Some of you may have heard of Andras Pellionisz. He has three Ph.D.s (Computer Engineering, Biology, Physics) and he maintains that much of what we know in biology is wrong. This is especially true of genomes. Whenever you mention junk DNA on a blog, Pellionisz will show up. Same when you mention the Central Dogma of Molecular Biology. He has a blog site that used to be called Junk DNA but it has morphed into HoloGenomicsSome of you may have been wondering if this guy has all his marbles. Fortunately for us, he has published a YouTube video that answers the question. Ryan Gregory found it first but I have to put it here because Pellionisz has been pestering me for years.
Let's play a little game. How many, if any, misconceptions can you identify?
To be fair, I didn't find it. I was invited to the talk at Google but did not attend. The press person he seems to have employed emailed me with the link.
ReplyDeleteHere's a clue from uncommondescent: "11 January 2007
ReplyDeleteDNA researcher, Andras Pellionisz gives favorable review to a shredding of Dawkins and TalkOrigins
scordova
DNA researcher Andras Pellionisz has found unwitting friends in the ID community."
Ungh... Sorry but I don't have the time to watch this stuff. I browsed their website and there's nothing on here that couldn't be addressed in the normal scientific journals. Instead they talk-about required 'paradigm shifts' and so on. Apparently they're having problems shifting those paradigms because there aren't many 1st-world researchers in the club. But this is a good thing I guess:
ReplyDeleteA clear trend is that regions less endowed compared to the USA wish to leapfrog in a paradigm-shift [Hologenomics], by directly jumping into "the PostModern era of Genetics", PostGenetics ("Beyond Genes"). Thus, membership includes even one of the 5 poorest countries in the World.
I'm so glad that science doesn't work that way. I remember reading about how the Soviets had a little trouble with their own paradigm shifts in genetics several decades ago...
listening to this speaker invoked a few university flashbacks of falling asleep to boring lecturers. Sorry but I don't have the patience to listen if the speaker doesn't make it worth my while.
ReplyDeleteKooks are not the only scourge of our times. Indeed I think they produce less harm than cyics that are actuallyt very ifgnorant, and amazingly shallow, acting like "know-it-all" and pontificating about almost anything, most of the time talking out of their asses.
ReplyDeleteIt's another form of intellectual degeneracy, quite common in both rich AND poor countires.
No, he isn't a kook -- you guys are dummies.
ReplyDeleteHis far-sighted work has found vindication in epigenetics, whereas you wouldn't know an original idea if it puked in your shoes.
Why anyone would give a rat's ass what Dawkins thinks (if that is not too strong a word) is beyond me.
This comment has been removed by the author.
ReplyDeleteThe kook and the cynic can meld into each other.
ReplyDeleteFor instance, "quantum consciousness" people can abuse some kind of frivolous physics-worshipping and surround themselves with a patina of avant-garde, while forgetting the value of good old-fashioned neurobiology and neuroanatomy. This is frivolous, not unlike the cynic.
I doubt there will be much progress in the understanding of the variosu attributes we designate through the term "consciousness" without close attention to brain circuitry. I also think comparative, evolutionary neuroanatomy and neurobiology is bound to be very enlightening as to how we obtained our particular human brand of emotion and cognition.
It seems to me that people dealing with "quantum consciousness" do not realize this and are thus profoundly mistaken. They seem to believe some marvelous explanation at the quantum level will allow to bypass this. This "quantum" promise may sounds awful sexy, sciencey and futuristic but is awfully poor in biology and practically barren in terms of expanding our phenomenological comprehension of mechansims underlying cognition.
Similarly, this "Junk DNA is a thing of the past" or "outdated" also seems to me a somewhat close to being cynical. Sure, it is also cynical to say that we have not advanced quite a lot lately in our understanding of how non-coding DNA particpates in different processes. We have, but to say junk DNA is simply "old-fashioned" or "outdated" is also awful shallow and based on frivolity.
Flanagan--
ReplyDeleteHis far-sighted work has found vindication in epigenetics, whereas you wouldn't know an original idea if it puked in your shoes.
OMFG! He discovered histones?? Here I thought they were discovered 125 years ago! My education has been a sham!!
Oh you meant he discovered siRNA? He was cheated out of a share of Fire and Mellos Nobel?
Or you mean he is a blithering old man who finds 'vindication' in other peoples work to make himself feel 'important' and 'revolutionary'?
For Petes sake, in this paper, 'Molecular epigenetics, chromatin, and NeuroAIDS/HIV: Translational implications', he likens himself to McClintock, Baltimore, Temin, and Prusiner. A paper on HIV-1 with only one JOURNAL OF VIROLOGY citation. He has no goddamn idea what he is blithering about, but hes a PARADIGM SHIFTER like Temin *rolleyes*
Its sad. Shame on you for encouraging him.
Well, I emailed him some citations of papers hypothesizing/identifying function in 'junk DNA' dating back to 1975 (in response to his mantra about how Malcom Simons all but discovered junk DNA in 1989 after being 'threatened' professionally for mentioning that he was thinking of looking into the matter), that is proving that he was wrong, and his response was to totally ignore them and prattle on about epigenetics.
ReplyDeleteMy vote:
Kook.
BJ Flanagan rants:
ReplyDelete"No, he isn't a kook -- you guys are dummies.
His far-sighted work has found vindication in epigenetics, whereas you wouldn't know an original idea if it puked in your shoes.
Why anyone would give a rat's ass what Dawkins thinks (if that is not too strong a word) is beyond me."
At first, I thought it a joke.
Pellionisz' "farsighted work" in genetics? Search medlinie and you get zip on relevant issues from him.
But it isn't a joke.
He writes:
"I'm delighted to report that Dr. Andras Pellionisz has recently been recognized for his far-sighted work in genetics."
Who recognized him? The Discovery Institute?
Like I said - kook.
Pellionisz is still banking on his conspiracy mongering - and the crap gets published:
ReplyDelete"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. "
Why don't reviewers maybe use Pubmed whenever they read hyperbolic claims in manuscripts?
"Doppelganger" and his equivalents may win disgrace in anonymous name-calling in blogs of desperate dead horse floggers, but are obviously disqualified from peer-review of published science papers. This blogger recommends unsigned entries trashed before reading in the interest of time.
ReplyDeletePellionisz_at_junkdna.com
lol, he seems to have shown up and attempted to pedantically insult doppelganger. Assuming it's really him, you have to wonder what he hoped to gain...
ReplyDeleteHi Andras the revisionist:
ReplyDelete"Doppelganger" and his equivalents may win disgrace in anonymous name-calling in blogs of desperate dead horse floggers"
Desperate about what?
I am not the one spewing revisionist nonsense to prop up my megalomaniacal fantasies.
Yes, you are flogging a dead horse with your LIES about the 'suppression" of junk DNA research. I proved that long ago, and T Ryan Gregory has amassed a large volume of quotes from research done during the time in which you and your allies have maliciously and falsely claimed 'suppression' on the very subject.
Doubtless, in your quest for fame, you will continue to promulgate these malicious lies.
", but are obviously disqualified from peer-review of published science papers. "
No, I have published a few and have been a reviewer also. Rest assured, your lies about suppression would not have made it past me. I am considering writing a letter to 'Cerebellum' and inquiring as to the stringency of their review prosess, as it clearly lets easily documentable lies into print.
"This blogger recommends unsigned entries trashed before reading in the interest of time."
That blogger fabricates a self-serving revisionist history to prop up his own fantasies.
I wonder if DNA researchers can launch a class action suit against Andras for libel?
LOL!
ReplyDeleteLarry wins +30 internets.
"For instance, 'quantum consciousness' people can abuse some kind of frivolous physics-worshipping and surround themselves with a patina of avant-garde, while forgetting the value of good old-fashioned neurobiology and neuroanatomy. This is frivolous, not unlike the cynic."
ReplyDeleteFunny, I was just thinking "frivolous" and "cynic." You seem to have neglected "ignoramus," however, and so I would remind you of Schiller, who famously observed that, "Against stupidity the gods themselves contend in vain."
"I doubt there will be much progress in the understanding of the variosu attributes we designate through the term 'consciousness' without close attention to brain circuitry."
You may imagine my astonishment on being apprised of this news item. Now, to what elements do you suppose those circuits ultimately reduce? What physical interactions mediate all biochemical processes? O, sure, those would be quantum fields and quantum interactions - but we need not explore that stuff, for we know before the fact that it's all irrelevant. So why bother our heads about it? Why not stick to what we know? That will surely work out in the end -- everybody says so. Besides, quantum theory is hard.
"I also think comparative, evolutionary neuroanatomy and neurobiology is bound to be very enlightening as to how we obtained our particular human brand of emotion and cognition."
No, please, go on -- this is fascinating. So fresh, so insightful!
"It seems to me that people dealing with 'quantum consciousness' do not realize this and are thus profoundly mistaken."
O, gosh -- how could I have thus thoroughly forgotten so many things I learned in grade school?
"They seem to believe some marvelous explanation at the quantum level will allow to bypass this. This 'quantum' promise may sounds awful sexy, sciencey and futuristic but is awfully poor in biology and practically barren in terms of expanding our phenomenological comprehension of mechanisms underlying cognition."
"We are accustomed to regarding as real those sense perceptions which are common to different individuals, and which therefore are, in a measure, impersonal. The natural sciences, and in particular, the most fundamental of them, physics, deal with such sense perception." (Einstein)
Whom to believe? You? Or Einstein? That is a puzzler.
"Take some range of phenomenal qualities. Assume that these qualities can be arranged according to some abstract n-dimensional space, in a way that is faithful to their perceived similarities and degrees of similarity — just as, according to Land, it is possible to arrange the phenomenal colors in his three-dimensional color solid. Then my Russellian proposal is that there exists, within the brain, some physical system, the states of which can be arranged in some n-dimensional state space [...] And the two states are to be equated with each other: the phenomenal qualities are identical with the states of the corresponding physical system." (Lockwood)
"We shall now recall the data of a classical theory as understood by physicists and then reinterpret them in geometrical form. Geometrically or mechanically we can interpret this data as follows. Imagine a structured particle, that is a particle which has a location at a point x of R4 and an internal structure, or set of states, labeled by elements g of G." (Atiyah)
"Bohr suggests that thought involves such small amounts of energy that quantum-theoretical limitations play an essential role in determining its character." (Bohm)
"The solution that appears most plausible to me, and that is consistent with a thoroughgoing naturalism, is an identity theory of the mental and the physical, as follows: Certain neuro-physiological terms denote (refer to) the very same events that are also denoted (referred to) by certain phenomenal terms. The identification of the objects of this twofold reference is of course logically contingent, although it constitutes a very fundamental feature of our world as we have come to conceive it in the modern scientific outlook. Using Frege's distinction between Sinn ('meaning', 'sense', 'intension'), and Bedeutung ('referent', 'denotatum', 'extension'), we may say that neurophysiological terms and the corresponding phenomenal terms, though widely differing in sense ... do have identical referents. I take these referents to be the immediately experienced qualities, or their configurations in the various phenomenal fields." (Feigl)
"The abstract notion of information, as put forward by Claude E. Shannon of MIT, is that a of a set of separate states with a basic structure of similarities and differences between them. We can think of a 10-bit binary code as an information state, for example. Such information can be embodied in the physical world. This happens whenever they correspond to physical states (voltages, say); the differences between them can be transmitted along some pathway, such as a telephone line.
We can also find information embodied in conscious experience. The pattern of color patches in a visual field, for example, can be seen as analogous to that of pixels covering a display screen. Intriguingly, it turns out that we find the same information states embodied in conscious experience and in underlying physical processes in the brain. The three-dimensional encoding of color spaces, for example, suggests that the information state in a color experience correspond directly to an information state in the brain. We might even regard the two states as distinct aspects of a single information state, which is simultaneously embodied in both physical processing and conscious experience." (Chalmers)
"[All] chemical binding is electromagnetic in origin, and so are all phenomena of nerve impulses." (Salam)
"Physicists talk about two kinds of fields: classical fields and quantum fields. Actually, we believe that all fields in nature are quantum fields. A classical field is just a special large-scale manifestation of a quantum field. [...] There is nothing else except these fields: the whole of the material universe is built of them." (Dyson)
"The incorrect perception that the quantum system has only microscopic manifestations considerably confused this subject. As we have seen in preceding sections, manifestation of ordered states is of quantum origin. When we recall that almost all of the macroscopic ordered states are the result of quantum field theory, it seems natural to assume that macroscopic ordered states in biological systems are also created by a similar mechanism." (Umezawa)
"The text of this volume claims that the mathematical formulations that have been developed for quantum mechanics and quantum field theory can go a long way toward describing neural processes due to the functional organization of the cerebral cortex." (Pribram)
"Since matter clearly influences the content of our consciousness, it is natural to assume that the opposite influence also exists, thus demanding the modification of the presently accepted laws of nature which disregard this influence." (Wigner)
"I would like to again impress you with the vast range of phenomena that the theory of quantum electrodynamics describes: It's easier to say it backwards: the theory describes all the phenomena of the physical world except the gravitational effect [...] and radioactive phenomena, which involve nuclei shifting in their energy levels. So if we leave out gravity and radioactivity (more properly, nuclear physics) what have we got left? Gasoline burning in automobiles, foam and bubbles, the hardness of salt or copper, the stiffness of steel. In fact, biologists are trying to interpret as much as they can about life in terms of chemistry, and as I already explained, the theory behind chemistry is quantum electrodynamics." (Feynman)
"For the invisible reality, of which we have small pieces of evidence in both quantum physics and the psychology of the unconscious, a symbolic psychophysical unitary language must ultimately be adequate, and this is the far goal which I actually aspire. I am quite confident that the final objective is the same, independent of whether one starts from the psyche (ideas) or from physis (matter). Therefore,
I consider the old distinction between materialism and idealism as obsolete." (Pauli)
Quote-mining physicists? very impressive, hehe.
ReplyDelete"Now, to what elements do you suppose those circuits ultimately reduce?"
Hehe. So this is where reductionism leads to: quantum conciousness. Take note, Larry (he likes reductionism, too).
"What physical interactions mediate all biochemical processes?"
The same that mediate all non-biological processes. I guess everything has "quantum consciousnes".
Call me when you find a quantum-level physical process is shown to occur exclusively in the brain. Then, I might be interested.
"we know before the fact that it's all irrelevant. So why bother our heads about it? Why not stick to what we know? That will surely work out in the end -- everybody says so"
No, I think there is lots of work to be done at the neurobiologicla level. I think it's juts stupid to try to advance consciousness via quantum mechanics. It's like thinking that we will greatly understand the architecture of a cathedral by looking harder at the bricks, only because "without bricks there would be no cathedral". I can make many different kinds of buildings with the same bricks. Atoms and quantum physics are everywhere. It's not what the specific phenomenon of biology, or consciousness, is about.
"Besides, quantum theory is hard"
You got that right. I'm sure you fully understand it. Hehe
"how could I have thus thoroughly forgotten so many things I learned in grade school?"
Yeah, I'm also sure you know everything there is to know about comparative neurobiology. You learnt it in grade school! So now you can forget all about that dated ole stuff.
As I said, it takes cynism to be a kook.
"We are accustomed to regarding as real those sense perceptions which are common to different individuals, and which therefore are, in a measure, impersonal. The natural sciences, and in particular, the most fundamental of them, physics, deal with such sense perception." (Einstein)
"shrugh" It's obvious you will take einstein over me no matter what we are saying. In any case I like the chap and often agree with him. I do not take that quote to mean neurobiology is unnecessary for understanding consciousness. Do you have something more explicit from Albert in this sense?
Ok Brian. You're funny, haha.
Brian,
ReplyDeleteyou could also have quoted from Erwin Schrödinger (What is life? 1944), that
(according to Wikipedia)
--
"is a non-fiction book on science for the lay reader written by physicist Erwin Schrödinger. One of the discoverers of the structure of DNA, Francis Crick, credited What Is Life? as a theoretical description, before the actual discovery of the structure of DNA (the existence of the molecule had been known for nearly 2 decades, but its role in reproduction and helical shape had not even been guessed at this time), of how genetic storage would work and a source for inspiration for the initial research.
In the book, Schrödinger introduced the idea of an "aperiodic crystal" that contained genetic information in its configuration of covalent chemical bonds. In the 1950s, this idea stimulated enthusiasm for discovering the genetic molecule. In retrospect, it could be seen as having been a well-reasoned theoretical prediction of what biologists should have been looking for during their search for the genetic material.
--
However, for this (very) particular audience, IMHO you should have only quoted from Eugene Wigner who laid down the foundation for the theory of symmetries in quantum mechanics.
And even from his College Course 9 "Reading Materials" only the very first paragraph is digestible for "bored housewifes" (a.k.a. doppelganger et al.:
"THERE IS A story about two friends, who were classmates in high school, talking about their jobs. One of them became a statistician and was working on population trends. He showed a reprint to his former classmate. The reprint started, as usual, with the Gaussian distribution and the statistician explained to his former classmate the meaning of the symbols for the actual population, for the average population, and so on. His classmate was a bit incredulous and was not quite sure whether the statistician was pulling his leg. "How can you know that?" was his query. "And what is this symbol here?" "Oh," said the statistician, "this is pi." "What is that?" "The ratio of the circumference of the circle to its diameter." "Well, now you are pushing your joke too far," said the classmate, "surely the population has nothing to do with the circumference of the circle."
Pellionisz_at_junkdna.com
This is just pitiful...
ReplyDeleteWhen in doubt, play the Galileo gambit! Refuse to confront specific criticism and ignore, ignore, ignore!
My, what a shiny coat you have, so distracting!
These guys like quotes a lot. I think they read mostly reader's digest hehehe
ReplyDeleteIt always sickens me a bit to see mush-headed revisionist megalomaniacs joining with their drooling sycophants to hide behind a facade of gibberish.
ReplyDeleteThe only bored 'housewifes' I suspect are Andras' and Brian's.
Cerebellum will be getting a letter.
Larry gets +40 more internets!
ReplyDeleteLOL!!
let's make a precision, however. Larry tends to talk out of his ass when he criticizes epigenetics and evo-devo, topics on which he clearly does not know enough. It's as easy to be cynic about new fields as it is to be a cynic about old fields. I think larry lets himslef be misled by the fact that some kooks like to hang onto evo-devo or epigentics to promote themselves.
ReplyDeleteOh and Richard Dawkins? He gets kookish, too ("gentics is information").And, a cynic for adaptationism.
I think larry lets himslef be misled by the fact that some kooks like to hang onto evo-devo or epigentics to promote themselves.
ReplyDeleteEpigenetics is a new buzzword that kooks like Pellionisz grab onto to make themselves feel cutting-edge. Epigenetics research is 'sexy' research.
However, I actually *do* epigenetics research, and the more I get into it, the more Im with Larry, who is 'talking out his ass'. Epigenetics isnt any more 'epigenetics' than transcription factors are 'epigenetics'. Modifications are transient. The fun with epigenetics is figuring out what flags a bit of DNA for silencing vs activated-- ie why are ERV LTRs enriched at biotinylated histones, while HIV-1 LTRs are ignored? Can we figure out therapies for forcing the HIV-1 genomes to be silent?
Has buttf*cknothing to do with 'quantum mechanics blah blah blah *GAG*'.
"Epigenetics isnt any more 'epigenetics' than transcription factors are 'epigenetics'. Modifications are transient"
ReplyDeleteNo, modifications are not all transient. You need to read more.
Non-transient, environmentally induced modifications can explain observed cases of "inheritance of acquired traits". Epigenetic markings in the male or female germ line on imprinted genes get through the erasing phase that occurs shortly after fertilization(how else do you think that they affect the phenotype?)
Whenever Larry talks about epigenetics, all he does is whine about the definition of the term as if that invalidated everything. He never mentions that things like non-mendelian patterns of inheritance have been explained by DNA methylation. And of course he knows nothing about the "lamarckian" implications. Only igorance can allow such cynical short-sightedness.
He seems to think everything is in the primary sequence. Much in line unfortunately popular kookish metaphor that a "program" is "encoded" in the primary sequence. Bleagh.
Larrys gets even worse when talking about evo-devo...don't even get me started...Gould would roll in his grave.
"Has buttf*cknothing to do with 'quantum mechanics blah blah blah *GAG*'."
ReplyDeleteYou got THAT right
After 27 entries wasted mostly on uncalled-for "name calling" we are narrowing on the real subject.
ReplyDeleteIn my video (on a page that analyzes some deeper issues) from 1:21 but especially in the segment of 2:29 I was trying to direct "name calling" to our field of research, technology, preventive and personalized medicine, (and up to a genome-driven economy). It is no longer a “Genome Revolution”, it is the era of HoloGenomics.
In the video-segment I pointed out that "Epigenetics" originated in 1942 with Waddington, but (as Wikipedia explains) "The word epigenetics has had many definitions, and much of the confusion surrounding its usage relates to these definitions having changed over time".
It is hardly, therefore, the well-identified "big tent" where new approaches, among others uniting Genomics with Epigenomics expressed in Informatics, could come together.
Moreover, both epigenetics.com and epigenomics.com are URLs of an (excellent) Berlin-based company that might result in infringement with their trade marking. Unlike that glitch, HoloGenomics.com (and org) were secured for International HoloGenomics Society, that will absolutely not be monopolized by any government, any country (not even the USA), and certainly not by any company.
The need is clear and timely for HoloGenomics, not only as an International Society but as a holistic approach to heredity (where there is no discrimination against even quantum-theory, as long as it is similarly constructive to science, technology and medicine as Crick recognized it as an inspiration of his research).
With International PostGenetics Society (pre-ENCODE as an Avant-Guard organization, as it branded "junk DNA" as a scientific misnomer 8 months before the Old Establishment did so) we already have 60+ Founders, and members from 35+ Countries poised to hold our Inaugural meeting of the new International HoloGenomics Society.
Pellionisz_at_junkdna.com
A. Vargas says,
ReplyDeleteWhenever Larry talks about epigenetics, all he does is whine about the definition of the term as if that invalidated everything.
I'm one of those strange people who think that we should all agree on what we're taking about before we have a discussion.
Perhaps you'd be so kind as to enlighten us with a definition of "epigenetics"?
He never mentions that things like non-mendelian patterns of inheritance have been explained by DNA methylation.
Yes I have, although I don't use the words "non-Mendelian inheritance" 'cause that phrase is very misleading.
I remember giving my first lecture on stable patterns of DNA methylation back in 1978. It was the restriction-modification system in bacteria.
And of course he knows nothing about the "lamarckian" implications.
I know a great deal about it. There are none.
Andras Pellionisz writes,
ReplyDeleteAfter 27 entries wasted mostly on uncalled-for "name calling" we are narrowing on the real subject.
Speaking of kooks, I realize that I forgot to post a definition. Here's one from die.net.
kook [Usenet; originally and more formally, `net.kook']
Term used to describe a regular poster who continually posts messages with no apparent grounding in reality. Different from a troll, which implies a sort of sly wink on the part of a poster who knows better, kooks really believe what they write, to the extent that they believe anything.
The kook trademark is paranoia and grandiosity. Kooks will often build up elaborate imaginar support structures, fake corporations and the like, and continue to act as if those things are real even after their falsity has been documented in public.
While they may appear harmless, and are usually filtered out by the other regular participants in a newsgroup of mailing list, they can still cause problems because the necessity for these measures is not immediately apparent to newcomers; there are several instances on record, for example, of journalists writing stories with quotes from kooks who caught them unaware.
This comment has been removed by the author.
ReplyDelete"I'm one of those strange people who think that we should all agree on what we're taking about before we have a discussion"
ReplyDeleteThen, you should give up on most of the field of biology. There's hardly any word that does not have more than one use or meaning (unless it is something completely trivial and boring). Try "gene" for example. Is there a unanimous meaning?
Even so, some things almost anybody will agree must fall under epigentics (for instance, DNA methylation). Some things DO make sense despite the lack of a crisp consensus. Only Physicists feel the need to have their feet on the ground all the time. In Biology, you need to know how to swim.
Whe you demand unanimity for "epigenetics" alone, while ignoring how rarely this requirement is satisfied for many great terms in biology, you prove yourself to be a selective cynic.
WHy? I suspect, because you (mistakenly) believe it's all about sequence. Pretty dumb reductionism.
My preferred definition of epigenetics? Any heritable change affecting the phenotype that is not a change in the primary sequence of DNA.
specilly those "close" to gentics itself: DNA methylation, chromatin arrangement, histone modifications... you know "epi-GENETICS"
Notice I demand heritability; yet there is lots more biological phenomena biology that are not determined by the primary sequence, such as phenotypic plasticicty in general. Some people would call this epigenetics too, but a much older and better term exists:
"epigenesis", the notion that the phenotype is not "preformed", either in the DNA or in any other "homunculus"-like blueprint. This term is really neat and goes back to Wolff.
"Yes I have, although I don't use the words "non-Mendelian inheritance" 'cause that phrase is very misleading."
Pfft. Cynic's bullshit. Say "Parent-of origin effects" then. When have you EVER discussed this
form of inheritance of this blog? When have you EVER acknowledged the importnace of DNAmethylation to explain? yet you criticize epigenetics...from here, it looks like you're simply totally ignorant on this topic.
"I know a great deal about it. There are none" [lamarckian implications]
You're ignorant. As I said, Non-transient, environmentally induced modifications can explain observed cases of "inheritance of acquired traits"
All you know is that you can take advantage of a popular and ignorant "historiographic" demonization of lamarckism. As simple as that.
Larry,
ReplyDeleteSince you provoked me by calling me names, the definition you picked from at least 30 definitions, after 30 entries (rather than at the outset), clearly does not apply.
But let me first reciprocate the favor of publicizing my YouTube and thus my paper with a pointer to your video taken at Centre for Inquiry, Ontario. (Don't worry, I will refrain from calling you names for what I strained to see/hear).
Based on your lecture I better understand why bloggers here throw around names instead of scientific definitions and rigorous debate.
If Richard Dawkins is a "kook" as well, I am not in a very bad company. In your video you throw names at James Watson as "damn", "silly", "stupid". It is a somewhat bizarre way to express compliments, but maybe it is just your style. It seems contagious, however, having an imprint on your blog - and as you say at 4:52 of your video your daughter, learned in harder sciences, calls you "pretty stupid" (not my words, yours).
It is fine that you say "as a scientist I am very comfortable talking about biology, biochemistry, chemistry but less comfortable about topics outside of my discipline"..."I don't understand tensor calculus".
It is okay that you were not trained for interdisciplinary research - as long as you kindly refrain from extrapolating your name-calling (lack of) manners to those who contributed with a tensor geometry explanation of biologically existing neural networks, and build fractal geometrical algorithmic approach based on the principle of recursive genome function.
Not trained in exact sciences, it may follow that you seem to have a problem with definitions. Towards the end of your video you say "We have to keep the definition open to all the various possibilities".
One finds it revealing that both in this blog and in your video, rather than starting with definitions as is customary in science, you end with definitions, moreover with clearly invalid ones.
One can't "keep a definition open" - the definition of the definition is that it creates a closed set, bounded by the exact necessary and sufficient conditions.
You may have to run this through your daughter/colleagues, who actually seem to know better.
Pellionisz_at_junkdna.com
"WHy? I suspect, because you (mistakenly) believe it's all about sequence. Pretty dumb reductionism."
ReplyDeleteOK, so, what causes DNA methylation?
Methyltransferases. What are they? Enzymes. What are enzymes? Proteins. Where do proteins come from?
Jonny Wells - I'm sure you've heard of him - did some experiments in colleges in which he removed nuclei from fertilized xenopus eggs. Amazingly, these denucleated eggs continued to divide. A couple of times. Then they died. He extrapolated this to mean that there are extra-nuclear factors that drive mitosis. He mentioned proteins and other compouiunds in the cytoplasm/cytosol. But Jonny never mentioned where such things would come fro, nor did he explain why it could be that mitosis only occurred a couple of times.
If genes are so unimportant, why did the mitosis stop?
The same basic 'argument' seems to be the norm for the epigenetics/junkDNA conspiratorialists like Pellionisz, etc. crowd - epigenetics and non-coding DNA are so special and important and our notions are going to overturn classical genetics! We are amazing! The 'old school' one-gene one-protein crowd just 'doesn't get it'. They keep saying totally old-school, ignorant, things like "genes are the ultimate source for your epigenetic compounds" and othersuch suppression of research techniques.
Give the reality based commuity a break.
You might like sticking up for a revisionist who likes conspiracy theories and self-promotion, but look what that did for McCain.
HoloGenomics
ReplyDelete"OK, so, what causes DNA methylation?
ReplyDeleteMethyltransferases. What are they? Enzymes. What are enzymes? Proteins. Where do proteins come from?"
what is this, "dumb and dumber"?
Proteins are produced using DNA as template. But then what bits of DNA are transcribed depends on things such as trancription factors, and well, methylation.
There are many, many, many obvious reasons why it's not all downstream from the dna primary sequence. It's pretty boring to enumerate them; anyone that just can't figure this on his own self is pretty much a simple DNA worshipper. Beyond help.
Some of you calling each other names actually share heros such as Dawkins and Watson. Those are no heros of mine.
ReplyDeleteIn the end you are all "brothers in reductionism".
"they keep saying totally old-school, ignorant, things like "genes are the ultimate source for your epigenetic compounds" and othersuch suppression of research techniques"
ReplyDeleteHehe. You know, you REALLY should not pay that much attention to the silly things they say. Ultimately, you only fool yourself.
No one is repressing epigenetics research, despite vocal cynism and opposition. It's hot stuff that very well takes care of itself. It does not need characters like Pellionisz or Flannegan whining over it.
If anything, you alone are fueling their galileo complex, with dumb arguments such as "genes are the ultimate source of everything"
Delightful!
ReplyDeleteLike a Gary Larson cartoon: A bunch of silly moo-cows rear up on their hind legs to make pronouncements upon matters metaphysical.
So much lip service to science!
So little reason or evidence!
So many tedious ad hominems!
What can it mean?!
It's as though self-deception hooked up with self-indulgence and from their incestuous union sprang forth a malignant herd.
With all due respect, and if it's not too late, could you perhaps look into having yourselves neutered? (I mean sexually, not intellectually, as that would clearly be redundant.)
"These guys like quotes a lot. I think they read mostly reader's digest -- hehehe."
ReplyDeleteThat is merely a trail of bread crumbs for you to follow, such as might be available to (what we, for the purposes of argument, shall agree to call) your "intellect."
In this wise, please be advised that it is only by an infinite (and indeed godlike) act of condescension on my part that you are able to understand me at all.
Incidentally, I do not have a Galileo complex -- although I'm sure he would be flattered by the comparison. Rather, this recourse to knee-jerk reactions is merely symptomatic of your global inability to comprehend anything on its own merits.
Finally, your "arguments" would be better served were you to master simple punctuation.
Off you go, now! Your time at the foot of the radiant (and indeed transcendent) splendor of my being is at an end.
Shoo!
Actually, the quotes were better
ReplyDeleteMr. Flanagan,
ReplyDeleteIt is clear that you have something of a man-crush on Pellionisz and even help promulgate his dishonest self-promotion regarding junk DNA (see your gushing woo here:
http://www.prweb.com/releases/genomics/biotechnology/prweb1102764.htm
Which is a real shame, for in propping up your hero, you are insulting those whose work you clearly didn't bother to learn about.
Pellionisz has sold people like you a bill of goods. ANd you are too blinded by hero-worship to see that.
Vargas spews:
ReplyDelete"what is this, "dumb and dumber"?"
Between you, Pellionisz, and Flanagan, it is a hard call. Add 'dumbest' to the list.
See footnote on the sad case of "Doppelganger" here
ReplyDeletepellionisz_at_junkdna.com
The link to footnote on the sad case of bored housewife "Doppelganger" is here
ReplyDeletepellionisz_at_junkdna.com
"Jonny Wells - I'm sure you've heard of him - did some experiments in colleges in which he removed nuclei from fertilized xenopus eggs. Amazingly, these denucleated eggs continued to divide. A couple of times. Then they died. He extrapolated this to mean that there are extra-nuclear factors that drive mitosis"
ReplyDeleteVery interesting he got cell division, but true mitosis requires formation of tow new nuclei.
"He mentioned proteins and other compouiunds in the cytoplasm/cytosol. But Jonny never mentioned where such things would come from, nor did he explain why it could be that mitosis only occurred a couple of times."
They don not "come from' DNA, you dumbass. DNA is necessary to produce them, but DNA alone is insufficent. What do you think, that nuclei alone sitting in a tube will sprout protoplasm and start dividing?
DNA needs proteins to replicate AND to transcribe and synthesize protein. It's feedbakc, not a one-way arrow.
Because of this, too, it's pretty clear why the cells did not keep dividing. DNA is required: but this does not mena that the entire cell comes from DNA, stupid.
A. Vaergas rants:
ReplyDelete"They don not "come from' DNA, you dumbass. DNA is necessary to produce them, but DNA alone is insufficent. "
Ah, I see Vargas is unfamiliar with short-hand language. Forgive me for incorreclty assuming that most fo the readers here were rational, intellignet folk who would understand that a thesis need not accompany such statements.
DNA alone may be insufficient, however, as you so eloquently state it is necessary, therefore, my point stands.
But thanks for the namecalling.
Oh - Andras, old, old old pal - didn't you know that referring to yourself in the third person is a sign of mental illness?
So, your thyroid is necessary for you to grow. Therefore, you "come from" your thyroid.
ReplyDeleteKeep up the good thinking
Vargass spews:
ReplyDelete"So, your thyroid is necessary for you to grow. Therefore, you "come from" your thyroid.
Keep up the good thinking"
I know that english is not your native tongue - oh, look at that! I must think that language comes from your tongue!
But seriously, let us think about what Vargass is trying to indicate.
I used common 'shorthand' in describing the relationship between a gene(DNA) and its protein product. Rather than taking what I figured was an unnecessary step in describing the specifics of protein synthesis, I simply wrote that proteins 'come from' DNA. I doubt that any sensible person would have interpreted what I wrote to mean anything other than the use of 'shorthand.' But not Vargass - oh, no, Mr.Pedant prattles on with insults about how I must be dumb or something for not writing it all out. And goes on to try to show how dumb I am by coming up with a silly "analogy."
But let us take a look at it:
So, your thyroid is necessary for you to grow. Therefore, you "come from" your thyroid.
In order for an analogy to have merit, it actually has to be analogous. You can live without a thyroid, but you cannot make a specific protein without the appropriate gene.
Good thinking, nitwit.
It is pitiful that even after 49 trials The Principle of Recursive Genome Function was not addressed at all - while in a more intelligent blog "chemist99" could pin down an actually experimentally (chemically) testable power of predictions of The Principle of Genome FunctionMaybe some blogs are just more intelligent than others. One tends to fell in the lowly darkness of oblivion, while another thrives on adhering to issues of science.
ReplyDeleteOdd that it took a 'blog' to come up with a test for YOUR paradigm-shifting ground breaking, histoiry-revising new amazing model.
ReplyDeleteIt is not odd at all, that a concept pops up in obscure places, like by Alexander Grosberg in Moscow in the nineties (now at New York University) relating the Hamilton and Peano fractal curves to the ultra-dense but knot-less folding of DNA.
ReplyDeleteTwo decades later, the fractal structure of DNA strands is now delivered to the Prez on the Science cover by a team, hallmarked by the Presidential Science Adviser (and Director of Broad Institute by Harvard and MIT) Eric Lander et al. One hears the fading voice of "objection" of the blog owner (in conflict with his own readership), hiding his head in his sandwalk "The Director of Broad Institute and the Prez he advises on Science matters are Kooks"
Andras,
ReplyDeleteDon’t let these bitter adversaries trouble you. They don't have your insight and perspective. Your thoughts will be widely known, appreciated and quoted in the future...just like it has happened to you in the past.
You just go (sprint) ahead and leave these antiquated minds behind.
Prof. Larry Moran harbors contempt for anyone, who does not share his rigid and atheist ideologies. As a scientist he is severely restricted to biochemistry “only”, while he lacks adequate knowledge of mathematics /physics and informatics.
ReplyDeleteHow dare he attack Pellionisz, who holds Ph.D s in these disciplines? That’s a long shot for Moran.
I don't see where these ideas represent a paradigm shift. Junk DNA isn't junk and recursion is a standard process in complex systems.
ReplyDeleteSo where is the paradigm shift?
I don't think the guy is a kook but he doesn't bring any substance to the table either, he just sort of rambles.
I do think the idea of PGC is a good one that will eventually come to pass, why wouldn't it?
The genes are the software, the non-coding area represents all the sub-routines, parameters required to execute the code.
I make an exception and answer "LargelyPolitical" since it exudes much unlike the malice and venom oozing from most of those putting their heads in the sandwalk. I am happy to note that LP finds my Principle a good one that will prevail (though for the question "why wouldn't it" the answer is the libelous and name-calling blog owner itself - who now put a disclaimer on top that he is not pontificating as a Professor of University, but is at odds with just about anybody in the planet).
ReplyDeleteI wish, however, that readers would not stop at the dismissal of the "Junk DNA" harmful misnomer (see the last nail in the coffin at HoloGenomics "news" on Feb. 23, 2009 - reports that deletion of non-coding DNA highly significantly affects expression of genes over 100,000 bases apart) ... blowing away lame excuses that "oh, we have always considered nearby promoter regions as regulatory part of genes".
Even the dismissal of the outright ridiculous "Central Dogma" should not be the end of study (though readers might note that just simply because Crick confessed in writing that he did not know what the word "dogma" meant is enough for LOL).
Careful readers proceeding in reading my Principle beyond the removal of the two show-stoppers will discover that "it connects the dots" and the genome function becomes recursive, and in addition my paper actually went far beyond, by specifying what the (software enabling) algorithm of recursion is: it is Fractal Iterative Recursion, generating Fractal Hierarchies. If anybody thinks that my FractoGene may be wrong, or Lander et al. 2009 October 9th Science cover article "Mr. President, the DNA is Fractal" is missing the point, should come forward with their (better, but at least as software enabling) algorithm. I would be happy to serve as a referee of contending submissions to peer review.
Lastly, those who wish to glance how quickly my Principle leads to practical applications might want to view this YouTube - showing the HolGenTech' Genome Computing Architecture, empowering the consumers to make daily choices based on interoperability of genomic-, health-data governed by personal preferences.
pellionisz_at_junkdna.com
Eric Lander, Director of the Broad Institute, Science Adviser to the US President confessed at the 10th Anniversary Celebration of the completion of the "Human Genome Project", with Nobelist Watson, NIH Director Collins, NIHGR Green safely buckled in their seats that "the fundamental assumptions were all wrong" and admitted that the structure of the DNA was fractal. (See details here).
ReplyDeleteYet, anyone is free to roam around for Centuries that the Universe rotates around the Earth, pay their dues through the nose to the Flat Earth Society, or parrot forever that Barbara McClintock was a "kook" with her (correct) idea of "jumping genes" - way beyond her Nobel belated by so many decades.
Another leading scientist whom this particular blog likes to feature as a "kook"; John S. Mattick (Foundation Director of the Australian Genome Research Facility and the Institute for Molecular Bioscience, an Associate Member of the European Molecular Biology Organisation and a Fellow of the Australian Academy of Science, Sidney, Australia) has just followed the example of Eric Lander (Director of the Broad Institute, Science Adviser to the US President). Dr. Mattick, with a long record of asserting that "Junk DNA" was anything, but, this time addressed the World Conference (HUGO), and said "It appears that the genetic basis ... has been misunderstood for the past 50 years... it appears most orthodox assumptions about human genetic information have been incorrect, and that what was dismissed as 'junk' because it was not understood will hold the key to understanding human evolution, development, variation, cognition and disease"
ReplyDeleteIs Larry Moran a Detractor?
ReplyDelete"Detract": "To speak ill of". For Moran's hate speech see his 2007 entry: "Should we pity America, or hate it?" He calmed to an ad hominem, on my YouTube 2008 - now over 11,000 hits.
"To Detract": "To diminish the importance, value, or effectiveness". Bingo. That is what Moran aims at 98.7% of DNA. The Battelle Study (see here) values the Genome Project at $796 Bn. Just in the US; Battelle lists 100 global offices. In contradiction to Moran, Battelle says:
"Non-coding DNA, previously termed "junk DNA" because it was thought to be a relic of evolution with little biological function, was instead confirmed to have specific functionality in transcription and translational regulation of protein-coding,i.e., most of it is not junk at all, it is central to life functions. This finding alone supports the vision of undertaking whole genome sequencing, since prior to the HGP some detractors argued that the budget would be better spent simply studying known protein coding genes and ignoring the rest"
Moran still detracts, not just with name-calling junk, also by clinging to the Central Dogma, by falsely claiming that proteins can not change the sequence information of DNA (denying The Principle of Recursive Genome Function). Moran's not realizing the effectiveness of proteins (methylesterase) disabling retrieval of DNA sequence-information bespeaks of his inability to define abstract concepts. This became deadly when the subject, biology, became informatics. Battelle says:
"Sequencing the human genome made clear information sciences, mathematics and biological investigation are now inexorably intertwined. The sequencing of the genome was as much a mathematical and computational achievement as it was a biological one and has helped to give rise to new fields of biological science in "computational biology" and "systems biology". It has been noted that "The revolutions that have been generated by the first draft of the Human Genome Project have barely been felt, but there is one profound change that has already occurred, and that is the realization that biology is fundamentally an information science."
Hopefully Moran knows basic tools; his inability to understand what "information on a hard disk for the OS" means is shown by "deleting files". The OS, looking up the directory, will return zero info on the file (though it may physically be there), but the biologist would have to struggle what "information" is - without an ability to retrieve! I had enough with teaching tensor network theory (and now fractals) thus will refrain from re-training old schoolers to appreciation of genome informatics.
Suffice to quote from Battelle "recurrent targets of somatic mutation in cancer. These discoveries are propelling research throughout academia and industry Eric Lander, Nature. Vol. 470. 2011". He has told off the audience of NIH (10th of HGP) that "fundamentals were wrong", showing his fractal folding of DNA - and now pointing to structural variants as recurrent targets. Genome misregulation leads to cancer when the recursive genome function is derailed.
The Myth of Junk DNA will NOT be resolved by ideologies - immune to academia or even a $trillion industry. It will be resolved by consumers (formerly patients) demanding that their cancer therapy cease to be experimentation, and be guided by full DNA sequencing ("before and after") to document involvement of all DNA - regardless if it used to be ignored as "Junk". For those suffering from Junk DNA diseases, history will not be kind to selfish detractors.
Andras you have made very reasonable points.
ReplyDeleteNot everyone is as blinkered as Moran.
So, Mattick is still spininig yarns to prop himself (and his company...) up and old Andras is claiming it is all perfectly correct.
ReplyDeleteNothing new under the sun.
Only took a decade since my FractoGene (2002) for the fractal approach to be supported by at least three top-notch independent experimental Proofs of Concept (see write-up 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. Now, with the next challenge of a geometrical interpretation of the RNA system, the detractor engages his name-calling the freshly decorated Dr. Mattick as "stupid and irrational".
ReplyDeleteIn one of my rare visits of his sites today (July 9, 2012) I noted with pleasure that Prof. Larry Moran has removed all of those side-bar "statistics" (opinions on "Junk DNA") that were incapable to properly round numbers. Sure, just by having published them, hurt his credentials that he apparently cares about. As he knows at least from history that ridiculing fellow-scientists is a burden on their credentials (e.g. calling Dr. Barbara MCclintock a "Kook" cost her 40 years for waiting for a Nobel, she was lucky that her longevity permitted her to wait out detractors), I request that Dr. Moran kindly retracts henceforth as a response to this public notice from his blog remarks calculated to ridiculing me, to inflicts considerable harm to my reputation - assuming that he cares about reputation of colleagues.
ReplyDeleteAn interesting thing - Ralph Steinman never compared himself with Barbara MCclintock, even after his data was originally met with a lot of skepticism. However, many a person who will never get the call from Stockholm seem to think they need to...
DeleteI care very much about the reputation of scientists and science. That's why I wil not retract or delete any of the comments I've made about Andras Pellionisz.
ReplyDelete:) It was sick... you know while I was reading this correspondance before my eyes appeared a bunch of biol students trembling from anxiety of the math exam and can't pity them. Nevertheless don't forget Mathematics is just a baloney (but most valuable than other disciplines) without it can be translate to the language ('mother tongue') of Logic, aka Philosoph... God Bless You All :D:D:D:D
ReplyDeleteC2=E/m
I'm confused...
ReplyDeleteWhen I took genetics as an undergrad at UC Davis in the 80s, "Junk DNA" was considered noncoding DNA of unknown function. Same held true in graduate school. The notion that it was useless was considered a hypothesis worthy of testing as technology improved - not as God's truth. If regulatory functions are found in "Junk DNA," where's the controversy?
Likewise the "Central Dogma" was presented as a notion to be tested until invalidated. Not as the kinds of dogma forced on me by my fundamentalist Christian high school. So if proteins induce methylation, which causes heritable change, then I see this as a refinement of what we know, and not the complete rebirth of Lamarck.
I do see a ton of value to looking at non-coding regions. If Andras algorithms help, then that's interesting. I am concerned by the invocation of Newton's laws, and what appears to be manufactured controversy. But I'm still keeping an open mind. Even if he's bombastic, he may develop a useful algorithm for looking at noncoding DNA. Not my field though, so I can't pass judgement on Holgentec.
I'm sorry, but not surprised, that your undergraduate and graduate education at UC Davis were deficient.
DeleteBy the 1980s there was plenty of direct evidence that large parts of the human genome were junk. All of it supported the genetic load arguments from the 1960's, the Cot curve results from the early 1970s, and the early C-value "paradox" work with multiple groups of species.
BTW, I don't know if you understand the difference between "noncoding DNA" and junk DNA. Please try and keep the distinction in mind. There's lots and lots of noncoding DNA that's functional and this has been known for fifty years.
Re: Interested Party
ReplyDeleteHuh? Me bombastic? Is it true that when promulgating my abstract cogitations, or for others articulating profane sentimentality and pseudo-philosophical or quasi-psychological observations about them, am I cognizant of platitudinous ponderousness of libels?
Maybe. But that’s not it.
"Teachers using English as a second language may have difficulty using simple words and end up using bombastic words instead, author and educator Dr Pumadevi Subramaniam said today. This was a trend among "second language teachers", she said, adding that some Mathematics teachers used "subtract by regrouping" and "standard algorithm", when they could have phrased it simply as "borrowing" and "writing it vertically"”.
English is not my second language. It is my sixth. Due to my earlier familiarity especially with the Latin and German languages I tend to favor words originating from Romanesque literature rather than the more Celtic vocabulary of typical monolingual workers. My mother tongue, the perhaps esoteric Hungarian language has both a flamboyance, as well as a precision that urges me to carefully select, as opposed to vaguely pick, expressions that I believe are the most appropriate. My dear friend, the late Edward Teller was also known to interpolate from his native Hungarian and German languages his third spoken language (the English, in addition to his earlier compulsory studies of classical Greek and Latin), thus he was likewise labeled “bombastic”.
Labels, however, change. Just like tables turn fast. This blog introduced lately an interesting re-definition: “Most people now know that ENCODE did not disprove junk DNA (with the possible exception of creationists and a few kooks)”. Thus, the latter community (this September spearheaded by some top ~450 genome specialists) comprises those who hold, using a line from Dr. Francis Collins, that “a certain amount of hubris was required for anyone to call any part of the genome 'junk'”.
Please bear with me; “don’t bite my finger, look where I am pointing” (Warren McCulloch).