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Invasion of the IBM Engineers



IBM today announced its researchers have discovered numerous DNA patterns shared by areas of the human genome that were thought to have little or no influence on its function and those areas that do.

As reported today in the Proceedings of the National Academy of Sciences (PNAS), regions of the human genome that were assumed to largely contain evolutionary leftovers (called “junk DNA”) may actually hold significant clues that can add to scientists’ understanding of cellular processes. IBM researchers have discovered that these regions contain numerous, short DNA “motifs,” or repeating sequence fragments, which also are present in the parts of the genome that give rise to proteins.

If verified experimentally, the discovery suggests a potential connection between these coding and non-coding parts of the human genome that could have a profound impact on genomic research and provide important insights on the workings of cells.

“Our goal is to apply advanced computational techniques to analyze the workings of processes and systems, in this case the function of the human genome,” said Ajay Royyuru, head of the Computational Biology Center at IBM Research. “Using these tools, we’ve been able to shed new light on parts of the DNA that were traditionally thought of as not having a specific purpose. We believe the innovative application of technology can provide further understanding in the life sciences at large.”

The IBM team used a mathematical tool called pattern-discovery, often applied to mine useful information from very large repositories of data in both business and scientific applications, to sift through the approximately six billion letters in the non-coding regions of the human genome and look for repeating sequence fragments, or motifs.

Among the millions of discovered motifs, the team identified approximately 128,000 that also occur in the coding region of the genome and are significantly over-represented in genes involved in specific biological processes such as cell communication, regulation of transcription, transport and others. In fact, copies of one or more of these motifs can be found in over 90 percent of all known human gene sequences, as well as some genes of other animals where they associate with similar biological processes.

The report on this work “Short blocks from the non-coding parts of the human genome have instances within nearly all known genes and relate to biological processes” by Isidore Rigoutsos, Tien Huynh, Kevin Miranda, Aristotelis Tsirigos, Alice McHardy and Daniel Platt of IBM’s T. J. Watson Research Center, Yorktown Heights, NY appeared on April 24th in the early edition of the journal PNAS.


Using an unsupervised pattern-discovery method, we processed the human intergenic and intronic regions and catalogued all variable-length patterns with identically conserved copies and multiplicities above what is expected by chance. Among the millions of discovered patterns, we found a subset of 127,998 patterns, termed pyknons, which have additional nonoverlapping instances in the untranslated and protein-coding regions of 30,675 transcripts from 20,059 human genes. The pyknons arrange combinatorially in the untranslated and coding regions of numerous human genes where they form mosaics. Consecutive instances of pyknons in these regions show a strong bias in their relative placement, favoring distances of {approx}22 nucleotides. We also found pyknons to be enriched in a statistically significant manner in genes involved in specific processes, e.g., cell communication, transcription, regulation of transcription, signaling, transport, etc. For {approx}1/3 of the pyknons, the intergenic/intronic instances of their reverse complement lie within 380,084 nonoverlapping regions, typically 60-80 nucleotides long, which are predicted to form double-stranded, energetically stable, hairpin-shaped RNA secondary structures; additionally, the pyknons subsume {approx}40% of the known microRNA sequences, thus suggesting a possible link with posttranscriptional gene silencing and RNA interference. Cross-genome comparisons reveal that many of the pyknons have instances in the 3′ UTRs of genes from other vertebrates and invertebrates where they are overrepresented in similar biological processes, as in the human genome. These unexpected findings suggest potential unique functional connections between the coding and noncoding parts of the human genome.

[...] I will pursue this more perhaps in another post, but I point out, IBM may have unwittingly detected designs which would otherwise elude the fitness test. See: Invasion of the IBM engineers [...] Airplane magnetos, contingency designs, and reasons ID will prevail | Uncommon Descent
All we’ve really identified so far is the easy stuff - we have the equivalent of a hex dump from the human genome project and genes that code for proteins are the ascii strings which any idiot can pick out of a hex dump with no problem. The hard part is unravelling the code segments not the data segments. We don’t even have an instruction set yet to say nothing of figuring out what exactly its doing. -ds How marvellous! the way you put it!! I had forgotten what Hex dump contains, and it took me a while to understand what you say here. And when I understood, I recalled what Hex dump contains. And I had a good laugh for many, many, many minutes! O dear God. It's the biologists' job to read the ASCII. Who's job to unravel the CODE segment? Hey! the biologists are Darwinist lah! And the anti-Darwinists are...? Doctors, engineers...have to be software engineers! MatthewTan
Farsad, Let us agree that Rigoutsos et al. (and all who find mathematical patterns in the "junk") are *not* invaders. A better word for such a pioneer is "discoverer". Dr. Pellionisz pellionisz@junkdna.com Pellionisz
Dr. Pellionisz: "Regardless if one is an ID believer or not, I think the ID camp should avoid looking at “Rigoutsos” (a class by himself) as a “turf invader” (from mathematics to biology)" Well, the ID camp is not the side who is looking at “Rigoutsos” as an invader. The results from this computational research are totally in favour of the ID camp. On the other hand the Darwinist(Evolutionist) camp as usual is trying to classify such researchers as "invaders" and "outsiders". Farshad
Gentlemen, I bumped into this blog and think that it might be important for me to comment on the discourse, as a person with decades of professional career towards mathematization (geometrization) of biology (See my professional homepage at http://www.usa-siliconvalley.com). With doctoral degrees in computer technology, then in experimental biology, followed by that in physics, I am well familiar with "turf wars"; especially between biologists/biomedical R&D professionals who occasionally or even typically not overy "mathematics friendly" versus those professionals (one class is that of biophysicists) whose philosophy dictates that if the non-living part of nature could, to a large degree, enlightened by mathematics (yielding physics, even quantum mechanics, etc.) the living part of nature is also likely to be blessed by a trend towards mathematization. My first few decades yielded so-called a "neural net" algorithm (Tensor Network Theory, the lion share of the work I did as Prof. of New York University Medical Center, for 14 years) that not only provided experimentally testable quantitative predictions, but actual experimental verification occurred (independently, and by those young and skeptical scientists who really wished to prove the mathematical (tensor geometrical) theory of cerebellar function wrong. "Neural nets" are now a flurishing and widely accepted discipline (though inherently mathematical), to the extent that its initial opponent (the establishment of Artificial Intelligence) was declared "brain dead" by the very person who established the "AI lab of MIT" (Prof. Minsky). Subsequent to pioneering "neural nets", I anticipated that the Internet would pose formidable "Information Technology" challenges and opportunities. Thus, I spent some time at NASA Ames (I laid out the plans to fly an F15 controlled by a neural net, accomplished some $ M-s and too many years later), while I switched for a decade into an Executive (Software Architect) of a slew of Silicon Valley companies throughout the "Internet boom". Anticipating that Genomics will need all "Information Technology" it can get, I have been doing Genome Informatics since 2000. Since I am a scientist/technologist/entrepreneur, I don't wish to mix issues of belief (such as ID/ET) and/or philosophy with hard facts of science. Regardless if one is an ID believer or not, I think the ID camp should avoid looking at "Rigoutsos" (a class by himself) as a "turf invader" (from mathematics to biology), if for no other reason, since the facts he (and his group) found will put a "full stop" to the increasingly hollow "debate" in the last few years, if "Junk DNA" is really "Junk" - or actually treasure. (See a LOT more at http://www.junkdna.com) The facts, long heralded by Dr. Malcolm J. Simons (1987) that the "Junk DNA" was way too "patterned" to be random ("junk"), have now been irrefutably turned to undeniable evidence. 66 million motifs and 128,000 pyknon-s in the (human) DNA, *are there*. (Anyone can check the self-similar repetitions). Philosophycally, it is arguable if they are results of Creation, or Evolution (for one, I don't see them as mutually exclusive categories). However, the importance is their biomedical interpretation - at least for those hundreds of millions who are dying of "non-coding DNA diseases" (see http://www.junkdna.com/junkdna_diseases.html), or might be diagnosed only in the future with some of the most dreaded diseases of this sort (including Alzheimers' Parkinsons', AIDS - and New York Times put the number of junk DNA diseases to a potential 150,000). It is true that Dr. Rigoutsos "stuck with his guns" (bioinformatics), and "only" laid out what he found, without going much further. I would not, however, turn this against him, because this may well be one of the biggest strength of their paper. He does not just say "patterned" - but provides ample evidence to see, moreover to further discover such patterns (e.g. in DNA of other species, see http://www.pyknon.com). He is not biased towards any particular interpretation. That is a good thing. Especially, since some of us *are*. For instance, somebody mentioned that the "Pattern in the DNA" shows fractal properties. Rigoutsos' finding catapults such observations *and* my FractoGene approach (connecting fractality of the DNA with the fractality in organisms that DNA helps develop, in a causal manner, see http://www.fractogene.com) from what could be "labeled" as "Pellionisz' fiction" - into FractoGene theory *much* substantiated (albeit, admittedly, not [yet] mathematically proven by the Pyknon-s). Interestingly, ID could actually benefit from the massive paradigm-shift triggered by the Rigoutsos paper. Since the patterns of pyknon-s is a *fact*, it cries for explanation. Thus, people will no longer argue IF "junk DNA" is "junk" or Creation/Evolution put it there for a purpose. The most serious of the serious scientists (matematicians) will/are engage(ing) in diligent analyses *what* the implications may be, or (as FractoGene already does) what experimentally verifiable/falsifiable predictions can be drawn in consideration of these findings. Please don't regard mathematicians either "invaders" or even non-believers. Just think of Einstein (or Newton, or Maxwell, or Schrodinger/Heisenberg) who went on record with some pretty awesome algorithms (E=mc^2...) to show that "algorithms" are not alien to Mother Nature, at all. In addition, some (albeit admittedly not all) scientists are not only highly respectful of believers, but themselves (like Einstein or my late friend and fellow-Hungarian Edward Teller) are believers. Malcolm Simons stands validated by Rigoutsos - "there is a pattern in the junk, beyond his wildest dreams". ID may consider the victory of validation of existing patterns "in the junk" as their own prediction came through (that junk may serve some unknown function). Finally, one day, it may become a "life or death question" if we knew (in time) what some of the "glitches in the junk" are doing to the genome, to make us gravely ill, or at least significantly affected by "Junk DNA diseases". We are all in the same boat, believers or non-belivers. Dr. Pellionisz Pellionisz
Farshad, I don't know whether there is a theory for the evolution of flight, let alone a testable one. I guess insects (or their ancestors) were the first flying animals, but how the evolution of the first flying insect occurred, I have no idea. There probably are some theories out there. There is not a lack of engineers in biology though, as far as I know. I know some engineers who are working on the hydrodynamics of fish and the aerodynamics of birds. They are trying to figure out to what extent the body shape of these animals is "optimal" is some sense, assuming that NS optimizes body shape I guess, which sounds like a reasonable assumption. Raevmo
Raevmo, I do not mean that all engineers are opponents of Darwinism. There are many engineers who believe darwinian mechanisms are able to explain the mechanisms and the complexity, however I highly doubt that theories like evolution of flight are challanged by specialized engineers from relevant fields. The problem is that such evolutionary claims are simply assumed to be true without taking the technical difficulties into account. Do we have a testable model for evolution of flight which is throughly tested and verified by engineers? Farshad
Farshad, one of the great evolutionary thinkers, Sir John Maynard Smith, was an aeronautical engineer by training. Raevmo
When I originally read this PNAS article what originally caught my eye was that (1) methods developed for use in Computer Science easily cross over to Biology and (2) the software is designed to search for information that shouldn't occur by chance. Patrick
The bio mechanisms in life forms are closely related to their relevant engineering fields. No one bether than an aeronautical engineer can understand the flight of bumblebee. It is closely related to the aerodynamics not pure biology. The main reason that evolutionary biologists want to keep away engineers is philosophical not scientific. An aeronautical engineer may find the idea of evolution of flight totally absurd, as the rules of aerodynamics might be too complex to allow an step by step wing development. Indeed it may really turn out that flight is also an IC system. The real headache for Darwinists is the fact that many engineers are quite skeptic for their proposed evolutionary mechanisms. As more engineers become interested and involved in this field, more exposure of fake darwinian mechanisms will become inevitable. Farshad
"The only excuse I’ll offer is the shear frustration from my perspective as an aspiring biologist whose also savy in c.s./stats who repeatedly hears that engineering/physics/compsci types are necessary to solve the problems that plague our field." They are necessary, BUT so are you. In the workplace you will meet all types. Whenever we had adjustments, new people were brought into the mix. Now, when I was young, a few times I made the mistake of following some who would be against new talent. What I learned later - is to learn from the new talent. So, great - your CS/Stats savvy, that's great! It means you have an upper hand on others and can work with CS people at a higher level and learn more from them in their fields. "This isn’t just promulgated on ID blogs, it’s widespread in the scientific establishment. t’s as if nonbiological scientists think we’re all just busy twiddling our thumbs and disecting frogs until someone comes along and shows us how to do proper hard science." Personally, I'd never think that at all. Its just a revolution taking place across all fields. I remember old engineers complaining about computers and CAD/CAM. But the ones who didn't complain, bought their own computers, learned the new CAD tools actually had the new kids beat by far - because they had rl/experience that CAD could not give anyone. Change/Info increase is increasing exponentially and people must train themselves on the fly. So, sounds like you'll need to sign up for a few night classes or attend lectures. Ongoing education is a must in your field and most. But its exciting! Otherwise, I got a paint brush for ya ;-) "There are even funds earmarked for engineers/phys/mathematicians to learn biology in order to set us straight, but no such monies–to my knowledge–for biologists to acquire the tools they need themselves." Excellent point, so write your Dean and other Associations to improve the educational direction. "Scientific snobbery is embedded in the system at all levels." I tend to think of it as people problem which can become institutionalized from on high. "The *problem* is that biological systems are really really complicated. (You fellows here should appreciate that, at the very least.) Some of the worst papers I’ve seen are from physicists forraying in biology." For some bio-systems are easy/others complicated. For me, the complication is created by the scientist at times, with arcane nomanclature and systems that are not intuitive. I do not think anyone set out to make it so. You live in exciting times where much will change in your field. I do not doubt your observations of 'outsiders'. But, imagine working with someone like them who are as inspired like you to learn new things about life? But they took a different path. Now - instead of coming to a fork in the road where you both take different routes - look at it differently. Imagine the opposite direction: you come from three paths which circle like a mixmaster into a large road on the same direction together. One is engineering, 2nd is math, 3rd is cs/linquitics. They get extra funding to learn about biology. You didn't. What will you do? Hold a grudge against them? Or learn from their expertise? "The problem is that there is a huge background of information concerning biological systems to properly integrate in your mind before embarking on analytical adventures. As a result, many nonbiologists make the mistake of oversimplifying systems b/c they problems they are trained to deal with have a limited number of “moving parts.” (metaphorically speaking, of course)" So you know something they don't. Voila, you can teach each other. If 'they' happen to be arrogant, time will take care of them. But if they're open, they'll want to learn just like you. Michaels7

"As far as chemists, physicists, and computer scientists are concerned biology is a cross between pipetting and stamp collecting. You really need a second major in a hard science for anyone to take you seriously." ;-) -ds

Sadly this is the prevailing perception. The funny thing is, according to this sociology professor's seminar I attended, some researcher--I need to dig up this reference--actually set out to rank academic disciplines according to how their members scored on standardized IQ tests. Just to address some of the anecdotal notions of what departments have the sharper tools in the shed. As expected, the lowest ranked were among the humanities,(e.g. psychology,history,literature) with the exception being economics, which scored right up there with basic sciences. At the bottom of the totem pole in science, surprisingly enough, was not biology but chemistry. Chemists grouped with the upper tier of humanities and below econ. And yet no one makes fun of chemists because the discipline fits the stereotype of what "hard science" is supposed to look like. In my opinion, there's an intrinsic messiness in biology that makes it seem softer. Partly because there are fundamental limitations in how one can query the target system without killing it.(or, in the case of evolution, dying of old age while waiting for an answer). And, with notable exceptions, the rules and behavior don't translate well--if at all--into mathematical language. This last point being the litmus test for respectable science.

So yes, more of us will be getting second degrees. Not because it's *necessary* for biology to progress, though. People who possess the proper motivation and aptitude for research will learn what they need to know to answer the questions they want to address. That's my philosophy, anyhow. It doesn't matter what your degree is in; it's what you produce. People will, however, increasingly be stacking on extra degrees in order to be taken seriously.

Get your second degree in computer science. Humans aren't going to be able to decipher the genome without massive computational resources and you don't want to be at the mercy of computer geeks to turn your ideas into algorithms. Computer science is fun, up to a point, anyhow. I didn't get sick of it for 20 years at 70 hours per week. The last 5 years was pure torture. -ds


"Don’t forget that in the design paradigm we should expect to find static and dynamic link libraries in the non-data segments of the code and if the front loading hypotheses is true we should find some template libraries containing templates of things never expressed in the ancestral lineage. Templates of things never used in the past that could be used in the future would be unambiguous evidence of design - one thing NeoDarwinian theory can never be twisted into explaining is anticipation of future needs. All we’ve really identified so far is the easy stuff - we have the equivalent of a hex dump from the human genome project and genes that code for proteins are the ascii strings which any idiot can pick out of a hex dump with no problem. The hard part is unravelling the code segments not the data segments. We don’t even have an instruction set yet to say nothing of figuring out what exactly its doing."

Your statement about unexpressed templates is an interesting one. However, the keep-design-out-at-all-cost folks would have a ready answer: the templates were developed and used in the past by unknown and now-extinct organisms. What else *could* they say. Again, RM+NS can "explain" it, since it can "explain" anything, despite absence of evidence.

RM+NS is the naturalistic-explanation-of-the-gaps ideology. I want precise detailed blow-by-blow accounts of how bio-processes evolved. If they can't provide them, their ideology is no better than "God did it."

Ya think they can shrug off an amoeba with a genome that contains the recipe for a neuron? :razz: -ds


I clearly stretched my case and concerning the detrimental nature of the "invasion" of nonbio sorts into the realm of biology, and I didn't give the proper acknowledgement to the past and continuing contributions they make to the field. For that lapse of judgement, I deserved admnonishment. And no, I had no earthly idea the extent of the resources IBM was putting into bioinformatics--aside from my acquaintance with bluegene. The only excuse I'll offer is the shear frustration from my perspective as an aspiring biologist whose also savy in c.s./stats who repeatedly hears that engineering/physics/compsci types are necessary to solve the problems that plague our field. This isn't just promulgated on ID blogs, it's widespread in the scientific establishment. t's as if nonbiological scientists think we're all just busy twiddling our thumbs and disecting frogs until someone comes along and shows us how to do proper hard science. There are even funds earmarked for engineers/phys/mathematicians to learn biology in order to set us straight, but no such monies--to my knowledge--for biologists to acquire the tools they need themselves. Scientific snobbery is embedded in the system at all levels. The *problem* is that biological systems are really really complicated. (You fellows here should appreciate that, at the very least.) Some of the worst papers I've seen are from physicists forraying in biology. The problem is that there is a huge background of information concerning biological systems to properly integrate in your mind before embarking on analytical adventures. As a result, many nonbiologists make the mistake of oversimplifying systems b/c they problems they are trained to deal with have a limited number of "moving parts." (metaphorically speaking, of course)

Although I did sadly and mistakenly leave that impression, I didn't mean to insinuate that the team at IBM, *shouldn't* be addressing biological questions in the manner they are... Only that going at it without bringing in folks well-versed in genomics and fundamental biology can lead to bad science b/c key pieces of the puzzle are too easily neglected. Even bringing in the wrong *kind* of biologists might lead you astray. It's a really broad field. These IBM guys resumes are more than impressive. No question about it. It's just that in my quick glance before posting my rant, I didn't see anyone involved who was fundamentally a biologist. Maybe I missed someone. And this whole issue of factoring biologists out of biological problems pushes my buttons.

As far as chemists, physicists, and computer scientists are concerned biology is a cross between pipetting and stamp collecting. You really need a second major in a hard science for anyone to take you seriously. ;-) -ds great_ape
arrogance and conceit go hand in hand with deep ignorance. Erudition is not the same as "knowledge", and it is why so many scholars are arrogant. The dictum 'the measure of wisdom is the recognition of one's ignorance' might be a useful insight for such know-it-alls who seek recognition through denigrating the insights of their peers. tinabrewer
"I think the young man was unaware of the scope of IBM’s research programs and the people they employ. That’s understandable." Dave, I know and I'm being sincere - that g_ape's sharp. More knowledge in his young mind than I'll ever attain in biology or genetics. But I hope he keeps an open mind. Blanket statements re: Math/CS professionals invading Biology are robotic repeats of old-line neo-Darwinist and tee me off a bit. Its an outdated worldview, misleading to students and future scientist to hear such rubbish. One does not survive future trends in bio-tech without the best in all fields integrating knowledge and resources. Letting go of some ego to work with others on new ideas. Its a team effort. Isidore and Zhou have degrees in physics, math and chemistry, but their group members have vast knowledge in biology and life sciences, plus the collaborators vary far and wide. Talented professionals cross lines of work in their careers. Expertise in one field can lead to great insight in other fields of work if one is lucidly aware of pattern recognition and efficient methodology transfer. In fact, the greatest leaps in science at times occur precisely because someone with scientific pedigree in another field steps in with a new approach. This is true especially at times of great movement in fields like genetics. Demand/money draws the brightest, hardest workers who produce doctoral quality work every single day. Math, CompSci, even EE's(signal processing) and nano engineers will come to the forefront of new genetic breakthrus. IBM's research is well planned for the future. Of course, there are areas where competitive research emerges in Universities. I was to rough on academics with a broad brush stroke. Funded by foundations, commerce, or DOD, they do serve as incubators and research hubs. But business is demanding, at times cruel and unrelenting in requirements to constantly produce better product. Companies need people to think outside the box, not in it. Otherwise they do not survive. Arrogance may serve some rare genius, but most people have to work together across boundaries. In fact, its quite efficient - team work. Managers of such teams put together by IBM do not have to be "degreed" biologist(just ability to comprehend Genetics at detailed levels) and the proof is in the production. If Isidore's team was not producing, they'd quickly be canned. To much money is riding on it. Grrrr correction to above post(repute=rebuke). Michaels7
Sorry about that! -ds No problem, I wrote an allegory a while ago and thought of you when I did:The Law of laws and the predestination of its effects. It has all the subtely of a sledgehammer to the forehead in using notions about a programmed unfolding of events in a Christian allegory. And I shrug at that. By the way, thanks for the line about trying to design flying things that run on sunflower seeds before sitting in judgment on the way things are designed and the like as Darwinists often do, I've made use of it. mynym
Smiles... thanks J for that chuckle. ;-) Michaels7
Perhaps they will babble about how wonderful and precise the Natural Selection is working and nature is the ultimate “software designer” and “the programmer”. Exactly, all apparent optimal design will be explained by the near infinite powers of natural selection* while apparent subopitmal design is to be mixed in with negative theology and more of the sort of "explanations" typical to those who seem to be easily overwhelmed by their own imaginations. *Which is itself a metaphoric polution of language given that there is no evidence of Nature "selecting" anything and loading down differential rates of reproduction with a whole philosophy of Life is absurd. There seems to be a philosophy about ultimate "selection" and the explanation of all that is in the background that Darwinists want assumed based on the mere fact of differential rates of reproduction. The contradiction becomes clearer once they begin to speak of metaphoric Blind Watchmakers and the like that supposedly evolve organisms that see, select to live, or select to make up stupid stories about how pretty much nothing "selected" everything. There is no such thing "blind selection," yet they use contradictory language. Then they place the sight that is necessary for selection anywhere but where it is empirically observed to be, e.g.: "....from the point of view of the selfish genes themselves, there is no paradox." Genes with points of view, and they're selfish too? Next thing you know there will be little gene diplomats to make peace among the selfish genes, as well as half-wit genes who believe that blind processes give rise to both the warring selfish genes, the peacemakers, as well as all that is genetically. Isn't it ironic that Darwinists complain of vitalism when confronted with different ideas based on empirical facts, yet use silly and blind metaphors to explain sight that certainly seem to be vitalism in a cheap tuxedo? (Not that there is necessarily anything wrong with vitalism or cheap tuxedos.) mynym

great-ape said,
"If they had a proper background to be doing this sort of work..." Ask the researchers if they understand the obvious connections you make.

"So yes, this paper in PNAS is a lovely example of what can happen when engineers/computer scientists invade biology."

I have no doubt you're one sharp minded individual.

Overview of BioInformatics and Pattern Discovery "In Broad Strokes".

Individuals/institutions embrace them. Collaborators utilize concepts of Bio-Dictionary and Isidore's team research:

Lead researcher Isidore Rigoutsos; 14 patents, multi-articles, peer-reviewed in broad areas of expertise: Journal of Molecular Biology and IEEE:

List of who disagrees with g_ape's conclusions of those who "invade biology":
Assoc. Editor Genomics 2003-present
Assoc. Member Gene Therapy and Molecular Biology, 2004-present
And the list goes on....

Ruhong Zhou, PhD. Chemistry, 7 patents, leading researcher, publishings including Nature:
Working with protein folds, ligan bindings and molecular structures. But he could use some obvious insights.

"Also, the only reason I’m hiding my identity is that I’ll be on the job market soon, and it’s tough enough already for us young folks. I don’t want to upset anyone, at any point on the philosophical spectrum, that might have the potential to impact hiring/tenure."

Now, this is a wise statement young man, I'll grant you, but lets look closer at the fear factors involved on two sides of the coin. It is arrogant statements like those you made about researchers at IBM that are embraced by the likes of Panda and PZ in academia today on one side of the coin. The Do Not Step in My Territory crowd.

But IBM and foundations like HHMI must adapt to survive in a free market society. They must bypass outmoded concepts in stuborn minded academics or go extinct. There is a reason many end up reclusives in Ivory Towers. Its not because they love educating young minds so much, as it is they cannot adapt to real world pressures. Its easy to teach the same concepts over and over again to blank minds not schooled well in the art of discernment. Indotrination is well understood by Mao, Marx, Lenin, Stalin, and others.
This is why the old paradigm of Darwinism survived for so long. But with internet, free speech, they can no longer regulate what is indoctrinated by media gatekeepers and dusty institutions. Its a mind-numbing occupation if one is not open-minded to view outside the box like Dave states. Darwin's black box is also a similie for blind arrogance imho.

Now, to the other side of the coin. Look into the real life consequences of Richard Sternberg. The Smithsonian scientist(neo-Darwinians) with arrogant hyper-inflated Egos of the worst kind abused him ruthlessly because he allowed a peer-reviewed paper into publication which went against status-quo neo-Darwinist attitudes and atheist leading prima-donnas like Eugenie Scott.

This arrogance grows from small seeds like the statements you made regarding the "invasion of biology" and therefore linkage by association to being unqualified without the least bit of support or research effort on your part into the background of the researchers of this paper.

This is why I laid out the links I did. To repute your absurd inuendo and false reductionist statements. See for yourself false statements you made about boundaries in science. This grows out of the materialist-reductio crowd who cannot see beyond their bio-geek, self-servicing, neo-Darwinian lobotomy. Isidore and others like him recognize a holistic appoach to life sciences irregardless of McEvo or little Evo.

Neo-Darwinian views are the dominant dogma in today's scholastic associations and academic hallways. So you have no fear of being discovered for such ascerbic, outdated comments you displayed in this post. On the contrary, this side of the coin is yours to drop in the hand of militant evolutionist. But dare you to mention the word ID, I warn you then to read up on Richard Sternberg who is himself an evolutionist, scoured before the alter of Darwin.

However, if you are deciding to walk down the the path less traveled in more advanced areas where capitalism is king of innovation - maybe you are wise for keeping your identity hidden. Because bizness does not wait upon ideological devices to modernize. They could care less about neo-darwinian rants of what must be taught. This is why a President of Intel could care less about SciAm editors opinions on macro-evolution. It is completely unworthy of progress in today's science and will not amount to a hill of beans for the people Intel must hire today in the workforce.

Bizness forges ahead despite prejudice and antiquated sentiments of decidedly political overtones. This is why free societies based upon free markets produce innovative solutions to problems. If ideas like Dembski's, et al. will not be recognized in Academic dusty halls, it certainly will make its way heard in bizzzznesss.

If it achieves new breakthrus in which RM/NS cannot produce then we will know about it eventually in the halls of academics after the fact. After the innovation. Remember, schools do not lead us in innovation. Business does. Business in a free market combines with universities to fund and lead new innovation. The free market of ideas leads, not dogmatic assertions.

IBM, HHMI and many others provide funds and scholarships exactly for interdisciplenary graduate level programs which demand that math majors and computer scientist - indeed cross over the boundaries of biology. They bring together math, physics, ee's, me's, ce's, various compsci's and all other areas in life sciences and genetics to focus teamwork and wide areas of knowledge in the hope of unlocking the Code of Life. Not only is this the future of where you must collaborate with others, it is the present as you can see by the links I provided you.

While you're looking to enter the job market - these people do it. A company like IBM does not invest its money and research on projects without sure return on investment.

These good people you so easily put down as 'invadors' are producing research that is breaking down old boundaries, shining light on areas once hidden, and are being utilized by Biological Sciences at top levels of research in academia and private enterprize.

So, don't be so quick to pull the trigger. Your future is much more bright if you will keep an open mind to the New Design Paradigm. The very research being done by thinkers like Isidore are paving the way for your future.

All the best in your job search.

I think the young man was unaware of the scope of IBM's research programs and the people they employ. That's understandable. Who would guess that IBM has been funding bioinformatics research to the tune of hundreds of millions of dollars beginning in 2000. With greenbacks like that on the table you get the best talent in any discipline you need beating down your door. -ds Michaels7
According to Dawkins, no function is just fine with NDE since the purpose of DNA is to survive:
...it appears that the amount of DNA in organisms is more than is strictly necessary for building them: a large fraction of the DNA is never translated into protein. From the point of view of the individual organism this seems paradoxical. If the 'purpose' of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing. Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true 'purpose' of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA. -- Richard Dawkins, The Selfish Gene (1976), p. 47. :-)

/"Exactly what was the prediction made? Was it something other than “some use will be found for the parts of the DNA for which a use has not yet been found”?
What group of ID researchers actually carried out the empirical verification for which they should receive credit?"/

There are many predictions made by IDist/Creationists that Junk DNA can't be just Junk, however it'no surprise that you will not be able to see any of them in any scientific issue until engineers from IBM made similiar claims.

I'm a software engineer and my own humble personal understanding of this convinced me that Junk DNA must be an advanced control mechanism. The distribution of data in Junk DNA has a fractal distribution that resembles codes/words of a language, a control mechanism or a program.

If DNA is a program then it's no wonder that it must contain two parts. CODE and DATA. The non-coding pattern resembles what we call CODE in a computer program. The coding pattern is the output or the DATA. The role of non-coding "Junk" seems to be a regulator or a complex program that sychronizes the timing and order of operations in a cell. I also believe that Junk DNA has a very important role in regulating timing of the complex process called "Cell Differentiation".

I'm not a biologist and there is no way for me to verify this, but those who are directly in field will never take such claims seriously. The problem here is precommitment of biologists to the Blind Watchmaker philosophy. Their first assumption was that non-coding part must be junk and this "Junk DNA" argument has been used by them against ID several times. Now it is clear that their argument was "Junk" not the DNA.

I wonder if in near future it turn out that Junk DNA has a very important role in inter-cell processes, what will be the new make-up that Dawkins types will find for their theory? Perhaps they will babble about how wonderful and precise the Natural Selection is working and nature is the ultimate "software designer" and "the programmer".

Don't forget that in the design paradigm we should expect to find static and dynamic link libraries in the non-data segments of the code and if the front loading hypotheses is true we should find some template libraries containing templates of things never expressed in the ancestral lineage. Templates of things never used in the past that could be used in the future would be unambiguous evidence of design - one thing NeoDarwinian theory can never be twisted into explaining is anticipation of future needs. All we've really identified so far is the easy stuff - we have the equivalent of a hex dump from the human genome project and genes that code for proteins are the ascii strings which any idiot can pick out of a hex dump with no problem. The hard part is unravelling the code segments not the data segments. We don't even have an instruction set yet to say nothing of figuring out what exactly its doing. -ds


Let's look at a particular episode in science: the adoption of relativity theory. While elements of Einstein's theory were present in the work of earlier scientists, it was Einstein who put it together in a form that a) was easily accessible (by those with the appropriate background) and b) produced predictions that others could then construct experiments to test. For example, gravitational lensing (bending of light by a massive object) and gravitational time dilation (gravity can affect the rate at which a clock ticks). And though more accurately termed a postdiction, the theory of relativity could also calculate the orbit of Mercury (an orbit with irregularities not easily accounted for by other theories). There have been many tests of relativity theory, all of them derivable from the theory.

Could Einstein's theory have been accepted without these tests? Probably not, or at least not easily. Moreover, the way in which the predictions were arrived at is important: Einstein could show explicitly how his theory would lead to a particular observable phenomenon. He did not rely on something akin to "The speed of light is constant, therefore clocks will go slower in a gravitational well." If he had, scientists would have greeted him with a collective "huh?" It is also important to note that Einstein was not an experimentalist -- he did not set up his own experiments to test his ideas -- but he could express his ideas clearly enough so that others could see not only the ramifications of his theory but also how to test them.

Now let's look at the situation with ID. To claim the PNAS article in support of ID, one would need to show how the theory of ID leads to the prediction that was supposedly experimentally verified. How does the prediction "uses will be found for 'junk' DNA" follow from the theory "life/the universe/everything was designed"? (Yes, those are very general statements -- feel free to fill in the appropriate details.) Perhaps DeWitt does this -- if so, I'm curious to know the details.

Also, it costs nothing to derive the consequences of a theory and from those develop experiments that might test the theory. Make a list of predictions, show how they are consequences of the theory, and at the very least make these available for others to view (and possibly test themselves). In any event, lack of funding is a red herring, distracting away from the central question of what are the testable consequences of ID.

The testable consequences of ID are that irreducible structures exist in biological systems which cannot be produced by any means devoid of intelligent agency. Structures put forward as irreducible include the bacterial flagellum (a simpler case) and the protein factory formed by DNA and ribosomes (a more complex case). Are that any parts of this you don't understand? Junk DNA having function isn't really a prediction, it's a paradigm engendered by the principle that intelligent agency *as we know it* isn't likely to be needlessly wasteful of resources. And whether or not junk DNA has a function or not RM+NS will happilly accomodate it either way. There are already myriad ad hoc hypotheses that are perfectly compatible with RM+NS ready to explain useless DNA as well as ad hoc hypotheses ready to go to explain the absence of it. This is really the history of RM+NS - it doesn't predict it explains the facts after the facts are discovered because it is no longer theory it is dogma. -ds Kipli

If there's no such thing as an (effectively) neutral substitution at the DNA level, there's a silent epidemic that's destroying humanity. People are walking around in the population that are polymorphic for chunks of chromosomes missing, segmental duplications, retroviral insertions,and all sorts of frightening nucleotide differences. They seem to get along okay, though. You might argue that it's functionally affecting their personality in some as-yet unknown way. Neutrality seems a more parsimonious explanation for their viability in my opinion.

Also, the only reason I'm hiding my identity is that I'll be on the job market soon, and it's tough enough already for us young folks. I don't want to upset anyone, at any point on the philosophical spectrum, that might have the potential to impact hiring/tenure. Once established, I'll have no problem commenting and/or blogging under my real name. I just don't want to wait that long to enter into the fray because I believe such discourse is important for testing and otherwise refining my thoughts on various subject matters.

As for how complex instincts are encoded in DNA, I don't know. As you suggest, it is a lot of info to encode. Maybe these IBM guys have indeed stumbled across a new regulatory network that might help explain it. I'm just saying there's very likely a more simple explanation for their data, and they must dispense with it first before proceeding to such grand speculations. As for *how* this instinctual info would otherwise be encoded, IMHO, the thousands of genes that exist, along with their splice variants and regulatory systems, can be tweaked like nobs and dials here and there to yield all sorts of behavioral tendencies. Instincts are ultimately behavior, and lots of tweaks you make to the biosystem via altering the genetic sequence, if they don't negatively disrupt basic biology, can result in behavior changes (output). So RM+NS stumbles across a good tweak that results, when combined with the environmental input, in a useful instinctual behavior. And it locks it in via selection. It may seem complex when analyzed behaviorally, but, biochemically, it was just the twist of a nob and the flip of a switch at a couple of places. Minute changes at some levels can make big differences. And their information storage requirements, because much of the pertinent context is in environment and existing biogoly, could be remarkably low. Behavioral complexity with very low information overhead in the DNA.

If there's no such thing as an (effectively) neutral substitution at the DNA level, there's a silent epidemic that's destroying humanity.

Very good! The silent epidemic is called "extinction". In the natural course of events it's almost guaranteed that humans will eventually become extinct. This is the fate of 99.9% of all species that ever existed and probably 100% given sufficient time (some just haven't been around long enough yet). All hominid lines except us have already become extinct after very short durations.

I figured you were a young biology major because you have the dogma from a few textbooks down very well but you haven't yet begun to cross correlate to come up with things you didn't learn by rote. That takes time, broader exposure to knowledge, and a high IQ in pattern recognition. I think you're just missing the broad exposure. You had a really good breakthrough with the silent epidemic! That was original thinking on your part but you weren't the first to figure it out and you didn't correlate epidemic with extinction. You have to think inside the box to get good grades. To make a real mark in your profession you must think outside the box.

Twisting knobs and tweaking dials is an awfully flippant answer for how instincts are encoded in the DNA molecule. If by that you mean to say that complex instinctual behaviors are somehow encoded in the DNA molecule and we don't have a clue how or where the encoding is accomplished then I'll agree. It's okay to admit the unknown. An important and basic part of being really smart is knowing what you don't know and being able to admit the gaps in your knowledge. There's an immensity of complex instinctual behaviors that are somehow encoded into the molecule of heredity. You might find some hormones that disable or trigger the submission reflex in a dog but you have no clue how he knows that he should roll over on his back and avoid eye contact to communicate submission. That is a very complex response requiring the coodinated action of hundreds of voluntary muscles. And it's no less remarkable that the dog he's submitting to knows it is an act of submission. And that's just one tiny bit of instinctual pack behaviors that dogs are born knowing as sure as they are born knowing how to bark and wag their tails. -ds


"RM+NS explains junk DNA with or without function. It explains everything! Thus it explains nothing. -ds"

Uh, no. As the Mayr quote points out (if you would take the time to actually read and understand it), junk DNA with no function would pose a problem for RM+NS.

The researcher who coined the phrase "junk DNA" pointed out shortly afterwards that he didn't call it "trash DNA". The difference being that you take out the trash, but save junk in the attic, because a use for it might be found later.

So, as usual, you ID types start out with a misconception based on reading a jargon term without bothering to research its precise meaning in the field. Biologists have long assumed that some function would eventually be discovered for so-called junk DNA. References predicting this go back as long ago as 1977.

Exactly what kind of "problem" is it for RM+NS if there are non-functional stretches of DNA? I can't wait to hear this! You might want to keep in mind I'm going to be pointing out all these explanations for how functionless DNA can become resident in the DNA molecule and note that none of them pose "a problem" for RM+NS. -ds


By the way, there will be a Great Doom one day. That much is certain, then all the people who predicted the end of the world as we know it will finally be right.

Okay, cool. This comment didn't get trapped in the moderation queue. You must have used a spam keyword in two comments in a row. Sorry about that! -ds mynym

What group of ID researchers are actually trying to verify any of those predictions?

Irrelevant. Yet I suppose that now they cannot get any State grants or money for such research. That is what the actions of fear-mongering bigots who argue that treating elements of ID as science will lead to a theocracy and so on are about, after all. Now you demand research from a group of ID researchers? If it was cited then you'd probably point out that they receive private instead of public funding and claim that taints it. I've noticed something about the Panda's Thumb and the NCSE types, they're very concerned about how ID gets funded and this sort of thing. In fact, their main concern seems to be politics and not the empirical facts. Maybe that was the design of their site all along, yet it bores me. But let's play the political game for a moment. It is the NCSE types who often work themselves into a position to make use of the State for funding and supposedly that indicates that everything they say is in the public interest. It isn't all in our interest though and sometimes it degenerates into crises mongering for more funding: "Watch out, epidemic! Don't eat this it will kill you. No wait, yes eat because it is good for you! No, not that, this again." "There's going to be a New Ice Age by the mid 90s. Wait...well, the mid 90s only passed without an Ice Age because of global warming. And now it is too late to do anything to avoid the next Great Doom that awaits us! Okay, things seem to just keep going on but we're all going to die eventually. Great Doom, I says!"

Supposedly Leftist scientists' State funding and legal control of State schools and the like means that they are pure as the driven snow, yet the private funding of any who oppose them means that their science must be tainted and the like. Is it really that surprising that they turn out to tend to be socialists and Leftist almost to a man? Maybe it is their funding that taints them, just taints it all. This is all irrelevant to the empirical facts but if you're going to dance a political and legal dance, then be ready for the politics of it all.

Mynym - your last two comments were caught in the moderation queue and I don't know why. I don't have your name in the moderation list so I didn't want you to think you'd done anything to warrant moderation. It may that your comments contained a sequence of letters that matches a spam word but none were obvious to me and that usually doesn't happen twice in a row. -ds mynym

Exactly what was the prediction made? Was it something other than “some use will be found for the parts of the DNA for which a use has not yet been found”?

Just last week I watched a DVD put out by creationists called 'Junk' DNA is not junk featuring a lecture by Dr. David Dewitt as I'm researching creationism. He goes into the empirical details based on the perspective that "junk DNA" will generally turn out to be like inane Darwinists claims about numerous "vestigial organs." If I had a book I would quote it because it is been my experience that in general Darwinists have never actually read or researched the work of creationists or ID types either. It seems that only some charaltans at the top read a little bit or go to some lectures, murmur about science to those easily wowed by the very word, then the Herd runs whatever way they tell it to while mooing about whatever it was told.

Or they do what PZ Myers' did in his recent posts about his attending a lecture by Kent Hovind, who is a rube, so therefore all creationists are rubes and so on. The funny thing is that even in his reply to the rube Hovind that makes liberal use of ad hominem against him for being a rube he still makes mention of the old gill-slit canard and the like himself. Hovind creates the ethos that creationists are rubes while Myers creates an ethos that all Darwinists are Leftist academics and pointy headed charlatans more interested in their own intellectual vanity than the truth. Just as a political matter, I would bet on the populist rubes there with their dumb folksy jokes and all. Perhaps like most geeks that inherit the earth Myers is socially and therefore politcally inept, so he cannot see how the populist will always win politically. Historically, the only way that Leftists like Myers have ever won politically is from forms of socialism that take a totalitarian top down approach of indoctrination as in Nazism and Communism.


Data belongs to everyone. You seem to be struggling under the common fallacy that ID theorists can’t use data unless they do the gathering of it. That’s utter nonsense and shows a basic misconception of how science works.

No, I'm not saying that. I originally read mynym's comment as claiming that ID proponents should get credit for an empirical verification. They should not, since they did not carry out the verification. Credit for a prediction, perhaps, but not for the verification; though I still don't know what the prediction was other than "we'll find a use". However, when I read that comment again I can see how it doesn't mean what I took it to mean.

In any event, my other questions were more important. If they can't be answered, then one must wonder about the status of ID as science. Are ID `researchers' merely piggybacking on the work of others? Almost all of the results I've seen posted on this blog that are supposedly related to ID are performed by scientists who were not specifically investigating an ID claim. Instead, their results are co-opted as supposedly providing verification of an ID prediction. While that might be appropriate in some situations, it's not how science works in general.

Data may not belong to one `side', but it makes for a curious situation when only one side is coming up with the data.

You don't think any scientists who believe life was designed come up with data? The problem is that any scientist who dares interpret the data in a way contrary to the evolutionary dogma risks considerable damage to his career. Few are willing to risk that over something they really don't care about as hardly anyone actually has a vested interest in the mechanism behind a past evolution that is a non-repeatable one-time event where the proposed mechanism works so slowly its larger effects (the creation of novel cell types, tissue types, organs, and body plans) takes millions of years and can never be observed taking place in any practical way. -ds Kipli
chunkdz@3 What I wanted to say is in essence what you have demonstrated: any given biological discovery is hijacked by Darwinists as evidence for their version of evolution. A Darwinist once said that "Genetics is at the core of evolution". However Dr Jon Wells correctly said that Mendel had no use whatsover of evolutionary knowledge to formulate his theories. Once again, this goes in line with one of the former trends: "Evolutionary prediction is an oxymoron". Mats

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