I'm repeating an observation that I read somewhere else. The term "junk" is preferred over "trash" because junk will eventually prove to be useful in some way, but trash is just something to be thrown out.

The existence of junk DNA can be predicted, but not from Darwinism or creationism. It can be predicted by knowing the mechanism by which DNA replicates and reproduces. You know that pieces of DNA will be added by various means (insertions, repeats) and that having a function is not at all relevant. In addition, small deletions will leave stuff behind, but that stuff will have lost its function because a vital part has gone missing. Since all these nonsense DNA groups, if you will, are reproduced by the appropriate enzymes, they will continue to exist even though they have no immediate function. Later on, of course, they may be exaptations (Gould's term) that are converted to some new function.

If the term "junk DNA" were merely inaccurate, it could be tossed into the trash bin of discarded but historically interesting scientific ideas, like "homunculus". But it also reveals a hubris which encourages deep distrust from the non-scientific community. In this age of GM food, stem cell research and human-animal research chimeras, geneticists should recognize that the language of humility is in their interest.

Just because functions have been identified for some regions of genomes thought to be non-functional does not mean that all regions thought to be junk are functional. This is particularly true for bloated genomes (like the human genome) which are loaded with parasitic elements. Mike Lynch's nearly neutral model for the evolution of eukaryotic genome structure explains how genomes can accumulate non-functional elements.

Ryan, Nick, David, ? I respectfully disagree that ?press offices may be THE problem?. (For sure they are A problem, see below).

THE problem IMHO is the biggest paradigm-shift in the history of science/technology with the most profound implications to every individual and entire societies. (Perhaps with the earlier exceptions of our "change of view" that Flat Earth was no longer the Center of the Universe, and our uneasy abandonment of the dogma that the atom would not split and elements could not be changed).

It would be absolutely miraculous if PostModern Genomics could just seamlessly flow from Modern Genomics without major turmoil. After all, not only the ?junk DNA? but also the ?Gene?, ?Central Dogma? of DNA>RNA>Protein, ?Monopoly of WC recombination? etc. became ALL obsolete). Indeed, some of us should be happy that we are not (literally) burned for heretical views (by the way, based on hard-core experimental evidence, also in medieval times?)

I am speaking with a little experience in paradigm-shifts (child-play compared to the switch from Modern to PostModern Genomics). My earlier experience was with the AI/NN (Artificial Intelligence/Neural Networks) paradigm-shift.

Cybernetics was taking off in the fifties with McCulloch-Pitts, Wiener, von Neumann and Frank Rosenblatt (etc) towards "BioCybernetics" - until the rival friend of Frank Rosenblatt (Marvin Minsky) "framed" research funds for about 15 years solely to "Artificial Intelligence". With some hubris, Minsky proposed based on scientifically false ?proof? in Perceptrons, 1969 that nothing was to be learned from biological intelligence. This ?framing? was very much like dr. Ohno?s ?framing? (attempted as ?garbage DNA? and stuck 2-years later as ?junk DNA? in 1972).

For AI/NN, it took the pioneers (working diligently on biological neuronal networks) about 2 decades to recover. Finally, in the late seventies, my kind of LINK">geometrization of neuroscience led to experimental proof (Stan Gielen in Holland, cf. ibid) and even to a new branch of philosophy (Neurophilosophy by Pat Churchland, UCSD, cf. ibid). I came up with the idea of a Society (International Neural Networks Society) its Journal and Meetings ? but those were relatively easy. The harder part was to break through in the media and finally in funding.

Looking back, nothing can be expected by a ?spontaneous? media-transformation, though one should never exclude a slim likelihood that some leading journal/journalist might seize the ?ZeitGeist?. For ?Neural Networks?, it took a special person (John Hopfield, now at Princeton Advanced Studies) already with NAS membership and highly accomplished career in a related field to fledging neurocomputing (semiconductors) ? with masterful skills in communication to the media and Society at large. (When people asked where he published his "Neural Network" research, his true anecdote was "in the Los Angeles Times" - at that time John worked out of Caltech). John Hopfield and I presented to the prestigious ?Neuroscience Study Program? in 1978 mathematical inroads to neuroscience.

For funding, it took Yale/Stanford graduate and distinguished Stanford professor Bernie Widrow, to hold in Boston a ?Neural Network Study Program? for DARPA initial funding (forgot, it was a meager $1 or 2 M).

Oh, yes ? nothing would have happened, if Soviet submarines did not have to be monitored perilously close to San Diego, and sonar pattern-recognition would not have been something in which neural network algorithms truly excelled. Defense provided vital funding, with NIH coughing up precious little, much later.

Therefore?

PostModern Genomics (that we call ?PostGenetics? in IPGS, LINK">International PostGenetics Society) we need a ?Hopfield?, a ?Widrow?, a ?DARPA? and some strategic application to emerge.

Nick, it is unlikely that Chief Editor of Science (Don Kennedy) would become the new ?Hopfield?. (Don is stepping down from Science, but did not take an opportunity to announce IPGS before "ENCODE" was out, anyway). You can see what LINK">Editor-in-Chief of The Scientist Richard Gallagher did with my direct pitch to "formally abandon Junk DNA". (I have written up a much more elaborated scholarly piece that only appeared in an abbreviated version as an ?Obituary? in LINK">JunkDNA.com. Should a suitable journal ask for the full manuscript is a question, but I have my upcoming book to publish it without tampering.

Collins and Venter are pitched (again?) for the pivotal personal role - but I can not speak for them. Quite likely, the paradigm-shift itself will hone and catapult the most suitable person for the required role.

Now comes the good thing, the part that is just hard work ? but thus no problem at all. PostModern Genomics (PostGenetics; ?Genomics beyond Genes?) has not one, not two, not three, not four, not five but at least six cardinally important strategic applications LINK">see here

1) LINK">JunkDNA diseasesmay (and usually do) effect every one in every society. Accordingly, pressure is enormous. Big Pharma is already buying up IP of ?short genome sequences" in $300 M -$1.1 B chunks.

2) Synthetic Genomics needs software enabling ?Algorithmic design? principles that can only come from PostModern Genomics.

3) Bioenergy applications are essentially based on ?better regulated? existing genomical mechanisms ? PostGenetics harbors clues for H2-based economy, renewable petroleum, etc.

4) Biodefense applications need diagnostic and therapeutic methods of ?newly regulated? sequences (just as computer defense applications can?t live without ?virus checkers?)

5) Big IT (Google, Microsoft, etc) already positions, both for "Genomics for the masses? and for ?Software tools for PostModern Genomics?.

6) PostGenetics Centers of R&D will spring up, with the steepest growth curve. There are plenty of ?Genetics Institutes? ? the leading edge is already clear.

Last but not least, massive paradigm-shifts always stir great turmoil (see a plethora of ideological and fear-driven pseudo-debates), but the most spectacular beneficiaries often are the "just do it" fresh companies. (See paradigm-shift from computer mainframes to home computers; with Apple pitched against IBM with great hype - Microsoft was created by seven brave guys and walked away with by the far largest profit. You can also recall GenenTech for Modern Genomics. Look for PostGeneTech for PostModern Genomics?)

Getting bogged down in hollow shouting over ideological trenches gets nowhere. Those who *really* care about what used to be called ?Junk DNA? before Dr. Ohno?s most harmful "framing? will just find out what the Algorithmic Design of the Genome might be (deferring rushed judgment if the design to be found will be characterized as intelligent or not).

It is certainly more intelligent than we presently are, or we would know it already :-)

pellionisz_at_junkdna.com

Well, this is just tragic -- literally. As if scientists aren't already perceived as unstoppably arrogant makers of monsters and machines of destruction, stomping on other social institutions and demanding to have the final say in matters of religion, politics, and anything else they feel like. Now we're being told they should proudly cling to their mistaken notions, and smugly attack any other views rather than having a bit of sensible humility and openness towards alternative ideas.

The Editor Richard Gallagher is right on many counts.

First, "Junk DNA" is worth keeping; just as I registered the LINK domain when nobody did so - and junkdna.com will keep running in some form for its historical/journalistic value as a catchy moniker of something that does not really exist. (It is not even my first time to do that. I registered and subsequently sold to Knight-Ridder Publishing the "siliconvalley.com" domain - although you don't find "Silicon Valley" on the map, at all.) Legends live forever in many shapes and forms, "looming larger than life". "Junkdna.com" will live on - quite possibly in an acquired version.

One also agrees with the Editor of "The Scientist" that "Junk DNA" was a classical "framing" of science, and I am particularly thankful for Dr. Gallagher for naming the next frame; PostGenetics; LINK

An abbreviated obituary is found in the column of LINK its full version, with publication to be decided goes further, features actual contents in the new PostModern frame).

"The Scientist", since it is a journal about Science and not of science, does not squarely face one issue, however. "Junk DNA" is dead *as a scientific term* - and for its social implications we bear responsibilities.

The Editor of "The Scientist" duly mentions my criticism that "scientific progress was inhibited" by "Junk DNA" - as the frame became much-much too small for Genomics that just grew beyond the straightjacket of 1.3% of human DNA (the "genes"). This is a dealy serious issue that overrides, in my opinion, our journalistic interest of "keeping things interesting".

Millions (if not hundreds of millions) of people are afflicted with "Junk DNA diseases", see LINK - and if an obsolete "frame" is abused for denying resources, not in journalism but in the US Congress (NIH), or hindering the EU PostGenetics Initiative from taking off - two particular consequences will be tied to decision makers.

One is the direct responsibility for suffering and/or death of those afflicted with "Junk DNA diseases". Second is the direct responsibility for global shift in "Genomics beyond Genes" for the benefit of those regions that are the first to reject a *science frame* proven to be obsolete.

pellionisz_at_junkdna.com