in "America" as he sloppily downgraded one greatly different Country of the Northern part of the Continent) Eric Lander was freshly appointed to the US Presidents' Science Advisory Board. Thus, it has gotten very hard finding anyone remotely claimed to be a scientist who would still subscribe to the absurdity that the human DNA is mostly functionless "junk". That follows the turnaround of Francis Collins last summer, by his saying on the web that "nobody talks about 'junk' any more". The obstacle is not so much Eric's Office - but more the fact that his group has published two weeks ago a major article in Nature; showing a new huge batch of over 1,600 large intergenic transcripts, highy conserved large non-coding RNAs (lincRNA-s) in mammals: .

    "In sharp contrast to previous collections, these large intervening non-coding RNAs (lincRNAs) show strong purifying selection in their genomic loci, exonic sequences and promoter regions, with greater than 95% showing clear evolutionary conservation. We also developed a functional genomics approach that assigns putative functions to each lincRNA, demonstrating a diverse range of roles for lincRNAs in processes from embryonic stem cell pluripotency to cell proliferation."

    Larry conducted a survey in his blog about a year ago (still there, on the extreme left margin, please scroll down) deeply bothering him and his handful of hold-outs that about half of his own readers deem only about half of the DNA "dismissible" (with the other half obviously not "junk" according to half of his readers). The new finding by Lander et al. could not be included in that survey, since the finding is brand new (published online February 1, 2009) - and thus tilts the balance even higher from Larry's 46% that he was forced to admit already, over a year ago . (That admission did not include ultraconserved elements, copy number variations, etc., etc). It would be good if Larry at least followed-up on his own tally - even though he ignores others'.

    Based on what Larry says in his YouTube about his daughter's opinion on him (at 4:50-5:24) it does not come as a surprise that he can't even cite my paper The Principle of Recursive Genome Function, free full text available.

    Given Larry's admitted inability to grasp abstract mathematical concepts - contrary to my audience at Google (see YouTube) or on the Panel at Churchill Club (see see link to another YouTube on same site), Larry perhaps rightly fears for any new paradigm surpassing the Central Dogma/Junk DNA obsolete axioms, that would call not only for biochemistry (his forte) but also for informatics, with definitions and other annoyances (in which he is apparently clueless).

    Eric Lander's first degree is in mathematics - he has long maintained (as another Canadian blog quoted: "'Rather than the genes, junk DNA is actually the challenge right now,' says Eric Lander of the Massachusetts Institute of Technology, who is himself a prominent Human Genome Project researcher".

    It is rather well accepted by now that the real science today is not some "guessing game" how many percent may or may not be functional - but what are the functional principles of what used to be overlooked for so long, with so many millions dying miserable deaths of "junk DNA diseases"?

    The few hold-out morons are also rather useful to mark today's time, since in the rather near future lots of people are likely to parrot "Oh, we have always known it wasn't junk... Oh, we have always known that the Central Dogma wasn't true... Oh, we have always known that genome function was based on fractal iterative recursion!"

    So why didn't you write the The Principle?

  5. I'm happy to let the words of András Pellionisz serve as evidence that he is a kook.

    But just for the record, in addition to misunderstanding modern studies of the genome and my definition of junk DNA, he also appears to misunderstand my position on The Central Dogma of Molecular Biology.

    I'd also like to note, for the record, that Lander's paper (Guttman et al. 2009) was an attempt to identify functional transcripts among the thousand s that are most likely just "transcriptional noise."

    Using fairly reasonable criteria to separate the wheat from the chaff, the authors ended up with ~1600 RNA-encoding genes that were strong candidates for genes with a biological function.

    The average size of the functional RNA transcripts was ~1500 bp. The total amount of the genome devoted to these potential genes is 0.08% of the genome.

    This isn't a surprise and it isn't going to change our understanding of overall genome organization. Most of the genome is still junk.

  6. I sent a kind private letter to Larry Moran. I notified him of both past and present leaders in the USA now declaring that "junk DNA is anything but"; Francis Collins last summer, and now a member of US President's Science Advisory Committee, Eric Lander.

    Those young Canadian students interested in the merging of genomics, epigenomics and informatics, who actually read Ohno's original 1972 abstract and saw Crick's original 1956 Figure know fully well that their "new ideas" have long passed away.

    Today, there are two questions.

    One is for people how to gracefully let go old dogma even if they have long-time personal investments in them and thus their first reflex is in what weird reincarnation can they try to keep them alive by artificial ventilation.

    The other question is for a new generation of scientists, not yet broken through the bulwark of oppressive hardliners, to find their way to HoloGenomics - even if it takes a healthy dose of informatics.

    As his twisted provocation in public speaks for itself, Larry Moran of Toronto, as a notorious "name caller", is a sad liability towards the quest of understanding genome function to Canadian Universities. This may be a reason why Canadian taxpayers are close to pulling the plug on their questionable "scientists" who are costly to keep, yet cause much public harm by painting a retrograde image of scientists who are immune to advancement of science.

    In passing I mention that in my paper to show what lies beyond for our understanding of the mathematical principles of genome function for those getting over obsolete dogmas of Crick and Ohno, I did not "misinterpret" Moran's science on the Central Dogma, as there was nothing to "misinterpret". I would have gladly discussed his publication (not blogs) among my 93 citations on Central Dogma - if I could find any.

    I am happy to invite all to share the excruciating experience of suffering through Larry's own YouTube to see/hear (if they can, in the cacophony that amounts to a mockery of science videos) how he calls names at US scientist James Watson "damn", "silly", "stupid" - and on his blog even UK scientist Richard Dawkins is called "kookish" for he admitted that "genomics turned informatics".

    For me, it is a privilege to be in the company of Watson and Dawkins. I may not agree with them all the time, but if they are called names like "kook", I am proud to close ranks with my respected colleagues who actually said meaningful messages to history.

    Moran says at 4:52 of his YouTube that his daughter (an astrophysicist) calls her father "stupid" when it comes to exact sciences, calling for mathematics/informatics. In some contrast, I seek the company of those, either at Google Tech Talk or at Churchill Club's Panel who are actually eager to step beyond obsolete dogmas hindering Genomics for over half a Century, and we certainly don't shy away from a science just because it is turning into informatics.

    Thus, it is a privilege for me to distance myself by not sinking to the level of Moran's and his cohorts in their lowly darkness, hallmarked by shady "Doppelgangers"; emotionally disturbed bored housewives of Vancouver, who anonymously but publicly exercise their confessed favorite pastime of "swearing").

    I wish for a better future to Canadian science if and when it could cleanse itself from the root causes of its present malaise.

    Given the sweeping force of "Genome Revolution" I very much doubt that retrograde characters like Larry Moran will long oppress free thinkers at bay. (Yes, Nick, science occasionally calls for "thinking"; "Wow, the guy [Einstein] broke through the limits of Newtonian mechanics, just by thinking about it". I, and hopefully your Ph.D. advisor, would find nothing objectionable about thinking through the sea of data, often by employing the power of mathematics - if one aspires to be a real scientist, not just a worker turning out more and more data till science dies of suffocation).

  7. Since Pellionisz's skill at following links is on par with his skill at doing simple lit reviews re: junk DNA, I submit that theonly 'bored housewife' around is his own.

    It doesn't matter how indignant AP is. It doesn't matter that he got a patent on something irrelevant - look at Ron Popeil.

    What does matter is the shameless self-promotion that this individual engages in, with his unnecessarily verbose, meandering diatribes and irrelevant anecdotes. What does matter is the fact that he continues ot misprepresent the hisrtory of 'junk DNA' to suit his own needs.

    His small legion of hoodwinked followers will discover - too late - that they've been had.

  8. [Clip from another Canadian blog that is more sensitive about the image of Canadian scientists - and is less likely to risk legal action of libel against the blog owner. In a particularly crass case an anonymous slanderer Doppelganger even hides his/her jurisdiction, gender, and science qualifications, if any. No spine to hide - anonymous trash discarded without reading - AJP].

    "I think I will close down the anonymous comments feature. I don't get many comments on the blog in any case, but I find it frustrating when people are not confident enough in their statements to sign them. I also find it is used as an excuse for bombast at the expense of reasonable discussion." - T. Ryan Gregory

  9. There is an option to post anonymously. You clivk on a button that says "anonymous" - I'm sure you've seen it. If you do not click on this button, you have to sign in with your Google/Blogger ID or your you can use your name/url.

    One of the reasons some may choose to be 'anonymous' as in not employing their real names is that maybe they do not want to be hounded by people like you sending them unsolicited emails filled with self-aggrandizement and disinformation.

  10. Annual Check-up

    A year ago someone professed: “Most of the genome is still junk”. It was “Lonely Moron” (this a riposte to a crass name-caller from Canada, with hubris to resort to an attempt to dismiss a University student because of belief system).

    I am parsimonious with my time on L.M. since his (scientist) daughter declared her father as “stupid” – she probably learnt it the hard way. I take her word (quoted by her father) as she had plenty of experience.

    For the annals, this check-up is to see how someone is doing now, who is in opposition not just to his own scientist daughter, but also to the majority of his blog readership, moreover leadership of his country (Canada) and now is in opposition to the President of the USA, giving top praise to Francis Collins’ new book in which he states (pp. 5-6) “if you thought the DNA molecule comprised thousand of genes but far more ‘junk DNA’, think again”. “A certain amount of hubris was required for anyone to call any part of the genome ‘junk’” stated Francis Collins in his earlier book. Apparently, L.M. as someone whose forte is exactly in the hubris department, feels no need to heed Francis Collins.

    The President is to follow in science matters his Science Advisers, Dr. Eric Lander (et al.) who delivered the message on the cover of Science Magazine, Oct. 9., 2009; Mr. President, the DNA is fractal!

    The gist of the paper is (with the famous Hilbert-curve on the cover), that the 2m long DNA “noodle” fits into the 6 micron-radius cell-nucleus by conforming to the “maximal density yet knot-free” fractal folding.

    The single most important lesson of ENCODE (2007) was that “the genome is pervasively transcribed”. Now we learn that mother Nature literally goes into great lengths to fold the entire DNA in a “maximally dense” manner -rather than getting rid of “needless junk”- with some of the ultraconserved elements preserved over hundreds of millions of years. It is only important to be “knot-free” if the DNA is actually transcribed – if not, why the fractal effort to keep “the junk” knot-free?

    Given his daughter’s single-word sentence, I don’t expect L.M. to ever reach an understanding of abstract concepts such as fractals. It would be too late (for him) anyway.

    FractoGene was presented at Cold Spring Harbor last September – without a single word of opposition,

    Oh yes. Yet another Continent that has long disqualified the “Junk DNA misnomer” is Australia. Professor John Mattick (of Sidney) has just gotten one of the most prestigious Australian awards, since “Professor Mattick has pioneered the theory that this ‘junk’ DNA actually specifies a hidden layer of regulatory information … scientific vision is to transform our understanding of human genomic programming..”

    Meanwhile, “ivory tower” empty debates of exactly how many percent of DNA we may not know some function became likewise superseded by utilization, just as the “Flat Earth” gang of backward hold-outs still conducts their useless “debates” – while astronauts visually observe the Globe’s roundness in their time of leisure while assembling space stations, and satellite telecommunication by transmitting stations rotating around the Globe is a business of extreme utility – though it would not be possible on the (flat) grounds.

    The Principle of Recursive Genome Function, wherein information from protein recurses to DNA (to modify e.g. the methylation pattern on the DNA – more in the “non-coding” than “coding” sequences), has been designed and presented to put into automated, practical use for consumers to practice personalized, participatory prevention, see YouTube.

    I regret if I overlooked any relative, person, science group, country, continent, abstract science thinking (etc) that L.M. is at odds. I will make up for them in the next annual check-up (2011).