Discussion Group about PostGenetics

Monday, October 31, 2005

PostGenetics FAQ

POSTGENETICS (IPGS) FAQ

WHAT IS “POSTGENETICS”?

GENETICS is the discipline focused on the genes (directly protein-coding DNA sequencing). "Genes" constitute 1.3% of the (human) DNA. The rest used to be considered “junkDNA”. For some time, this "rush to judgement" has been widely regarded "the biggest mistake of molecular biology". Mistakes in the sciences must be corrected, sooner or later. Thus, at some time, Genomics, the discipline of the entire DNA (Genome) was destined to break out from a solitary confinement. "POSTGENETICS is Genomics Beyond Genes”.

WHAT IS INTERNATIONAL POSTGENETICS SOCIETY?

The community which puts first and paramount priority in R& D of the understanding, and practical utilization of the understanding, of the 98.% of the (human) DNA (the now formally abandoned notion of “junkDNA”)

IPGS – WHY NOW?

One of the two immediate triggering factors was the announcement of the sequencing of the Chimpanzee on the eve of the 1st of September, 2005. (IPGS was immediately filed on the 1st). It turned out that there is a forty times larger difference between the DNA of the chimp and the human in the 98.7% "junkDNA". There is a widespread (and often scientifically pointless) debate why and how humans are different from the rest of the living organisms. As for “how”, this is the time for scientists to directly address the most likely biggest difference – in the usual scientific manner of predictive and thus experimentally supportable or refutable theories.

The other timely factor has been that staggering amounts of US taxpayer dollars are allocated in a hurry, for “gene discovery” for dreadful hereditary diseases as well as connected human behavior and lifestyle. “Gene Discovery” has been around and ‘genes’ have been extensively looked at as the origin of the above. Some genes (BRCA1 and BRCA2 are two excellent examples) were in fact identified as associated with certain breast cancers, and medication (Herceptin) could be produced to stop them in their track. However, the number of "genes" is extremely limited in the Genome (1.3% in the human DNA) while there is an increasing number, inclulding some of the most common hereditary diseases (e.g. fragile x syndrome, causing autism and more severe health challenges, or the incurable terminal disease of multiple myeloma), that are already know to be originating not from any gene (they are pristine, intact) – but from errors in the “junkDNA”. The philosophy of how human kind is different from other living organism is not necessarily a vital or even an urgent issue for Society to address. It may, in fact, become divisive, especially if continues to be handled in a non-scientific manner. However, helping people who are needlessly suffering and dying because of a neglect of looking for the likely (or known) cause of their diseases in the “junkDNA” has a truly vital humanitarian urgency. In fact, for some officials whose sole and solemn duty is to help Society(Representatives of Congress, Health Program Administrators, etc) the appropriate distribution of the available resources is a sine qua non of their “job description” - and intentional neglect can even be considered a crime.

IPGS – WHY SO LATE?

PostGenetics is disruptive. Genetics has a 100 year history – and the establishment consolidated and grew its colossal intertia accordingly. We already witness a “conceptual meltdown” to be followed by Academia- and Industry—wide disruption. It will result in breakdown and collapse for some, while a historically unprecedented opportunity of most lucratively catapulting for others. Disruption is painful, and revolutions often end up “eating their children" (unless we are experienced, having lived through more than one disruptions and thus protect ourselves; AI/Neural Nets for one example, and Government/Private Industry development of Internet, for a more recent instance). For a historical perspective, just consider the disruptive switch from the steam-engine to internal combustion engines and electric motors in technology, or the “paradigm shift” of a Geo-centric philosophy to more modern theories of just our Solar System - not to mention black holes and light routinely travelling along the curvature of gravitation in more modern Astronomy. In the 21st Century, those advancing science are somewhat less likely to be literally burned alive, but don’t naively expect your grant, paper (etc) to be funded/accepted without the clout of collective bargaining power. Others will bite our finger instead of looking where PostGenetics is pointing. Thus far, examples could be quoted how the establishment turned true pioneers against each-other, or rejected paper by some well-known pioneer of a remote land just because “it did not feel right”. [not "yours truly" - see http://www.junkdna.com/fractogene/05_simons_pellionisz.html] )..

On the other hand, it is "not too early" - neither "too late" for the R&D and Applications to skyrocket, since "Disruptive Technologies" yield the most spectacular returns for the experts of Public Sector. Of course, one has to be alert and ready – and appropriately schooled by the “state of art” e.g. from Harvard Business School scholars (Clayton Christensen, Juan Enriquez) how disruptive technologies can be played to the hilt - to outdo "sustaining technologies" by a few orders of magnitude.

OKAY, HOW CAN I HELP POSTGENETICS?

Join the leadership by contacting PostGenetics [at] junkdna.com. (Use regular e-mail sign, this format is to avoid automated traffic). By the time the declaration will appear in a major magazine, the presently 12 "original signatories" will have expanded – as some of them have simply not been reachable. Only a single Venture Capitalist personal member and Corporate Membership will be added initially - to avoid the very usual “tumult and divergence”, falling over one-another, in the early stages of an organization. Likewise, only one Sponsor of the “Inaugural Congress of IPSG” will be clinched, to ensure a streamlined and proven operation. IPGS like most any Society will elect leadership from its ranks, from those who signal that they are "able, willing and available".

Donate to IPGS– this is the biggest issue in the history of Philanthropy. Think of those hundreds of millions of people with hereditary diseases who have so far been “junked” – since their health challenge lies, or may very well lie, in the "junkDNA".

Become a regular member. It is expected that once our Declaration will appear in a major scientific Journal ranks of "Regular Individual and Corporate Memberships" will fill at a rapid rate. Even among the original co-signatories of our “Letter” one already finds professors of Genetics, Pharmacogenomists, Neurobiologists - those who are keenly aware of the 100 year old distortions ossified in Genetics. In addition to Biotechnologists, (protein-based) Nanotechnologists and Information Technologists are “pools” for our membership (including workers of the now vast and established field of Neural Networks - itself a disruptive R&D a quarter of Century ago…).

Speak up, express your opinion. Use this BLOG to drop a note – or use other related newsgroups. Put in your two cents worth of your opinion to Newsmedia. Most importantly, write to your Representative in Congress that you insist on putting your tax dollars to work for the heretofore actively discouraged field, labeled with a pejorative manner – that even scientists universally agree that “it was the biggest mistake in the history of molecular biology”. If your Congressperson is not likely to pick up the “ZeitGeist” – vote for his/her competitor.

If you are already a worker, and fully convinced, why don’t you secure your participation in the first "Open" Symposium" of IPGS in Budapest, Hungary (Oct, 2006)?

Dr. Andras J. Pellionisz
(408) 732-9319
Founder of PostGenetics

6 Comments:

Anonymous Anonymous said...

This is a test if anonymous comments can be made by clickin on "Post a Comment"

9:02 AM

 
Blogger Sohail S. said...

interesting!

My comment (from a science-fanatic student, who likes to take part in ideas with other disciplines) :

In an abstract view, I consider this very similar to some aspects of the concept of “attention”, which as you know is an umbrella term for a series of neural mechanisms in brain. Here, brain is just a metaphor for the genome. In normal conditions (lets call routine genomic tasks!), the genome’s “focus of attention” is concentrated on those 1.3%, (which are spatially arranged in few spots localized in the folded chromosome) but in some situations, other parts may be activated and take roles for those specific “novel” situations. This novelty does not occur often, but those junk DNA may have a high degree of importance, yet with a lower probability or frequency of being expressed. Maybe that's why they have been left out of interest or neglected so far. This was an ontogenic analogy but a similar metaphor can be considered in phylogenic level as well. There may be some functions for those junk in the evolutionary mechanisms which may be not known yet (for example as hidden or spare variables for some genomic algorithms).

Generally, I think mechanisms discovered in neuroscience (which is my passion) can have some lessons for molecular biology too, and a paradigm shift in both fields may occur. By “genomic attention” I mean the degree (distribution) of expression for the genes. This concentration distribution can be seen as a dynamic probability distribution changing in time.

Besides, another (stereotypical) account can be: if there were no use for the remainder, then keeping them is not economical and the organisms should have got rid of them before, during evolution. The 1.3/98.7 ratio of information/junk content is too far from Pareto principle.

(Sincerely yours, Sohail - a curious (non)student from Iran who is interested about these topics)

2:48 PM

 
Blogger Dr. Andras J. Pellionisz said...

Sohail,

your most important comments are right on target:

1) Malcolm J. Simons makes a point even in his "Genius of Junk" video (see transcripts http://www.abc.net.au/catalyst/stories/s898887.htm

"Under Darwinistic notions you would think that junk would drop off under the theory of natural selection just like species drop off if they hit ecological niches which is incompatible with survival. If they can adapt to those niches, then those that can survive and those that can’t die. There’s the notion. If you apply that to the DNA sequence, then the coding region genes which survived have a function and by the way the non coding sequences have survived as well. So the proposition would have to be that if they’re there, they’ve got a function".

2) For your comment "There may be some functions for those junk in the evolutionary mechanisms which may be not known yet (for example as hidden or spare variables for some genomic algorithms)"

See: http://www.fractogene.com that specifically puts forward a genomic (recursive fractal) algorithm, in which the "junk dna" information contents were predicted (2002) to be useful for such purposes. Meanwhile, the "fugu prediction" of FractoGene has been experimentally confirmed (http://www.junkdna.com/fractogene/05_simons_pellionisz.pdf)

I invite you to also see the "news column" on junk dna at
http://www.junkdna.com/new_citations.html

That news column also have a (separate) blog for you (and anyone) to comment and discuss issues.

Regards, Dr. Andras J. Pellionisz

3:25 PM

 
Blogger Dr. Andras J. Pellionisz said...

Since e-mail communication is occasionally blocked these days, the public site where "Genius of Junk" transcripts are found are at

http://www.abc.net.au/catalyst/stories/s898887.htm

5:05 PM

 
Blogger Sohail S. said...

Thanks for answering personally. I am information-flooded a bit! That paper is so interesting. My current idea about fractal in brain (dim=1.23) is according to a figure in
Laughlin and Sejnowski. Communication in Neuronal Networks. Science 301 2003.
Would you mind if I ask for a pdf version of the following paper? (current html version is hard to read) :
9. Pellionisz AJ. Neural Geometry: Towards a fractal model of
neurons. In: Cotterill RMJ, editor. Models of brain function,
Cambridge: Cambridge University Press; 1989. pp 453–464.
(Pardon for using here for communication)
Best regards,
( sohale@gmail.com )

12:35 PM

 
Blogger Dr. Andras J. Pellionisz said...

FractoGene references (answer to Sohale).

The reference Pellionisz AJ. Neural Geometry: Towards a fractal model of neurons. In: Cotterill RMJ, editor. Models of brain function, Cambridge: Cambridge University Press; 1989. pp 453–464.

is found at

http://fractogene.com/89_fractal/89_fractal.html

(Second item once "Pellionisz" is typed into Google).

FractoGene references are found at
http://www.fractogene.com

Though several groups have already jumped on the bandwagon (see "endorsed" box in same fractogene websites), Terry Sejnowski's 2003 paper or diagram (a year after FractoGene's 2002 patent submission...) does not make any reference to fractals at all. (It took to the Sejnowski group 14 years to adopt and quote the "covariant and contravariant tensors" of my Tensor Network Theory - but they are at least in the "elite league" to belatedly credit the approach - thus far the only algorithmic explanation of the function of cerebellar neural networks):

http://www.cnl.salk.edu/~zhang/jnp-reconst.pdf

The fractal approach to "junk DNA function" is already developing into a "fractal frenzy"...

Dr. Pellionisz

1:04 PM

 

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