Pellionisz Google Tech presentation.

Those of you who read this blog or others that discuss non-coding DNA will, for better or worse, be familiar with regular commenter Andras Pellionisz. Whether he has managed to convince anyone of his views on non-coding DNA is something readers should judge for themselves. Thus, here are links to his website, a recent article, and a recent Google Tech presentation.

www.junkdna.com (home of the “avant-garde society that formally abandoned ‘junk DNA'”)

Pellionisz, A. 2008. The principle of recursive genome function. Cerebellum 7: 348-359.


10 comments to Pellionisz Google Tech presentation.

  • Andras

    It speaks highly of scientist Dr. Gregory to kindly bring my peer-reviewed science publication, within five months of its appearance, “The Principle of Recursive Genome Function”; to the attention of all (free full text is available here). “All” includes those I classified in my comment here as stuck in “Stage I” (ignorance), probing “Stage K” (knowledge) and going for the higher goal of “Stage U” (understanding, in terms of algorithmic i.e. software-enabling manner), how directly protein-coding and non-genic vast majority of human DNA may function in a concerted fashion. (Who would sort the greatest pieces of music according to what percentage of the instruments were playing at certain times, or on average?)

    While we agreed that the advancement of science, under normal circumstances, is not a matter of scientist- and in some other cases impossible-to-scientifically-argue-with bloggers (rather, dead horse floggers) to decide, I am also grateful for Dr. Gregory’s pointer of my Google Tech Talk on YouTube. I am convinced over just one week’s time, that such wider perspective is very constructive.

    My only reservations about his great entry, if any, are the following:

    a) His pedantry as of yesterday, how instead of “Mr. Gregory” the appropriate way to address him is “Dr. Gregory” should perhaps been also applied today, in his own posting on me. At long last, he could rectify, rather than still parrot, a “name calling” that is much more derogatory than what he lamented. Name calling is tolerated from those habitually disregarding courtesy (say, some children with sub-sophisticated manners). Or – as in my case used to be – when someone’s solid information-theoretical work could not be accepted as long as the establishment was mistaken, as novelty ran dead-against not one, but two prevailing and now patently false dogmas. My stealth-work was conducted mostly in the “wilderness” precisely because of a keen awareness that it was prone to be targeted for superficial/careless mud-slinging.

    It is more pleasing to note that in another blog it is now recognized that what used to be my “lucid heresy” now turns out to be the only algorithmic approach to DNA, which e.g. can explain non-genic yet “ultraconserved elements” (and even his own “Onion test” – though it is only obvious for mathematically and software-savvy experts such as at Google that iterative recursion, say their PageRanking, in some cases converges to much higher peaks than usual. For the mathematically savvy, the web is known to be fractal, and such recursive surges are called “The Slashdot Effect” – explained in others’ research publication that I featured in my YouTube).

    Much more importantly for Genome Informatics (both Theory and Technology) my approach can point out where to look for genomic glitches (e.g. as fractal defects in the now rapidly more affordably available full human DNA sequences).

    b) Dr. Gregory is twice mistaken that my point is that “all non-coding DNA is functional”. I am on record having repeated (maybe not in sufficient number of recursions :-) that it is a “non-issue” exactly what percentage of formerly “Junk” DNA is “anything, but Junk”. What matters for those still dying of genome regulatory diseases is to reach an understanding (beyond ignorance and sheer knowledge) of genome regulation, that is now universally accepted to involve formerly discarded “Junk” regions of the DNA. His second mistake is to overlook my real and quite different point, that beyond reversing both mistaken dogmas I actually provided in my science paper a theoretically sound principle that surpasses mistaken dogmas.

    I invite all to elevate discourse from name calling to real scientific debate – preferably not about “non-issues” and not necessarily fixated on blogs, but perhaps on accepted science platforms but e.g. publishing in peer-reviewed science journals where anybody is welcome to submit alternative (mathematical) Principles of Genome Function. As I demonstrated (most recently with my Google Tech Talk), I am not shying away from explaining my information-theoretical insights and their information-technological realization, upon invitation.

    Moreover, I am happy to celebrate my birthday today with the pleasant note that such enlightened discourse is rapidly converging to large-scale applications help those dying because, suffering from, or fearfully anticipating becoming patients at any time of formerly “Junk DNA diseases”.

    pellionisz_at_junkdna.com

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  • Doppelganger

    Ah, junk DNA diseases – all the fault fo the evil darwinist conspiracy and orthodoxy, bent on suppressing the amazing Dr. Pellionisz and his associates, who are, sadly, only a few decades behind the times and a few lurid tales of suppression short of the truth…
    You’ve seen it before, and blown it off, but it certainly demonstrates, along with myriad other papers on junk DNA that came out well before Simon’s tales of suppression arose, that the claims of junk DNA being ignored by the orthodoxy are just made up:

    Cell. 1975
    Feb;4(2):107-11.

    The general affinity of lac repressor for E. coli DNA: implications for gene regulation in procaryotes and eucaryotes.

    By equilibrium competition experiments, the dissociation constant (K(RD)) of lac repressor for E. coli DNA carrying a deletion of the lac operon was measured at a variety of salt concentrations. These data are used in the consideration of several aspects of protein-DNA interaction: Quantitative estimates of specificity are made. Specificity changes only slightly with salt concentration. We calculate that in vivo, 98 percent or more of repressor is bound to DNA predominately at sites other than the lac operator. Inducers shift repressor from operator to nonoperator DNA, but do not free it from DNA. The general affinity of repressor for E. coli DNA is sufficient to support a model where repressor slides along DNA for significant distances. The effective dissociation constant of repressor for operator (K(eff)) is very sensitive to the total DNA concentration. We propose that “junk” DNA in eucaryotes functions to maintain total DNA at an optimum concentration. We consider the lac operon in the nucleus of a lymphocyte, point out that severe difficulties would be encountered, and suggest possible solutions.

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  • Philip Haynes

    Please excuse my naive question – my field is distributed computing. But I am intrigued. It appears in min 33:30 of the presentation Dr Pellionisz states that serial a view of the DNA + RNA => Protein algorithm breaks the 2nd Law of Thermodynamics and that a recursive algorithm solves this lemma.

    Have I understood the point? If so, how well acknowledged in the literature is this (apparently quite significant) claim?

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  • Andras

    Philip,

    The new claim is indeed significant that the Principle of Recursive Genome Function by means of recursion from proteins to DNA (for more than half a Century a dogma maintaining that such “never happens”, a groundless dogma that prevailed against scores of evidence against it), invalidates the general assumption that the hereditary system is closed, i.e. that the 2nd Law of Thermodynamics through the entropy-increase dooms the system.

    The novelty and potential significance of this claim (that the system is not a priori doomed) has escaped the attention of bloggers here, I believe for two substantial reasons.

    One is that thermodynamics and similar disciplines of hard sciences are at a very early stage penetrating the very young science of biology (physics is over two Millennia old, while biology is much less mature with its 231 years of its history).

    The other reason may be that most Old School scientists of 100+ year old Genetics, lacking an interdisciplinary training, (mistakenly) perceive a threat in anything they don’t understand – even if it has the potential of saving their life.

    Hopefully, with the help of you and others who immediately grasp the significance of the Principle of Recursive Genome Function, the lemma will be both theoretically and (by means data by leading scientists who already expressed their interest testing experimental predictions) will be rapidly proven both theoretically and experimentally.

    Meanwhile, the Principle provides a “Circle of Hope” that no genome glitches doom anybody by the sheer predestination of inescapable entropy-increase.

    Pellionisz_at_junkdna.com

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  • Philip Haynes

    Dear Dr Pellionisz,

    Perhaps it is the old chemist in me. I am interested in the science, rather than examples of Kuhn scientific revolutions.

    As context to my question, I recently did a survey into the thermodynamics of information systems as applied to software systems development. It turned out to make any definitive statement appeared to be distinctly non-trivial, requiring a career (or two) to make significant progress on the matter.

    Thus my understanding from your comments, two hypotheses are made:

    a) A linear model of Protein production from DNA/RNA is not possible due to the second law of thermodynamics as it is a closed system.
    b) Protein synthesis works via a recursive algorithm.

    I also take it from your comments that the work to spell out the detailed thermodynamic argument, supported by experiement and have it generally accepted in the literature is yet to be done.

    Have I got the exact status correct?

    Your clarification would be much appreciated.

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  • Andras

    Philip, my statement is definitely not your (a), since the linear model of protein synthesis from DNA to RNA to PROTEIN is a well-established fact. (But sticking with “half the story” would have us left with a “Closed System”). My lemma is your (b) that “protein synthesis works via a recursive”…- I would rather say biological process, governed by an intrinsic – “algorithm”. As for Genomic Entropy, I tend to agree with you that this field is currently underdeveloped. There are essentially two reasons for the early stage; one is that biology (including genomics) is yet to be fully penetrated by exact sciences, and the other reason is a violent over-reaction from old-fashioned (though sometimes quite young) biologists who lack training in interdisciplinary sciences. To avoid taking the issue personally, I could mention that the very scholarly mathematical approach of the Princeton-group (with Dr. Herschel Rabitz, a Harvard Ph.D. having published 400+ science papers) is dismissed as “mathemagics” by some who are not even interested (!) in following math (thus, even less inclined to understand software development). Pellionisz_at_junkdna.com

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  • Doppelganger

    “Dr. Herschel Rabitz, a Harvard Ph.D. having published 400+ science papers”

    I am always a bit leary of claims like this. 400 papers?
    Actually, his Princeton website says he has 730. I mean, seriously…

    He earned a PhD in chemistry in 1970.

    38 years. That is 19 papers a year. About a paper every every 2 and a half weeks.

    Raise your hand if you think that is even possible….

    These courtesy authorships are embarrassing.

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  • Andras

    The Structure of Genome Revolution

    This blog appears to be the second that has reached the “crisis” stage – so brilliantly described by Thomas Kuhn in his “The Structure of Scientific Revolutions” (1962). As Genomics became Informatics, the acid test is mathematics, if one can go with the present paradigm-shift or become a hold-out for obsolete dogma.

    For both “Genomicron” and “Sandwalk” to cross the Rubicon of mathematical abstraction appears to remain a challenge. Sandwalk owner says on his video that her daughter finds him “stupid” in exact sciences, while owner of this blog is expressly uninterested in “methamagics” of a superbly accomplished Harvard Ph.D. with 730 paper published. For Doppelganger even the concept of having 730 papers is incredulous.

    Obviously, neither of Doppelganger’s Janus ears have heard of mathematician genius Paul Erdos, with over 1,550 publications! Of course, in mathematics an idea (conjecture, lemma, theorem) can be a paper; may be a matter of minutes to write up the equations (proofs often take much longer; some theorems go hundreds of years unproven):

    “…Erdos decided for once to ride the train. As luck would have it he found himself seated next to a stunningly beautiful young woman. The two struck up a conversation, and one thing led to another. By the time the train was pulling into Penn Station, they had written a joint paper…” (The mathematical journeys of Paul Erdos, by Schecter, Touchstone 1998).

    There is a well-justified envy towards mathematics by “biologists” overly narrowly defined as experimentalists. Experiments are usually expensive, take much preparation and time, the process is intensely regulated (occasionally forbidden!) and typically result in data only – often with no advancement in understanding.

    Kuhn’s fundamental thesis is precisely that knowledge does not automatically transform into understanding. Rather, a knowledge-steamroller (“sprint for genes”) may often trample advancement, and a revolution is needed to re-interpret discarded data (“junk DNA”). Or, as Neurophilosopher Pat Churchland wrote: science every once in a while needs a “Galilean trio of revolution: simplification, unification, and above all, mathematization”.

    Francis Collins (mastermind of ENCODE) clearly expressed upon publication in 30 journal-articles of results (June 14, 2007), that “The scientific community will have to re-think long-held beliefs”. He knows best how painful is not only to re-think “beliefs” (axioms and dogma, rather), but also to re-structure the establishment of experimentation – yet he had to say what he did say. As for Doppelganger’s dismissal that “Collins does not mandate”, she/he is right, since as of today Dr. Collins is not at the NIH. However, the US Government does mandate. And once US taxpayers paid ~ $100 M for the ENCODE-1 study that reached a scientific consensus (i.e. that “Junk DNA is anything, but”) – angry US patients mortally sick with “Junk DNA diseases” could indeed win even legal battle against those accepting US government funds for their work, and continue to overlook “Junk DNA”.

    Like it or not, the “Genomics became Informatics” paradigm-shift will prevail. Mathematics intrinsic to genome function might (re)call for quantum mechanics, fractals, chaos (etc). Indeed, the Second Law of Thermodynamics will be a life-or-death issue in prevention.

    Again, as Kuhn wrote: “Rather than a single group conversion, what occurs is an increasing shift in the distribution of professional allegiances. At the start a new candidate for paradigm may have few supporters, and on occasions the supporters’ motives may be suspect. … they will improve it, explore its possibilities, and show what it would be like to belong to the community guided by it. .. Gradually the number of experiments, instruments, articles and books based upon the paradigm will multiply. Still more men, convinced of the new view’s fruitfulness, will adopt the new mode of practicing normal science, until at last only a few elderly hold-outs remain”… the man who continues to resist after his whole profession has been converted has ipso facto ceased to be a scientist…” .

    Thus, the easiest and most elegant turn-around, that also provides an alibi, muting any chance of “negligence” charges, is Membership in the now broadly featuredInternational HoloGenomics Society.

    pellionisz_at_junkdna.com

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  • For more recent dissemination of evidence, please add <a href=http://www.junkdna.com/youtube>YouTube-s</a> and presentation (without opposition) at Personal Genomes conference in<a href=”http://www.junkdna.com/pellionisz_csh.html”>¬†Cold Spring Harbor</a>.

    For independent evidence for the Fractal Genome, see Oct. 10 cover issue of Science by Eric Lander (Science Adviser to President of USA and Director of the Broad Institute) et al, October 9, 2009

    Pellionisz_at_junkdna.co

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  • Only took a single decade since my FractoGene (2002) for the fractal approach to be supported by at least three top-notch independent experimental pieces of Proof of Concept that fractal defects cause hereditary diseases, most notably cancer; (see <a href=”http://www.junkdna.com/hologenomics_history.html#fractogene_poc”>write-up</a> with a clickable “timeline” citing 32 significant entries and listing at least 150 devoted workers). The revolution of a geometrical unification of neuroscience and genomics had to sustain damages, yet could only be delayed a couple of years, while it unlocked half-a-Century of delay.

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