Andrea Bottaro posted Entry 3249 on July 19, 2007 02:10 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/3237

Over at the Discovery Institute’s Media Complaints Division, Casey Luskin is keeping himself busy trying to fudge assert that the notion of “junk DNA” (which ID advocates consider erroneous, despite the fact that strong, independent lines of evidence indicate that a large fraction of genomic DNA in most eukaryotic organisms is phenotypically non-functional) was the result of application of Darwinian principles.

Several people (e.g. T. Ryan Gregory, Larry Moran and Steve Reuland, as well as myself ) have already pointed out that, on the contrary, a strict application of the Darwinian paradigm, also known as “panselectionism” or “adaptationism”, led many prominent evolutionary biologists to initially resist the idea that some DNA may be non-functional, an opposition which was later mostly lifted (sometimes partially, as we will see) by the progressive acceptance of neutralist views.

Indeed, as late as 2001 Ernst Mayr, one of the “deacons” of Darwinian adaptationism, thought it appropriate to state, in “What Evolution Is”:

A remarkably high proportion of DNA in the chromosomes seems to perform no obvious function, such as coding for RNAs and proteins. Such DNA, probably incorrectly referred to as “junk,” is estimated for humans to be as much as as 97 percent of the total DNA. […] There is widespread belief among Darwinians that such apparently unnecessary DNA wouldhave been eliminated long ago by natural selection if it did not have some, as of yet undiscovered, function.

(E. Mayr, 2001, What Evolution Is, Basic Books, p. 108)

[Note that for Mayr, never much the pluralist, true DarwiniansTM essentially included only strict followers of the Neo-Darwinian New Synthesis, with minor - ahem - adaptations.]

In “The Growth of Biological Thought” (1982), Mayr also rejected the idea that “junk DNA” may be largely composed of parasitic, “selfish” elements, which, while not strictly non-functional, only serve the goal of their own propagation. Such an idea, Mayr wrote:

is inherently distasteful to a Darwinian. Surely natural selection, a Darwinian would say, should be able to come up with a defense mechanism against such an expensive type of parasitism.(E. Mayr, 1982, The Growth of Biological Thought, Belknap Press, p 579; quoted by Maxine Singer in From Genomic Junk to Human Disease, Proc. Am. Phil. Soc. 138, 11-24, 1994)

In 1971, shortly after the seminal papers by Kimura, King and Jukes and others had formalized and begun to test the Neutral Theory, Mayr threw the gauntlet with words that would fit perfectly in the mouth of most of today’s ID advocates:

More and more sites even in the largest molecules are found to have specific functions. A “functionless site” is simply one the function of which has not yet been determined.

(E. Mayr, Populations, Species, and Evolution , 1971, Harvard University Press, p. 127; cited by Gert Korthof .)

So much for the claim that “junk DNA” was a direct consequence of Darwinian ideas.

But there is a far sweeter contradiction at play here.

On the one side, ID advocates certainly like to claim that the functionality of “junk DNA” is a direct and necessary consequence of the design approach. For instance, in a paper in the now defunct “peer-reviewed” ID journal PCID, Jonathan Wells says:

From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much “junk.” It is much more likely that noncoding regions have functions that we simply haven’t discovered yet.

while on the other, they have expended significant amounts of effort countering what they claim is the fallacy of the “argument from optimal design”, which points out that biological “design” is at times clearly haphazard and inefficient, reflecting more the contingencies of an undirected evolutionary process than any foresight or intelligent planning. Thus, Bill Dembski wrote, in an article entirely devoted to this topic:

Nevertheless, taken strictly as a scientific theory, intelligent design refuses to speculate about the nature of this designing intelligence. Whereas optimal design demands a perfectionistic, anal-retentive designer who has to get everything just right, intelligent design fits our ordinary experience of design, which is always conditioned by the needs of a situation and therefore always falls short of some idealized global optimum.

[Incidentally, note that this article, written for a religious audience, is not shy at all about using the G-word, and while claiming that ID “refuses to speculate about the nature of this designing intelligence”, it eventually goes off the deep Biblical end:

This is a fallen world. The good that God initially intended is no longer fully in evidence. Much has been perverted. Dysteleology, the perversion of design in nature, is a reality. It is evident all around us. But how do we explain it? The scientific naturalist explains dysteleology by claiming that the design in nature is only apparent, that it arose through mutation and natural selection (or some other natural mechanism), and that imperfection, cruelty, and waste are fully to be expected from such mechanisms. But such mechanisms cannot explain the complex, information-rich structures in nature that signal actual and not merely apparent design–that is, intelligent design.

The design in nature is actual. More often than we would like, that design has gotten perverted. But the perversion of design–dysteleology–is not explained by denying design, but by accepting it and meeting the problem of evil head on. The problem of evil is a theological problem. To force a resolution of the problem by reducing all design to apparent design is an evasion. It avoids both the scientific challenge posed by specified complexity, and it avoids the hard work of faith, whose job is to discern God’s hand in creation despite the occlusions of evil.[8]

But this is another story.]

The problem of suboptimal design is so important in the ID advocates’ mindframe, that it deserved its own entry in their self-produced, unpretentiously named “Encyclopedia of Science and Philosophy”. Alas for Luskin, that entry readily concedes that “junk DNA” can not only exist, but is a predictable result of an intelligent design process analogous to human software design (the genome as bloatware, so to speak):

Dead code is code that was written into the program in high level programming language, either erroneously, or originally, for some now redundant purpose (such as testing other code), and remains in the program source code doing nothing. Modern compilers, programs that convert source code into computer-interpretable code, usually strip out
such unused code during the process of compilation, analogous to the way in which DNA polymerase excises introns (non-coding sequences) out of a gene and splices together its exons (coding sequences) when transcribing to mRNA. However, the dead code can happily sit in the source code (as perhaps can the ‘junk’ DNA stay in the DNA) forever - doing nothing but causing confusion to later intelligent observers - engineers who must update the program for example.

Sometimes software engineers will leave code that is not dead code, but does not perform a function, in the source code intentionally. Such code is sometimes called a stub, and is incorporated for the purposes of extensibility - extending the capabilities of the code later on. The code is correct and required effort to produce, was deemed unnecessary to the current version of the software, but is desirable to add functions to the next version, and therefore is purposefully left in - by design. Of course, depending on a number of factors - whether requirements for the next version of the software change or other software makes it obsolete before the next version - even code for extensibility might never be used. There are many other examples of code, that might never actually be used, being purposefully incorporated into software programs. Take interface code for example. Software engineers might build software A to talk to or interoperate with software B written by other software engineers. The source code that facilitates this interoperability is called interface code. However, if the software B project is cancelled, then the interface to B from A will likely never be used, but might never be removed. This is just another example of designed flaws or non-optimal design by intelligent designers.

It is also noteworthy that in computer science and engineering, what is actually considered optimal is contingent on many factors relating to the requirements for the design (what people need or want it to do) and how powerfully the design must implement functions to cater for those requirements. For example, the speed of a software module that runs a screensaver is likely to be considered optimal at a much lower bit-rate than one that renders visual radar feedback on the space shuttle.

Ultimately, of course, software engineers are imperfect designers with limited capabilities operating in imperfect conditions (budget, fatigue and delivery schedules etc.), and so no rational person expects their designs to be perfect, flawless, or even necessarily optimal (although they may converge on some of these some of the time). However, even a putatively perfect or superhuman intelligent designer - one capable of designing the biochemical underpinnings of life - is arguably not required to produce perfect, flawless or optimal designs.

So, Intelligent Design predicts efficient design and no “junk DNA”, except when of course it doesn’t. Ah, the power of having a heuristically empty theory!

Ultimately, I think ID’s current infatuation with the “no junk DNA” mantra, jumping on the bandwagon of some recent discoveries, is an altogether bad move for them, for several reasons:
- First, it puts them in the uncomfortable position of aligning themselves with ultra-Darwinian pan-selectionists, who not only have clear dibs on who first expressed skepticism at the existence of “junk DNA”, but also can explain why all DNA should be functional based on a much more elegant and parsimonious theory (based on straightforward, “micro-evolutionary” negative selection effects that even the most close-minded ID advocates would find hard to argue against).
- Second, it forces them into a contradiction with respect to the “argument from optimal design”: either design is optimized, in which case neither “junk DNA” nor our prostates and inverted retinas should exist, or it isn’t.
- Finally, and most importantly, it still leaves them facing the daunting task of explaining away the currently overwhelming evidence (from the c-value paradox, to the existence of large deletion polymorphisms, to the phylogenetic evidence for neutral “drift” of most stretches of intergenic sequence, etc) that much of genomic DNA in many eukaryotes has no phenotypic effect.

Of course, I don’t expect ID advocates to change course at this point, as their penchant for painting themselves into corners (see Behe’s testimony at the Dover trial for a masterpiece in the art) is now the stuff of legend. Still, it will be fun to see how they will cope when reality catches up with them.

[Note added in proof:
As I am re-editing this, I see Mike has made some of these points already in an independent post. Repetita iuvant, I guess.]

[UPDATE:
Casey Luskin has posted another piece at the Discovery Institute’s Media Complaints Division ominously entitled: “Is Panda’s Thumb Suppressing the Truth about Junk DNA?”, in which he alleges that I have suppressed a comment from one Andras J. Pellionisz, who seems to be a rather cranky biophysicist (“of Information Geometry of Nature”, according to his own self-description) who claims to have identified the function of “junk DNA” based on its “fractal geometrical” properties.

In fact, Dr. Pellionisz’s extensive comment has been posted on this blog since Friday morning, which is when I realized it was stuck in the pipeline awaiting authorization, simply because its unusually large number of links triggered our spam-detection system.

The real irony is that Luskin complains of a non-existing instance of censorship here while writing on a site that does not allow any comments whatsoever, and has systematically rejected track-backs from the Panda’s Thumb for years (I am sending one from this post, let’s see if it goes through).

Of course, the “Evolution News & Views” site has no interest in having its readers fairly and publicly evaluate its arguments, like we do at PT. Its goal is simply to administer the Discovery Institute’s Kool-Aid, without interference from uncomfortable questions or pesky facts. ]

[UPDATE II:
Luskin has added the following addendum to his original piece:

Update 8:00 am, July 23, 2007: Unsurprisingly, Dr. Pellionisz now reports that after my post went live, he discovered that Panda’s Thumb chose to post his comment.

Since the comment in question was in fact authorized for publication long before Luskin’s post went live with Pellionisz’s erroneous accusation, either Luskin or Pellionisz (or both) are still blatantly misrepresenting the truth. I’ll let them sort out between themselves who is in fact responsible for the falsehood; in the meanwhile, bets are open.]

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Comment #188848

Posted by Kevin W. Parker on July 19, 2007 3:00 PM (e)

Don’t you get the feeling that if current reports were saying that junk DNA didn’t have a function that the ID proponents would come up with some way of claiming credit for that as well?

Comment #188851

Posted by mark on July 19, 2007 3:13 PM (e)

Sure, ID predicts the presence of lots of junk DNA. If you go in any house you will almost certainly see some pictures hanging on the wall, or flowers in a vase, or hand-woven baskets on top of the kitchen cabinets. The Interior Designer has included non-functional elements in her design. Non-functionality is a direct and necessary consequence of Interior Design. We can extrapolate, knowing what we do about Interior Designers, how Go–er–the Intelligent Designer designs. On the other hand, if you visit a house furnished by the Bauwowhaus school of Interior Design, functionality rules. The conclusion is that you are absolutely correct when you say

Intelligent Design predicts efficient design and no “junk DNA”, except when of course it doesn’t.

Comment #188853

Posted by Glen Davidson on July 19, 2007 3:21 PM (e)

Of course, what are the alternatives? I mean, if they had some good arguments, I’d ask why they don’t focus on those instead of fighting to assert predictions from evolution that never existed, and their insistence that patently worthless junk must have function (it’s probably possible that nearly all has function (if in some redundant capacity, perhaps), but no reasonable scientist would supposes that it did at the present time).

What are they supposed to do, bring up their research triumphs, genuine predictions of ID that have succeeded (well, in fact they failed spectacularly), and their great understanding of malaria evolution? Are they going to tell us how “design” differs from what is expected from evolution, or why the patterns of “design” in prokaryotes differs from the patterns of “design” in eukaryotes (but not from what would generally be predicted from evolution under known constraints)?

They might as well stick with their earlier claims until these no longer sell to the gullible. Then, because they’re fulfilling a need to deny evolution rather than any imperative to deal with models and evidence, they can just find another argument that has no legs scientifically, but can be foisted onto their naive constituents.

Glen D
http://geocities.com/interelectromagnetic

Comment #188856

Posted by Andras Pellionisz on July 19, 2007 4:08 PM (e)

On September 1, 2005 when I originated the International PostGenetics Society http://www.postgenetics.org and established PostGenetics (“Genomics beyond Genes”) we reached the “eye of the JunkDNA cyclone”; with an organization standing up against casting out 98.7% of human Genome as “Junk” the overwhelming wind was no longer blowing individual scientists into a junky direction. There appeared an organization, led by scientists, to provide anchorage of research of what this 98.7% actually does. On the 12 of October 2006, on the “European Inaugural” of IPGS there appeared the first international organization that formally abandoned the “JunkDNA” misnomer as a scientific term.

On the 14 of June, 2007, with the publication of the NIH-led ENCODE-report(with $53 M tax-dollars spent), we have reached the dead center of the eye of the cyclone. Yes, as appeared in The Scientist Gallagher Editorial “http://www.the-scientist.com/2007/7/1/15/1/”, in July, the discredited misnomer will liver forever as a memento of “framing” Modern Genetics into an establishment where resources were denied, papers were rejected (ask e.g. Mattick and Taft of their excellent manuscript which was never accepted as intended, or even Rigoutsos whose breakthrough publication on pyknons sustained at least a year of delay). Worse, as I pointed out in my “comments” to The Scientist, elaborated in more detail in an Obituary of Junk DNA ” http://www.junkdna.com/#obituary_of_junk_dna ” uncounted millions of people died of miserable deaths while scientists were looking for the “gene” causing their illnesses - and were not even supposed to look anywhere but under the lamp illuminating only 1.3% of the genome (the genes).

One person with a Junk DNA disease ” http://www.junkdna.com/junkdna_diseases.html ” is my dear friend and fellow-pioneer of Junk DNA scientific research; Dr. Malcolm J. Simons, the Honorary Chairman of IPGS “http://www.junkdna.com/ipgs_staged/founders.html…

As documented in the full transcript of the video Genius of Junk “http://www.abc.net.au/catalyst/stories/s898887.h…” award-winning science documentary (never aired in the USA, guess why), Malcolm, as a Darwinist voiced in the 2003 filming his 1987 conviction against the “Junk Frame” this way:

“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” [MJS]

How do you think his fellow-Darwinist scientists received his assertion (1987) that “Junk DNA” had a function? Read on the transcript:

“When I showed the professional geneticists the data, which indicated to me that the 95% non-coding region wasn’t junk, and was ordered…The reaction was smiling disbelief at best – you’re off your friggin’ head and if you’re any good at squash – stick to your day job” [MJS]

(For those asking, I may give you a copy for your personal perusal of the video that you would never in your life forget – especially if you or your loved ones encounter one the gezillions of “junk DNA diseases”. If you have gotten rich – and old enough that some of these regulatory diseases start popping up - your best investment may be to endow frantic research precisely for PostGenetics Centers. Probably unlike dear Malcolm himself, you might actually buy some years to live)

Thus, although when we are already re-entering the cyclone with an opposite wind building up with accelerating speed, “it is too easy” (and looks quite childish, though very human) to “back-pedal” in post-June 2007 on the issue of “Junk DNA”. Most everything is on record, already.

For instance, that it is probably the understatement of Genomics that science pioneers were doing so to get rich by going against dogma (dear Malcolm is anything but “materially rich”). He just knew that he could never publish in the establishment views branded (“framed”) as heretical views - tried to maintain his integrity, leadership and perhaps earn some living from those with dollar signs in their eyes buying up IP “on the cheap”. (Gregor Mendel got any rich? Rosalind Franklin? How about Barbara McClintock who stopped publishing rather than getting ridiculed by a majority of PR firing power but minority of intellectual marksmanship?)

Instead of engaging in a “blaming game” (that may not be the best use of time, unless you enjoy it), you may also wish to drop shouting over some arbitrary ideological trenches. Try doing some actual R&D towards the “Algorithmic Design” of the Genome. We are all united on that one – Malcolm and myself even published (yes, in peer-reviewed science journal…) experimental support “http://www.junkdna.com/fractogene/05_simons_pell…” of quantitative predictions.

Yes, FractoGene even passes “the Onion-test” at least as well as any competitor “Junk DNA theories” in our times of PostModern Genomics (PostGenetics).

pellionisz_at_junkdna.com

Comment #188857

Posted by Tyrannosaurus on July 19, 2007 4:08 PM (e)

When your “hypothesis” predicts everything the result is that it explains nothing. All of their supposedly predictions are a posteriori after real scientists have studied, researched, tested and come up with publications. Like grandma used to said; “after you see the dog’s [Enable javascript to see this email address.] you can tell is a male.” That is why ID is not science, it has no explanatory nor predictive powers.

Comment #188872

Posted by Popper's Ghost on July 19, 2007 5:25 PM (e)

Whereas optimal design demands a perfectionistic, anal-retentive designer who has to get everything just right, intelligent design fits our ordinary experience of design, which is always conditioned by the needs of a situation and therefore always falls short of some idealized global optimum.

This is typical of theistic intellectual dishonesty. Sure design is always conditioned by the needs of a situation, but that just means that optimality is locally defined, it doesn’t explain lack of optimality – what explains that is that the designers we are familiar with lack omniscience and omnipotence.

But such mechanisms cannot explain the complex, information-rich structures in nature that signal actual and not merely apparent design–that is, intelligent design.

Ah, but they can. Despite refutation after refutation of Demsbki’s work, he bleats on as if they had never been written. And throwing in the word “intelligent” explains nothing at all – intelligence isn’t some magic loophole through which the laws of physics, information, or logic can be avoided. If Dembski truly had a theorem showing the
impossibility of natural processes producing design, then we couldn’t produce any of the designs we produce. But, just as human intelligence arises from the actions of dumb molecules constrained by the laws of physics, so can
everything else we observe in the world, including the biological world. Despite the strongest possible illusion that
we are ghosts above and beyond our physical bodies, science has demonstrated in considerable detail that we aren’t. The claim to free will shatters when scientists can measure a decision being made in the brain before the subject consciously “makes” the decision, and when they can generate experiences, including “seeing God”, by poking appropriate places in the brain. It’s mechanism all the way down.

The good that God initially intended is no longer fully in evidence. Much has been perverted.

So much for omniscience, eh? And how did the world get perverted? Even if God created man with free will who then abused God’s intent, how does that explain the “perversion” of nature? Did man create malaria, or did God? Or does one go where evidence and reason lead and conclude that neither did.

the hard work of faith, whose job is to discern God’s hand in creation despite the occlusions of evil

Ah, yes, faith. Faith is what requires one to be intellectually dishonest, to ignore or pervert evidence and reason, whether on the grand scale of Dembski and the fundies or with lesser sophistries. Faith spawns apologetics, which is a euphemism for sophistry and dishonest argument. It goes directly against Quine’s dictum, a dictum that is so evident in the way that biologists have moved away from Mayr’s panadaptationism as the evidence has unfolded:

The desire to be right and the desire to have been right are two desires, and the sooner we separate them the better off we are. The desire to be right is the thirst for truth. On all counts, both practical and theoretical, there is nothing but good to be said for it. The desire to have been right, on the other hand, is the pride that goeth before a fall. It stands in the way of our seeing we were wrong, and thus blocks the progress of our knowledge.

Comment #188876

Posted by Sili on July 19, 2007 7:13 PM (e)

Just out of curiosity: what is the problem with the prostate?

Comment #188878

Posted by raven on July 19, 2007 8:07 PM (e)

It will take decades to determine what noncoding DNA does. It will never be answered by sitting on the sidelines and making noise which is the standard mode of operation for the DI.

The provisional simple minded answer right now is, some is functional, some is just there. We’ve rehashed this often, I posted a few threads ago for the third time, the mouse megabase deletion results which is at least novel empirical data.

Here is another recent experiment. Which indicates that some noncoding does something. What is interesting about this stretch of DNA, is that it codes for a common allele which raises the risk of coronary heart disease, the major killer in the USA, and was found by standard statistics linkage analysis. So far so good. But there is nothing in this stretch of DNA. No protein coding regions. No obvious small regulatory RNAs. Definitely a mystery and it could be a long time until it is known what it is about this stretch of DNA that raises the risk of CHD.

Science. 2007 Jun 8;316(5830):1488-91. Epub 2007 May 3. Links
A common allele on chromosome 9 associated with coronary heart disease.McPherson R, Pertsemlidis A, Kavaslar N, Stewart A, Roberts R, Cox DR, Hinds DA, Pennacchio LA, Tybjaerg-Hansen A, Folsom AR, Boerwinkle E, Hobbs HH, Cohen JC.
Division of Cardiology, University of Ottawa Heart Institute, Ottawa K1Y4W7, Canada.

Coronary heart disease (CHD) is a major cause of death in Western countries. We used genome-wide association scanning to identify a 58-kilobase interval on chromosome 9p21 that was consistently associated with CHD in six independent samples (more than 23,000 participants) from four Caucasian populations. This interval, which is located near the CDKN2A and CDKN2B genes, contains no annotated genes and is not associated with established CHD risk factors such as plasma lipoproteins, hypertension, or diabetes. Homozygotes for the risk allele make up 20 to 25% of Caucasians and have a approximately 30 to 40% increased risk of CHD.

PS Wonder what the DI explanation is for the very ancient 8% defective retroviruses that make up the human genome? The ones that go back in the primate lineage 10’s of millions of years. On second thought, I doubt it would be very specific.

Comment #188879

Posted by David Stanton on July 19, 2007 8:35 PM (e)

Slli,

Are you male? Are you over 50? If so you shouldn’t need to ask. If not, well as someone once remarked, why run a waste disposal system through an amusement park?

Seriously, an enlarged prostate can cause many problems with excretory function. That’s because the excretory system runs right through the prostate. Not very intelligent design. And of course then there’s always prostate cancer to worry about. Every male over 50 should be screened regularly.

Comment #188889

Posted by Coin on July 19, 2007 10:48 PM (e)

So Luskin is incompetent.

And this proves there is no God.

Doesn’t that about sum it up?

You said it, not us…

Comment #188890

Posted by Sam Corpin on July 19, 2007 10:48 PM (e)

The following is an excerpt from Science Daily and it clearly explains the latest research finding on “junk DNA”.

“Science Daily — A tiny opossum’s genome has shed light on how evolution creates new creatures from old, showing that change primarily comes by finding new ways of turning existing genes on and off.

The research, by an international consortium led by the Broad Institute of MIT and Harvard, revises our understanding of genetic evolution. Scientists previously thought that evolution slowly changed the genes that create specific proteins. As the proteins changed, so did the creatures that owned them.

The current research shows that opossum and human protein-coding genes have changed little since their ancestors parted ways, 180 million years ago. It has been the regulation of their genes - when they turn on and off - that has changed dramatically.

“Evolution is tinkering much more with the controls than it is with the genes themselves,” said Broad Institute director Eric Lander. “Almost all of the new innovation … is in the regulatory controls. In fact, marsupial mammals and placental mammals have largely the same set of protein-coding genes. But by contrast, 20 percent of the regulatory instructions in the human genome were invented after we parted ways with the marsupial.”

The research, released Wednesday (May 9, 2007) also illustrated a mechanism for those regulatory changes. It showed that an important source of genetic innovation comes from bits of DNA, called transposons, that make up roughly half of our genome and that were previously thought to be genetic “junk.”

The research shows that this so-called junk DNA is anything but, and that it instead can help drive evolution by moving between chromosomes, turning genes on and off in new ways.”

Well, that should clarify things alot. How this can take either side of the evolution-creation debate is beyond me, though.

http://www.sciencedaily.com/releases/2007/05/070…

Comment #188896

Posted by Popper's Ghost on July 20, 2007 12:46 AM (e)

either design is optimized, in which case neither “junk DNA” nor our prostates and inverted retinas should exist, or it isn’t.

Has any IDist ever mentioned in the same sentence both “junk DNA” and prostates or inverted retinas or … [from Wikipedia]

ectopic pregnancy and the gap between the ovary and the fallopian tube

that the human birth canal passes through the cervix, barely allowing passage for the enlarged human head

migration of the human testes and resultant hernias

the human appendix

the recurrent laryngeal nerve that loops around the aortic arch

the immense dystrophin gene

congenital diseases and genetic disorders such as Huntington’s Disease

the common malformation of the human spinal column

the pharynx, used for both ingestion and respiration

crowded teeth and poor sinus drainage

the inability of humans to produce vitamin C

Comment #188897

Posted by Popper's Ghost on July 20, 2007 12:54 AM (e)

So Luskin is incompetent.

And this proves there is no God.

Doesn’t that about sum it up?

You asked this incredibly moronic question in a previous thread and it was pointed out by many people in that thread why it is immensely moronic. Why ask it again, if not to prove that you are stupid and dishonest?

Comment #188914

Posted by Rolf Aalberg on July 20, 2007 4:04 AM (e)

Popper’s Ghost listed a number of rather non-intelligent designs, but omitted my favorite, the “ductus deferens” (also called the “vas deferens”) - see Wikipedia.

Comment #188923

Posted by Frank J on July 20, 2007 6:32 AM (e)

So Luskin is incompetent.

And this proves there is no God.

Doesn’t that about sum it up?

No. Luskin is a very competent bait-and-switch artist. And the only thing that it “proves” is that he and his fellow IDers have no scientific alternative to evolution, and know it. If these scammers didn’t need YECs and OECs for political support they’d be saying something like “we have the real theory of evolution.” Of course it would still be pseudoscience.

Comment #188924

Posted by Popper's Ghost on July 20, 2007 6:57 AM (e)

Syntax Error: mismatched tag 'kwickxml'

Comment #188925

Posted by Popper's Ghost on July 20, 2007 6:57 AM (e)

Say, Popper, I think they asked the question again because the answers were obviously lies.

You’re obviously stupid and dishonest, as I said.

Comment #188927

Posted by Popper's Ghost on July 20, 2007 7:13 AM (e)

P.S.

Thats the goal, no doubt about it.

Even if that were the goal, it wouldn’t make the post from Banned any less stupid.

Here’s a clue for you: people as transparently moronic and intellectually dishonest as you and Banned are (and you’re most likely the same person) cannot and will not convince anyone of anything. I’m sure such powerlessness must be frustrating for you. But just think of the glory that awaits for you in heaven when your pathetic useless existence on this globe ends.

Comment #188934

Posted by demallien on July 20, 2007 8:21 AM (e)

Say, whatever…

I don’t suppose you have any, you know, links, showing people saying that evolution equals atheism do you?…

I for one shan’t be holding my breath.

Comment #188937

Posted by Andrea Bottaro on July 20, 2007 8:45 AM (e)

Yo - no troll feeding. It only makes them come back for more morsels.

Comment #188956

Posted by Torbjörn Larsson, OM on July 20, 2007 9:36 AM (e)

Nice analysis, indeed.

David Stanton wrote:

the excretory system runs right through the prostate

Analogous to how the equivalent of the esophagus runs right through the cephalopod brain AFAIU. Personally, I would find that hard to stomach. :-P

Comment #188962

Posted by Torbjörn Larsson, OM on July 20, 2007 10:25 AM (e)

Oh, I forgot this:

Andrea Bottaro wrote:

Repetita iuvant

Ex cathedra, alea jacta est. Audita altera parte acta est fabula, ab falso quod libet. Sic transit gloria mundi. Suum cuique tribuere, coram populo; ID delenda est.

[Pasted together from http://www.sabi.co.uk/Notes/miscPhrases.html but since I don’t know a word Latin I can just note in the face of any errors: Errare humanum est. :-P]

Comment #188966

Posted by David Utidjian on July 20, 2007 10:31 AM (e)

Kevin,

Most IDists that I have heard/read are claiming that all or almost all will turn out to have “function.” The more religious ID types and even the not so religious types, will accept the proposal that “junk” DNA is due to the “post-Fall” state we are in. That is to say, at one time all this DNA had function and all us critters were created perfect… but since the “Fall” we now have some de-activated and/or corrupted stuff in our genomes. Anyhow… that is how the story goes.

Relatively recently I think the IDists have been downplaying or ignoring the earlier “post-Fall” explanation for two reasons:

1. Pinning the reason for “junk” DNA on “the Fall” is definitely an explanation tied to religion. They are trying to avoid mixing up their “scientific” ID with any specific religious content. This is only politically expedient for them at present.

2. As always, IDists do no actual science in support of their movement, instead they snipe and cherry pick at real science done by real scientists from the sidelines. This behavior is especially targeted at the branches of science and fields that are making rapid progress, which is exactly what is going on with genomics at the moment.

The IDists are really that desperate. I think that deep down they understand that they don’t really have any real science that they can do. For their intended audience, it is enough that they call real scientists the pig fuckers and let them do the denying.

-DU-

Comment #188967

Posted by George Cauldron on July 20, 2007 10:40 AM (e)

So Luskin is incompetent.

And this proves there is no God.

Doesn’t that about sum it up?

You asked this incredibly moronic question in a previous thread and it was pointed out by many people in that thread why it is immensely moronic. Why ask it again, if not to prove that you are stupid and dishonest?

This question implies that Banned is capable of doing better.

BTW, why isn’t Emanuel Goldstein (‘whatever’) being deleted?

Comment #188972

Posted by David Stanton on July 20, 2007 11:04 AM (e)

David wrote:

“Relatively recently I think the IDists have been downplaying or ignoring the earlier “post-Fall” explanation for two reasons:”

You make some excellent points. Please allow me to add another reason why the “Fall” scenario is unfeasible.

3) Several “junk DNA” features are shared with Chimpanzees and other primates, such as retroviral transposons inserted into specific genes. Obvioulsy the “Fall” cannot possibly explain such shared features.

Comment #188973

Posted by Andrea Bottaro on July 20, 2007 11:14 AM (e)

David (Stanton) is correct. The main reason why neither IDists (except perhaps the token few who genuinely accept common descent) nor “traditional” Creationists can accept the idea of “junk DNA” is that non-functional DNA features shared between species are prima facie evidence of phylogenetic relationship.

Comment #188982

Posted by Incorygible on July 20, 2007 12:03 PM (e)

Andrea Bottaro wrote:

The main reason why neither IDists (except perhaps the token few who genuinely accept common descent) nor “traditional” Creationists can accept the idea of “junk DNA” is that non-functional DNA features shared between species are prima facie evidence of phylogenetic relationship.

Exactly. Much like the argument from Evil for the theists, the argument from Junk (especially shared junk) is simple and devastating for the IDists. They must therefore resort to the same twisted apologetics to convince their audience that “[the Designer] works in mysterious ways”. Their attempts range from “who are we lowly humans to say it’s junk?” (for audiences favouring a simplistic, literal interpretation of [a Designer]) through to the “who are we to say what [the Designer] would or would not do?” (for those sophisticated theological sorts who are willing to reinvent [the Designer] to fit the data). It’s no surprise that Luskin is so obsessed with junk DNA.

Comment #188989

Posted by Moses on July 20, 2007 12:26 PM (e)

Comment #188917

Posted by whatever… on July 20, 2007 5:34 AM (e)

Others like Dawkins, Dennet, PZ Myers (who seems to think his blog counts as peer reviewed literature) will come right out and say it: science equals atheims, religion must be eliminated.

Thats the goal, no doubt about it.

Your “science equals atheism” and PZ thinks his “blog counts as peer reviewed literature” characterizations are gross distortions to the point that they’re deliberate lies.

Comment #189001

Posted by Sam Corpin on July 20, 2007 1:05 PM (e)

How can any of you be so sure, concerning whether there is a creator of the (human) genome, or not?

You thought you had almost all> the answers when you thought that humans were expressed genetically by only 5% of their genome, and that the other 95%, for the most part, was just “junk DNA”.

Now; since May 2007, at least, it has been proven that at least half of the “junk DNA” regulates the whole genome expression in a creature by turning genes on and off.

This creates quite a different picture of how main stream science had been thinking the genome worked. (That is evidenced even in this blog.)

I, myself, am not sure if there was a creator behind our genome or not. My question to you is, how can you be so sure that there was no intelligent design behind our creation, when you really didn’t even know how the genome really functioned, for the most part, anyway?

Have any of you come to question that maybe you really don’t have enough answers to make a definite statement as to the creation issue yet?

In the future, when we have all of the facts straight, then, and only then, can anyone say for sure whether our genome was created or not. Anyone who believes absolutely one way or the other, using the information we have compiled on the genome so far, is not being very scientific. It is one thing to have opinions, debates and evidence interpretations - it is quite another to be absolute about something that isn’t any where near done being investigated yet.

Having worked in an investigative capacity for years at a previous job, as a seasoned investigator, I realized that sometimes; even when all evidence pointed toward one thing; sometimes that evidence, in the final analysis, summed up to something entirely different than we had originally conceived.

In dismissing God at this early stage of our genome intrepetation, we are not even giving him the chance that we, as Americans, would give a citizen in a court of law.

I know you guys will be screaming as you write, insulting me with your poison key pads :) - and why will you be doing this? Because you know, deep down inside, that I am right.

Comment #189002

Posted by Glen Davidson on July 20, 2007 1:24 PM (e)

Having worked in an investigative capacity for years at a previous job, as a seasoned investigator, I realized that sometimes; even when all evidence pointed toward one thing; sometimes that evidence, in the final analysis, summed up to something entirely different than we had originally conceived.

Wow, that’s what you learned? That’s the depths of banality.

In dismissing God at this early stage of our genome intrepetation,

Too bad you know nothing of science. God isn’t dismissed, for God isn’t even introduced by any evidence. If you’re an investigator, you’re a pathetic one, since you have no business bringing up “possibilities” which have no evidence for them.

Should you ever find evidence for God, present the evidence. That’s all we demand of IDists, and they never present any real evidence.

we are not even giving him the chance that we, as Americans, would give a citizen in a court of law.

I suppose that’s because we don’t know that he exists. How bright are you?

I know you guys will be screaming as you write, insulting me with your poison key pads :) -

You claim to be bringing up something new (God hasn’t been disproved by science), when virtually all of us acknowledge this fact. Learn something about your interlocutors before you decide to grace us with the wisdom of your trite and banal cliches.

and why will you be doing this?

It’s because it’s a very stupid and old PRATT (point refuted a thousand times), and has nothing to do with the statements made by science.

Because you know, deep down inside, that I am right.

Because it means as much as the fact that we can’t disprove that a teapot orbits Mars, to use Russell’s famous example. IOW, you’re trivially right, and there’s not the slightest reason we should care about that fact.

Perhaps as an investigator you’re incapable of noticing that we’re discussing what’s appropriate in science, not whether or not God exists. Just because ID is really only concerned with the latter issue doesn’t mean that we’re generally interested in that fact at all. What we’re concerned about is what any decent investigator is interested in, following the rules of evidence to the best conclusion possible at a given time. And at this time the conclusion that God had something to do with the genome is wholly unwarranted, for nothing in it differs from what “natural processes” would be expected (given our state of knowledge) to produce.

I’d like to see you try to bring up the fact in court that it is impossible to show that God tampered with the crime scene. You’d be laughed out of court, because that’s so obviously true and unimportant to the case that only an idiot would bring it up.

Glen D
http://geocities.com/interelectromagnetic

Comment #189003

Posted by CJO on July 20, 2007 1:26 PM (e)

How can any of you be so sure, concerning whether there is a creator of the (human) genome, or not?

Why so hung up on the (human) genome? Is it Special somehow?

What about the sea anemone genome or the skunk cabbage genome? Is the jury still out there too, or are we only entertaining the idea of special creation of humans?

If the latter is the case, then we have to ask, why does the human genome show so much similarity to the genome of our closest relatives, including a whole lot of no-kidding junk, derived from ERVs?

You seem to be making much, also, out of the provisional nature of scientific discovery. Such flexibility in the face of new evidence is a strength of the method. But please explain how finding some regulatory function in stretches of the genome once thought to be non-functional makes any stronger a case for its special creation, especially in light of all the features of the genome that attest to its continuity with the genomes of all other life on earth.

Comment #189004

Posted by Andrea Bottaro on July 20, 2007 1:27 PM (e)

How can any of you be so sure, concerning whether there is a creator of the (human) genome, or not?

I don’t know who you are referring to, but I suspect no one here is “sure”, one way or another. The existence, or not, of a creator is certainly not the issue here.

You thought you had almost all> the answers when you thought that humans were expressed genetically by only 5% of their genome, and that the other 95%, for the most part, was just “junk DNA”.

Now; since May 2007, at least, it has been proven that at least half of the “junk DNA” regulates the whole genome expression in a creature by turning genes on and off.

Nothing of the sort has been proven, or even suggested by the investigators in question. That’s just a crude misinterpretation/misrepresentation of the data, which as published simply showed that a large amount of the genome undergoes transcription, at some detectable level. The fact is, we don’t know what that transcription does for the organism, and it may well do nothing at all. It’s like saying that because garbage smells, and some smelling things are useful, garbage must be useful.

Comment #189005

Posted by David Stanton on July 20, 2007 1:28 PM (e)

Sam,

No one is making any claims about God except you. Many of us who have spent a life time studying genetics have concluded that there is absolutely no evidence to contradict the assumption that natural causes are sufficient to explain the human genome. The genome also has many features that appear (baased on our present knowledge) to be extremely unlikely to have been the result of any intelligent planning. If you want to believe that God did things that way no one can stop you. Just don’t go around claiming that scientists are the ones jumping to conclusions without evidence. We have come a long way in figuring out the fundamentals of inheritance and gene expression. Of course we still don’t know everything, but that is no reason to assume that what we do know is worthless. We are far from being in the “early stage of our genome interpretation”. And as far as a court of law goes, that is not how scientific questions are answered. And even if it was, we know how that worked out in Dover don’t we?

By the way, as far as we can tell, there are still millions of copies of defective viruses in the human genome, many of which we share with other primates. They don’t do anyhing at all except predispose us to premature death and disease. Sure, anything may have an undiscovered function, but the burden of proof is on you to determine what it is. Go do some research and tell us what the function is if you want to be taken seriously.

Comment #189007

Posted by Aagcobb on July 20, 2007 1:51 PM (e)

Sam, if the genome was designed, why did God think the onion needed five times more non-coded dna than humans?

Comment #189008

Posted by Sam Corpin on July 20, 2007 1:58 PM (e)

Glen: It would be a case of premeditation or not, and of who was involved, (or more like a case of natural occurrence or murder, even); not a matter concerning “whether God tampered with the crime scene, or not.”

It’s your comments that are stupid, not mine.

CJO: I’m not hung up on the human genome, that’s why I put “human” in quotes (_)when I referred to the human genome in my previous comments.

But please explain how finding some regulatory function in stretches of the genome once thought to be non-functional makes any stronger a case for its special creation, especially in light of all the features of the genome that attest to its continuity with the genomes of all other life on earth.

The only way this makes a stronger case for its special creation, is in light of the fact that it makes a weaker case for its “non-creation”; in that it weakens the argument of the anti-IDists, by showing that the main expressive regulatory control contained in the human genome has been misintrepreted, for the most part.

If we think something works one way, only to take it apart and find that that is not the way it works after all, then many of our assumptions up to that point are now in question, because they were based in how WE THOUGHT the thing worked, not in how it really does work.

This type of scenario also inherently implies that how WE THOUGHT something was created, may not be HOW IT WAS created after all, if it’s cause to be in existence is in question.

The research, by an international consortium led by the Broad Institute of MIT and Harvard, revises our understanding of genetic evolution. Scientists previously thought that evolution slowly changed the genes that create specific proteins. As the proteins changed, so did the creatures that owned them.
…>“Evolution is tinkering much more with the controls than it is with the genes themselves,” said Broad Institute director Eric Lander.

This makes quite a difference in how science intreprets the genome.

Comment #189009

Posted by Glen Davidson on July 20, 2007 2:18 PM (e)

Glen: It would be a case of premeditation or not, and of who was involved, (or more like a case of natural occurrence or murder, even); not a matter concerning “whether God tampered with the crime scene, or not.”

Of course it would be, banal idiot.

That’s my point. How dumb are you?

Can’t you understand yet that in science and other investigative matters, that God, without any evidence for his interference, is simply left out of the picture?

Or are you too much in denial to understand a simple analogy, but have to smother it over with non-sequiturs?

It’s your comments that are stupid, not mine.

If they were stupid, you’d have made an intelligent comment, not simply related the fact that I’m right that you wouldn’t bring God as a “possibility” into the courtroom. You’re too stupid even to understand that you agreed with my remarks that you call “stupid”.

Can’t you back up anything you say, or do you have to deny all arguments and evidence that goes against your trivial nonsense?

This is why we use poison keyboards against dolts like you, you can’t understand the most basic issues, but have to try to run around normal practices to “save” your pet ideas, regardless of your inability to provide the requested evidence for them.

I hope you never work on any case with which I might be involved. While you sensibly don’t apply the same standards to legal cases that you do to the “God question,” I can hardly trust anyone who brings in mindless tripe to save a “hypothesis”.

Glen D
http://www.geocities.com/interelectromagnetic

Comment #189010

Posted by CJO on July 20, 2007 2:21 PM (e)

The only way this makes a stronger case for its special creation, is in light of the fact that it makes a weaker case for its “non-creation”; in that it weakens the argument of the anti-IDists, by showing that the main expressive regulatory control contained in the human genome has been misintrepreted, for the most part.

Right. So it doesn’t make a case for ID at all. There are two primary arguments of the “anti-IDists” (a curious circumlocution):
First, as Glen said, and you ignored, disproving the existence of a creator has never been the aim of science. Nothing about new information concerning “junk” DNA or previously unknown regulatory elements in the genome requires science to look for supernatural causes.
Second, ID is scientifically vacuous and as long as it’s focussed on supposed misinterpretations of past biology, and even if we accept inflated claims for the significance of these misapprehensions, it still can’t compete with ignorance, as it offers no positive account of “design.”

No recent discoveries, nor any likely future ones, do anything about either of these objections to ID, which is nothing more than a game played with words.

Comment #189012

Posted by Glen Davidson on July 20, 2007 2:40 PM (e)

The only way this makes a stronger case for its special creation, is in light of the fact that it makes a weaker case for its “non-creation”; in that it weakens the argument of the anti-IDists, by showing that the main expressive regulatory control contained in the human genome has been misintrepreted, for the most part.

No, it shows what an incompetent “investigator” you are. As I said, and as you idiotically were unable to comprehend, we make claims based upon the evidence. We didn’t make the claims based on the lack of evidence that you accuse us of making (you’re intellectually dishonest as well as incompetent), we simply used terms that indicated that we didn’t know of its function (some were misleading to ignoramuses like yourself, like the term “junk”).

It’s not that it was misinterpreted, it’s that claims weren’t made based on no evidence. Unlike someone as stupid as you, science didn’t end with the lack of evidence, rather evidence was sought by non-IDists. If your guys were so confident of your claims, why didn’t they actually do any research, instead leaving it to the real scientists and competent investigators?

And tell me, you who claim not to be stupid even as all of your posts are stupid, so what if it had been misinterpreted (a hypothetical, since your claims are merely lies)? What would that indicate about evolution? You seem either not to have read what Andrea wrote, or as usual, you were incompetent to understand it.

If we think something works one way, only to take it apart and find that that is not the way it works after all, then many of our assumptions up to that point are now in question, because they were based in how WE THOUGHT the thing worked, not in how it really does work.

OK, so you made mistakes in what you thought. What does this have to do with the many scientists who strove to discover the suspected regulatory functions? IOW, learn how to think, and how to investigate these questions.

This type of scenario also inherently implies that how WE THOUGHT something was created, may not be HOW IT WAS created after all, if it’s cause to be in existence is in question.

Non-sequitur, moron.

Why don’t you learn how to read, then read what Andrea Bottaro posted? Evolutionary theory did not predict junk, in fact a number of dedicated Darwinians made the mistake of suggesting that junk shouldn’t exist based on the negative fact that Darwinian theories don’t predict it. They don’t, however, exclude it, either.

The research, by an international consortium led by the Broad Institute of MIT and Harvard, revises our understanding of genetic evolution.

Yes, dimwit, research goes on in science, unlike among your incompetent IDists.

Scientists previously thought that evolution slowly changed the genes that create specific proteins. As the proteins changed, so did the creatures that owned them.

That was the initial concept, indeed. As research expanded our horizons, regulatory changes were thought to be more and more important, and regulatory functions were sought for the often mislabeled “junk DNA”.

One of the reasons regulation was considered for the changes occurring during evolution was that the genes were found not to change very rapidly. Gene changes didn’t seem sufficient for the observed evolutionary changes, hence other mechanisms were thought to be important.

Evolutionary thinking won out again, leading researchers into new paths of discovery. That’s how science works. If you ever become literate, you’ll need to read into science.

“Evolution is tinkering much more with the controls than it is with the genes themselves,” said Broad Institute director Eric Lander.

Yes, which was suspected for at least a couple decades in evolutionary research. What do you think evo-devo involves?

This makes quite a difference in how science intreprets the genome.

Yes, and what bearing does this have on evolutionary processes? You don’t know, do you? You just ape the IDiots and pretend that learning new things in biology undercuts the actual theories that have pointed scientists to that learning, notably evolutionary theory.

I think you need an education before you start meddling in matters that you obviously aren’t competent to discuss presently.

Glen D
http://www.geocities.com/interelectromagnetic

Comment #189014

Posted by ofro on July 20, 2007 2:43 PM (e)

Sam Corpin:
The research, by an international consortium led by the Broad Institute of MIT and Harvard, revises our understanding of genetic evolution. Scientists previously thought that … (snip) …

With your quote of a MIT or Harvard study about “Scientist previously thought…” you are falling prey to (more likely: are trying to propagate) a well-worn fallacy. You make it sound like scientist scrambled to find a fundamentally different explanation. Wrong! They are merely fine-tuning well-established principles worked out by hundreds of scientists before them.

Comment #189015

Posted by Sam Corpin on July 20, 2007 2:50 PM (e)

Hey, I am not an IDist! I do not have an opinion one way or the other; because, as far as I am concerned, enough of the evidence is not in to make a definitive decision one way or the other.

I am just pointing out the fact that all of the evidence is not in for you to say that there is definitely no “Intelligent Design”. As a matter of fact, I was definitely swaying heavily toward the fact that there in no “Intelligent Design” in the genome, until, that is, I discovered that we have been misinterpreting the major expressive action of the genome, which in turn tells me that we are not as far along as we would previously have liked to believe, in understanding the human genome.

The new evidence does not point toward Intelligent Design as far as I can see. However, it does bring to question our haste in creating a miasma without most of the relevant data being proven; and in this case, with an incorrect assumption of how the genome itself is expressed. This is a very big deal, dont’cha think?

Comment #189016

Posted by Sam Corpin on July 20, 2007 2:50 PM (e)

Hey, I am not an IDist! I do not have an opinion one way or the other; because, as far as I am concerned, enough of the evidence is not in to make a definitive decision one way or the other.

I am just pointing out the fact that all of the evidence is not in for you to say that there is definitely no “Intelligent Design”. As a matter of fact, I was definitely swaying heavily toward the fact that there in no “Intelligent Design” in the genome, until, that is, I discovered that we have been misinterpreting the major expressive action of the genome, which in turn tells me that we are not as far along as we would previously have liked to believe, in understanding the genome.

The new evidence does not point toward Intelligent Design as far as I can see. However, it does bring to question our haste in creating a miasma without most of the relevant data being proven; and in this case, with an incorrect assumption of how the genome itself is expressed. This is a very big deal, dont’cha think?

Comment #189017

Posted by Sam Corpin on July 20, 2007 2:50 PM (e)

Hey, I am not an IDist! I do not have an opinion one way or the other; because, as far as I am concerned, enough of the evidence is not in to make a definitive decision one way or the other.

I am just pointing out the fact that all of the evidence is not in for you to say that there is definitely no “Intelligent Design”. As a matter of fact, I was definitely swaying heavily toward the fact that there in no “Intelligent Design” in the genome, until, that is, I discovered that we have been misinterpreting the major expressive action of the genome, which in turn tells me that we are not as far along as we would previously have liked to believe, in understanding the genome.

The new evidence does not point toward Intelligent Design as far as I can see. However, it does bring to question our haste in creating a miasma without most of the relevant data being proven; and in this case, with an incorrect assumption of how the genome itself is expressed. This is a very big deal, dont’cha think?

Comment #189018

Posted by Sam Corpin on July 20, 2007 2:57 PM (e)

Please, accept my apology for the triple posting, it was not intentional. I had just hit POST, when I noticed I had typed in “human genome” where I should have just typed “genome”. I quickly took out the word “human” before the message had posted, and I hit POST again. Well, you see the result. I’m really sorry, I know this will just make some of you see red.

Comment #189019

Posted by Flint on July 20, 2007 3:00 PM (e)

Sam:

I do not have an opinion one way or the other; because, as far as I am concerned, enough of the evidence is not in to make a definitive decision one way or the other.

You do not understand the issue. There is no “decision one way or the other” because these are ships in the night. Not even 100% complete, perfect, validated evidence of anything in the Real World can rule out Design, because Design is not testable. It’s a statement of sheer, pure preference.

Here’s an exmple. Pick up a rock and look at it. There is very very little a geologist can’t tell you about that rock. But was it Designed? Nobody but you can make that decision, because evidence isn’t relevant. Only preference. Evidence can never point toward, or away from, Design. Design is irrespective of any possible evidence.

The issue here is whether something that cannot possibly be tested, measured, or ruled out should be regarded as scientific. And the answer is very clear: If it can’t be ruled in or out on the basis of evidence, it ain’t science. It might be right, it might be wrong, nobody can possibly ever know, so it ain’t science.

As time goes on, the genome will be understood better and better and better. NONE of that understanding has anything whatsoever to do with Design. Design is a statement of doctrine, completely outside the world of evidence.

Comment #189020

Posted by Glen Davidson on July 20, 2007 3:02 PM (e)

And by the way, it was Mendelianism that suggested that genes were the primary source of change during evolution, not Darwinian evolution per se. Darwinian evolution can work as well with regulatory sequences as with coding sequences, it’s just that Mendelian inheritance had been shown to be very important, and neo-Darwinism incorporated Mendelian inheritance into its synthesis simply because Mendelianism (so to speak) had the requisite evidence behind it.

So if the IDists, along with Sam, were competent critics, they’d be faulting Mendelianism for scientists supposedly not suspecting (which science didn’t, really) regulatory functions for “junk DNA”, not Darwinian evolution itself. But they’re not out to find a bunch of complaints against the well-established (but not complete) Mendelian mechanisms, they’re out to complain about well-established (but not completely understood) evolutionary mechanisms.

And so it goes. Then they complain that we call them IDiots.

Glen D
http://www.geocities.com/interelectromagnetic

Comment #189022

Posted by Werrf on July 20, 2007 3:20 PM (e)

Perhaps time for a less…ahem…’passionate’ response? :)

Sam Corpin wrote:

Hey, I am not an IDist! I do not have an opinion one way or the other; because, as far as I am concerned, enough of the evidence is not in to make a definitive decision one way or the other.

And enough evidence will never be in, because the only way to make any sensible judgement about design in living creatures, or the universe, would be to compare a creature KNOWN to be designed to one KNOWN to have evolved, and see which one most closely fits the life on earth. Since we cannot do that, design can never be proved - at least, not in the forseeable future.

Sam Corpin wrote:

As a matter of fact, I was definitely swaying heavily toward the fact that there in no “Intelligent Design” in the genome, until, that is, I discovered that we have been misinterpreting the major expressive action of the genome, which in turn tells me that we are not as far along as we would previously have liked to believe, in understanding the genome.

The problem you’re having is not with science, though, or with scientists, it’s with public perception of the science. The fact is that if scientists had been convinced that all ‘Junk DNA’ was true junk, and that we already knew and understood how things were working, nobody would’ve bothered examining the ‘junk’.

Science has never been as far along as popular science programs and sci-fi would have us believe. Take those reports with a strong supply of salt, and you’ll do okay.

Sam Corpin wrote:

The new evidence does not point toward Intelligent Design as far as I can see. However, it does bring to question our haste in creating a miasma without most of the relevant data being proven; and in this case, with an incorrect assumption of how the genome itself is expressed. This is a very big deal, dont’cha think?

Not really. Blame the pop science writers, those who created the ‘miasma’ - not sure what you mean by that, BTW :) - not the scientists. They were the ones who went looking for the evidence to support function in non-coding DNA inthe first place.

On the other hand, compare the ID-ists. They’ve sat around for years, doing no research, telling us that “well, of course there’s junk DNA - it was created by the Designer, and we can’t know the mind of the Designer. We’d expect to see junk DNA in a designed organism.” But now that scientists have found purpose for non-coding DNA, they’re all saying “Oh, yes, of course we knew there’d be function for this ‘junk’ DNA - it’s only those foolish scientists who said it was useless.”

One side makes excuses, the other side finds evidence - which would you rather place your trust in?

Comment #189024

Posted by David Stanton on July 20, 2007 3:29 PM (e)

Sam wrote:

“I am just pointing out the fact that all of the evidence is not in for you to say that there is definitely no “Intelligent Design”.

So, just when will “all” of the evidence be in? The human genome has been completely sequenced you know. Should we suspend judgement on every question until we understand everything completely? Exactly what is it you think we do not understand? Exactly what is it you thnk we do understand? Unless you have spent a life time studying genetics, you have no idea what we do and do not understand. One can always stand on the sidelines and shout: HA HA you guys don’t know everything.

Here’s a news flash, science is always provisional. The conclusions of science are always provisional. Science always yields to new evidence. Got any?

“All” of the evidence will never be in. So what? I don’t remember anyone saying “there is definately no intelligent design”. One could always argue that the human genome represents design, no matter what we understand or do not understand. So what? That doesn’t make it true.

At this point we definately do understand enough to say conclusively that if the human genome is designed, it is a very poor, very inefficient desgn that could be improved upon greatly with just a little more intelligence. And no matter whether it was designed or not, it is still related by common ancestry to other primates. That much we do understand.

Comment #189025

Posted by Eric Finn on July 20, 2007 3:31 PM (e)

Sam Corpin wrote:

How can any of you be so sure, concerning whether there is a creator of the (human) genome, or not?

Science can not decide whether there is a creator or not. Individual scientist may, and many of them do, have their private opinions.

Sam Corpin wrote:

Have any of you come to question that maybe you really don’t have enough answers to make a definite statement as to the creation issue yet?

Well, I guess many of us have.

Science works by building hypotheses and making predictions based on those hypotheses (which often involve building models, either mathematical models or other type of models). The creator-hypothesis is, in my opinion, a scientific hypothesis. However, science needs predictions as well. A hypothesis is not enough, if no verifiable predictions can be deduced. Science has no means to assess a hypothesis without predictions, and those types of hypotheses will inevitably fall outside science.

Sam Corpin wrote:

Having worked in an investigative capacity for years at a previous job, as a seasoned investigator, I realized that sometimes; even when all evidence pointed toward one thing; sometimes that evidence, in the final analysis, summed up to something entirely different than we had originally conceived.

That is quite possible, of course. It is most certain that scientists are wrong in many things. However, would you like to change the way scientists work in their attempt to work out verifiable predictions and to check if those fit in the data? Most of the time, they are trying to refute their own hypotheses, rather that trying to confirm them. A hypothesis with no predictions is not helpful in this process, no matter how much data it can explain. Or, are you perhaps indicating that there are verifiable predictions deduced from the creator-hypothesis?

Regards
Eric

Comment #189026

Posted by hoary puccoon on July 20, 2007 4:22 PM (e)

Another shot at Sam Corpin–
There is a much cheaper way of finding genes, Sam, than decoding an entire genome. Since genes are, by definition, pieces of DNA that code for proteins, you can take the proteins you’re interested in and work backwards. The entire reason for the Human Genome Project was that scientists already knew that there was a lot of interesting DNA in our genome that didn’t code for proteins. If they had really had the attitude the IDers imply they did– that everything except the protein-coding segments was just junk– they would never have done the Human (or any other) Genome Project. Are they making new and unexpected discoveries, now that they have a few genomes to study? Well, of course they are. But you know, Sam, THAT’S WHY THEY DID THE PROJECT IN THE FIRST PLACE. If they had really thought they’d find nothing but protein-coding genes and junk they’d never have bothered.

Comment #189033

Posted by Popper's Ghost on July 20, 2007 4:46 PM (e)

How can any of you be so sure … you know, deep down inside, that I am right.

You’re a hypocritical moron, Sam. You’re the one who is sure … sure of things that you are completely ignorant about or too stupid to undersstand.

Comment #189036

Posted by Popper's Ghost on July 20, 2007 4:53 PM (e)

It’s your comments that are stupid, not mine.

No one here other than you thinks so Sam, and just saying so is no rebuttal, whereas Glen gave you reason and evidence. You’re an intellectually dishonest moron addressing a strawman – whether God created the human genome isn’t the issue, but you’re too stupid to understand that. The issue is the arguments that people like Casey Luskin make – whether those arguments are valid, whether they agree with the facts, whether they support their conclusions.

Comment #189040

Posted by Popper's Ghost on July 20, 2007 5:08 PM (e)

The only way this makes a stronger case for its special creation, is in light of the fact that it makes a weaker case for its “non-creation”; in that it weakens the argument of the anti-IDists, by showing that the main expressive regulatory control contained in the human genome has been misintrepreted, for the most part.

Let’s suppose Sam, that every biologist who ever lived (except for the ones you quote approvingly) is a cretin who has misinterpreted everything he or she has ever laid eyes on. How does that strengthen the case for special creation? It doesn’t, you moronic dolt. Errors in interpretation of the genome are neutral in regard to the argument for special creation. What you’re saying is like saying that if an “anti-IDist” had argued that there are WMDs in Iraq, the fact that there weren’t “weakens the argument of the anti-IDists”. It’s bloody effing stupid and dishonest; it is only arguments for or against ID that matter, not “the argument of the anti-IDists”, as if anything said by an “anti-IDist” is such an argument and thus any mistake by an “anti-IDist” counts against “the anti-ID argument”. That’s the thinking of an ideologically blinded dolt.

Comment #189043

Posted by Popper's Ghost on July 20, 2007 5:12 PM (e)

I am just pointing out the fact that all of the evidence is not in for you to say that there is definitely no “Intelligent Design”.

It has been pointed out to you, moron, how trite that is – it’s the stupidest of all strawmen; no one here says that there is “definitely” no “intelligent design”. But what they do say is clearly well beyond your puny comprehension.

Comment #189046

Posted by Popper's Ghost on July 20, 2007 5:17 PM (e)

It’s a statement of sheer, pure preference.

No, actually, it isn’t. As folks like Richard Dawkins and Victor Stenger have pointed out, the world looks just the way one would expect if it were not intelligently designed. The odds are overwhelmingly against intelligent design, if intelligence has any sort of implication of foreplanning. Teleology is not in evidence.

Comment #189048

Posted by rimpal on July 20, 2007 5:27 PM (e)

Casey is in very kooky mood. He just can’t seem to get off the junk-DNA treadmill. Now in his 3rd post after having been shown up for a rube re the scientific findings on non-coding DNA, left with nothing else claims he has been an eyewitness to such assertions. Obviously Casey hasn’t heard the Russian quip, “…lying like an eyewitness”

Comment #189049

Posted by Moses on July 20, 2007 5:27 PM (e)

Comment #189001

Posted by Sam Corpin on July 20, 2007 1:05 PM (e)

How can any of you be so sure, concerning whether there is a creator of the (human) genome, or not?

You thought you had almost all> the answers when you thought that humans were expressed genetically by only 5% of their genome, and that the other 95%, for the most part, was just “junk DNA”.

Now; since May 2007, at least, it has been proven that at least half of the “junk DNA” regulates the whole genome expression in a creature by turning genes on and off.

Unlike theology, science is (eventually) self-correcting. You’d have us believe your disproved fairy-tales are true. Even though years of painstaking research into the origins of Christianity, Judaism and other Mediterranean religions clearly show that Judaism is a religion cobbled from many sources, primarily the Canaanite worship of El and the Yahweh cults of the Sinai, but with a lot cobbled from mythos of other cultures. If you look, you can learn. If you have the guts to face it. Which you don’t and won’t.

This creates quite a different picture of how main stream science had been thinking the genome worked. (That is evidenced even in this blog.)

Not really. You should look at the evolution of the understanding of the atom. It took scientists decades to come up with their current view of the structure of an atom. We had Thomson’s model which was pretty much like an old-fashioned plum pudding. It then went to Rutherford’s planetary model with discrete electrons freely moving their orbits. Bohr came along a few years later and added quantum mechanics to it and fixed the orbits at states which could only be changed by emitting or absorbing a photon. Then came the modern view which I’ll let you look up yourself since you have so much time.

I, myself, am not sure if there was a creator behind our genome or not. My question to you is, how can you be so sure that there was no intelligent design behind our creation, when you really didn’t even know how the genome really functioned, for the most part, anyway?

You lie. You are quite sure. Your post, considered in its entirety, and with adequate models from which to compare, says otherwise.

Have any of you come to question that maybe you really don’t have enough answers to make a definite statement as to the creation issue yet?

Did you ever wonder why there are two creation stories in Genesis? Did you not know that they both came from other religions? Has it ever occurred to you that some of us have a vast collection of work which shows Christianity is nothing more than a descendant of religions that you yourself say are false? That Christianity, itself, is a cobbled together religion of no more merit than the religions from which it was cobbled? Religions that you expressly dismiss as “pagan” and “false?”

See, I know this. So how could I possibly, after been socialized to believe that all non-Christian and virtually all other Christian religions were false religions, having been shown that my religion was based on lies, distortions and other religions, have some “faith” in a creator deity of such a mendacious and incompetent nature?

In the future, when we have all of the facts straight, then, and only then, can anyone say for sure whether our genome was created or not. Anyone who believes absolutely one way or the other, using the information we have compiled on the genome so far, is not being very scientific. It is one thing to have opinions, debates and evidence interpretations - it is quite another to be absolute about something that isn’t any where near done being investigated yet.

Having worked in an investigative capacity for years at a previous job, as a seasoned investigator, I realized that sometimes; even when all evidence pointed toward one thing; sometimes that evidence, in the final analysis, summed up to something entirely different than we had originally conceived.

Oh please. Spare us the logical fallacies about what we can or can’t determine. Your ignorance has no bearing on the understandings of the origins of the human genome by scientists. Just like your ignorance of the origins of your religious beliefs have any bearing on my understanding of the origins of modern western religions.

In dismissing God at this early stage of our genome intrepetation, we are not even giving him the chance that we, as Americans, would give a citizen in a court of law.

It’s not a court of law, which is a good thing. Stats say one-in-six verdicts is wrong, usually resulting in a false convicition, and judges are just as bad as juries. If science was wrong one-in-six theories we’d be in a lot of trouble.

I know you guys will be screaming as you write, insulting me with your poison key pads :) - and why will you be doing this? Because you know, deep down inside, that I am right.

I know you’re a liar. I know you’re a wind-up troll. I suspect you think you’re clever or original in your trolldom. You’re not. You’re cookie cutter. We see your kind all the time. Demanding respect for your religious beliefs and arguing for special creation of humans while pretending to be “open” and “not rush to judgement.”

Comment #189050

Posted by Popper's Ghost on July 20, 2007 5:30 PM (e)

And the common retort is “But that doesn’t rule out the possibility of God.” Well duh. But that’s nearly the same level of intellectual sophistication as a nine year old who thinks they have made a great intellectual discovery and goes around saying “Anything is possible.” It’s not quite true, of course – some things are self-contradictory. But that still leaves a lot of room for trite observation. And it’s amazing how many people never move beyond that, never realize the complete and utter lack of significance of things being “possible”, never grasp that there is a far more powerful sort of epistemology, despite that they use it every day in order to survive and make their way through the world. “There are no WMDs in Iraq.” “But it’s possible that there are.” “Yes, yes it is, dolt.” “There is no intelligent designer.” “But it’s possible that there is.” “Yes, yes it is, dolt.”

Comment #189051

Posted by Peter on July 20, 2007 5:35 PM (e)

Is it dysteleology or is it extensibility? Is there a way to test for either of these?

Comment #189052

Posted by Popper's Ghost on July 20, 2007 5:36 PM (e)

My question to you is, how can you be so sure that there was no intelligent design behind our creation, when you really didn’t even know how the genome really functioned, for the most part, anyway?

This is an incredibly stupid ad hominem. It’s like saying, how can you be so sure that there are no unicorns, when you really didn’t even know that Gumby had a sister named Minga?

Comment #189053

Posted by Popper's Ghost on July 20, 2007 5:40 PM (e)

Peter, what part of “is not in evidence” don’t you understand? It’s not a metaphysical claim.

Comment #189055

Posted by Popper's Ghost on July 20, 2007 5:50 PM (e)

In dismissing God at this early stage of our genome intrepetation,

Stupid effing moronic false dichotomous strawman basher. Various interpretations of the genome have no bearing whatsoever on whether there’s a God. That’s the point, as you would realize if you weren’t so stupidly dishonest – it is the IDiots who falsely claim, after the fact, that this or that interpretation was a prediction of ID (as if pre-diction had nothing to do with actually making a claim beforehand) and that therefore it supports the existence of God.

Comment #189056

Posted by Sir_Toejam on July 20, 2007 5:54 PM (e)

Sam:

I do not have an opinion one way or the other; because, as far as I am concerned, enough of the evidence is not in to make a definitive decision one way or the other.

which reminded me of something I read a few years back:

“At some point in an election, an ‘undecided voter’ becomes a euphemism for stupid and lazy, and that time is now,” says Tucker Carlson, a staff writer for the Weekly Standard and a commentator for CNN. Carlson’s solution: don’t encourage them. “We’ve got to stop pretending that everyone should vote. Maybe democracy by the interested is good.”

Comment #189058

Posted by Popper's Ghost on July 20, 2007 6:13 PM (e)

As a matter of fact, I was definitely swaying heavily toward the fact that there in no “Intelligent Design” in the genome, until, that is, I discovered that we have been misinterpreting the major expressive action of the genome, which in turn tells me that we are not as far along as we would previously have liked to believe, in understanding the genome.

This looks like the key. Sam was so stupid as to think that whether there is intelligent design hinged on our interpretation of the genome, concluded somehow from interpretation of the genome that there is no intelligent design, and then when that inference was undermined, decided to go attacking those that he thought were as stupid as he is. Despite being an “investigator”, he seems unable to realize that non-functional sequences in the genome would just be one of many arguments against intelligent design, and the main reason that it is discussed as such is because the IDists make such a big stupid deal of finding some function that wasn’t previously known – wow, imagine that, we now know things that we didn’t know before. And gee, some biologists leapt to insufficiently grounded conclusions about lack of function, largely due to panadaptationist biases that have already been roundly criticized … by biologists. Yes, indeed, biologists make mistakes. But that’s not a reason to become a radical skeptic, rejecting all evidence and argument and the conclusions reached from them, just because it’s possible that they are in error. Lack of certainty of P is not the same as “P and not P are equally likely.”

Comment #189059

Posted by Popper's Ghost on July 20, 2007 6:17 PM (e)

I do not have an opinion one way or the other; because, as far as I am concerned, enough of the evidence is not in to make a definitive decision one way or the other.

As if the only alternative to making a definitive decision is to have no opinion.

Comment #189060

Posted by Werrf on July 20, 2007 6:26 PM (e)

Poppers Ghost wrote:

Sam was so stupid as to think that whether there is intelligent design hinged on our interpretation of the genome, concluded somehow from interpretation of the genome that there is no intelligent design, and then when that inference was undermined, decided to go attacking those that he thought were as stupid as he is.

Sorry, but that’s not what he said.

Sam was mislead by the popular press into thinking that we understood everything about the genome, so he trusted scientific statements. When he learned that what he’d been told was wrong, his trust in scientific statements was shaken. He didn’t realise the difference between good scientists and the press - foolish, perhaps, but not as stupid as he’s being made out to be.

If you were told by your lawyer that there was absolutely no way in hell that ID could ever be taught in schools, you’d believe him. If another lawyer then came along and said well, actually, there’s this loophole… you might start wondering if you could trust ANYTHING lawyers told you. It wouldn’t make you automatically stupid.

Comment #189062

Posted by Sir_Toejam on July 20, 2007 6:35 PM (e)

Sam was mislead by the popular press into thinking that we understood everything about the genome, so he trusted scientific statements

nonsequitor.

Comment #189065

Posted by Torbjörn Larsson, OM on July 20, 2007 6:51 PM (e)

Andras Pellionisz wrote:

with an organization standing up against casting out 98.7% of human Genome as “Junk”

This seems to be a number familiar from the non-coding part of the genome. AFAIK the functional non-coding genome isn’t “junk”.

Werrf wrote:

the only way to make any sensible judgement about design in living creatures, or the universe, would be to compare a creature KNOWN to be designed to one KNOWN to have evolved, and see which one most closely fits the life on earth

There is an interesting design detection idea in this, the Multiple Designers Theory. It is the only design theory which seems feasible; it is basically the basis for detecting different natural designers in forensic science and SETI.

Venter’s designer cells will fit the bill soon, so “forensic science” will come to have a place in biology as well.

Eric Finn wrote:

The creator-hypothesis is, in my opinion, a scientific hypothesis. However, science needs predictions as well.

Agreed. However, a nitpick; IMO a non-predictive hypothesis (if it is alone) or theory is often said not to be scientific for that very reason.

Comment #189068

Posted by Werrf on July 20, 2007 7:19 PM (e)

Sir Toejam wrote:

nonsequitor.

A very common one, in the modern world - believing that what is reported in the media is the truth, rather than a compressed and distorted lie-to-children. It happens in many fields - politics, science, showbiz, economics, all over the place. Short sighted, but all too common. It doesn’t make one stupid.

Still, my point stands - he wasn’t stupid, just misled.

Comment #189069

Posted by Torbjörn Larsson, OM on July 20, 2007 7:26 PM (e)

Torbjörn Larsson wrote:

the basis for detecting different natural designers in forensic science and SETI

Heh. I must be low on caffeine. I just realized (I think) why this works formally - it is a meta-‘design’ detection. Since it is impossible to assign random patterns to designers, we assign meta-patterns of designers (their patterns of remains, behaviors, signals) to them.

Much like NBG sets aren’t collections of subsets (with members), but a class that is a member of some other class. (Roughly to avoid that sets can’t be members of themselves.) By proper encapsulation it works (assigning patterns/members in designers/classes), by naive set/design theory it doesn’t (assigning patterns/members).

Come to think of it, that is also how evolution ‘assign’ patterns ‘in’ genes - as patterns among genomes, i.e. phylogenetic trees.

RBH’s design theory rocks! Or, I need more coffee. :-P

And now we return to our regularly scheduled thread.

Comment #189072

Posted by Tim Fuller on July 20, 2007 8:34 PM (e)

Sam:

1. Self proclaimed non IDiot.

2. Self evident Christian apologetic

3. Possible pro IDiot Shill

a. Evidence suggests a mastery of the English language at the total expense of any scientific consistency. Sophistry at this level is proof that Sam isn’t dumb. However, his responses to the well written questions in his FIRST post expose his true intents (as have been documented by others - Comment #189049 nailed it) Feigned neutrality and civility that quickly morphs into obvious religious shillery. I recognized it in the first post (as I’ll bet many others did because it is so ‘cookie cutter’ also previously noted) This obliviousness to the facts (even when spoon fed to him) and his subsequent hysteria is seen in fundementalists conditioned by birth to doubt (fear) anything not true to ‘scripture’. No manner of fact will suffice. My fear is that many of the same people running around looking for God under every rock are the same ones who believe we found a big stockpile of WMD’s in Iraq (and need to get the big pile in Iran TOMORROW)

Enjoy.

Comment #189079

Posted by Andrea Bottaro on July 20, 2007 9:33 PM (e)

People, this thread is depressing. Either you try to lift the tone above kindergarten-level name-calling, or I’ll just close it. It is sad that trolls can so easily derail a discussion here. They must be having a ball at our expense.

Comment #189083

Posted by Eric Finn on July 20, 2007 11:01 PM (e)

Torbjörn wrote:

Eric Finn wrote:

The creator-hypothesis is, in my opinion, a scientific hypothesis. However, science needs predictions as well.

Agreed. However, a nitpick; IMO a non-predictive hypothesis (if it is alone) or theory is often said not to be scientific for that very reason.

I may have been too liberal in my use of the terminology.

From Wikipedia:
A hypothesis (from Greek ὑπόθεσις) consists either of a suggested explanation for a phenomenon or of a reasoned proposal suggesting a possible correlation between multiple phenomena. The term derives from the Greek, hypotithenai meaning “to put under” or “to suppose.” The scientific method requires that one can test a scientific hypothesis. Scientists generally base such hypotheses on previous observations or on extensions of scientific theories.

Your comment was not nitpicking, and Wikipedia seems to agree with you.
I was allowing for possible future predictions, although I do not expect that happening, unless the creator is defined in more detail.
Of course, the creator might exist or might not exist irrespective of the scientific status. All it means is that we can’t use science to to find it out.

Regards
Eric

Comment #189084

Posted by Eric Finn on July 20, 2007 11:33 PM (e)

Andrea Bottaro wrote:

People, this thread is depressing. Either you try to lift the tone above kindergarten-level name-calling, or I’ll just close it.

I have had problems in understanding the tone of some of the comments. Maybe the tone is selected because of having to explain the same basic things for the umpteenth time. On the other hand, that’s what the teachers do (not usually to the same pupil, though). Maybe some of the questions are rather provocative as well.

I do enjoy reading the threads here on PT, since I can find a lot of interesting items written by experts in their fields.

Regards
Eric

Comment #189088

Posted by Popper' Ghost on July 21, 2007 12:01 AM (e)

Sorry, but that’s not what he said.

I didn’t say he said it – it was an inference. A far better supported one than yours.

It wouldn’t make you automatically stupid.

Actually it would, and you’re stupid for thinking that “you can’t trust ANYTHING lawyers tell you” could possibly be a rational conclusion. Lawyers are individual people; there is no claim about them that is universally true. But the initial stupidity is thinking that “trust” is an appropriate epistemological method.

Comment #189089

Posted by Popper' Ghost on July 21, 2007 12:04 AM (e)

he wasn’t stupid, just misled

False dichotomy. He clearly is stupid, and not just for being misled in a way that non-stupid people wouldn’t be.

Comment #189090

Posted by Popper' Ghost on July 21, 2007 12:07 AM (e)

Either you try to lift the tone above kindergarten-level name-calling

It is your reaction that is kindergarten-level, reflecting how thoroughly you absorbed your kindergarten teacher’s admonishment to be a nice little boy. Appropriate levels and expressions of contempt are a sign of maturity.

Comment #189091

Posted by Alex on July 21, 2007 12:11 AM (e)

As usual, the ID folks also manage to get their biochemistry all wrong in their “encyclopedia”: So now DNA polymerases excise introns. Really? Does anyone still believe ID has anything to do with biology?

Comment #189092

Posted by Popper' Ghost on July 21, 2007 12:35 AM (e)

Of course, the creator might exist or might not exist irrespective of the scientific status. All it means is that we can’t use science to to find it out.

If we can’t use science to find it out then it can’t be found out. There isn’t any alternative to the scientific method for answering empirical questions.

But there’s a deeper problem here, which is that the creator hypothesis is incoherent. No one actually has the faintest idea what they mean by “the creator of the universe”. For instance, when we refer to someone creating something, we generally mean that they have assembled it from some materials; the creation consists of the causal activities performed by the creator on the materials, resulting in the creation. What are the materials from which the universe was created, and by what sort of process were they put together? If there were such materials, why aren’t those just another phase of the same universe? If there were no materials, and thus no process of assemblage, what warrants calling the “creator” a creator? Why can’t we just as well view it as the universe springing into being, with the alleged creator simply standing by? (Skipping over the problem of “standing by” could possibly mean.) Very rarely do people expend the intellectual effort or engage in the intellectual discipline and integrity of considering such problems. Rather, they blithely take everyday language and apply it to things it doesn’t apply to, as if anything grammatical is also meaningful.

Comment #189093

Posted by Popper' Ghost on July 21, 2007 12:37 AM (e)

Lawyers are individual people; there is no claim about them that is universally true.

Urgh … obviously not no claim, as I just made one.

Comment #189094

Posted by Popper' Ghost on July 21, 2007 12:45 AM (e)

Maybe the tone is selected because of having to explain the same basic things for the umpteenth time.

Or maybe it has something to do with the immense arrogance and hypocrisy that people like Sam Corpin display when they presume to lecture the entire scientific community with their strawman accusations. He has the audacity to ask “How can any of you be so sure” and then close with “I know you guys will be screaming as you write, insulting me with your poison key pads :) - and why will you be doing this? Because you know, deep down inside, that I am right.” That is not someone who wants to discuss something, who is open to challenge or learning. (Nor of course is it someone who has been innocently misled.)

Comment #189095

Posted by Popper' Ghost on July 21, 2007 12:50 AM (e)

It is sad that trolls can so easily derail a discussion here. They must be having a ball at our expense.

The trolls didn’t derail the discussion, they continued it. The subject is, after all, big honcho troller Casey Luskin, who represents a troll organization leading a troll movement. And they are indeed having a ball at our expense by creating the impression that there’s a “controversy”, a “scientific disagreement”. I think it’s as appropriate to be civil toward them as toward a Nazi or a tse-tse fly.

Comment #189116

Posted by Sir_Toejam on July 21, 2007 5:20 AM (e)

It happens in many fields - politics, science, showbiz, economics, all over the place. Short sighted, but all too common. It doesn’t make one stupid.

then it makes one lazy, if they are not stupid.

hell, you figured it out, yes?

anybody here who claims innocence of how poorly the media report scientific findings?

why make excuses for him? surely he can make excuses for himself, if he’s not stupid, right?

Comment #189152

Posted by hoary puccoon on July 21, 2007 12:17 PM (e)

I’m sure the trolls are having a laugh at our expense. This Sam Corpin character is just too slick. And it’s the same old stuff– basically pushing “the controversy.” Looks like the M.O. of the Disco Institute to me.
If you think about it, Corpin has no point at all. He’s basically saying, “gee, when the human genome was fully described, it turned out to lead to unexpected new research!” Well, surprise, surprise. The world spent how many hundreds of millions of dollars to decode the human genome? And we’re supposed to believe scientists did all that because they wanted to dot a few i’s on their old research?? Oh, come on. I don’t think anyone smart enough to write in complete sentences could be dumb enough to believe that. I imagine the “researchers” at the DI had a ball, though, coming up with yet another way to twist the truth.

Comment #189155

Posted by George Cauldron on July 21, 2007 12:51 PM (e)

Hey, I am not an IDist! I do not have an opinion one way or the other; because, as far as I am concerned, enough of the evidence is not in to make a definitive decision one way or the other.

I think I detect the presence of a Concern Troll.

(And not an especially convincing one.)

Comment #189183

Posted by Steviepinhead on July 21, 2007 4:06 PM (e)

Werrf:

Sam was mislead by

On a side-note, Stevie begins to get nervous that he may have to correct someone’s usage. Inevitably, whenever he feels “forced” to do so, he makes some egregious typo or usage error himself…
Werrf:

stupid, just misled.

Whew! No “correction” necessary…

Comment #189184

Posted by Sam Corbin on July 21, 2007 4:20 PM (e)

Okay, first let me say that I am not a scientist, yet. I am going back to college in the fall to study Molecular Biology. I have 1.5 - 2 years to go to get my Bachelors Degree in this area. I dropped out of college several years ago because I could not, at the time, come up with an area of pursuit that I felt truly interested in. I have all of my basics completed for a 4 year degree; however, that was several years ago.

It was 10 or 14 years ago while doing research on the ERIC database at the local library that I ran across my first information on the “Human Genome Project”. Let me tell you, I WAS ELATED. I researched everything I could about it at the time. I told other people about it at almost every instance for a while. I was very, very excited at the prospect of the advancements, cures, possible longevity and history of our origins that were to be discovered in the coming years. As a matter of fact, tears came to my eyes when I first heard on the news that the Human Genome Project had finished mapping the human genome - 10 years ahead of time!

Many of my friends, that I would speak to about the HGP, were actually hearing about it publicly for the first time. (Maybe this is where my -yes- stupid arrogance on the subject was born, even.) I did not feel arrogant at the time, though, just grateful, very grateful, to the scientific community.

I cringed when I read what I had written in my earlier posting here on this blog: “..Because you guys know that I am right!”
I am not offended by some of your hateful emotional outbursts, because I realized, when one of you pointed it out, that you hate it when non-scientists say something like this when you have been professionally researching this stuff for years.

*********

I did really well in school, but that was a long time ago. I see that I am not the straight A student here, but rather the Kindergartener, and I am humbled in my naivety. Forgive me.

I should add here, that my basic understanding of the human genome, at first, was that it was a “code”, which, to the layman such as myself, implies that the code was “created”.

I admit that the tone of my first posts were somewhat provoking, (admittedly in part, due to my misplaced and very embarassing arrogance), but the main reason for my questions, was a vain attempt to get definitive answers to the questions that keep plaguing my mind, and to which I cannot seem to get seemingly logical answers to, as a layman.

I have a better than (the) average (Joe) understanding of gene expression, viruses, DNA, RNA and chemistry; however, I cannot fully grasp the concept of how inorganic matter first starts to “desire” to survive.

I can see how like molecules want to bond together and how the building blocks of organic material can be created from inorganic material; however, my comprehension comes to a halt when I read that these first basic organic molecules started exhibiting survival instincts.

So, my question again is, how does the newly developed organic molecule(s) obtain it’s first survival instincts? What mechanism(s) are at work that awaken the organic molecules to their mortality? If awareness is too strong of a word, then what basic chemical and/or physical process takes place that is the basis of the survival instinct?

Understand, that it is hard for us laymen to move from the understandable, computer program-type model, to the spontaneous generation model, without a layman-comprehensible explaination for this phenomenon.

I have more basic questions, but I realize that most of you here are scientists, and are not interested in fielding my “stupid” questions. However, could one of you please, explain to me in layman’s terms, how this phenomenon (survival instinct) first came into existence, please?

[syntax error fixed - AB]

Comment #189186

Posted by Steviepinhead on July 21, 2007 4:29 PM (e)

Let me predict that syntax will hardly be the only error in Sam’s forthcoming comment.

Comment #189194

Posted by Andrea Bottaro on July 21, 2007 4:55 PM (e)

I have more basic questions, but I realize that most of you here are scientists, and are not interested in fielding my “stupid” questions. However, could one of you please, explain to me in layman’s terms, how this phenomenon (survival instinct) first came into existence, please?

It depends on what you mean by “survival instinct”. If you mean consciousness of one’s existence and voluntary avoidance of situations that may terminate it, then only rather sophisticated organisms with complex nervous systems have it. If you are talking about molecular/cellular homeostatic mechanisms that mechanistically (not consciously) act to preserve an organism’s physiological status, almost certainly all cellular organisms have at least some (but I’d say that viruses, for instance, probably don’t).

If you instead are referring simply to the ability of organisms to replicate themselves, that was probably one of the first, if not the first, property of living matter (depending on who you ask). Early replicating molecules (or aggregates thereof) could have been relatively simple nucleic acids and/or assemblages of proteins and membranes. But these replicating forms certainly dio\d not have “instincts”, awareness, or “drive” to do anything, they simply replicated, and the better replicators became progressively more common, and more sophisticated, by selection processes.

Comment #189195

Posted by Sam Corbin on July 21, 2007 5:08 PM (e)

It is very hard to believe that some of you are really scientists. I don’t see how childishly attacking my intelligence, and “pseudo pre-menstrally” changing the meaning of my posts, makes your responses what they should be: Based in fact, understandable to a layman and in line with what I had written.

Many of us laymen, have a problem with the evolution theory because the genome had been presented to us in the mass media as a “code”, which to us laymen, indicates something that has been created, like a computer progam.

The second problem us ignoramuses have, is the proper understanding of how the newly created organic material awakens to its mortality, and develops a survival instinct.

If “survival instinct” is too strong of a term to describe the phenomenon, then a logical and concise explaination of the physical and/or chemical processes that take place in the newly formed organic material that are expressed as survival mechanisms, which ultimately grow into what we know as survival instinct.

If any of you can accurately, logically and understandably explain where, how and why the survival instinct originates (with emphasis on how), then people such as myself, that you accuse of being IDists, could have a working knowledge, based in understanding, of what your argument is based on.

Comment #189196

Posted by Flint on July 21, 2007 5:21 PM (e)

It doesn’t strike me as all that baffling to suggest that a marginally better tendency to survive is itself a survival characteristic. As Andrea said, few critters (certainly no bacteria, for example) have any consciousness to use to make a conscious effort to stay alive. But no organism survives today, that lacks the ability to survive somehow. I doubt it makes much sense to project human fear of death onto other forms of life.

Comment #189213

Posted by David Stanton on July 21, 2007 6:01 PM (e)

Sam,

Sorry about all the name calling. However, you have to understand that when a non-scientist basically calls into question the professional integrity of all scientists, the response is not likely to be polite.

In response to your question, Andrea is correct. The only requirement for selection to act is the ability to replicate. After that, selection becomes almost inevitable, especially if replication lacks perfect fidelity.

As for how the first replicating organic structure arose, that is a complicated question. If you don’t want to wait until you finish your degree, I would recommend the following web site as an introduction to the topic:

talkorigin.org/faq/abioprob/origin oflife.html

The article is written for non-professionals and starts from the basics. I hope you find it useful. (Note that abiogenesis is a topic completely separate from that of evolution).

If you are sincere in your quest for knowledge, I wish you luck. If it is any consolation, IMO the fact that you are interested in these issues is evidence of your intelligence. Your choice of molecular biology as an area of study is IMO further evidence. Realizing that some others might know more about these issues than you do would also be good evidence and learning from them even more so.

Comment #189214

Posted by Andrea Bottaro on July 21, 2007 6:14 PM (e)

NOTE: I have added an update to the post above.

Comment #189241

Posted by CJO on July 21, 2007 7:39 PM (e)

What you’re concerned about is life itself. Break life down to its most basic features: discrete boundary (the cell wall), metabolism, and the ability to replicate with some degree of fidelity. Once you have these features in place (and the genetic “code” fits in here as the machanism behind replication), survival is just what happens. What must happen. For some lineages more than others, which is the slow engine of R&D that eventually led, here on earth, to the big complex nervous systems Andrea talked about. And hence your survival instinct.

That process is well understood in broad outline. Not well understood at this time is how organic chemistry gave rise to the three essential components in the first place. The ID approach is to embrace a foregone conclusion and prop it up with cherry-picked data and appeals to analogies like the genome as computer code that may mislead as much (or more) as they enlighten. The scientific approach rejects easy answers to hard problems and makes such gains as it can with methodical empirical inquiry. Origin-of-life research is a growing and exciting field –it’s much too early to give up. And, ultimately, accepting defeat is the only concrete contribution of ID to the question. I’ll stick with the provisional answers science can provide.

Comment #189254

Posted by Andras Pellionisz on July 21, 2007 9:02 PM (e)

I am glad for Panda’s Thumb that my contribution on my rather unique Darwinist friend and fellow-pioneer of research (of what used to be “Junk DNA”) could be dislodged and finally got posted here, in its original destination as well. This gives all of us a chance to carefully look at Malcolm Simons’ record from every viewpoint. (I do recommend to read/view the documentary “Genius of Junk” on him). Yes, there were Darwinists as early as in 1987 to risk everything they had for their scientific conviction that 98.7% of human DNA wasn’t “junk”.

While correcting the record is important for history, it may be wasted time to guess if instead of 1.3% the functional ratio is 20%, 30% … 90%, 100%, or if its algorithmic design can be best characterized by the adjective “intelligent” or not. International PostGenetics Society simply focuses on finding it out *how the functional whatever percentage* (beyond the 1.3% that used to be “genes”) work. There is no ideological aspect to IPGS, indeed there is no record (in fact, no question) what is the ideological background of the now 58 Founders and members representing 34 countries.

The Honorary Chairman of IPGS is Dr. Malcolm J. Simons (no time was wasted for ideology in our writing up the experimental support for quantitative predictions of the fractal-algorithmic approach to genome function, or in formally abandoning the “Junk DNA” notion as a scientific term at the “European Inaugural” of IPGS, 12 October, 2006). More on PostGenetics at “http://www.postgenetics.org”.

pellionisz_at_junkdna.com

Comment #189280

Posted by raven on July 21, 2007 10:38 PM (e)

Casey Luskin has posted another piece at the Discovery Institute’s Media Complaints Division ominously entitled: “Is Panda’s Thumb Suppressing the Truth about Junk DNA?”,

What truth about junk (sic) DNA. This is why the DI will always be a fringe pseudoscience group of nonentities. There is no truth about noncoding DNA right now.

What we know right now indicates in a provisional and simple minded way that some noncoding is functional, some, maybe most, is not.

To really answer the question will take far more data than we have, decades worth most likely. 3 billion bases is a lot of DNA. Science asks questions and answers them experimentally. Experiments are designed, run, data collected, analyzed, repeat over and over contingent upon the collective results at any given time.

Scientific questions are not answered by arguments, lies, posting emails back and forth, making baseless claims without data, insults, slander, and endless postings on message boards. Which is all the DI ever does.

This is why the Greeks and Chinese never went very far. There was always this thought that by just thinking things through and using logic, scientific problems would be solved. Empiracism was looked down upon on the basis that real scholars didn’t get their hands dirty. This works very well in mathematics and the Greeks made many contributions. In the real world, one needs a partnership between theory and experiment.

This is why I have absolute contempt for the DI. They are really pseudoscientistic pretenders taking potshots at real science and scientists from the sidelines while lying constantly about everything. The opposite of what any real science department anywhere is.

Comment #189300

Posted by Sam Corbin on July 22, 2007 12:17 AM (e)

Andrea, CJO, David and Flint: Thank you.

Werrf: Thank you for your support.

Comment #189301

Posted by Sam Corbin on July 22, 2007 12:17 AM (e)

Andrea, CJO, David and Flint: Thank you.

Werrf: Thank you for your support.

Comment #189303

Posted by PvM on July 22, 2007 12:52 AM (e)

Luskin should be embarassed but I am not sure if such a state of mind exists in his vocabulary. Ironically, it is the DI website which censors comments and trackbacks.

Which is why ID remains scientifically vacuous.

Surely intelligent design is not practiced by its proponents.

Comment #189316

Posted by Popper' Ghost on July 22, 2007 2:18 AM (e)

Um, have people here actually failed to notice that “Sam Corbin” != “Sam Corpin”? Someone’s messing with you.

my comprehension comes to a halt when I read that these first basic organic molecules started exhibiting survival instincts

Ah, the arrogance of impoverished intellect. Rather than having read anything so absurd, he most likely read something quite different that, with his sloppy mental habits, he misinterpreted as saying that but, in his arrogance, he failed to consider the strong likelihood that he misinterpreted it. And in his laziness he failed to seek out other sources that explained things differently and more clearly – it must be laziness in the extreme, because they are plentiful.

If “survival instinct” is too strong of a term to describe the phenomenon, then a logical and concise explaination of the physical and/or chemical processes that take place in the newly formed organic material that are expressed as survival mechanisms

This is so simple to understand that it baffles me that people have trouble with it. Consider mountains that erode quickly and those that don’t. The latter survive while the former don’t – not because they have a “survival instinct” or “survival mechanisms” but because they have features that make them more survivable. The same goes for organisms, or even replicating molecules; some have features more conducive to survival than others. There’s nothing baffling or mysterious or magical about that. But unlike mountains, replicators replicate, and in so doing replicate the “code” that produced the features conducive to survival, so over time there is more of that “code” and less of the “code” that results in features less conducive to survival. Voila, natural selection. There isn’t some specific “chemical process” that confers survival, survival is simply a statistical existential consequence; any processes that result in relatively higher survival will do, and the processes that do are very dependent on the environment of the organism; it’s the environment, “nature”, that does the selecting.

There are all sorts of features that can result in an increase in the statistical likelihood of survival. Some of those features are like the hardness of mountains – they simply make the organism more robust, less subject to damage – calling these “survival mechanisms” is quite misleading. And some of the features are behavioral – e.g., avoidance of potentially harmful circumstances. This can be simply a matter of an organism having a sensor that triggers movement away from light or vibration or high or low concentrations of salt or oxygen or whatever. It’s utterly mechanical; the organism doesn’t need to have any “instinct” or awareness or anything else; it’s just a machine that acts a certain way, and machines that act one way tend to survive to produce more of the “code” that produces that sort of action while machines that act another way tend to survive less. Voila, natural selection.

Back when no one had ever thought of this, there was an excuse for having trouble understanding it. But there’s no excuse these days. And the same goes not just for Sam Cor{b|p}in, but also to people who have posted things like “competition (aka natural selection)” on this board. Natural selection does not equate to “competition” (in fact cooperation is often preferentially selected) or “survival instinct”; it is much broader and much more basic than that.

Comment #189317

Posted by Popper' Ghost on July 22, 2007 2:24 AM (e)

This is why the Greeks and Chinese never went very far.

It’s not just the IDiots who are simplistic fools.

Comment #189318

Posted by Popper' Ghost on July 22, 2007 2:29 AM (e)

Not well understood at this time is how organic chemistry gave rise to [discrete boundary (the cell wall), metabolism, and the ability to replicate with some degree of fidelity] in the first place.

This is true, but that’s at a far more sophisticated and detailed level than Mr. Cor{b|p}in’s notion that molecules developed a desire to survive.

Comment #189319

Posted by Popper' Ghost on July 22, 2007 2:50 AM (e)

But no organism survives today, that lacks the ability to survive somehow.

So do rocks that don’t erode have “the ability to survive somehow”? “ability” is fundamentally the wrong way to look at evolution, and invariably leads to error. How about dinosaurs vs. mammals, or non-feathered dinosaurs vs. feathered dinosaurs? Did the latter have an “ability to survive” while the former didn’t? Hardly. Rather, the latter had features that resulted in greater survival of the K-T boundary event vs. the features of the former. Survivability isn’t intrinsic to an organism, it’s an existential consequence of the interplay between the features of the organism and the environment in which it is embedded. As the environment shifts, or as organisms enter different environments, the differential survival of organisms shifts. Understand this and you will understand a great deal about evolution. Fail to understand it and you will fall into all sorts of normative nonsense like Social Darwinism.

Comment #189320

Posted by Popper' Ghost on July 22, 2007 3:08 AM (e)

The second problem us ignoramuses have

Ignoramuses are people who are willfully ignorant. Pick up any basic biology book at the bookstore or library and you can learn the basics of natural selection. There are millions of “laymen” (including me) who don’t suffer from your bizarre misconceptions about molecules having desires or being “awakened to their mortality”; take responsibility for your own unique confusion.

As for a “code”, which to us laymen, indicates something that has been created, like a computer progam – yes, the code was created, by natural processes. Just because one sort of code was produced by humans doesn’t mean that all sorts of codes were. You could just as well talk of the lens of the eye, which to us laymen, indicates something that has been created, like a camera. It isn’t being a layman that is your problem, it’s being illogical, which stems from being mentally lazy.

Comment #189322

Posted by Popper' Ghost on July 22, 2007 3:19 AM (e)

I can see how like molecules want to bond together

Molecules, don’t “want” to bond together, any more than rainwater “wants” to fill holes, and being “like” has nothing to do with it. I suggest a basic chemistry book – something on the eighth grade level, as that seems to be about where you’re at.

Comment #189328

Posted by Popper' Ghost on July 22, 2007 3:29 AM (e)

If you are talking about molecular/cellular homeostatic mechanisms that mechanistically (not consciously) act to preserve an organism’s physiological status, almost certainly all cellular organisms have at least some (but I’d say that viruses, for instance, probably don’t).

What’s relevant in biology isn’t preservation of an organism’s physiological status, it’s preservation, through replication, of the means of producing like organisms (that in turn, through replication, preserve the means …). And viruses have that property in spades, resulting in their long term survival – as an abstract set organisms with a similar physiology, not as individual physiological organisms, the survival of which doesn’t matter. I think someone wrote a book about that – the selfish something or other – but the concept has yet to sink in.

Comment #189336

Posted by Popper' Ghost on July 22, 2007 3:50 AM (e)

Andras J. Pellionisz, who seems to be a rather cranky biophysicist

He does seem to score high on The Physics Crackpot Index.

Comment #189337

Posted by Eric Finn on July 22, 2007 3:52 AM (e)

Popper' Ghost wrote:

There isn’t some specific “chemical process” that confers survival, survival is simply a statistical existential consequence; any processes that result in relatively higher survival will do, and the processes that do are very dependent on the environment of the organism; it’s the environment, “nature”, that does the selecting.

I found your post (Comment #189316) very instructive.

Sometimes it takes a lot of thinking to tell simple things apart from the more complicated ones.

Regards
Eric

Comment #189346

Posted by Popper' Ghost on July 22, 2007 5:19 AM (e)

Sometimes it takes a lot of thinking to tell simple things apart from the more complicated ones.

Especially when there’s been so much muddying with bogus notions of Social Darwinism and “survival of the fittest” (Darwin’s greatest error, IMO, was allowing that grossly ambiguous and misleading phrase to be attached to his theory). So people have this notion that the “survival” relevant to evolution has something to do with how sharp your claws are or how big your club is. But all those cavemen and all the cats that sometimes took a swipe at them are dead, regardless of their “survival instincts” or “survival mechanisms” – none survived, just as no individual survives for long. (I think this mistaken view of “survival” is like religion in that both stem from denial of death.) Survival of individuals is irrelevant, beyond lasting long enough to produce some offspring. Fecundity beats a big club any day, as does mutually beneficial collective behavior (contrary to free market ideologues, unions are natural). Just imagine some Social Darwinist sitting on the grass under a shade tree thinking about how his (an appropriate pronoun) superior qualities allow him to get ahead in this dog-eat-dog world – ignoring the grass, the tree and all the other noncombatting organisms around him, as well as the fact that dogs don’t eat dogs and that getting ahead is a largely irrelevant social construct. Much of what people believe about the biological world is obviously stupid – obvious to anyone who isn’t intellectually lazy, anyone who bothers to try to think things through. Fortunately for the survival of the human species, it doesn’t have much to do with that trait, which may well explain why it’s so rare. (Yes, that’s another one of those stupid beliefs, that intelligence is, per se, a survival trait. It’s kind of funny how many of those most sure of this are childless geeks.)

Comment #189347

Posted by Popper' Ghost on July 22, 2007 5:49 AM (e)

BTW, as an example of just how perverted the common view is, consider the eugenicists who sterilized low-IQ women lest they have too many babies. As if it were IQ points, rather than reproduction, that is the driving force of evolution. And who is more dangerous to the species, a 90 IQ woman with 10 children or the CEO of ExxonMobil or the former CEO of Halliburton? Not that that’s either here or there; evolution doesn’t work on such global scales, and it doesn’t “care” whether species go extinct or – more likely for us – are decimated. The point is that while we put great value on intelligence, it doesn’t have much value in the biological world. Our big brains developed in response to a specific sequence of conditions that are still not well understood – there wouldn’t be much to understand if intelligence were a survival trait per se. But there are billions of organisms without any brains that have done and will continue to do a lot better at the (species) survival game than us.

Comment #189351

Posted by Popper' Ghost on July 22, 2007 6:13 AM (e)

This is why the Greeks and Chinese never went very far.

As a response to the immense stupidity and ignorance of that comment, let me offer

http://en.wikipedia.org/wiki/History_of_Greece
and
http://en.wikipedia.org/wiki/History_of_China

BTW, this paragraph may provide some foresight about where we are going:

Archaeology shows a collapse of civilization in the Greek world in this period. The great palaces and cities of the Mycenaeans were destroyed or abandoned. The Greek language ceased to be written. Greek dark age pottery has simple geometric designs and lacks the figurative decoration of Mycenaean ware. The Greeks of the dark age lived in fewer and smaller settlements, suggesting famine and depopulation, and foreign goods have not been found at archaeological sites, suggesting minimum international trade. Contact was also lost between foreign powers during this period, yielding little cultural progress or growth of any sort.

Comment #189365

Posted by Andrea Bottaro on July 22, 2007 6:54 AM (e)

Dr. Pellionisz, your comment wasn’t “finally” published, it has been for 2 days now, long before your complaint became public, and was held for approval by our software for reasons having to do with the way you composed it (too many url links), and none other.

It would be appropriate for you to apologize for your baseless accusations, which reflect poorly on you, and contact Casey Luskin requesting to issue a correction on his blog (good luck with that, however).

Incidentally, once again our trackback to the misnamed “Evolution News and Views” site has been rejected - just to stress where the censorship resides in this debate.

Comment #189371

Posted by Popper' Ghost on July 22, 2007 7:05 AM (e)

Here’s a more direct piece about Greek science:
http://galileoandeinstein.phys.virginia.edu/lect…

Strato, like Aristotle, believed in close observation of natural phenomena, but in our particular field of interest here, the study of motion, he observed much more carefully than Aristotle, and realized that falling bodies usually accelerate. He made two important points: rainwater pouring off a corner of a roof is clearly moving faster when it hits the ground than it was when it left the roof, because a continuous stream can be seen to break into drops which then become spread further apart as they fall towards the ground. His second point was that if you drop something to the ground, it lands with a bigger thud if you drop it from a greater height: compare, say, a three foot drop with a one inch drop. One is forced to conclude that falling objects do not usually reach some final speed in a very short time and then fall steadily, which was Aristotle’s picture. Had this line of investigation been pursued further at the Lyceum, we might have saved a thousand years or more, but after Strato the Lyceum concentrated its efforts on literary criticism.

Strato did, however, have one very famous pupil, Aristarchus of Samos (310 - 230 B.C.). Aristarchus claimed that the earth rotated on its axis every twenty-four hours and also went round the sun once a year, and that the other planets all move in orbits around the sun. In other words, he anticipated Copernicus in all essentials.

Archimedes, 287 - 212 B.C., lived at Syracuse in Sicily, but also studied in Alexandria. He contributed many new results to mathematics, including successfully computing areas and volumes of two and three dimensional figures with techniques that amounted to calculus for the cases he studied. He calculated pi by finding the perimeter of a sequence of regular polygons inscribed and escribed about a circle.

Two of his major contributions to physics are his understanding of the principle of buoyancy, and his analysis of the lever. He also invented many ingenious technological devices, many for war, but also the Archimedean screw, a pumping device for irrigation systems….

Such a shame that the Greeks, the rediscovery of whose works led directly to the Renaissance and the Enlightenment, “never went very far”.

Comment #189403

Posted by raven on July 22, 2007 9:46 AM (e)

Wikipedia: Aristotle

“His writings provide an account of many scientific observations, but there are some curious errors. For example, in his History of Animals he claimed that human males have more teeth than females. In a similar vein, Galileo showed by simple experiments that Aristotle’s theory that the heavier object falls faster than a lighter object is incorrect.

In places, Aristotle goes too far in deriving ‘laws of the universe’ from simple observation and over-stretched reason. Today’s scientific method assumes that such thinking without sufficient facts is ineffective, and that discerning the validity of one’s hypothesis requires far more rigorous experimentation than that which Aristotle used to support his laws.

I should have said ancient Greeks and Chinese, not that it wasn’t obvious from my context. While we are wiki-ing, the old Greek and Chinese scholars were big on talking and writing, not so big on experimentation. That is why the Greeks made major contributions in philosophy and mathematics where sitting around with a piece of paper and pencil works well. Their contributions in the physical and biological sciences where experimentation is necessary were nowhere near the same level. The most well known ancient scholar Aristotle, “goes too far in deriving ‘laws of the universe’ from simple observation and over-stretched reason.” A lot of what Aristotle wrote about what we call science these days is just wrong.

It is clear that the ancients made some progress in science and then stalled out. It wasn’t until the end of the medieval period in Europe when the modern scientific method(s) were developed that the stunning progress weve made since started.

This is a sideline to this thread in general and the DI in particular. To reiterate the main point:

To really answer the question [noncoding DNA] will take far more data than we have, decades worth most likely. 3 billion bases is a lot of DNA. Science asks questions and answers them experimentally. Hypthothesis are formulated, experiments are designed, run, data collected, analyzed, repeat over and over contingent upon the collective results at any given time.

Scientific questions are not answered by arguments, lies, posting emails back and forth, making baseless claims without data, insults, slander, and endless postings on message boards. Which is all the DI ever does.

They don’t do science. They sit on the sidelines and twist whatever real scientists discover to fit their religious and political objectives.

Comment #189405

Posted by Popper' Ghost on July 22, 2007 10:04 AM (e)

I should have said ancient Greeks and Chinese, not that it wasn’t obvious from my context.

What you were saying was obvious … and obviously stupid and wrong.

While we are wiki-ing, the old Greek and Chinese scholars were big on talking and writing, not so big on experimentation.

The point of my citations is that Greeks such as Aristotle, Strato, and Aristarchus were big on observation, not just “talking and writing”. And if the Chinese weren’t so big on experimentation, one must wonder how they managed to come up with the compass, paper, printing, and gunpowder, among many other technical innovations.

Their contributions in the physical and biological sciences where experimentation is necessary were nowhere near the same level.

Gee, maybe that’s because advanced experimentation requires advanced technology. Their contributions were well advanced over their contemporaries. Your understanding of the history of science is horrendously bad.

Comment #189495

Posted by Andras Pellionisz on July 22, 2007 8:25 PM (e)

Dr. Bottaro, I truly appreciated that you, as a scientist, opened a thread pointing out that a few Darwinists did not fall (and I would add, hardly any of the God-believers ever fell) for Dr. Ohno’s deliberate framing of DNA with unknown function as “Junk”. You made a very good point. For instance, prompting me to draw attention to Darwinist Dr. Simons’ remarkable pioneering since at least 1987. Therefore, I was just as “cranky” as you were “depressed” to see your pithy thread degenerate (beyond my bounced though I think meaningful posting) to “kindergarten-level name calling”:

Comment #189079
Posted by Andrea Bottaro on July 20, 2007 9:33 PM (e)
People, this thread is depressing. Either you try to lift the tone above kindergarten-level name-calling, or I’ll just close it. It is sad that trolls can so easily derail a discussion here. They must be having a ball at our expense.

I would like to join you in encouraging bloggers, first to identify themselves (just as you and I are doing) with actual accomplishments or at least some degree in science, and second to focus on science, since supposedly Panda’s Thumb (as opposed to other blogs for which I am not responsible) is about science. We at International PostGenetics Society, http://www.postgenetics.org now with 60 Founders representing 34 countries even have a name and very clear agenda for this new branch of PostModern Genomics: PostGenetics (“Genomics beyond Genes”).

You may wish to help raising the level of your thread with actual debate on the topic you brought up, instead of lowering yourself to the level of name-callers.

Sincerely
pellionisz_at_junkdna.com

P.S. Regretfully, I have to take exception to your name-calling-type of posting (regarding “baseless accusation”). At the time of my release of my posting, intended for Panda’s Thumb but not appearing there and meanwhile the debate sinking towards levels that somewhat later even you found “depressing”, I was 100% justified to seek alternative public outlets. (Since you can have no idea when I released my posting to be published in other blog(s), please be rest assured that I acted when my posting to PT was bogged down in what you characterize as technical delay).

Can we, pleeeeese, focus on your original well-put science topic? People suffering from Junk DNA diseases “http://www.junkdna.com/junkdna_diseases.html” would not only be “cranky” or “depressed”, but outright dying on us if we proceed on an unproductive thread?

Comment #189496

Posted by Andras Pellionisz on July 22, 2007 8:31 PM (e)

just a quick note that I tried to post my answer to Dr. Bottaro but the reply screen signalled:

…I have enabled a feature that allows your comments to be held for approval the first time you post a comment. I’ll approve your comment when convenient…

Please stand by to see whenever my answer appears

pellionisz_at_junkdna.com

Comment #189499

Posted by Andrea Bottaro on July 22, 2007 9:04 PM (e)

Dr. Pellionisz:
maybe what I am going to suggest will sound perplexing and unsettling to you, but next time a comment of yours doesn’t show up on a site, you would be better off asking questions directly to the people managing that site first, rather than constructing rather bizarre conspiracy theories in your mind and complaining about them to third parties, especially if those parties’ only and transparent goal is to peddle pseudoscientific propaganda.

As for the where the discussion here is going, I have as little control over it as you do. You are welcome to continue posting on this site if you stay on topic and stick to the site rules, but I cannot guarantee that people will find your comments of any interest, and answer them. Moreover, that not everyone here has a degree and/or accomplishments in science is irrelevant. As I am quite sure someone may have mentioned to you before, scientific credentials are no insurance against error, foolishness or lunacy.

Comment #189502

Posted by Andras Pellionisz on July 22, 2007 9:56 PM (e)

Dr. Bottaro,

You say “As for the where the discussion here is going, I have as little control over it as you do.”

I don’t think anyone should “control” the discussion, but you initiated a very important thread, and I am trying to help you raise the level of discussion to citing Dr. Malcolm J. Simons’ “triumph and tragedy”.

For history, I think it is important to set the record straight that because of a deliberate “framing” (by Dr. Ohno) the few individuals, for which Dr. Simons as a Darwinist is an outstanding example, were seriously jeopardized in their effort (in his case, since 1987) to point out that “junk DNA” was anything but “junk”. In this thread I have yet to see if anyone actually looked up his science-story (see full transcript of “Catalyst”, link provided above).

If there is a apparent impossibility to refute, we might as well conclude your precious thread with the summary that “a few Darwinists tried to go against the whirlwind of the JunkDNA cyclone but were trampled under - now AFTER we left the dead-center of the eye of the cyclone wind is blowing with a rapidly increasing force into the opposite direction; the junky trend is dying out and people suffering from (or fearing) JunkDNA diseases have a hope, especially if united in PostGenetics”.

Any SCIENCE comments? (If for nothing else, for dear Malcolm’s sake?)

pellionisz_at_junkdna.com

Comment #189533

Posted by hoary puccoon on July 23, 2007 3:30 AM (e)

Re the science of ‘junk’ DNA– as James Watson points out in “DNA the Secret of Life,” (p. 180) ‘There is actually an extremely quick-and-dirty way to secure a snapshot of all the coding genes in the genome, using… reverse transcriptase technology….’
In other words, as I pointed out in two previous posts, if scientists had really believed that all of our DNA except protein-coding genes was ‘junk,’ there would have been no reason whatsoever for the Human Genome Project.
Andeas Pellionisz’s characterization of a few, embattled ‘Darwinists’ crying in the wilderness against the ‘junk’ orthodoxy is simply wrong. In fact, it was the proponents of ‘nothing but junk’ who ended up crying in the wilderness, while legendary scientists like Watson secured vast amounts of money, basically on the hypothesis that non-coding DNA wasn’t just junk.
Casey Luskin’s argument, in my opinion, is so misleading as to be immoral. The Discovery Institute did nothing to further the Human Genome Project. But now that the project has turned out to be as scientifically fruitful as its proponents hoped it would be, he is trying to grab the glory.

Comment #189544

Posted by Andrea Bottaro on July 23, 2007 7:53 AM (e)

Dr. Pellionisz:
The point of my post above is historical, and namely that, contrary to the Discovery Institute’s fabrications, the idea of “junk DNA” did not affirm itself because of some “Darwinist conspiracy”, but was in fact initially resisted by strict Darwinians (and still is in some cases, such as your friend - see below). I take no credit for this insight, as this is all well known to anyone who was there, or has read the relevant literature rather than making stuff up.

As for your comment, I strongly doubt Ernst Mayr, quite possibly the most influential evolutionary biologist of the second half of the last century, was “trampled over” (or would have let anyone trample him, who tried) about his ideas on “junk DNA” - I’d like to see any evidence of that. Secondly, Dr. Ohno in his original paper readily acknowledged that regulatory elements would be found in intergenic DNA, which is precisely where we stand now, since no one denies (or for that matter, ever denied) that intergenic regions contain some regions of function.

Going back to the quote you provided:

“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” [MJS]

note that it makes exactly the same point of my post above: Darwinian principles of natural selection, strictly applied, would predict that there would be no such thing as “junk DNA”. In other words, if “junk DNA” exists as such, it is in spite of natural selection (i.e. because it is effectively selectively neutral). This is the opposite of the pseudoscientific propaganda that the ID advocates have been peddling, and that you helped support with the unwarranted accusations you have leveled against this blog.

Regarding the science, and your idea of “fractal properties” of intergenic DNA, I won’t claim I can judge the mathematics behind it, but even assuming it is sound, I have to say I am very skeptical of its biological significance, in the absence of any proposed actual mechanism linking such properties to phenotypes.

Comment #189554

Posted by Flint on July 23, 2007 8:38 AM (e)

As folks like Richard Dawkins and Victor Stenger have pointed out, the world looks just the way one would expect if it were not intelligently designed. The odds are overwhelmingly against intelligent design, if intelligence has any sort of implication of foreplanning. Teleology is not in evidence.

This statement makes the implicit assumption that no god can cover its tracks so well that Popper’s Ghost can’t see them! Sorry, but I don’t accept this presumption. While I’ll cheerfully grant that there’s no evidence of any gods with the tendencies and motivations attributed to the standard ones, and that the machinations of such gods would most probably be very hard to ignore, this only makes a certain sort of god unlikely.

I think that if Popper’s Ghost had the power to manipulte coincidence generally, he could over time produce a biosphere to his liking without leaving the slightest sign of his activities visible to its inhabitants. In fact, PG could use this power to produce a *drastically* different world, within a matter of days, and remain utterly invisible.

Comment #189637

Posted by Glen Davidson on July 23, 2007 1:51 PM (e)

“Evolution is tinkering much more with the controls than it is with the genes themselves,” said Broad Institute director Eric Lander. “Almost all of the new innovation … is in the regulatory controls. In fact, marsupial mammals and placental mammals have largely the same set of protein-coding genes. But by contrast, 20 percent of the regulatory instructions in the human genome were invented after we parted ways with the marsupial.”

The research, released Wednesday (May 9, 2007) also illustrated a mechanism for those regulatory changes. It showed that an important source of genetic innovation comes from bits of DNA, called transposons, that make up roughly half of our genome and that were previously thought to be genetic “junk.”

The research shows that this so-called junk DNA is anything but, and that it instead can help drive evolution by moving between chromosomes, turning genes on and off in new ways.”

The big problem with our “Sam Corbin/Sam Corpin” is that he really doesn’t understand what he reads. How does anyone use the above to “argue” for anything but virtually the same version of evolution that we’ve always had?

His quote itself mentions how it is that evolution occurs by utilizing the so-called “junk DNA”, and the only argument that the relevant DNA in that quote isn’t “junk” is that it is serving as a resource for evolution. There isn’t the slightest hint of anything like “design”, rather it’s all following the evolutionary pathway.

As I mentioned, and which he, as you’d expect of a dishonest IDist (whether he is one or not), he ignored, if anything was seriously changed by the discovery of regulatory functions in the “junk DNA” it was the Mendelian view of genetics. Of course not even the latter was overturned by any means, our views of inheritance have expanded.

Nothing he presents either supports ID, or at all questions evolution. It’s all the usual blather of the IDists (whether or not he is one), with not even the slightest hint of an intelligent question in there. Everything being found, including what’s in his quote, fits evolutionary theory as it has been understood for a couple decades or so, and we’re supposed to question evolutionary theory based upon, well, what?

Glen D
http://www.geocities.com/interelectromagnetic

Comment #189646

Posted by Glen Davidson on July 23, 2007 2:41 PM (e)

Okay, first let me say that I am not a scientist, yet.

Like that isn’t obvious.

I am going back to college in the fall to study Molecular Biology.

Why? I mean, if you think that professors and scientists are lying to you about the evolution of the molecules found in biology, why would you bother? Or do you in fact think that the scientific enterprise is generally sound, and that one ought to learn from the experts instead of using pseudoscience in order to fault what you yourself don’t understand?

I was very, very excited at the prospect of the advancements, cures, possible longevity and history of our origins that were to be discovered in the coming years. As a matter of fact, tears came to my eyes when I first heard on the news that the Human Genome Project had finished mapping the human genome - 10 years ahead of time!

That pretty much sounds like a crock. And if not, you had a rather odd emotionalism attached to a fairly reductionistic project which really didn’t promise much except further research into proteins, regulation, and the complexity of life.

Many of my friends, that I would speak to about the HGP, were actually hearing about it publicly for the first time. (Maybe this is where my -yes- stupid arrogance on the subject was born, even.) I did not feel arrogant at the time, though, just grateful, very grateful, to the scientific community.

I hope you’ve followed the many other discoveries, like siRNA. If you did, you’d know what scientists know, that life is very much unlike a designed phenomenon, rather it is extremely complex in part because it evolved in various directions, and was not made with the sorts of ordered regularities that machines are (we see regularities, but they’re evolved, not ordered).

I cringed when I read what I had written in my earlier posting here on this blog: “..Because you guys know that I am right!”

Since it was the soppiest creationist nonsense, you should cringe.

I am not offended by some of your hateful emotional outbursts, because I realized, when one of you pointed it out, that you hate it when non-scientists say something like this when you have been professionally researching this stuff for years.

What makes you think we’re hateful when we have some contemptible ignoramus coming in here and spouting off IDist/creationist claptrap? We, most of us anyway, don’t hate you, we just recognize complete BS and treat it with the contempt it deserves.

*********

I did really well in school, but that was a long time ago. I see that I am not the straight A student here, but rather the Kindergartener, and I am humbled in my naivety. Forgive me.

I should add here, that my basic understanding of the human genome, at first, was that it was a “code”, which, to the layman such as myself, implies that the code was “created”.

What else would it be called?

And btw, you claim that you tended to oppose ID in the past, which makes no sense if you simply took the code to have been created. It’s really hard to believe that you could have the prerequisites for Molecular Biology down and still have the nonsense “code=created” in your head.

I admit that the tone of my first posts were somewhat provoking, (admittedly in part, due to my misplaced and very embarassing arrogance), but the main reason for my questions, was a vain attempt to get definitive answers to the questions that keep plaguing my mind, and to which I cannot seem to get seemingly logical answers to, as a layman.

That makes no sense at all. You didn’t ask questions, you claimed to have answers.

I have a better than (the) average (Joe) understanding of gene expression, viruses, DNA, RNA and chemistry; however, I cannot fully grasp the concept of how inorganic matter first starts to “desire” to survive.

Why do you suppose that organic or inorganic matter would “desire” to survive? At best, only humans can be thought of as “desiring to survive,” however it seems very unlikely that our aversions to danger and to “death” actually come out of our “desire to survive”.

And it really doesn’t take much thought using the concept natural selection to recognize that aversions to situations causing injury and death would have survival and reproductive value.

There’s something IDist in your question, for you really ought (given your claims) to be able to think this out rather better than you have. Perhaps you are not an IDist, however you are asking their questions, and we know why they ask them, which is that they can become exceedingly complex philosophically and scientifically if one has the desire to avoid the best answers we have today.

The question you ought to ask is, why do organisms avoid death and injury. For that we have general answers, and in some cases, specific answers regarding avoidance and repair of injuries. Indeed, the clotting mechanism famously involves a number of factors co-opted from other bodily processes.

I can see how like molecules want to bond together

No, you cannot see that, or if you can you’re worse off than we ever suspected. There is no tendency for like molecules to bond together, indeed some “like molecules” repel each other.

and how the building blocks of organic material can be created from inorganic material; however, my comprehension comes to a halt when I read that these first basic organic molecules started exhibiting survival instincts.

Basic organic molecules do not exhibit survival instincts. Again, you’re asking the most doltish questions, the sort that we get from Egnor and other IDists.

If there is anything worth calling a “survival instinct” (and I think it’s an OK term, so long as we realize that it’s a catch-all term covering a variety of cognitive and behavioral phenomena), it only shows up in relatively advanced animals. Plants almost certainly do not have “survival instincts”. Animals have aversive behaviors and more complex repertoires of neural activity and what we might call “instincts”.

Ask yourself why animals feel pain under evolutionary theory. Then, if you succeed in understanding that, try to apply that to more generalized avoidance of dangerous situations.

So, my question again is, how does the newly developed organic molecule(s) obtain it’s first survival instincts?

It doesn’t. Are you really going into molecular biology thinking that organic molecules have survival instincts? I don’t believe it, which is why I find your line of questioning disingenuous.

What mechanism(s) are at work that awaken the organic molecules to their mortality?

None. Molecules act according to quantum physics and forces.

If awareness is too strong of a word, then what basic chemical and/or physical process takes place that is the basis of the survival instinct?

Perhaps you need to learn what “survival of the fittest” means. Apparently you have no concept of evolution as explaining how it is that organisms adapt without having to rely upon “survival instincts” and similar evolved characteristics which appear only late in evolution (and not in most organisms). In other words, you really need to learn the basics, not insist that we give answers to your gross misconceptions regarding biology.

Understand, that it is hard for us laymen to move from the understandable, computer program-type model, to the spontaneous generation model, without a layman-comprehensible explaination for this phenomenon.

You aren’t supposed to go from a computer program-type model, you’re supposed to learn evolutionary processes quite separately from that type of ordering of matter. Again, I don’t believe your claims of what you have taken in college, unless, of course, you did very badly in your courses.

Seriously, go off and learn the basics of evolution, rather than believing the nonsense of IDists. Talkorigins.org is a good place to go for it.

I have more basic questions, but I realize that most of you here are scientists, and are not interested in fielding my “stupid” questions.

We don’t mind answering well-meant questions. But if you really are so badly misled as to believe that organic molecules are supposed to gain “survival instincts” there isn’t much that we can tell you except that you need a high school education in biology.

However, could one of you please, explain to me in layman’s terms, how this phenomenon (survival instinct) first came into existence, please?

Where it can be said to exist, the survival instinct came into existence out of the continuing evolution of animals who first evolved aversive behaviors. That is to say, when the ability to understand situations as something other than simple perceptions of dangerous phenomena (hurt, etc.), anticipations and aversions to potential dangers evolved. Presumably this was somewhere beyond the evolution of the angleworm.

The fact of the matter is that this “question” does not sound like an honest question of someone open to the evidence, but rather as a “stumper” that IDists and creationists pose because they can’t deal with the masses of evidence in favor of evolution. That the “survival instinct” would evolve with greater cognitive powers is readily understandable under evolutionary understandings, of course.

What Sam needs to do is to explain how everything appears to be related in basically the same manner that humans can be known to be related to each other (as families, or as a species) without the known processes of evolution being responsible for this. What I’m saying is that biology is best understood at the physiological and genetic levels, not at the level of cognition and of cognitive evolution, and nothing at the physiological and genetic levels make any sense as anything but evolution by known means. That’s true of cognition as well, however much about cognition and its evolution is not well understood at this time.

Glen D
http://www.geocities.com/interelectromagnetic

[syntax error fixed - AB]

Comment #189657

Posted by Glen Davidson on July 23, 2007 3:02 PM (e)

It is very hard to believe that some of you are really scientists.

It is hard to believe that you are asking the honest questions that a dropout from college could ask.

I don’t see how childishly attacking my intelligence,

Why, do children attack your “intelligence” as we do? I mean, do you seem stupid even to children? Not that I’d find it surprising, considering how poorly you’ve handled yourself here.

You’ve been given a whole lot of answers, yet you ask stupid ID-inspired BS as if it was really something that had just occurred to you.

and “pseudo pre-menstrally” changing the meaning of my posts, makes your responses what they should be: Based in fact, understandable to a layman and in line with what I had written.

You don’t write understandable sentences, you know. What was that last monstrosity?

Many of us laymen, have a problem with the evolution theory because the genome had been presented to us in the mass media as a “code”, which to us laymen, indicates something that has been created, like a computer progam.

Even the mass media not too infrequently notes that the “genetic code” was not created. If you’re really stumbling over that misinterpretation, you have no business going to college.

The second problem us ignoramuses have, is the proper understanding of how the newly created organic material awakens to its mortality, and develops a survival instinct.

Only humans are known for certain to have awakened to their mortality, though there are indications that some apes may have as well. Newly created organic matter most assuredly does not.

What’s so stupendously wrong about your whole approach is that you seem to be confusing natural selection as if it were the “survival instinct” operating in organisms. When in fact natural selection is quite the opposite.

In other words, it seems that you ought not to be here. You ought to be learning the very basics about evolution at Wikipedia or some such thing. You need to clear out the completely incorrect notions that you have about evolution before you begin to ask questions of those used to answering the questions of those who actually have some conception of what evolutionary theory states.

If “survival instinct” is too strong of a term to describe the phenomenon, then a logical and concise explaination of the physical and/or chemical processes that take place in the newly formed organic material that are expressed as survival mechanisms, which ultimately grow into what we know as survival instinct.

It’s natural selection. Go and read up on it, seriously. There isn’t something internal to the organism that makes it have survival mechanisms, all that happens is that the best surviving and reproducing molecules and organisms are what survive. And no, we don’t have the concise physical and/or chemical processes that take place, we have a general principle which you fail utterly to understand. The point of the principle of “survival of the fittest”, or better, the survival of the best reproducing, is that any number of processes are possible, which is why we end up with a variety of processes and methods of “making a living”.

Look up “natural selection” on Wikipedia. You need it.

If any of you can accurately, logically and understandably explain where, how and why the survival instinct originates (with emphasis on how), then people such as myself, that you accuse of being IDists, could have a working knowledge, based in understanding, of what your argument is based on.

This isn’t the place to correct your horrible misconceptions of what DNA and evolution are about. Again, go read some basic material. Wikipedia is, in fact, a much better source for someone as ignorant as you than Talkorigins.org is. I repent for thinking that you could handle Talkorigins.

The fact of the matter is that if we knew all of the steps of the evolution of the “survival instinct”, we still couldn’t explain it to you because you have no idea of how natural selection works.

Glen D
http://www.geocities.com/interelectromagnetic

Comment #189658

Posted by Glen Davidson on July 23, 2007 3:17 PM (e)

Dr. Bottaro, I truly appreciated that you, as a scientist, opened a thread pointing out that a few Darwinists did not fall (and I would add, hardly any of the God-believers ever fell) for Dr. Ohno’s deliberate framing of DNA with unknown function as “Junk”. You made a very good point. For instance, prompting me to draw attention to Darwinist Dr. Simons’ remarkable pioneering since at least 1987. Therefore, I was just as “cranky” as you were “depressed” to see your pithy thread degenerate (beyond my bounced though I think meaningful posting) to “kindergarten-level name calling”:

Oh right, a few did not. Why don’t you, who pretend to have high standards, come up with some actual evidence that “Darwinists” believed that non-coding DNA was junk, rather than merely treating it as if it did until such a time as function could be found out?

I would like to join you in encouraging bloggers, first to identify themselves (just as you and I are doing) with actual accomplishments or at least some degree in science,

What accomplishments do you have in science? You don’t seem to put out anything worth writing.

and second to focus on science, since supposedly Panda’s Thumb (as opposed to other blogs for which I am not responsible) is about science.

I’m sure you’d like to control this forum, but because it isn’t really intended for crank scientists like yourself plus those who understand science legitimately. We end up with almost completely uneducated people like “Sam Corbin” who have to be dealt with according to their arrogance and ignorance.

We at International PostGenetics Society, www.postgenetics.org now with 60 Founders representing 34 countries even have a name and very clear agenda for this new branch of PostModern Genomics: PostGenetics (“Genomics beyond Genes”).

Wow, you have a name for it. As long as that’s your major claim about it, I think I’ll give it a pass.

You may wish to help raising the level of your thread with actual debate on the topic you brought up, instead of lowering yourself to the level of name-callers.

You might wish to be above the level of dishonest posters, so that you won’t attract the kinds of names thereby deserved.

Can we, pleeeeese, focus on your original well-put science topic? People suffering from Junk DNA diseases “www.junkdna.com/junkdna_diseases.html” would not only be “cranky” or “depressed”, but outright dying on us if we proceed on an unproductive thread?

Pot, meet kettle, so to speak.

Glen D
http://www.geocities.com/interelectromagnetic

Comment #189663

Posted by Glen Davidson on July 23, 2007 4:12 PM (e)

Mapping and Sequencing the Human Genome: How to Proceed
Lloyd Smith, Leroy Hood

SUMMARY: The proposal to map and sequence the genome has engendered a controversy among biologists?a controversy that involves personalities and politics, as well as scientific judgments of the pr

CONTEXT: …human genome than to identify and characterize all or most of the individual genes. Second, much of this so-called junk DNA could have functions that are as yet unknown. The chromosome is an organelle that self-replicates and…

Nature Biotechnology 5, 933 - 939 (01 Sep 1987) Review

Here’s one article in a major journal arguing in 1987 for sequencing all of human DNA, because the “so-called junk DNA could have functions that are as yet unknown.” And for the most part, these people won, so that everything was eventually sequenced.

And btw, there’s an opinion piece that asks the same question of “junk DNA” in 1980 in Nature.

That said, I think it’s fair to say that today’s evolutionary understanding (but not natural selection per se) does predict junk DNA. It’s really the same thing as saying that vestigial organs exist, which they do, there’s really little question that at least some junk has to exist, due to duplications in some of the most telling examples.

And, of course, such junk does exist, and is found. It’s perhaps worth pointing out that one reason IDists are trying to gloat over the fact that some functions of “junk DNA” exist is that we have often pointed out that some rather undeniable junk exists (most of us didn’t say that “junk is junk and that’s it”, however).

That is to say, retroviruses and the vitamin C gene are shared across primate genomes, a fact that we’ve been generous enough to point out. The attack over “junk DNA” does, I think, relate primarily to this, because they never were able to answer our points, and instead they want to do what they often try to do, which is to claim that some “higher principle” negates our “pathetic level of detail”.

Of course they can’t back up their claims, nor can the IDists show that retroviruses and the “broken vitamin C gene” exist for any reason other than that useful DNA (whether older viruses or genes) became corrupt, just as present evolutionary theory states that they did.

Glen D
http://geocities.com/interelectromagnetic

Comment #189675

Posted by Andrea Bottaro on July 23, 2007 5:27 PM (e)

Please note update #2 above.

It seems like Evolution News & Views has problems reporting even basic facts honestly, but what’s new?

Comment #189676

Posted by Andras Pellionisz on July 23, 2007 5:45 PM (e)

[Glan Davidson] Why don’t you, who pretend to have high standards, come up with some actual evidence that “Darwinists” believed that non-coding DNA was junk..

[Andras J. Pellionisz] Historically the most famous is Dr. Ohno (a Darwinist) first tried to frame it in 1970 as “trash DNA” - it did not stick. In 1972 he wrote the paper “So much junk in the DNA” – unfortunately, the misnomer stuck. (See refs on “http://www.junkdna.com” ). As of today, perhaps the most famous Darwinist who still hasn’t turned around from “junk DNA” is Richard Dawkins.

[GD] What accomplishments do you have in science?

[AJP] Dr. Bottaro was kind enough (without the asking) to link my professional website with 100++ science publications and other accomplishments. 40 years worth is a bit too much to list here… “http://www.usa-siliconvalley.com

[GD] I’m sure you’d like to control this forum

[AJP] Dr. Bottaro said: “As for the where the discussion here is going, I have as little control over it as you do.” I answered (please read): “I don’t think anyone should “control” the discussion”

[GD] Wow, you have a name for it [International PostGenetics Society].

[AJP] You forgot to look up the Founders, the clear agenda of putting #1 priority on what formerly was dismissed as “Junk DNA”, and the historical fact that ENCODE was the second in 2007 (after IPGS as the first in 2006) to formally abandon the notion of “Junk DNA”, see “http://www.postgenetics.org”. Re-writing history is not possible. Anybody can (and will) turn around “post-ENCODE”.

[GD] You might wish to be above the level of dishonest posters

[AJP] Till you could (you can’t) name what you mistakenly interpret as different from fully honest I will kindly disregard your name-calling.

pellionisz_at_junkdna.com

Comment #189691

Posted by Glen Davidson on July 23, 2007 7:50 PM (e)

[Glan Davidson] Why don’t you, who pretend to have high standards, come up with some actual evidence that “Darwinists” believed that non-coding DNA was junk..

[Andras J. Pellionisz] Historically the most famous is Dr. Ohno (a Darwinist) first tried to frame it in 1970 as “trash DNA” - it did not stick. In 1972 he wrote the paper “So much junk in the DNA” – unfortunately, the misnomer stuck. (See refs on “[…]www.junkdna.com” ). As of today, perhaps the most famous Darwinist who still hasn’t turned around from “junk DNA” is Richard Dawkins.

Anecdotes. You must have some idea of what evidence is, even if you boost the “Information Geometry of Nature”.

Meanwhile, I included a bit from Nature that made the case in the same year as your “martyr” did, and I mentioned the 1980 piece as well (I only mentioned it because I couldn’t find out who authored it at the time—though I could now if it was important).

[GD] What accomplishments do you have in science?

[AJP] Dr. Bottaro was kind enough (without the asking) to link my professional website with 100++ science publications and other accomplishments. 40 years worth is a bit too much to list here… “[…]www.usa-siliconvalley.com”

Well finally (what, I’m supposed to be watching for updates?). Looks kind of flaky, just on the surface. I don’t wish to say that it necessarily is, but come on, you’re going to have to give us a reason to think that a “Fractal approach to DNA” is worthwhile before we accept it as some great accomplishment rather than as a questionable approach.

[GD] I’m sure you’d like to control this forum

[AJP] Dr. Bottaro said: “As for the where the discussion here is going, I have as little control over it as you do.” I answered (please read): “I don’t think anyone should “control” the discussion”

I read what you wrote there, and what you’d written beforehand. I think the first is likely to be more indicative of your intentions than your acquiescence with the guy who controls the forum is.

[GD] Wow, you have a name for it [International PostGenetics Society].

[AJP] You forgot to look up the Founders, the clear agenda of putting #1 priority on what formerly was dismissed as “Junk DNA”, and the historical fact that ENCODE was the second in 2007 (after IPGS as the first in 2006) to formally abandon the notion of “Junk DNA”, see “[…]www.postgenetics.org”. Re-writing history is not possible. Anybody can (and will) turn around “post-ENCODE”.

Yeah, I saw that. It just doesn’t tell us anything. You’re going to have to include something of substance, and not a bunch of bleating about non-coding DNA diseases, the latter of which are reported in the mainline journals.

[GD] You might wish to be above the level of dishonest posters

[AJP] Till you could (you can’t) name what you mistakenly interpret as different from fully honest I will kindly disregard your name-calling.

I don’t want to escalate or anything, but you know very well to what I was referring. Luskin isn’t blithering about “suppression” or whatever without any help, I’ll warrant (sure, it’s an educated guess, but I can’t just trust your claims based on the record till now). Plus, so far your name-calling, lack of inclusion of your own accomplishments when you were saying others ought to give theirs, and the uncertain nature of those “accomplishments” to those of us not knowing more than that they “sound flaky”, puts you in a less than brilliant light thus far.

–snip sig–

Who knows, maybe you could do rather better than you have. It’s just that so far we’re singularly lacking in evidence for your claims, and it appears as though your claims are unjustified up to this point.

Glen D
http://geocities.com/interelectromagnetic

Comment #189693

Posted by Glen Davidson on July 23, 2007 8:29 PM (e)

And btw, I fail to see the connections in Pellionisz’s Fugu “argumentation”. If they’re there, I hope they’ll be spelled out, but so far it appears as though the fact that Fugu has less-branched Purkinje cells and a smaller genome is somehow assumed to be causally connected. But it would appear as if, should we accept that P-cells are fractal in growth (certainly looks possible from 2-D images), that this would be the result of an iterative developmental program, not of some kind of templated fractal “determinism” in the DNA.

That programmatic growth would take advantage of iterations leading to fractal growth would hardly be surprising. Considering the evolution of the genome, however, it would seem likely that natural selection would interfere with any sort of fractal development of DNA, as would “neutral evolution”. Hence fractal growth seems a reasonable and not particularly new idea, while the fractal nature of the DNA information would not seem likely to be evolutionarily beneficial, nor to be positively selected like iterative developmental programs would be.

Perhaps Pellionisz has much better arguments. One would hope so.

Glen D
http://geocities.com/interelectromagnetic

Comment #189709

Posted by Andras Pellionisz on July 23, 2007 11:57 PM (e)

Dr. Bottaro:

Thank God :-) (or just the efforts by you and me as two scientists) there seems to be a trend now from pseudoscientific deterioration of your precious thread from the lowliest name-calling, by self-declared non-scientists and drop-outs, towards real science. Thus, you no longer should be depressed, and I can revert to my usual happy mode when dealing with science (may be strange, but I am disgusted by garbage, junk, name-calling). Your point about Ernst Mayr and my point about Malcolm Simons are mutually reinforcing; what used to be a matter of opinion (shall we call it belief?) turned into a matter of science of 98.7% of human genome.

This is unfortunate to most bloggers whose knowledge of science is marginal at best, since their void of substance is typically masked by kindergarten behavior without a semblance of decorum. Therefore, I would even risk suggesting that “post-ENCODE” the role of Panda’s Thumb became vacuous or outright self-destroying as a “PR frontline”. Science issues (under normal circumstances) are not decided by the volume of popular vote (shouting), but as I saw declared at another blog, they are determined by “the scientific method (i.e. observation, hypothesis, and experimentation)”.

While we both despise “kindergarten name-calling”, history is definitely justified as a topic – and I think we both agree, again. Shall we conclude that even Chief Editor of “The Scientist” (Richard Gallagher) in his current Editorial openly confesses that that Dr. Ohno deliberately “framed” Genetics? (I never used the term “conspiracy” anywhere - but fully agree with Gallagher that Ohno’s “framing” was deliberate). If that is not enough, Sidney Brenner’s Nobel Lecture explains the purposeful intent of inhibiting progress in the field of regulatory DNA.

http://www.junkdna.com/#brenner

[Brenner] “In 1985, when the first suggestions were made to sequence the human genome, I thought that the sequencing techniques, even with incremental improvements, would not be equal to the task, and would require a factory scale operation to do it. I had also come to the conclusion that most of the human genome was junk, a form of rubbish which, unlike garbage, is not thrown away. My view at the time was that we should treat the human genome like income tax and find every legitimate way of avoiding sequencing it. It could therefore be asked whether a genome existed in Nature which perhaps had very much less junk but nevertheless had the full repertoire of vertebrate genes?”

If you need contemporary “PR specialists” additional to Gallagher, another notable example is Richard Dawkins, a scientist by training but (unfortunately) he turned from science to become an “anti-God evangelist” (excuse the befitting oxymoron), who is also yet to admit that he was on the wrong side of truth, along with the overwhelming majority of Darwinists. What is wrong with saying “we were wrong”? Ego?

The bigger a person is in science, the more one can afford to admit earlier mistakes. Take, for instance Francis Collins. At the 2003 February 50th Anniversary of DNA I personally asked him (and many others) about “Junk DNA” (I was curious, since one year prior I formulated the FractoGene concept, and shopped around to see how it was catching interest. Not well – it was years too early in the deafening silence of “few genes” and still is a few months too early for most bloggers with equal to or less than one science publications in their life. The 50th of DNA was more of a funeral. With the Human Genome project just completed *everybody* knew that there weren’t enough genes - but they did not have a concept to cart into the vacuum). Francis Collins conveyed a dismissal of “Junk DNA” at that time to me, specifically mentioning in the reception dinner at Monterey Aquarium the huge and widely varying genomes of sub-species (onion, frog, salamander, etc). As he is a learned mathematician (and an M.D.-Ph.D.), since 2003 he found both DNA and Mathematics to be divine languages - and the “http://www.junkdna.com” collection uses his turnaround slogan from his book “It took certain hubris to call any part of the DNA Junk”. Three months after the Monterey conference Francis Collins went to the Congress to ask for the next chunk of money. ( “Junk DNA” was never mentioned, not even “non-coding DNA”, the closest he talked about was “non-protein coding genes”; with the meaning of “non-protein” left undefined…). He got the money in for the ENCODE project – smuggled in by 5% of the text of his testimony. With the ENCODE first Report released, now you have a God-believer (Collins) who has proven with his ENCODE that most Darwinists were simply wrong on “Junk DNA”…

Francis Collins is alive and well, Malcolm Simons is alive (not so well), Sidney Brenner (and others) are still active and are large-format scientists. Why do you think they don’t even drop one line in Panda’s Thumb? Because it is so big on badmouthing, and not big enough on science…

With the decorum and history issues re-dressed, we are cleared to talk about science. Phew!

I made the hard choice of appearing in PT because a much-respected young scientist (T. Ryan Gregory) put out his “The Onion Test” here. What a brilliant move!

New Scientist (UK) did a much better job compared to The Scientist (USA) about the demise of “Junk DNA”. (Too bad that the article is behind a pay-wall, but because of its importance will be excerpted at http://www.junkdna.com ). New Scientist cites:

“One of the biologists trying to find out what conserved non-coding DNA does, Edward Rubin at the Lawrence Berkeley National Laboratory in California, recently added extra copies of some of these sequences to mice. “It’s like taking a few extra pages and stapling them into a book,” he says… His team added copies of the “ultra-conserved” sequences that are almost exactly the same, base for base, in the mouse, rat and human. Nearly half of the sequences the team tested boosted gene expression in specific tissues, especially genes involved in nervous system development, the team reported last year (Nature, vol. 444,p 499)”.

Dr. Bottaro, you said about my FractoGene:

“even assuming it is sound… I am very skeptical of its biological significance [of intergenic DNA], in the absence of any proposed actual mechanism linking such properties to phenotypes”.

While a skeptical stance is very healthy for a scientist, you can not overlook experimental evidence.

Dr.Bottaro, now you have independent and widely quoted 2006 evidence (not only in Nature but also quoted even in New Scientist) that the added intergenic (“Junk”) DNA expressed itself in obviously very important phenotypes of the nervous system. Further, the same New Scientist article would inform those truly interested in science that:

“For instance, there are specific sequences to which certain proteins bind, and the presence of these proteins call boost or block the expression of genes nearby. Although it does not code for any protein, this “regulatory DNA” plays an important role”.

FractoGene is an algorithmic design approach based on recursive iteration of protein synthesis, based on the fractal DNA, with the directly protein-coding sequences in a fractal arrangement with non-directly-coding DNA generate a fractal hierarchy of proteins. My 1989 paper “http://fractogene.com/89_fractal/89_fractal.html…” shows the specific fractal phenotypes (of the arborization of a particular brain cell) with different amount of “auxiliary information” in the DNA (formerly “junk DNA”) in several species (and yes, the slow or fast convergence of fractal process only with slight differences in the parameters does pass “the onion test” at least as well as any other explanation one knows of. Please anyone come forward with a better one if you can; I am interested in science).

By the way, the FractoGene also provides an explanation for a slew of other “mysterious” phenomena, for instance “ultraconserved elements” (truncated common fractal recursive iterations) - and indeed why is it that the entire organism is not very sensitive to some of the “fractal recursive iterations” deleted (this “mystery” is also very much harped on in New Scientist).

Granted, 5 years of R&D is built on quite a bit of Intellectual Property amassed, that is not most wisely disseminated by a blog format – but (hint, hint) for a well-known Mandelbrot Set it does not alter the fractality of the picture very much if some of the repetitive “motifs” are taken out, does it? On the other hand, if you look for “refinement”, it is handy to let the process run more recursions, isn’t it? Lastly (in a blog…) think of “Ontogeny mimicking Phylogeny”; isn’t that spooky that an apparent “fractal algorithm” runs through the phases of a worm, a frog, a mouse, a rabbit - as *your* embryo develops into a human?

Learn more through more appropriate channels than blogs, e.g. in my upcoming book of what should be disseminated at list price,

pellionisz_at_junkdna.com

(I certify that in the conflict of two antagonistic blogs I am not responsible for deficiencies, if any, in either. Further, I attest that all my communications with both were true and correct)

Comment #189710

Posted by Andras Pellionisz on July 24, 2007 12:10 AM (e)

yet another “hold”, I believe the 6th. Till this moment 3 of my 6 “held postings” did eventually appear, 3 have not. Would be nice to see (as in science papers…) not only the date-stamp of submission (received), but also the date of “authorization” (accepted) and the date of actual publication (published; watch for the subtlety that the second and third are typically *different* time-points…)

Comment #189727

Posted by Rolf Aalberg on July 24, 2007 5:41 AM (e)

Andrea Bottaro, responding to Pellionisz:

As for the where the discussion here is going, I have as little control over it as you do. You are welcome to continue posting on this site if you stay on topic and stick to the site rules, but I cannot guarantee that people will find your comments of any interest, and answer them. Moreover, that not everyone here has a degree and/or accomplishments in science is irrelevant. As I am quite sure someone may have mentioned to you before, scientific credentials are no insurance against error, foolishness or lunacy.

For what it may be worth, here is the opinion of an uncredentialed but very long-time “student” of science and evolution: I do not find Pellionisz’ comments of any interest.
Moreover, it seems to me that a debate about who (maybe) and who (maybe) didn’t believe or make comments that may be construed as evidence pro or con belief in the junkiness of some parts of DNA is rather useless and can only be of academic interest. As far as the theory of evolution and evolutionary research is concerned, the issue seems to be rather unimportant.

Being mere mortals, scientists may of course make errors, but so what? Again, for what it may be worth, it seems to me that science has a respectable track record when it comes to correcting it’s own errors.

Comment #189748

Posted by Andrea Bottaro on July 24, 2007 7:19 AM (e)

yet another “hold”, I believe the 6th. Till this moment 3 of my 6 “held postings” did eventually appear, 3 have not. Would be nice to see (as in science papers…) not only the date-stamp of submission (received), but also the date of “authorization” (accepted) and the date of actual publication (published; watch for the subtlety that the second and third are typically *different* time-points…)

Dr. Pellionisz:
0ne single message of yours was being held as of this morning, it was submitted at 11:57 pm last night, and I authorized it a few minutes ago (btw, “authorization” and “publication” are the same thing, and occur coincidentally). Another duplicate message of yours, identical to comment 189676, was deleted yesterday, as I do with any duplicate comments I notice (I just did the same with 2 comments by Glen Davidson, for instance).

If you had paid any attention to what I said before, you would know that your comments are being repeatedly held because you put too many url links in them (indeed, your last comment, without url’s, went straight through). Since in most cases these are just links to pages you have linked to many times before, namely to your web site, and whoever wanted to go there probably already has, try dropping them from your future comments. You’ll see that, as if by magic, your preoccupation with Panda’s Thumb’s alleged suppression of your opinions will vanish. (Or not, but anyway.)

As for

While a skeptical stance is very healthy for a scientist, you can not overlook experimental evidence.

that was precisely my point - I find your “evidence” unconvincing to say the least. I am using quotemarks because the only actual evidence you have, at least that I can find, is your claim that the fractal properties of DNA in fugu correlate with their Purkinje cell arborization, compared to mammals. Frankly, assuming that is true (it’s unclear from your paper to what extent the analysis was conducted) that’s not surprising to me. I would be far more impressed if you successfully predicted that the lungfish (30-something as large a genome as human) had much more developed cerebella than we do, or that Xenopus tropicalis and X. laevis (sister species, the second a tetraploid of the first) did differ according to their genome size in their cerebellar structure. (To be fairly blunt, I actually think that what is most missing from your hypothesis is even more basic, and namely any actual biological model of how the “fractal properties” of DNA would be reflected in Purkinje cells - i.e. a series of proposed and plausible causal mechanisms that would go from one to the other.)

The experiments I mentioned above are relatively simple, so they should be a straightforward task for you to perform. I hope you do not subscribe to the Mike Behe approach to experimental science, according to which your opponents have the duty to test and invalidate your hypothesis, because you already know it’s right, while you do not have to test theirs, because you already know it’s wrong and it would be “unproductive” to work on it. The approach does leave one a lot of free time, but is not conducive, from what we have witnessed, to scientific productivity.

Comment #189777

Posted by Apeman on July 24, 2007 9:56 AM (e)

Self-Inflating-Crank-Scientist wrote:

Learn more through more appropriate channels than blogs, e.g. in my upcoming book of what should be disseminated at list price,

That’s very generous of you.

Comment #189808

Posted by Torbjörn Larsson, OM on July 24, 2007 12:10 PM (e)

Glen Davidson wrote:

I fail to see the connections in Pellionisz’s Fugu “argumentation”.

Thank you Glen, this is is my challenge as well, as I noted in the last thread about Pellionisz’s claims.

That simple iterative mechanisms can create power laws and/or fractal distributions is no surprise. But here it is assumed that one presumed fractal distribution creates several others presumed ones by some unknown non-trivial transformation (protein distribution) or worse (neuronal growth) - “like creates like” as it where.

There is also a suggestion of correlation but no firm data as you note, even less suggestions for tests of the promised causality. No, the more I look at it the more it becomes fragmented.

Comment #189821

Posted by Andras Pellionisz on July 24, 2007 1:27 PM (e)

Dr. Bottaro,

You wrote:

[Andrea Bottaro] “the only actual evidence you have, at least that I can find, is your claim that the fractal properties of DNA in fugu correlate with their Purkinje cell arborization, compared to mammals. Frankly, assuming that is true (it’s unclear from your paper to what extent the analysis was conducted) that’s not surprising to me. “

[AJP] So why didn’t *you* write the paper? As far as I can see my brain cell explanation is the closest answer to Dr. Gregory’s “Onion Test”. (If there is a better one, let’s see).

[AB] “I hope you do not subscribe to the Mike Behe approach to experimental science, according to which your opponents have the duty to test and invalidate your hypothesis, because you already know it’s right, while you do not have to test theirs, because you already know it’s wrong and it would be “unproductive” to work on it”

[AJP] You are absolutely right – I don’t subscribe at all to any antagonism, *certainly not* to an alienation of experimentation and theory. I am one of the few who have always, over 40 years, conducted research with experimentation and theory both hallmarked with excellence and working as a team. It is simple to see; just kindly look up my co-authors over 40 years. Those few who actually read the “fugu” paper (and I command you for it) would sharply observe that I am not the first author. I had to be convincing enough for an experimentalist-clinician (Dr. Simons, an M.D. with whom bloggers should by now be familiar) that the fractal approach is what he considers the best effort for a “triangulation” of biophysics-morphology-genomics. Those familiar with his ouvre would know that he never claimed an understanding what was the function of Junk DNA (before he travelled from Australia 4 times to collaborate with me in Silicon Valley and with his physical presence in Budapest help declare, half a year before ENCODE that “Junk DNA” *had* a function). He based his patent on his experimental conviction that the “junk DNA” wasn’t either “junk” or “random” - good to be used for diagnosis. With my fractal approach he is convinced that presently this is the best explanation of what the function is. (My earlier experimentalist team-workers – bright enough to be open to the inevitability that at some day experimental facts must be brought into a synthesis with hard-core [mathematical] theory were likewise of “world-class” caliber; the late Prof. John Szentagothai (a morphologist) Prof. Rodolfo Llinas (a physiologist), just to round the number to the minimal 3 for a triangulation of “morphology”, “physiology” and genomics.

As for your technical comment on blog mechanisms, it would be nice if the “bouncer page” would tell the truth. It informed me about 6 times that I was “posting for the first time” (untrue), while never mentioned (you don’t, either) what is “too many” for embedded links? Since links don’t cost anything and can be very helpful for those wishing to be precise, I am somewhat skeptical that an unspecified number (1? 2? 3? 6?) should be used as an excuse.

pellionisz_at_junkdna.com

Comment #189827

Posted by Apeman on July 24, 2007 2:36 PM (e)

I am one of the few who have always, over 40 years, conducted research with experimentation and theory both hallmarked with excellence and working as a team.

There’s no need for false modesty.

As for your technical comment on blog mechanisms, it would be nice if the “bouncer page” would tell the truth.

They probably added an exception handler to their script to specifically annoy you personally.

Since links don’t cost anything and can be very helpful for those wishing to be precise, I am somewhat skeptical that an unspecified number (1? 2? 3? 6?) should be used as an excuse.

Would you like to buy some FractoGene-inspired male enhancement pills (patent pending) from me? Just click on my link right here.

Comment #189829

Posted by Glen Davidson on July 24, 2007 2:54 PM (e)

Thank you Glen, this is is my challenge as well, as I noted in the last thread about Pellionisz’s claims.

I hadn’t paid attention to the last go-around, so I really didn’t know what had been written. It’s good to hear that the same things were noted beforehand.

That simple iterative mechanisms can create power laws and/or fractal distributions is no surprise. But here it is assumed that one presumed fractal distribution creates several others presumed ones by some unknown non-trivial transformation (protein distribution) or worse (neuronal growth) - “like creates like” as it where.

There is also a suggestion of correlation but no firm data as you note, even less suggestions for tests of the promised causality. No, the more I look at it the more it becomes fragmented.

No improvements from the later posts, either. A bit of reliance on authority, a half-admission that a kind of prejudice is driving their conclusions, and absolutely nothing to rule out the myriad of other possible causes for differences between Purkinje cells in guinea pigs and puffer fishes—nor any causal mechanisms to link the posited but not yet-found “cause” (supposedly fractal DNA) and the purported effect.

It’s not clear why UDites and other IDists are drawn to Pellionisz, except that the latter hints at similar religious drives, and the fact that neither “science” cares much about finding adequate evidence for their “conclusions”. Pellionisz seems to have fallen for the fractal fad that existed a while back, more or less assumed along with others that DNA must be fractal, and grasps at straws to “support” his belief in it as well as in an ill-defined set of religious presuppositions.

And he lectures us to stick with science as he babbles on meaninglessly about others who agree with him, and how one or more scientists have set the establishment against him and others like him.

Apeman responds well, though I’ll go ahead and agree with Pellionisz that the “bouncer page” could speak to the issues rather better (can Andras really be so dense and/or ignorant as not to know why the links are limited, namely the spam factor?).

Glen D
http://www.geocities.com/interelectromagnetic

Comment #189865

Posted by David Utidjian on July 24, 2007 5:35 PM (e)

I have diddled around in the Pellionisz website(s) for a few days now and I am a little mystified as to all this hullabaloo over patents and intellectual property rights. I was curious so I did a search over at the US PTO for ‘fractogene’ (no hits) and ‘pellionisz’ (8 hits) but only one of which was issued to ‘Pellionisz; Andras J’. It is US Patent number: 4,450,530 issued on May 22, 1984 with the title ‘Sensorimotor coordinator’. I leave to those who are really interested to go and look it up.

My question is this: If one has a current patent OR pending patent OR a submitted patent application, does one not also have some protection? If one has applied for a patent then it is on file with the US PTO and pretty hard for someone else to claim it as theirs, no?

I am pretty confused about all the hype about ‘fractogene’ this and ‘helixometry’ that and with all that linking between 3-4 sites with almost no real information content.

I am also confused about the affiliation with NYU Medical Center. No record of Pellionisz on their faculty pages. It does list Rodolfo Llinas as a professor in the Physiology department.

Amongst the dozens of links on the Pellionisz ‘Accomplishments’ page there is a link to a bulletin from NYU College of Arts and Science (2006-2008), it is a 500 page PDF file. Doing a search for ‘Pellionisz’ yields nothing (I also tried misspellings).

Now I see that Pellionisz has collaborated with Paul Werbos (who is listed as the holder of some of the patents I found).

I have undergraduates that put up more consistent and informative sites about their accomplishments and interests.

In any case I can’t figure out what it is about Pellionisz ideas that he is afraid to tell the world about. The site and the hype remind me of some of the ‘cold fusioneers’ (back in the day).

-DU-

Comment #189879

Posted by Apeman on July 24, 2007 7:37 PM (e)

My question is this: If one has a current patent OR pending patent OR a submitted patent application, does one not also have some protection? If one has applied for a patent then it is on file with the US PTO and pretty hard for someone else to claim it as theirs, no?

It is the filing date that matters, and patent applications are published after about 18 months anyway, so there is no real reason to hide anything - unless you’re out to make a buck by selling your “discoveries” in book form “at list price” in the meantime.

Unfortunately, FractoGene is not much more than the Thinking Man’s Time Cube.

Comment #189884

Posted by Apeman on July 24, 2007 7:56 PM (e)

I am also confused about the affiliation with NYU Medical Center. No record of Pellionisz on their faculty pages. It does list Rodolfo Llinas as a professor in the Physiology department.

There are 7 publications in ISI by Pellionisz, AJ. The three that have been cited by others originate from the 1980s and list his affiliation as NYU Med Cetr. His affiliations on the later pubs are NASA AMES and this company of his.

Comment #189897

Posted by Andrea Bottaro on July 24, 2007 9:53 PM (e)

I’m off for a few days, so nobody freak out if comments don’t show up. As for the maximum allowed number of links, three is obviously too many, and one seems to be OK. I’ll leave it to better mathematical minds to figure it out.

Comment #190129

Posted by slpage on July 25, 2007 7:50 PM (e)

Syntax Error: mismatched tag 'url'

Comment #190132

Posted by slpage on July 25, 2007 7:56 PM (e)

Hmm…. OK. I’ll try it the old fashioned way -

I think Luskin and Pellionisz are out to lunch:

http://all-too-common-dissent.blogspot.com/2007/…

Comment #190133

Posted by slpage on July 25, 2007 8:00 PM (e)

Andras writes:

“He just knew that he could never publish in the establishment views branded (“framed”) as heretical views -“

What garbage. A simple literature review shows that there were many folks not just suggesting - but looking for and finding - function in ‘junk DNA’ before your good buddy ever uttered a word about it.

Your’s (and Simons’) seems to be a typical tall tale spewn by fringe types trying to gain sympathy for thier cause.

Comment #190207

Posted by hoary puccoon on July 26, 2007 4:14 AM (e)

It’s been pointed out ad nauseum that the Disco Institute doesn’t do published-in-peer-reviewed-journals research. But from this thread it’s obvious they don’t even do night-before-the-high-school-term-paper-is-due research. Casey, where, exactly, did you find the bible verse that told you it’s okay to exploit troubled souls like Pellionisz and Egnor? Oh, I forgot. Actually reading the bible, instead of just thumping it, would be too much like research, wouldn’t it?

Comment #190659

Posted by Andras Pellionisz on July 27, 2007 7:25 PM (e)

Re:

You (and Simons) seem to be … trying to gain sympathy for their cause.

[AJP] Yes, I am trying to gain sympathy not only for Dr. Simons for his double role of working for decades against the headwind of the “Junk DNA” cyclone, but also for him as well as so many hundreds of millions of people (quite possibly including you) who are, or on any day can be, diagnosed with one of the already astounding number of (formerly) “Junk DNA diseases”. Make a quick count. About 1.3% of the human DNA is composed of “genes”. Has Modern Genetics been useful for screening/diagnosis/(therapy) of genic hereditary diseases? Is it, therefore, likely that with 100% focused on PostGenetics will even more effective? With the present tailwind, beyond the eye of the “Junk DNA wing” of the cyclone, there are already results (e.g. intronic and intergenic fractal defects, microRNA results, etc, see junkdna.com )to be hopeful for at least early diagnosis, up to and including cure in the future (depending on public support).

pellionisz_at_junkdna.com

Comment #190687

Posted by Henry J on July 27, 2007 10:46 PM (e)

Re “Has Modern Genetics been useful for screening/diagnosis/(therapy) of genic hereditary diseases?”

Have any such been screened or diagnosed by any other method other than the use of modern genetics?

Henry

Comment #190730

Posted by Dr. Andras Pellionisz on July 28, 2007 2:28 AM (e)

Henry answers

Re “Has Modern Genetics been useful for screening/diagnosis/(therapy) of genic hereditary diseases?”

this way:

Have any such been screened or diagnosed by any other method other than the use of modern genetics?

[answer by AJP]

Modern Genetics (1953-2005) has been very successful, since a Century from the nascence of PostGenetics (PostModern Genetics, PostGenetics from 2005) historians will be amazed how much was accomplished with the ignorance of 98.7% of the human genome. (Paraphrasing the motto by Graeme O’Neil on “http://www.junkdna.com”).

Some (if not most) hereditary diseases, however, eluded the search for genic causes - since for most regulatory genomic diseases medicine could not (probably will not) find a single gene, not even a combination of genes as the established root-cause. It is extremely common that the problem lies beyond the bounderies of “genes”.

Perhaps the most important case is Parkinson’s disease, where the *promoter* (“Junk DNA”) part of the SNCA gene contains an already identified fractal defect.

PostGenetics (“Genomics beyond Genes”) that is the PostModern era of Genomics, is already on record with fractal defects, microRNA-s (and other non-genic causes) to catapult “PostGenetic Medicine” far beyond what was accomplished by limiting ourselves to a mere 1.3% of the human genome (the “genes”).

If only a single person’s life can be saved, all the “nay-saying” and “badmouthing” needlessly inflicted by this thread on pioneers has been well worth it.

pellionisz_at_junkdna.com

Comment #190864

Posted by Henry J on July 28, 2007 7:52 PM (e)

I guess the way I phrased that question didn’t work.

It just sounds to me as though the scientists who study DNA are and have been studying the non-gene parts of it, and have been doing so for years. That some non-gene problems have been diagnosed serves as evidence for that inference.

Henry

Comment #190874

Posted by Andrea Bottaro on July 28, 2007 10:05 PM (e)

Andras Pellionisz wrote:
Some (if not most) hereditary diseases, however, eluded the search for genic causes - since for most regulatory genomic diseases medicine could not (probably will not) find a single gene, not even a combination of genes as the established root-cause. It is extremely common that the problem lies beyond the bounderies of “genes”.

Perhaps the most important case is Parkinson’s disease, where the *promoter* (“Junk DNA”) part of the SNCA gene contains an already identified fractal defect.

Just for the record, this is what Ohno himself had to say on this possibility, in his 1972 “So much junk in our genome” paper:

Taking into consideration the fact that deleterious mutations can be dominant or recessive, the total number of gene loci of man has been estimated to be about 3x10^4 (Muller, 1967; Crow and Kimura, 1970). Even if allowance is made for the existence in multiplicates of certain genes, it is still concluded that, at the most, only 6% of our DNA base sequences is utilized as genes (Kimura and Ohta, 1971). Aside from conventional structural genes and regulatory genes, this 6% should include the promotor region and operator region which are situated adjacent to each structural gene, for these regions can certainly sustain deleterious mutations. [italics in text - AB]
(Ohno S, So much “junk” DNA in our genome. Brookhaven Symp Biol. 1972;23:366-70.)

I think it is worth pointing out a few things here:
1. Obviously, Ohno, like all molecular biologists of the time, was well aware of the existence of regulatory elements outside coding sequences (his nomenclature “promotor” and “operator” refers to the names given to regulatory elements in bacterial genes, the only ones characterized at the time).
2. He was also well aware that mutations can occur in such regulatory sequences.
3. He never included such regulatory elements among “junk DNA”.
4. Note that his argument here (as well as in the rest of the paper) owes much more to the work of Kimura and others on the Neutral Theory than on Darwinian mechanisms.
5. Note also how damn close the estimate of the number of genes was then, based entirely on genetic load considerations, compared to what it turned out to be. The reasoning is, if we had much more functional DNA than we actually seem to have (let alone if all all our DNA sequences were functionally significant), the rate of mutation in each generation would likely be prohibitive for survival of our progeny. Hence, we can afford to have at most a few percent of our genomic DNA sequences under negative selection constraints, and not much more. Therefore, the argument went, if “junk DNA” does anything, whatever it does is highly unlikely to be sequence-dependent. That argument still stands.

As for the medical genetics issues discussed by Dr. Pellionisz, the situation is rather different from what he portrays it. Genetic diseases due to a single or a few genetic loci can readily be established to be just that, and studied, in the total absence of any information regarding where the mutation resides (i.e. either in genic or non-genic DNA). Indeed, hundreds of such conditions have been studied in depth and, in the overwhelming majority of cases when the mutations have been identified, they were found to map to coding sequences or conventional regulatory regions (similar to those discussed by Ohno, above).

In addition to these “simple” genetic diseases, however, many other diseases with significant genetic components also exist, that are caused not by one or a few, but by the combination of many genetic mutations, often influenced by things like environmental factors, such as nutrition or infections. Such multigenic/multifactorial diseases are very hard to study, because their appearance in families is not regular, and patients with identical or very similar diseases may carry different combinations of genetic factors affecting susceptibility. Whether or not any of these genetic mutations map to “junk DNA” or not it is not known, but the reason that these diseases are a tough nut to crack for geneticists is not the location of the mutations, within or without the “boundaries of genes” - whatever that means -, let alone “Darwinist conspiracies” and such claptrap, but the complexity of the factors that cause them.

Comment #190885

Posted by Science Avenger on July 28, 2007 11:48 PM (e)

A little off topic, but am I the only one that perceives a general edge in readability of legitimate scientists vs cranks? I don’t have enough biological knowledge to have a bias one way or another as to the details of the science, but with most of the cranks I find their basic train of thought often difficult to discern. They also seem to use more arcane technical jargon. This sends up red flags for me, because in my profession, when I feel my position is weak and I need to bamboozle a layman, that’s what I do.

Comment #190901

Posted by Andras Pellionisz on July 29, 2007 1:06 AM (e)

I congratulate to Dr. Bottaro that we managed to salvage his precious thread back to delightful science from some really ugly kindergarten levels (hopefully never to revert). It is particularly impressing that upon the death of Dr. Ohno’s “Junk DNA” scientific concept and 35th Anniversary of the “framing” to “genes only” finally we have a chance here to focus on this core-issue. (I previewed the Obituary elsewhere; “http://www.junkdna.com/#obituary_of_junk_dna

Of course, at the time of Dr. Ohno’s abstract in 1972 (and the whole world, even beyond biologists) were well aware of regulatory elements outside “coding sequences” – since Jacob and Monod won their Nobel Prize seven years before, in 1965 for the “Operon” regulation, with promoter regions pinpointed (Jacob and Monod discovered the Operon regulation in 1961, eleven years prior to Ohno’s deliberate “framing” to limit scientific progress only to “genes”). Of course Dr. Ohno (and everybody else) were well aware that mutations could occur in such regulatory sequences (and everywhere else).

I am not aware, nonetheless, that Dr. Ohno (or anybody else, please correct me if I am mistaken) identified fractal defects corroborated with non-genic hereditary diseases compared to my list at “http://www.fractogem.com” . Readers who actually took the time, as Dr. Bottaro did, to look up the entire Ohno abstract (a mere 3.5 double-spaced typewritten pages) as well my comparably dense listing (quoted above) would note that Ohno’s loose definition of “gene loci” certainly did not include “intergenic” regions (his abstract does not use this term at all) - while I can confide without compromising IP that my FractoGem Miner found fractal structures not only in promoter and intronic regions, but also in precious intergenic areas (the “open high seas” of “Junk DNA” that Dr. Ohno deemed “untranslated”). In this sense, while Dr. Bottaro’s #3 observation is true that “He never included such regulatory elements among “junk DNA””, the present state of art surpasses Dr. Ohno’s precisely by finding precious fractal (regulatory) elements in what he attempted to dismiss as “Junk”.

Dr. Bottaro’s #4 determination on Ohno’s argumentation is interesting. Although it is true that in Dr. Ohno’s abstract one does not find the word “Darwin” at all, “natural selection” is certainly there (while “Neutral Theory” is nowhere to be found). I leave this bone to others to chew on.

I find Dr. Bottaro’s #5 note “muted” by the ENCODE Report, published on the 14th of June, 2007. To me, both “counting genes” and “gene discovery” appear as obsolete past-times, since “gene” used to have about as many different definitions as many geneticists you asked, while ENCODE blew essentially all of them away. (The “boundary of a gene” could have been practically interpreted as the sequence within an “open reading frame” - but much to the surprise of uninformed workers of the field exons were found by ENCLODE far outside such ORFs, yet belonging to a particular “gene” – hint: FractoGene).

I am particularly grateful to Dr. Bottaro for joining me in the effort to focus attention to hereditary diseases that I call “Junk DNA diseases”, since this agenda is far more of a life-or-death issue to each of us, than any foul-mouthed shouting over mostly arbitrary ideological trenches.

I partially agree with Dr. Bottaro that “the reason that these diseases are a tough nut to crack for geneticists is … the complexity of the factors that cause them”.

Of course “these diseases are a tough not to crack”, I totally agree. My partial disagreement is summarized by my motto: “complexity is in the eye of the bewildered”. Faraday said “there is nothing simpler than a problem solved”. Electricity used to be incredibly mesmerizing. Faraday helped a lot, but the real breakthrough came when the Maxwell equations emerged.

Let’s work at identifying the algorithmic design (and its defects) of the full genome. Since we need to muster all our efforts for such a vital agenda, I urge all to kindly drop less worthwhile, though apparently habitual, swipes.

pellionisz_at_junkdna.com

Comment #190987

Posted by slpage on July 29, 2007 12:26 PM (e)

Dr. Pellionisz,

Are you still of the impression that geneticists and evolutionary biologists disregarded ‘junk DNA’ prior to Simons’ supposed groundbreaking ‘discoveries’?
If so, it is fairly easy to discard this notion by performing a simple literature search. Doing this, one can see that possible functions for ‘junk DNA’ were being proposed very early on in, in the 1970s. And in 1981, Zuckerkandl in fact published a paper on binding sites in ‘junk DNA’ and identified one of the first promoter sequences known.

I also note that as the notions of Darwinists and others ‘disregarding’ junk DNA have fallen by the wayside, supplanted by facts, that you have focused on inserting FractoGene into your replies. What has FractoGene identified?

Comment #191153

Posted by Andras Pellionisz on July 30, 2007 2:02 PM (e)

I posted a reply yesterday. The “bouncer page” claimed that it was for reasons of protection in case of “first users”.

pellionisz_at_junkdna.com

Comment #191200

Posted by Andras Pellionisz on July 30, 2007 8:08 PM (e)

Re:
==
Dr. Pellionisz,

Are you still of the impression that geneticists and evolutionary biologists disregarded ‘junk DNA’ prior to Simons’ supposed groundbreaking ‘discoveries’?
==

[Andras J. Pellionisz] It should not matter what my personal impression is. Suffice to look up e.g. an authority’s Nobel Lecture (given by Dr. Sydney Brenner at 2002 on his rather clear explicit views around 1985):

nobelprize.org/nobel_prizes/medicine/laureates/2002/brenner-lecture

“In 1985, when the first suggestions were made to sequence the human
genome, I thought that the sequencing techniques, even with incremental
improvements, would not be equal to the task, and would require a factory
scale operation to do it. I had also come to the conclusion that most of the
human genome was junk, a form of rubbish which, unlike garbage, is not
thrown away. My view at the time was that we should treat the human genome
like income tax and find every legitimate way of avoiding sequencing it. It
could therefore be asked whether a genome existed in Nature which perhaps
had very much less junk but nevertheless had the full repertoire of vertebrate
genes? It is easy to ask the question if one already has the answer. Towards the
end of the 1960’s I spent time in Woods Hole and took advantage of the library
where I first discovered the papers of Hinegardner (10). At the time, I
was puzzled by the enormous variations in the amounts of DNA in different
organisms. Indeed, whereas most physicists thought that organisms did not
have enough DNA to specify their complexity, it was clear to me that many organisms had too much. I discovered from Hinegardner that one group of
fish, the Tetraodontidae, which included the Japanese pufferfish, Fugu, had
very small genomes, with a haploid content of about 400 megabases as opposed
to the 3000 megabases of mammalian genomes. Although teleost fish
are distant from humans they are still vertebrates, with the same body plans,
development and physiological systems as ourselves. Because of these basic
similarities it seemed unlikely that Fugu, with a haploid DNA content one eighth
that of mammals would have eight times fewer genes, making it much
more probable that what was missing in Fugu was junk DNA. If Fugu had the
same gene repertoire as humans, then its genome would be more compact
giving us the human gene inventory for eight times less work and expense.
We proved that this was indeed the case and proposed the genome of Fugu as
the ideal model vertebrate genome (11), with a DNA content only 4 times
that of C.elegans.”

[AJP] Nobelists have much influence on papers published, resources allocated (or not), etc. If Sydney Brenner is on record with his Nobel lecture having had been a discouraging influence on R&D of “junk DNA” please take *his* word for it regardless of my opinion. (There is a flood of more evidence, e.g. Dr. Mattick’s very public outcry to the same effect in the Genius of Junk transcript, also published in Sci. Am. Your two citations only prove that “junk DNA” R&D wasn’t *totally* suppressed. Total suppression, as we know in PT, is very difficult).

Re: “I also note that as the notions of Darwinists and others ‘disregarding’ junk DNA have fallen by the wayside, supplanted by facts, that you have focused on inserting FractoGene into your replies. What has FractoGene identified?”

[AJP] The “discouragement” is on record (see above). I don’t have much claims at PT – was triggered to step in by Dr. Gregory’s direct Onion Test Challenge. Note that Sydney Brenner also floated (applied to the Fugu) what is known in PT as T. Ryan Gregory’s Onion Test – and FractoGene IMHO is still the best explanation by its peer—review published paper (referenced several times) for the fugu-(salamandra-onion) tests by Brenner/Dawkins/Gregory. If there is a better explanation than what FractoGene offered, please post it in your kind reply.

Please also note that the argument above by Sydney Brenner was utterly pragmatic “to treat the genome as the income tax” with minimal attention to anything but what formally appears to be vital to pass an audit. (Frankly, I don’t even know the ideological proclivity of Dr. Brenner, if he had/has any). However, somebody else with a declared ideological agenda (Editor-in-Chief of The Scientist, Richard Gallagher) expressed in his current editorial what is now evident: Dr. Ohno quite successfully framed genetics to be effectively limited to genes only. FractoGene I inserted in an attempt to break a multiple impasse which I find very troubling and harmful. First, IMHO circling the wagons around Intelligent Design contra Primitive Darwinism antagonistic camps is outright detrimental to the advancement of science, that in general should *not* be motivated by any ideological agenda (and in our case fighting “junk DNA diseases” is a far more important challenge for human kind than ideological warfare). FractoGene, as a concept (by identifying that the known fractality of DNA and the also known fractality of biological organisms are in a cause and effect relationship and thus provide opportunities to novel utilities) may be useful here for toning down harmful antagonisms by offering an Algorithmic Design approach (with utilities to diagnose/fight JunkDNA diseases). I am reasonably (?) hopeful that both camps could benefit from loosening up from their present rigid extremisms. I would urge one camp to open eyes for the obvious design (pattern) of the DNA (rather than insisting on an obviously false view that the Junk DNA is either junk or random). At the same time, I would urge the Intelligent Design camp workers towards revealing what the actual Design is (in a way Francis Collins does it) – such that we can all defer the adjective for later time when labeling the design is based on the actual (though always partial) knowledge of the investigated design. (I don’t a priori object to an intelligent use of the adjective, since the design is certainly smarter than we presently are – otherwise we would know the actual design much better than the flabbergasted ENCODE suggests, wouldn’t we?)

With the public (for which PT may be a reasonable [skeptical] microcosmos) taking a turn towards close attention to junk DNA diseases, professionals e.g. in. the pharma, bioenergy, IT and nanotechnology communities have no problem satisfying needs of society at large, using IP of novel approaches through their established means (beyond blogs). Fractal defects identified by FractoGem Miner (based on the FractoGene concept and algorithmic approach), e.g. as listed on www.fractogem.com should be more than plentiful advertisement. If interested in joining the utilization of FractoGene IP, contact me as others do at

pellionisz_at_junkdna.com

Comment #191219

Posted by Henry J on July 30, 2007 10:29 PM (e)

A couple of things occur to me. One, part of DNA being “junk” wouldn’t necessarily rule out also causing a disease, if some portion of it were to have a detrimental effect.

And two, fractal patterns, iirc, are caused by repetitive duplications of parts of something. Wouldn’t that suggest that if there are fractal patterns, those would less likely to contain useful parts of the genome than the non-fractal areas on the DNA?

Henry

Comment #191227

Posted by Andras Pellionisz on July 31, 2007 12:40 AM (e)

Henry J,

So delightful to talk about some basic questions of science. Let’s start from the beginning.

For your first question, you are absolutely right, since you posted a truism:

“One, part of DNA being ‘junk’ wouldn’t necessarily rule out also causing a disease, if some portion of it were to have a detrimental effect.”

Of course if something is “detrimental” could not rule out “causing a disease”.

IMHO the very question is targeted mistakenly, however. Nobody (that I know of) would, or can, rule out that some percentage of the DNA may be “junk”, meaning that it is not doing anything useful. That is a non-issue e.g. for me. In my opinion, it is also a non-issue to “guess” the exact number; 1-10-20-90-98.7 percent of the DNA (formerly called “Junk”) that is now found “functional”. (On junkdna.com see an interesting, but not-so-important “bet” between Drs. Birney and Mattick on this “numbers’ game”.)

At least for now, I keep focused on the “newly found functional DNA” that was formerly dismissed as “Junk”, with the (admittedly ambitious) goal of revealing its “algorithmic design”. Fortunately, fractal defects my FractoGem Miner finds in the sequences known as “regulatory” already appear to yield clues to a slew of some (literally) “mind boggling” diseases, increasingly deemed “junk DNA disease”; e.g. Alzheimers’.

As for your second question:

“…fractal patterns, iirc, are caused by repetitive duplications of parts of something. Wouldn’t that suggest that if there are fractal patterns, those would less likely to contain useful parts of the genome than the non-fractal areas on the DNA?”

Yes, this is also rather basic issue - emerged at the 2002 interview, see www.junkdna.com/#junk_dna_revisited

“The genes we know about today, Pellionisz says, can be thought of as something similar to machines that make bricks (proteins, in the case of genes), with certain junk-DNA sections providing a blueprint for the different ways those proteins are assembled”.

What is “less likely to contain useful parts of the genome” – the building materials (bricks, glass, timber, concrete) or the “design” how to put the parts together? I don’t think it is a very good question (reminds me of the “competition” which of our organs are the most important; heart, lung, liver, kidney - none can do it without the others). You must have all necessary components AND the design.

pellionisz_at_junkdna.com

Comment #191268

Posted by hoary puccoon on July 31, 2007 5:39 AM (e)

Dr. Pellionisz’s long quotation from Sydney Brenner leaves the misimpression that Brenner thought everything in the genome except genes was junk. James Watson’s popular-science book, “DNA, THE Secret of Life,” gives a completely different impression. Watson points out Brenner was working at ‘the relatively cash-strapped Medical Research Council in Britain….’ and that using reverse transcriptase to sequence genetic DNA ‘was the most cost-effective way of using what little money he had.’ Watson also says, ‘under Brenner’s leadership, the fugu rough draft was completed for some $12 million, a genuine bargain by genome-sequencing standards.’ It seems hardly likely that Brenner would have put the effort into sequencing the entire fugu genome, two-thirds of which does not code for proteins, if he thought everything but genes was junk. It seems much more likely that Brenner was simply responding to the financial realities of Britain in the Thatcher years, than that he had any basic scientific objection to studying non-coding DNA.
I don’t know what Dr. Pellionisz’s Ph.D. is in. Perhaps he feels I have no right to comment, since my Ph.D. is in sociology, not science proper. But I must say, if my work in the sociology of science had played as fast and loose with historical accuracy as Dr. Pellionisz’s does, I would have been booted out of the program before I got my MA.

Comment #191321

Posted by Andras Pellionisz on July 31, 2007 11:24 AM (e)

Edge of tongue and scientists (off topic)

“am I the only one that perceives a general edge in readability of legitimate scientists…?” – asks Science Avenger (a non-scientist).

I am guilty (though not at all “as charged”) of having some roughness to my English language. One reason might be that for smooth-talking salesmen with a native English language composing kindergarten level postings comes easy as child-play (they often need no more than a handful of four-letter words as opposed to e.g. using expressions that are seven times longer; “singlenucleotidepolymorphism”).

However, I am a scientist for whom the English is not the first, not even the second language. (After my native Hungarian, compulsory Russian, acquired Latin, German and French, the English language is my 6th).

I find very telling the following confessions of “Science Avenger”: “I don’t have enough biological knowledge … of the science, but with most of the cranks I find their basic train of thought often difficult to discern. They also seem to use more arcane technical jargon. …In my profession, when I feel my position is weak and I need to bamboozle a laymen, that’s what I do”.

Since “Science Avenger” is admittedly a “non-scientist” I don’t think he/she is qualified to be a “flagperson” to recognize “crank” or “not crank” scientific jargon, and IMHO is further disqualified for his admittedly phony use of technical terms to confuse readers.

If one embarks on reading scientific expressions, one has implicitly accepted the fundamental criterion that in science precision is more important than “easy listening”. Reading science *is* hard – this is why we scientists had to be educated for so many years. (From elementary school to have 3 Ph.D.s [computer engineering, biology, physics – since one of you asked] took me 40 years – more precisely to be a scientist, one is committed to “lifelong continuous education”. Please forgive me).

I am further “guilty” since both my *not* Indo-European native Hungarian (an outstandingly precise language) and my first acquired language formative for science (classical Latin; a highly structured Indo-German Romanesqe language) trained neural nets of my brain to memorize easier those words of the English language that originated from the highly structured classical Latin, German and French, as opposed to the simpler and more “rural” vocabulary of English words with Celtic origin. I am cognizant to have e.g. the proclivity of using “sophisticated” over the much less expressive “clever” – perhaps appearing more “arcane” to some. My English vocabulary is simply much richer in words of the more Romanesque than Celtic origin. This I was told - to my surprise - by my learned colleagues while I stayed in Great Britain, since this phenomenon is also rather well known there. Good ears, especially of the Welsh, can rather easily tell “more aristocratic” and “more rural” English speakers apart. For those preferring entertainment over science, the mix of “My Fair Lady” could be useful to get familiar with this subject. In the USA, with zillions of further linguistic components; African, far-Eastern, and indeed even Hungarian; e.g. Gulash and Hussar, though both with incorrect spelling (and “Hungarian notation” in computer programming by Charles Simonyi) analysis of the lingual mosaic is a science itself.

Contrary to “Science Avenger”’s admittedly phony jargon to intentionally obfuscate (you would say, “snow under”, or would use the slang of rural celtic origin “bamboozle”) readers, my style is genuine and honest – while admittedly rather difficult for a bed-time reading. Therefore, I refer readers wishing to fall asleep or have easy fun (on others’ expense) to kindergarten English.

pellionisz_at_junkdna.com

P.S. Don’t worry, I am in the (difficult) process of negotiating the best possible co-author/lector for my FractoGene book.

Comment #191334

Posted by Henry J on July 31, 2007 12:40 PM (e)

Re “What is “less likely to contain useful parts of the genome” – the building materials (bricks, glass, timber, concrete) or the “design” how to put the parts together?”

No, the part less likely to be useful is the part that “are caused by repetitive duplications of parts of something”. That pretty much excludes organs.

Re “Of course if something is “detrimental” could not rule out “causing a disease”.”

My point there was that something with no useful function (i.e., “junk”) could cause a problem, not that something that’s detrimental could cause a problem - that’s pretty much the definition of “detrimental”.

Henry

Comment #191341

Posted by Andras Pellionisz on July 31, 2007 1:01 PM (e)

Henry, for the most part, we are bogged down with semantics (detrimental/disease, etc).

Re: your comment:

“the part less likely to be useful is the part that ‘are caused by repetitive duplications of parts of something. That pretty much excludes organs”

Wow, I don’t think so… I spent a few decades with ‘repetitive duplications of parts’ (of a rather important organ [to some], the *brain*). I can recommend my fractal model of the Purkinje brain cell

fractogene.com/89_fractal/89_fractal.html

While the paper is somewhat “difficult” (concepts about Non-Euclidean geometry in biology) I believe the pictures speak for themselves.

(Other spectacular organs where ‘repetitive duplication’ is visibly stunning are the lung, the heart circulatory system

fractogene.com/full_genome/fractal_visual_gallery.html

Pictures are worth a thousand words…

pellionisz_at_junkdna.com

Comment #191347

Posted by Henry J on July 31, 2007 1:42 PM (e)

I’m thinking that duplicate of organ parts is not analogous to duplication of sections of DNA - in the case of organs, more of the same increases capacity for that organ. Capacity issues don’t apply to DNA in that way.

Henry

Comment #191374

Posted by Andras Pellionisz on July 31, 2007 4:10 PM (e)

Dear Hoary Puccoon (Ph.D. in sociology),

Of course in my opinion anyone has the right to comment (though it appears that some are screened more than others…). I would debate not the “right to comment” but the *rushing to pretend to be the judge* in particular scientific issues - if one is not a specialist in that science. Dr. Hoary Puccoon (sp?) would even qualify to be a member of the IPGS, see www.postgenetics.org since “beyond Junk DNA” has trans-disciplinary core-issues, very much welcoming contribution from the science of sociology.

As for Dr. Brenner, you misquoted him: “Dr. Pellionisz’s long quotation from Sydney Brenner leaves the misimpression that Brenner thought everything in the genome except genes was junk”.

Please read Dr. Brenner again: “I had also come to the conclusion that most of the human genome was junk” (and kindly note that “most” is not identical to “everything in the genome except genes”). We don’t need to judge Dr. Brenner as he is fully capable of speaking for himself. As a scientist closer to Dr. Brenner’s field, I would just add that I have personal knowledge that during his USA career, as a boss, he discouraged a brilliant friend of mine (who was working for Dr. Brenner) from looking into “regulation” *instead of* the task he pragmatically assigned to him.

And I agree with you, that pragmatism is not bad in itself - the last thing I would wish is to “blame” a genius like Dr. Brenner. (I have actively discouraged any “blaming game” in this thread).

Instead, I submit (you be the judge, since it is your field) that sociology might help in compelling societies to occasionally re-evaluate what the finite resources should be distributed for.

In the present paradigm-shift, I would imagine that society at large may set a different pragmatic agenda for Genomics than before the realization that each of us may actually suffer, and/or die miserable deaths, because of “junk DNA diseases”.

What is your opinion/judgment for instance about US taxpayers spending a proposed double ticket in the future (above $100 M) to continue ENCODE “as is” (already having cost $53 M)? Do you think that spending at least a part of new funds could be more effective if we don’t beat the dead horse of “Junk DNA” even deader (for a second and a third time) - but rather, direct at least a fraction of R&D funds to fighthing “Junk DNA diseases”?

As a sociologist (with obvious interest in PostModern Genomics) do you think NIH or NSF (or other agencies relying on tax-dollars) might be more suitable to seed/lead?

pellionisz_at_junkdna.com

Comment #191423

Posted by Andras Pellionisz on July 31, 2007 10:34 PM (e)

Henry J,

You wrote:
“duplicate of organ parts is not analogous to duplication of sections of DNA - in the case of organs, more of the same increases capacity for that organ. Capacity issues don’t apply to DNA in that way”

Capacity issues don’t apply to DNA?

You may wish to look up the “Onion Test” (another thread of PT), and see that presently the phenomenological explanation of “C-value” of DNA is that it correlates with cell SIZE (“capacity”).

The required “Onion Test” for non-coding DNA theories is answered in the paper

www.junkdna.com/fractogene/05_simons_pellionisz.pdf

is best passed by FractoGene, since e.g. the Fugu - Zebrafish - Mouse - Human genome’ (c-value) correlates not only with the P-cell size (“capacity” to receive parallel fiber input) but also with the hierarchy of fractal arborization. Currently, I know of no better explanation - let me know if you do.

pellionisz_at_junkdna.com

Comment #191426

Posted by Henry J on July 31, 2007 11:00 PM (e)

Re “Capacity issues don’t apply to DNA?”

I said IN THAT WAY.

Yes, more DNA will take up more room in the cell, but that wasn’t the point.

Duplication of parts of an organ increases the capacity of that organ.

That doesn’t apply to DNA - the overall amount of DNA doesn’t determine how much of something can be processed by an organ.

As for more DNA fitting in a larger cell, yep, with more space there’s less detrimental effect of having unneeded stuff, so more junk accumulates.

Henry

Comment #191495

Posted by Andrea Bottaro on August 1, 2007 8:24 AM (e)

Sorry for the leave of absence from the thread, I just wanted to add some comments on factual issues:

Dr. Bottaro’s #4 determination on Ohno’s argumentation is interesting. Although it is true that in Dr. Ohno’s abstract one does not find the word “Darwin” at all, “natural selection” is certainly there (while “Neutral Theory” is nowhere to be found). I leave this bone to others to chew on.

This word-search approach reminds me of Behe arguing that scientists don’t really know squat about molecular evolution because their papers contain words like “may” “might” and “possibly”. Ohno’s original argument for “junk DNA was two-fold: on the one side, the “genetic load” argument (discussed in a comment of mine above, see also below), and on the other the issue of phylogenetic conservation of protein sequences, which is restricted to “active sites” (Ohno’s nomenclature) while the rest behaves according to Kimura’s predictions under neutrality (cited in the paper). Thus, Ohno argues, the fate of duplicate genes is most often to become inactivated by mutations that destroy their product’s active site, and then drift off into neutral oblivion. (Ohno thought that the vast majority of non-functional, “junk” DNA would be comprised of pseudogenes and their unrecognizable remnants - in this he was incorrect, but of course he did not have the benefit of knowing any genomic sequence, let alone all of it like we do.)

I find Dr. Bottaro’s #5 note [on the issue of genetic load] “muted” by the ENCODE Report, published on the 14th of June, 2007. To me, both “counting genes” and “gene discovery” appear as obsolete past-times, since “gene” used to have about as many different definitions as many geneticists you asked, while ENCODE blew essentially all of them away.

This is simply false, all that anyone can conclude from the ENCODE data is the bare fact that more of the genome undergoes transcription than we suspected. The ENCODE paper makes no point (and its authors are careful not to) about the function of this transcription. On the contrary, the genetic load argument applies to genome size regardless of ENCODE: if the primary sequence of intergenic DNA was under selective constraints (similar to, say, protein-coding or regulatory element sequence), then organisms with genomes of the size of ours (or even much smaller), would simply suffer a biologically unbearable rate of deleterious mutations. Thus, most intergenic DNA sequences (“fractal” or not) cannot be under significant selection, and are therefore functionally neutral (which doesn’t mean that intergenic DNA cannot be functional in some other, sequence-independent way - e.g. as “spacers” etc).

The required “Onion Test” for non-coding DNA theories is answered in the paper

www.junkdna.com/fractogene/05_simons_pellionisz.pdf

is best passed by FractoGene, since e.g. the Fugu - Zebrafish - Mouse - Human genome’ (c-value) correlates not only with the P-cell size (“capacity” to receive parallel fiber input) but also with the hierarchy of fractal arborization.

And once again, your paper does not do this at all. It lacks the critical data, on P-cell arborization in zebrafish, to even approach reaching such a conclusion - missing data that is marked by huge question marks in your own figure 4. (By the way, I cannot believe these data do not already exist somewhere, and even if they don’t, they could be obtained by any neurobiology grad student in less than a week, let alone the 2 years that have elapsed since your paper was published.) It really hurts your scientific credibility to keep repeating this ridiculously inflated claim.

In the same vein, I looked for evidence of this other claim:

Perhaps the most important case is Parkinson’s disease, where the *promoter* (“Junk DNA”) part of the SNCA gene contains an already identified fractal defect.

and I could not find any either.

Comment #191512

Posted by Erik 12345 on August 1, 2007 9:56 AM (e)

Andras Pellionisz, what are the fractal features you’ve identified in some DNA sequences? In what sense are they “fractal”?

Comment #191520

Posted by hoary puccoon on August 1, 2007 10:49 AM (e)

Dear Dr.Dr.Dr. Pellionisz;
As a sociologist I would not presume to judge the NIH and NSF decisions on hard science grants without putting a considerable effort into studying the process and results of their grants. The work I did do in that area– which is now dated– indicated they were making, on the whole, pretty good decisions. The two crucial factors appeared to be that:
1.) The standards for performance in the physical sciences, as indicated by, among other things, the high ratio of published to submitted papers, are fairly straight-forward.
2.) The number of labs working in any one area is limited, so that the personal reputations of the major players are known.
On the whole, I believe these two factors result in a system which generally is hurt more than helped by second-guessing on the part of those who haven’t studied its inner workings.
As I said, I haven’t been active in this area recently enough to make a definitive statement about it. But I would certainly be cautious about criticizing the decisions of either the NIH or the NSF.

Comment #191532

Posted by Steviepinhead on August 1, 2007 11:55 AM (e)

Henry J:

…with more space there’s less detrimental effect of having unneeded stuff, so more junk accumulates.

That’s it, Henry! I’m never inviting you in to see my garage again!

Comment #191596

Posted by Andras Pellionisz on August 1, 2007 7:00 PM (e)

Dr. Bottaro,

Anonymous non-scientist bloggers have nothing to lose. This explains some extreme low points in the thread.

However, since you are one of those young scientists who still have a chance to make their spectacular careers in PostModern Genomics, you might wish not to needlessly compromise *your* credibility in some key science issues at crucial times. Rather, you may wish to adopt the more sober view that even an anonymous blogger expressed in another thread about Pellionisz’ FractoGene approach to function of formerly “Junk DNA”:

“GeoMor
Hell, he could be right…”

As even non-scientist bloggers can easily verify, one might wish to refrain from statements you made such as:

“all that anyone can conclude from the ENCODE data is the bare fact that more of the genome undergoes transcription than we suspected”

Readers of the full ENCODE Report could reach their own conclusion by reading beyond the first “bullet point” (“The human genome is pervasively transcribed” as only the first of the 11 points of “Summary”) - see link to free Nature full text at:

www.junkdna.com/#junk_dna_is_dead

and only count just the number of bullets (eleven). Dr. Bottaro hits only on the first, while leaves the next ten bullets more-or-less similarly disregarded as the 89.7% “Junk DNA” used to be…

Of course, the trauma of ENCODE on Genomics (as we knew it) is reflected in a mix of reactions. Dr. Bottaro seems to be still stuck in the first, “denial” phase. Others are at the next “rage”, “depression” phases or reached “acceptance” – while a few have worked half a decade already based on “what if Junk DNA is anything but”.

I submit as an interesting open attitude towards some new approaches “what’s in it for me if it proves to be right?”

Dr. Bottaro’s “criticism” is more like to what I usually answer “Don’t bite my finger – look where I am pointing”. (Dr. Bottaro may be stuck in denial of the 6-week-young ENCODE but in the rage mode about my 5-years-young FractoGene…)

Let me gently suggest that Dr. Bottaro is missing the point. The “critical data” in the “Fugu FractoGene paper” is not the P-cell of the zebrafish, nor the that of the guinea pig. Critical to science is the P-cell of the fugu (and to human “Junk DNA diseases” the human P-cell).

Dr. Bottaro bites:

“your paper … lacks the critical data, on P-cell arborization in zebrafish, to even approach reaching such a conclusion - missing data that is marked by huge question marks in your own figure 4. (By the way, I cannot believe these data do not already exist somewhere, and even if they don’t, they could be obtained by any neurobiology grad student in less than a week, let alone the 2 years that have elapsed since your paper was published). It really hurts your scientific credibility to keep repeating this ridiculously inflated claim.”

Thanks for making my day with the first part, the huge question marks in Fig. 4. of www.junkdna.com/fractogene/05_simons_pellionisz.pdf
I have been waiting for someone to pick them up - otherwise I would not have put them in :-)

Why? It is not good for any approach to exude that “I solved it all”. (There is no such thing in science, ever). Since FractoGene is on its early curve, I think it is helpful to pinpoint (predict) some potential results that – exactly as Dr. Bottaro says – “could be obtained by any neurobiology grad student in less than a week”. I would be extremely glad to review a manuscript by Dr. Bottaro et al. on e.g. the P-cell of the zebra fish; they typically cost $0.20 apiece – a bargain compared to the delicacy of Fugu. Besides, I can guarantee success since I have seen with my very eyes the P-cell of the Danio and - as the paper says in two separate places – it is “interim” or “intermediate”. Frankly, I was rooting for some grad students in Dr. Mattick’ lab, since they claim tanks crowded with some 20,000 Danio apiece. However, nobody would rush to strengthen an initiative *before* one figures out “what’s in it for me”, would they?

Meanwhile, let’s talk about a much smaller question mark that meticulous readers might detect in the paper. It is E? of the same Fig. 4.

As true theories are, FractoGene is predictive. (My earlier, Tensor Network Theory was predictive, too; predicting such an incredible behavior of contravariant vectors compared to covariant ones that two young researchers were outraged enough to experimentally check out the prediction – much to their surprise the young man, now distinguished Professors – found prediction of TNT *correct*)

The “Fugu FractoGene” paper went out on a limb with the genome-size of the guinea pig (E?). (By the way, the paper was published not “2 years” ago, but last April, 2006; 5: 27-35). About 2 months after publication (not submission) of the paper, the genome was sequenced; proving that the very similar appearance of the arborization of P-cells of the mouse and the guinea pig is well reflected in their genome size. (Hint: another bunch of easy stuff for grad students).

I admit that I am somewhat puzzled. I thought that Panda’s Thumb (as opposed to other blogs) will love theories based on actual quantitative predictions, even if they are of the “Algorithmic Design” approach - as long as they are scientific, predictive,– and especially after they have received experimental support.

Where did I go wrong?

pellionisz_at_junkdna.com

Comment #191601

Posted by Andrea Bottaro on August 1, 2007 7:54 PM (e)

Readers of the full ENCODE Report could reach their own conclusion by reading beyond the first “bullet point” (“The human genome is pervasively transcribed” as only the first of the 11 points of “Summary”) - see link to free Nature full text at:

www.junkdna.com/#junk_dna_is_dead

and only count just the number of bullets (eleven). Dr. Bottaro hits only on the first, while leaves the next ten bullets more-or-less similarly disregarded as the 89.7% “Junk DNA” used to be…

Not at all. Essentially all the other observations are either related to the issue of transcription, or explicitly counter any claim that significant fractions of intergenic DNA sequences are involved in selectable functions. Indeed, here are the points from the paper (my comments in square brackets):

- The human genome is pervasively transcribed, such that the majority of its bases are associated with at least one primary transcript and many transcripts link distal regions to established protein-coding loci. [transcription-related]

- Many novel non-protein-coding transcripts have been identified, with many of these overlapping protein-coding loci and others located in regions of the genome previously thought to be transcriptionally silent. [transcription-related]

- Numerous previously unrecognized transcription start sites have been identified, many of which show chromatin structure and sequence-specific protein-binding properties similar to well-understood promoters. [transcription-related]

- Regulatory sequences that surround transcription start sites are symmetrically distributed, with no bias towards upstream regions. [transcription-related]

- Chromatin accessibility and histone modification patterns are highly predictive of both the presence and activity of transcription start sites. [transcription-related]

- Distal DNaseI hypersensitive sites have characteristic histone modification patterns that reliably distinguish them from promoters; some of these distal sites show marks consistent with insulator function. [transcription-related]

- DNA replication timing is correlated with chromatin structure. [not transcription-related, but makes no difference with regard to “junk DNA” issue]

- A total of 5% of the bases in the genome can be confidently identified as being under evolutionary constraint in mammals; for approximately 60% of these constrained bases, there is evidence of function on the basis of the results of the experimental assays performed to date. [supports the lack of selectable function of the majority of DNA]

- Although there is general overlap between genomic regions identified as functional by experimental assays and those under evolutionary constraint, not all bases within these experimentally defined regions show evidence of constraint. [supports the lack of selectable function of the majority of intergenic DNA, in that even within conserved regions, only some sequences are under selection]

- Different functional elements vary greatly in their sequence variability across the human population and in their likelihood of residing within a structurally variable region of the genome. [supports the lack of selectable function of the majority of intergenic DNA, in that even the sequence of identified biochemically active regions can vary extensively between individuals]

- Surprisingly, many functional elements are seemingly unconstrained across mammalian evolution. This suggests the possibility of a large pool of neutral elements that are biochemically active but provide no specific benefit to the organism. This pool may serve as a ‘warehouse’ for natural selection, potentially acting as the source of lineage-specific elements and functionally conserved but non-orthologous elements between species.[supports the lack of selectable function of the majority of intergenic DNA]

As for the following:

Let me gently suggest that Dr. Bottaro is missing the point. The “critical data” in the “Fugu FractoGene paper” is not the P-cell of the zebrafish, nor the that of the guinea pig. Critical to science is the P-cell of the fugu (and to human “Junk DNA diseases” the human P-cell).

That would be the case if one could seriously extrapolate a trend and derive a correlation from two (2) data points, as you are attempting to do. However, that is not the case. As I suggested, your prediction, to be meaningful, has to hold for critters like lungfish and salamanders (up to tens of times the human genome size), sharks (genomes about human size, or a bit larger), and lampreys and chickens (slightly smaller). Care to make a prediction right here as to the arborization of P-cell dendrites in these species? Should be straightforward.

I am not sure where you are going with all this bluffing and posturing. I am pretty sure that you are unlikely to hook up with venture capitalists here at PT willing to invest in your ideas (and this is regardless of the actual value of your ideas, by the way - I just doubt there are many venture capitalists among PT readers).

Comment #191630

Posted by Andras Pellionisz on August 2, 2007 12:15 AM (e)

Dr. Bottaro,

“I am not sure where you are going… I am pretty sure that you are unlikely to hook up with venture capitalists here at PT…”

I am wearing several hats. With my “PostGenetics Evangelist” hat on in PT, I am trying to make you non-believers in the functionality of (formerly) Junk DNA to be convinced by SCIENCE that it is the case for a whole lot more than 1.3% of the genome. You are right that VCs would never touch PT. At this time, I can’t think of any who would believe the “Junk DNA” fairy tale. It is the “public” that should produce an outcry for society to drum up a campaign against “Junk DNA diseases”. A “bully” as PT appears to be, its horns might be used better for mankind if turned against a real enemy.

Since even you admitted that ENCODE has proven Dr. Ohno wrong (on at least one of his fundamental theses) somehow I have the funny feeling that Susumu would at this point of time be rooting for me…

And, you know, I just don’t think that if ENCODE could sum all their eleven bullets into one, they would not have done so…(We all could try to trivialize the genome e.g. that “it is nothing but A,C,T,G” or “nothing but fractals” – but at least we scientists should do better). That’s why I mess e.g. with “cell size” and “arborization prediction for Fugu”, and a few other details in my long years of R&D.

pellionisz_at_junkdna.com

Comment #191675

Posted by Andrea Bottaro on August 2, 2007 7:09 AM (e)

Since even you admitted that ENCODE has proven Dr. Ohno wrong (on at least one of his fundamental theses) somehow I have the funny feeling that Susumu would at this point of time be rooting for me…

That’s not what I said at all. And I suspect Dr. Ohno would be very pleased with the ENCODE results, vis-a-vis his original paper, and still side with the evidence.

2007 Encode paper, based on direct genome analysis: :

A total of 5% of the bases in the genome can be confidently identified as being under evolutionary constraint in mammals.

1972 paper by Ohno, based on theoretical considerations on “genetic load”:

Even if allowance is made for the existence in multiplicates of certain genes, it is still concluded that, at the most, only 6% of our DNA base sequences is utilized as genes.

Even assuming potential changes of a few percent points one way or the other for various reasons, that’s pretty damn close for a 35-year old back-of-the-envelope calculation.

I see you offered no prediction on the Purkinje cell arborization of lampreys, sharks, lungfish, salamanders and chickens, compared to fugu and human. Does the Fractogene approach only apply to fugu and guinea pigs?

Comment #191776

Posted by Andras Pellionisz on August 2, 2007 4:26 PM (e)

Dr. Bottaro said:

[AB] “Ohno thought that the vast majority of non-functional, ‘junk’ DNA would be comprised of pseudogenes and their unrecognizable remnants - in this he was incorrect, but of course he did not have the benefit of knowing any genomic sequence, let alone all of it like we do”

[AJP] To me, it does sound like an admission by Dr. Bottaro that Dr. Ohno was incorrect in one of his main theses… (Sure, I accept the excuse for Dr. Ohno being wrong not knowing what we know, particularly with ENCODE). It seems to me an exercise in futility to uphold Dr. Ohno’s mistake(s), when even e.g. Richard Gallagher (in The Scientist) succumbed to the obsolesce of ‘Junk DNA’ as a scientific concept, and retained the phrase for ‘framing’ purposes ‘to keep things interesting’. Scientists go beyond the goal of publicity. Further, about the ‘active loci’ (Ohno’s ‘definition of genes’ that degenerated into the ‘genes only’ frame set by Ohno), I added:

[AJP] “both ‘counting genes’ and ‘gene discovery’ appear as obsolete past-times, since ‘gene’ used to have about as many different definitions as many geneticists you asked, while ENCODE blew essentially all of them away”. I gently suggested that Dr. Bottaro is not yet in the acceptance phase set forth of the trauma-process by ENCODE. Since Dr. Bottaro was kind enough to copy the eleven “summary bullets” of the ENCODE Report, it is apparent that Dr. Bottaro is in a denial of even the second half of the FIRST bullet:

[ENCODE #1] “The human genome is pervasively transcribed, such that the majority of its bases are associated with at least one primary transcript and many transcripts link distal regions to established protein-coding loci”

[AJP] Kindly note that “many transcripts link distal regions to established protein-coding loci” goes beyond essentially all traditional definitions of “gene” (it is transparent in ENCODE starting with the first bullet). Certainly, when Dr. Ohno wrote his infamous paper (1972) even “introns” (“Junk DNA” parts of the genes) weren’t known, since Walter Gilbert introduced the term “intron” only in 1978. Many are in denial about the “blow up” of dogma of “JunkDNA” and, yes, of “genes as we knew them”. Young scientists from the present startline will do exceedingly well or will get stuck depending on if they pick up the speed of PostModern Genomics, or keep fondling their cheriched dogma.

Bottaro says: “I see you offered no prediction on the Purkinje cell arborization of lampreys, sharks, lungfish, salamanders and chickens, compared to fugu and human. Does the Fractogene approach only apply to fugu and guinea pigs?”

[AJP] You can only see that I did not find *this blog* the best scientific outlet to come forward with rather profound predictions of FractoGene (not limited to particular species). I communicated results through peer-reviewed science journal article - you are free to put your name on the record with different views likewise. (You are practically the only scientist in this field at PT and in addition not very receptive to PostModern Genomics - unfortunately it really looks to me that PT is not “science friendly”.) Rest assured that through more proper channels I can reach potential science co-workers how to tackle further e.g. the Fugu/Salamander/Onion test challenge, or they can reach me, including the possibility, as my Dutch young colleagues did, *with their accepted paper, having found experimental evidence supportive of my initiative*

pellionisz_at_junkdna.com

Comment #191782

Posted by Aryaman Shalizi on August 2, 2007 6:24 PM (e)

If you have time to get to a good medical library, you can locate comparative diagrams of Purkinje cell arborization across the vertebrate lineage in R. Niewenhuys, “Comparative Anatomy of the Cerebellum,” Progress in Brain Research 1967:25:1-93. At the tail end of this review he shows Golgi-stained sagittal profiles of the Purkinje cell from lamprey, shark, teleost, turtle, bird and human, each demonstrating a clear increase in dendritic complexity. This is nothing exceptional, as even Cajal noted in his 1904 “Histology of the Nervous System” that many anatomists had already observed the increasing complexity in dendritic arborization of the Purkinje cell across the vertebrate series. In Cajal’s chapters on the cerebellum (in vol II of the 1995 english translation), you can find similar Golgi-stained sagittal profiles of rainbow trout, frog (tadpole), pigeon, mouse and human Purkinje cells, showing an increase in dendritic complexity as you move up the vertebrate series.

Now neither Cajal nor Niewenhuys had the benefit of a nifty website like genomesize.org, but if they did, they could make the following table:

Organism ranked by increasing Purkinje cell arborization: genome size, in pg
Lamprey [clade average]: 1.6pg
Shark [assumed dogfish]: 6.8pg
Teleost fish [Rainbow trout]: 2.5pg
Frog [assumed generic Rana]: 6.7pg
Turtle [clade average]: 2.9pg
Pigeon [assumed Rock pigeon]: 1.5pg
Mouse [M. musculus domesticus]: 3.3pg
Human: 3.5pg

Dr.^3 Pellionsz even admits that Purkinje cells of the mormyrid family of fishes have extraordinarily elaborate dendritic trees, and they have a genome size of only 1-1.2pg. Given these observations, I’m fairly confident there are few ways you could put together a convincing trend line correlating genome size with complexity of the Purkinje cell dendritic arbor, without making the baby Gauss cry.

After going through Dr.^3 Pellionsz’s paper in Cerebellum more than a few times, I fail to grasp the rationale behind focusing on the morphology of the Purkinje cell, other than the fact that Mandelbrot said it looked like it was fractal and could be amenable to analysis using non-Euclidean geometry. So what?

What does FractoGene [patent pending] predict
[1] about other kinds of neurons? What predictions does it make about the relatively invariant morphology of, for example, cerebellar granule neurons, the single most numerous class of neurons in the central nervous system, which have an almost invariant morphology in all species that have cerebella? What predictions does FractoGene make about the structure of cortical pyramidal cells, which also show a much lower degree of morphological variation?
[2] about biological structures that do NOT have a fractal-like appearance? What does FractoGene say about cuboidal versus squamous epithelium? Or about teeth and bone, which scale to an organism’s physical (not genomic) size?

I have no problem with the idea that some sort of scaling or power laws or fractal dimensions may be involved in animal morphology and metabolism (In fact, I really like some of the work in this area), but I just don’t see anything to this FractoGene stuff beyond a lot of hand waving; certainly not any explanatory power.

Comment #191829

Posted by Andras Pellionisz on August 3, 2007 1:02 AM (e)

Wow, I got really excited by the posting of Aryaman Shalizi – with some really substantial science arguments, even if not all bona fide. Alas, not mentioning at all the Fugu (although the “Fugu Prediction of FractoGene” paper was aimed at the Fugu, in the first place…)

I will provide a more elaborate answer latest by this weekend, but in this quick preview let me point out two more features.

On one hand it is delightful that A.S. writes “I have no problem with the idea that some sort of scaling or power laws or fractal dimensions may be involved in animal morphology and metabolism (In fact, I really like some of the work in this area)” – and we’ll have some nice exchange regarding morphology, metabolism and fractals, since it is e.g. cardinal to Santa Fe Institute.

On the other hand, he does not seem to be a particular expert in Purkinje neurons (I can see no publications from him in Pubmed regarding P-cells) compared to my series of papers for the last 33 years. This is apparent from his comment on my comment on the P-cells in Mormyrid. I wrote “astounding refinement” as opposed to the trend of (fractal) complexity (or as he says, “elaborate”). My guess is that A.S. has not yet seen a P-cell of the Mormyrid fish. (If he has, he would immediately recognize its drastically distorted pattern).

Nor has anyone (certainly not Cajal not even Niewenhuys) published a P-cell of the Fugu (to our knowledge – that’s why I went out on a limb with a quantitative prediction for the Fugu, and independent experimentalists found my predicition on the Fugu correct). This was certainly a prediction, and supported by experimental evidence. Is there room for more predictions? Absolutely. Did I imply that “I solved it all”? Certainly not - see the “huge question marks” in the paper for the Zebrafish P-cell (also unmentioned by A.S.).

FractoGene is not only predictive for P-cells; e.g. the “Methylation Prediction” was not at all restricted for *any* cell at all…

More a bit later, as I come up for air from other past-times than blogging…

pellionisz_at_junkdna.com

Comment #191852

Posted by Andrea Bottaro on August 3, 2007 6:51 AM (e)

Aryaman, you are such a spoilsport! I was holding on for Dr. Pellionisz’s predictions before comparing them to the rather abundant info already available on Purkinje cells in various animals. ;-)

Anyway, I’ll try to scan the figures of P-cell Golgi stains from those critters over the week-end, and post them in an update above.

Comment #191978

Posted by Andras Pellionisz on August 3, 2007 6:22 PM (e)

Dr. Bottaro writes: “Aryaman, you are such a spoilsport! I was holding on for Dr. Pellionisz’s predictions before comparing them to the rather abundant info already available on Purkinje cells in various animals. … I’ll try to scan the figures of P-cell Golgi stains from those critters over the week-end, and post them in an update above”

Oh, no. Not at all a “spoilsport”. I could not be happier! In our paper with Dr. Simons we opened up a new opportunity:

“The genomes of many species have been sequenced. They provide a new opportunity for combining comparative anatomy and genomics, guided by mathematical conceptual frameworks… As yet, the genomic aspects of P-cell development have not been brought into similar focus”

From a PT thread, barely worth touching, in a few days I could trigger at least two real scientists (hopefully, with a good number of grad students in tow) towards the predicted very important trend of “triangulation”.

Mind you, posting a few Golgi preps already available since Golgi & Cajal’s Nobel (1911) or putting out a “table” where the actual (sub) species are guessed at best, may not be the highest quality work, though. Something original might be helpful (in our case, the Fugu P-cell and the “triangulation concept” on the specific platform of the P-cell. I will get to some key notes regarding the “mathematical conceptual framework” – it did not exist, did it, if some of us still believe “Junk is Junk”?)

Don’t forget that e.g. coming up with *new* data (as we did with the Fugu) or what we pitched for the zebrafish might be more worthy of a publication than a no-brainer of tabulation where 5 of 8 items are “average” or “assumed” species, especially since e.g. the zebrafish-work “can be easily done in less than a week”. I would even sponsor some zebrafish preps at $0.2 apiece “out of pocket”… (On second thought, I would not, since it might be an “inside job” where I already know the result …)

Most importantly, kindly focus on much-needed “mathematical conceptual frameworks” (would you please let me know what you find anything that tops FractoGene?) – and mining the “genomic aspects of P-cell development”.

As a result of the “Fugu P-cell prediction paper”, now I am Section Editor of the Journal “The Cerebellum” – and even have been commissioned for a “Special Issue” since we’ve eagerly awaited that the trend we set would, indeed, take off. Do you think that your separate/joint manuscripts after a week of gathering new data might be ready for my expedited review by Labor Day?

Would be super …

pellionisz_at_junkdna.com

Comment #192033

Posted by Andrea Bottaro on August 3, 2007 11:40 PM (e)

Dr. Pellionisz:
before you get people to do the hard work for you, you must make predictions that are not as shifty and ambiguous as you have done so far, to make it worth the while. Let’s start with these 3:

- If one provided actual species, their genome’s C-values, and some objective measurement of Purkinje cell morphology (in other words, much more information than provided in your fugu paper), what would be your prediction of the expected correlation? Be specific, please.
- Also, I am still trying to get you to commit to say something with regard to P-cells in lungfish, salamanders etc, which should really stand out with respect to P-cell arborization given their massive genomes. What do you think they look like? Will their arborization be, say, 10-fold higher than human? 30-fold?
- And if I gave you C-values of, say, 3 or 4 vertebrate genomes, could you align them in order of Purkinje cell complexity, without knowing the species beforehand?

You gotta give us something, otherwise it’s a pointless exercise. So far, the information Aryaman provided (several of the species names he provides are correct, by the way, and I have a few more) already clearly contradict your hypothesis, so you’ve got kind of a hole to climb out of.

There is actually a lot of information out there, although strangely almost none of it is included in your paper.

Comment #192272

Posted by Andras Pellionisz on August 4, 2007 5:38 PM (e)

Dr. Bottaro,

My heartfelt congratulations that we resuscitated your PT thread to the level of scientific cooperation, well under way with “protocol design”. This is really something! Such a phenomenon does not happen in every blog, though the scientific goal is (should be) identical in our PostModern times of Genomics (towards Post-ENCODE Genetics, PostGenetics).

I hope you realize that as in any algorithmic approach in PostGenetics, there is much more to FractoGene than the “minimum program of the Purkinje cell of the Danio” (that you deemed as doable swiftly). We wrote in the paper that “The Danio results … and other comparison are expected to blossom as a new branch of research”. I am happy that it really looks like this is the case.

Some “more global” answers will also be apparent from my deeper answer to Aryaman, but all PT bloggers should also be familiar with the “Onion Test” by T. Ryan Grigory - noting that the Purkinje brain cell is only one of the conspicuous platforms to FractoGene application. While the “Purkinje cell” prediction of FractoGene does not apply to the onion, the “Methylation Prediction of FractoGene” does.

Therefore, while with Dr. Simons we have already (from his viewpoint, quite heroically) pioneered the trail, for reaching highs of “full vistas” the types of “PostGenetics Centers” would ideally be required that integrate biology, statistics, computer science, mathematics, physics, and engineering and span from plants through bacteria to mammals, such as the undeclared but de facto emerging “PostGenetics Center” at Duke; www.junkdna.com/#duke_igsp

Since there is competition around, we better follow-up in private emails with specific plans. Nonetheless, abbreviated public answers to your 3 questions can be given as follows:

[AB] (1) “If one provided actual species, their genome’s C-values, and some objective measurement of Purkinje cell morphology (in other words, much more information than provided in your fugu paper), what would be your prediction of the expected correlation? Be specific, please”

As for specifics, I am sure you will correct your oversite that the “fugu paper” is closely coupled to my fractal modeling going back 17 years

fractogene.com/89_fractal/89_fractal.html

where I have long provided the “objective measurement of Purkinje cell morphology” (reducing “complexity” to levels of fractal hierarchy of e.g. a Lindenmayer-string fractal). If you (or others) would like to tackle e.g. the zebrafish P-cell, the “piece of cake” Golgi-staining might be entirely skipped to provide computer modeling of P-cells as I did since 1973, or like in more contemporary form; what DeSchutter et al. honed into a mastery: See #21 in the references of the “fugu paper”. Their prep was based on fluorescence-studies, concluding in a computer-reconstruction (of the guinea-pig PC), albeit they have not proceeded (yet) to fractal modeling and on. They might (have) at any time.

If even such a “laser-beam focused” mini-project is doable by an Assistant Professor in a Department of Medicine, you can tell better.

Since I suspect that you are determined to tie my integrity to integers, looking at my Figs. 3-4 in the “Fugu” paper, it appears that the Fugu (B in Fig. 4) is comparable to the “fractal template level” , while the Guinea Pig (E? – now established!) is comparable to the “fractal model, level 3” on Fig. 3). The Human PC is comparable to a level between 4-5 on the curve. (Sharply note that I did not imply “linearity”).

[AB (2) – “Also, I am still trying to get you to commit to say something with regard to P-cells in lungfish, salamanders etc, which should really stand out with respect to P-cell arborization given their massive genomes. What do you think they look like? Will their arborization be, say, 10-fold higher than human? 30-fold?”

No, I don’t think so. Andrea, are you also inclined to press me to commit myself to the P-cells in the Onion? – since the onion is part of what used to be the “C-value enigma”. In most (all) cases, we really don’t know if just one particular cell is the cause of the excess, and if that were the lucky case, which cell(s).

Sorry, the poor onion does not have a cerebellum (“invented” for the shark and on)… In science, one strives to find out first the rule (cf. Galileo’s planetary system centering NOT around the Earth) and then it is much easier to conclude on aberrations (e.g. finding Pluto).

If you insists on hearing my opinion on e.g. the Mormyrid P-cell (I know how they look like…), I don’t think that their level of fractality is high, at all. Since I happen to have a mathematical theory of the cerebellar function (TNT, yes, with predictions experimentally confirmed), I suspect that the electric fish operates its sensorimotor transformation not merely in the 4-dimensional Minkowski space-time manifold (under visual sensory control, as e.g. we do), but involving a much broader sensory-frequency-range (imagine including all ultraviolet and infrared domains of electromagnetic waves), and thus the P-cell needs a much higher number of parallel fibers (and thus, much higher number of granule cells) compared to cerebella at similar advancement in the phylogenetic ladder. Likewise, I don’t think that the exceptions in genome-size of lungfish, some frogs, different salamanders is likely to do either with the cerebellum in general (and thus, not with the Purkinje cell). It is much more likely, that these excesses reflect on the specifics of metamorphosis of various sub-species.

It is quite possible, however, thus well-worth of the chase, that we’ll succeed to “hit on a PC” with excessive fractality of one sub-species over another, and connect it directly to their differences in specific regions of (formerly) “junk DNA”. That will be a good time to open champagne. Kindly note that this rather deep question has to do with the “multifractal” as opposed to “monofractal” nature of vertebrate organisms. (I already have some leads on the onion, but, again, that can not involve any cerebella or Purkinje cells…)

[AB (3) – “And if I gave you C-values of, say, 3 or 4 vertebrate genomes, could you align them in order of Purkinje cell complexity, without knowing the species beforehand?”

If they represent “the rule”, yes. If they represent exceptions (see above) most likely not.

The “triangulation effort” is extremely important in either case. All blog readers will sharply note, that there are a good number of rather different cells in higher-order organisms (a “multifractal”). If development of the “trunk” or “hat” should “mushroom” in various cases, is exciting and useful target of research. Wherever there is a “peak” of excessive reverberate iterations (requiring, according to FractoGene, see also “Methylation prediction” the picking up of “auxiliary information lurking in what used to be ‘Junk DNA’”) I would immediately like to track it down “who – amongst the many - is/are singing such a long song”. This, however, will need tons of more Genomics (of the PostGenetic kind). At this point, we barely know even how the “genes” would “grow” a normal Purkinje neuron – let alone our very initial actual knowledge of the roles their intronic and intergenic regions play in physiological and/or pathological growth.

I said “very initial”. Of course, our knowledge is not equal to zero. For instance, the well-known intronic GAA triplet-repeat that is known to be the cause of the Friedreich Spinocerebellar Ataxia (a lethal hereditary syndrome, a veritable “Junk DNA disease”) has already been identified by FractoGem Miner as a fractal defect “in the junk” of X25.

There is a lot in any new approach. I am more than willing (delighted!) to share in proper formats.

pellionisz_at_junkdna.com

Comment #192294

Posted by Andrea Bottaro on August 4, 2007 7:27 PM (e)

[AB] (1) “If one provided actual species, their genome’s C-values, and some objective measurement of Purkinje cell morphology (in other words, much more information than provided in your fugu paper), what would be your prediction of the expected correlation? Be specific, please”

As for specifics, I am sure you will correct your oversite that the “fugu paper” is closely coupled to my fractal modeling going back 17 years

fractogene.com/89_fractal/89_fractal.html

where I have long provided the “objective measurement of Purkinje cell morphology” (reducing “complexity” to levels of fractal hierarchy of e.g. a Lindenmayer-string fractal). If you (or others) would like to tackle e.g. the zebrafish P-cell, the “piece of cake” Golgi-staining might be entirely skipped to provide computer modeling of P-cells as I did since 1973, or like in more contemporary form; what DeSchutter et al. honed into a mastery: See #21 in the references of the “fugu paper”. Their prep was based on fluorescence-studies, concluding in a computer-reconstruction (of the guinea-pig PC), albeit they have not proceeded (yet) to fractal modeling and on. They might (have) at any time.

If even such a “laser-beam focused” mini-project is doable by an Assistant Professor in a Department of Medicine, you can tell better.

Since I suspect that you are determined to tie my integrity to integers, looking at my Figs. 3-4 in the “Fugu” paper, it appears that the Fugu (B in Fig. 4) is comparable to the “fractal template level” , while the Guinea Pig (E? – now established!) is comparable to the “fractal model, level 3” on Fig. 3). The Human PC is comparable to a level between 4-5 on the curve. (Sharply note that I did not imply “linearity”).

OK, I take this to be your statement that an objective measure of P-cell fractal properties, using a suitable methodology (e.g., from a peer-reviewed paper), in a suitable series of organisms (vertebrates, of course, with genomes of not particularly unusual size - see below) should positively correlate with their genome’s C-value? Can we finally nail down this prediction of yours, and move on to test it? A simple yes or no will suffice.

[AB (2) – “Also, I am still trying to get you to commit to say something with regard to P-cells in lungfish, salamanders etc, which should really stand out with respect to P-cell arborization given their massive genomes. What do you think they look like? Will their arborization be, say, 10-fold higher than human? 30-fold?”

No, I don’t think so. Andrea, are you also inclined to press me to commit myself to the P-cells in the Onion? – since the onion is part of what used to be the “C-value enigma”. In most (all) cases, we really don’t know if just one particular cell is the cause of the excess, and if that were the lucky case, which cell(s).

Sorry, the poor onion does not have a cerebellum (“invented” for the shark and on)… In science, one strives to find out first the rule (cf. Galileo’s planetary system centering NOT around the Earth) and then it is much easier to conclude on aberrations (e.g. finding Pluto).

If you insists on hearing my opinion on e.g. the Mormyrid P-cell (I know how they look like…), I don’t think that their level of fractality is high, at all. Since I happen to have a mathematical theory of the cerebellar function (TNT, yes, with predictions experimentally confirmed), I suspect that the electric fish operates its sensorimotor transformation not merely in the 4-dimensional Minkowski space-time manifold (under visual sensory control, as e.g. we do), but involving a much broader sensory-frequency-range (imagine including all ultraviolet and infrared domains of electromagnetic waves), and thus the P-cell needs a much higher number of parallel fibers (and thus, much higher number of granule cells) compared to cerebella at similar advancement in the phylogenetic ladder. Likewise, I don’t think that the exceptions in genome-size of lungfish, some frogs, different salamanders is likely to do either with the cerebellum in general (and thus, not with the Purkinje cell). It is much more likely, that these excesses reflect on the specifics of metamorphosis of various sub-species.

Well, I did not mention onions at all here. Indeed, onions, amoebas, and thousands upon thousands of other organisms with very large genomes do not have cerebella, which is kind of a snag for your model. But anyway, while I take notice that you now agree your hypothesis does NOT address the “onion test” after all, what I really was getting to was vertebrates. Indeed, vertebrates that are phylogenetically closer to mammals than fugu is. (Invoking metamorphosis seems rather ad hoc, frankly, since most organism that undergo metamorphosis do not have particularly large genomes. You are not claiming that DNA fractality is generally associated with metamorphosis, right?)

Regardless, by refraining from making any prediction in this case, I assume you are saying your model does not apply to vertebrates with unusually large genomes either. In other words, it can pass neither the “onion test” nor the “lungfish test”. Although it’s unclear to me why the model should still apply to vertebrates with unusually small genomes (like fugu), I’ll take you at your word, and move on.

[AB (3) – “And if I gave you C-values of, say, 3 or 4 vertebrate genomes, could you align them in order of Purkinje cell complexity, without knowing the species beforehand?”

If they represent “the rule”, yes. If they represent exceptions (see above) most likely not.

Well, then, what is the rationale for considering some organism a “rule”, and another an “exception”? Why isn’t fugu, or zebrafish, an exception? Why isn’t lungfish the rule? You gotta be more specific on this, before we proceed.

Comment #192296

Posted by Andras Pellionisz on August 4, 2007 7:32 PM (e)

Some truly important points made by Aryaman Shalizi:

“I fail to grasp the rationale behind focusing on the morphology of the Purkinje cell, other than the fact that Mandelbrot said it looked like it was fractal and could be amenable to analysis using non-Euclidean geometry. So what?”

“I have no problem with the idea that some sort of scaling or power laws or fractal dimensions may be involved in animal morphology and metabolism (In fact, I really like some of the work in this area…)

[AJP] I composed a “longhand” answer, but in reference to the last and most fundamental comment I would really like first to know the feedback from Aryaman to the article (and my comments) at:

http://www.junkdna.com/#biology_unified

Some more detailed reflexions [AJP]

The first (“why Purkinje”) is a good question, since Aryaman (unfortunately for his interests) failed to grasp the important rationale of picking the Purkinje neuron as an excellent, perhaps the best, “platform” for “triangulation of genomics, morphogenesis and biophysics”. (There may be an “Onion cell” equivalent to Purkinje and/or Red Blood Cells – neither existing in plants. I have some leads but the story is not ready to print).

The second (“so what”) is also a pithy question, though a bit unnatural and quite foreign to Aryaman, as it sounds as a crudely phrased red-neck “bottom-line” question, like “what is in it for me?” “So what if we find non-Euclidean geometrical laws governing DNA structure and function”? Decide for yourself…

The last comment is by far the most important; “mathematical scaling laws ruling morphology and metabolism”.

Starting with the most important, it seems too bad that those obsessed with the “rule of random” usually are not very mathematically minded. This is a problem for biology. When mathematics becomes a barrier rather than an invitation, what you usually get is a lot of data – yet little understanding.

Since Dr. Shalizi knows a few things about cerebella, it is mostly for other bloggers to mention that the Purkinje neuron (of the cerebellum) is usually the biggest kind of brain cell. Why is that important? For instance, because of his most substantial comment (“metabolism”). It should strike learned bloggers that both the red blood cells that show best the correlation with C-value, as well as the Purkinje cells, are “metabolically distinguished”. However, it should also be clear to the mathematically minded (as pointed out in our paper) that “most animals are not a single monofractal, as appears to be the case in some simple plants, but are almost certainly multifractal. This seems evident from the different fractal properties of their separable organelles (lung, coronaries, intestines, etc.) Therefore, the FractoGene concept might have to be augmented with novel methods of sequence analysis” (after publication signaled in www.fractogem.com and www.fractoset.com).

Aryaman further asks:

What does FractoGene … predict
[1] about other kinds of neurons? What predictions does it make about the relatively invariant morphology of, for example, cerebellar granule neurons, the single most numerous class of neurons in the central nervous system, which have an almost invariant morphology in all species that have cerebella? What predictions does FractoGene make about the structure of cortical pyramidal cells, which also show a much lower degree of morphological variation?

[AJP] See “Methylation prediction of FractoGene” – it is not limited to Purkinje neurons at all.

[2] about biological structures that do NOT have a fractal-like appearance?

[AJP] First of all, that it may be worth looking if the appearance is NOT OBVIOUSLY fractal-like, nonetheless hidden fractal properties (and rules) may be lurking beneath… (People who already swung to the other extreme from “what a nonsense” to “everybody knew all along it was fractal”, usually ask me: “tell me one thing that is NOT FRACTAL in Nature”… Same story, different attitude…)

pellionisz_at_junkdna

Comment #192321

Posted by Andras Pellionisz on August 4, 2007 9:20 PM (e)

Dr. Bottaro:

You seem to be a good model of a “repetitive iteration” that converges very slowly. (Probably somebody else will do the zebrafish prep, though “it only takes a week for a grad student”).

Again (FractoGene Simplied):

PROCESS: Repetitive iteration to build fractal organelles by perusing fractal DNA information, including that in the “Junk”.

PLATFORM: Show the above to build a fractal Purkinje cell (Normal Purkinje cells shown, Onion, Lungfish etc. cells not shown)

RULE: Such fractal recursion iterates (converges to full grown status), taking an amount of “junk” that correlates with the number of recursions. (Purkinje cells shown in “fugu paper”)

EXCEPTION: Same recursion, with (small) changes of fractal process parameters can peruse excessive “junk” if repetitive iteration converges S.L.O.W.L.Y.

PROCESS passes Onion, Salamander, Lungfish tests with some (unknown) cell(s) taking excessive recursions to build.

CONSEQUENCE: It is unlikely that the Purkinje cell causes the excess in lungfish, frogs, salamandra, etc. but very possible that the Purkinje cell growth, as an illustration of the RULE, might be found in some sub-species as excessively slow to build (EXCEPTION).

LESSON: If one wants to go for the “quick and easy”, do the zebrafish PC (“satisfaction guaranteed, or your money back”).

Those with ambition and talent in
(a) Vertebrate research; identify PC with excessive fractality, requiring excessive recursion (and thus, “junk DNA”).
(b) Plant research; identify the cell(s) requiring excessive recursions to build.

Those with ambition and talent in
© aiming to pump more, pretending an ill-understanding; realize that it does not work with everyone.

pellionisz_at_junkdna.com

Comment #192427

Posted by Andrea Bottaro on August 5, 2007 7:52 AM (e)

Dr. Pellionisz,
I wrote:

OK, I take this to be your statement that an objective measure of P-cell fractal properties, using a suitable methodology (e.g., from a peer-reviewed paper), in a suitable series of organisms (vertebrates, of course, with genomes of not particularly unusual size - see below) should positively correlate with their genome’s C-value? Can we finally nail down this prediction of yours, and move on to test it? A simple yes or no will suffice.

You replied with 255 words, saying nothing to the effect that you are going along with this prediction. Do you? Don’t you? The advantage of this is that the data are already publicly available, so we could get an answer right away. Please provide a straight reply.

As for your comment, I still don’t get it: assuming nobody knows what Purkinje cells look like in salamanders and zebrafish, what is the actual, rational basis for your claim that salamanders will be the exception, and zebrafish the rule, to your prediction? This is crucial: let’s say we do the experiment and find that, contrary to your prediction, zebrafish have primitive PC arborization, and salamanders ultra-developed arborization, what will prevent anyone from then claiming that zebrafish must be the exception, and salamanders the rule?

Again, this is important with regard to the 3rd prediction highlighted above: if you tell us what makes an exception and what a rule, we can exclude the exceptions beforehand and just focus on a set of organisms that should, according to this yet unstated parameter, conform to the rule, and see if they indeed do.

I am trying to flesh out your predictions in an empirically testable fashion, but you don’t seem to budge.

Comment #192675

Posted by Andras Pellionisz on August 5, 2007 10:30 PM (e)

Dr. Bottaro:

Just because this thread is yours and I am a guest I don’t think you should feel entitled to interrogate me in a manner demanding “yes or no” answer to what is your re-phrasing of what I said. When quoting me, after you say “I take this to be your statement” please kindly apply a full stop. Rather not re-phrase, if you can resist.

From plenty direct communications I am getting, it is clear to me that most people agree with your (correct) opinion that Golgi-testing the zebrafish (Danio) PC is an easy game – and thus will be done swiftly (though for reasons I will not touch on in this public posting, most likely not by you).

In fact, our “Fugu paper” stated that:

“…we were curious to examine P-cell presence and dendritic complexity in Fugu and Danio. That study is to be reported separately (33). The authors have permitted us to refer to their results as “unpublished observations” for the Fugu. The Danio results (only partially available) and other comparisons are expected to blossom as a new branch of research”. [Fugu paper]

Readers will appreciate, however, that (especially regarding “other comparisons”) there is much more to a proper study by a Hungarian-Japanese joint program than coming up with a Golgi-stained Danio P-cell (as a preliminary result, I have seen *that*). Readers might come to the conclusion on their own (thus, after a sufficient lead-time, I don’t have to unduly jeopardize their publication priorities) that actually *two* curves have to be first plotted, and after curve-fitting (the customary way to tell apart what is “rule” and what is “exception”) the curve of the C-values of sequenced genomes along the emergence of species and the curve of “bifurcation levels” of the fractal models of P-cell over the axis of same sequenced species need to be compared. An appropriate time to open champagne is when particular species (in even luckier cases, sub-species) are found that yield exception in *BOTH* curves.

After the champagne will come some additional and even harder work - to plunge into genomic analysis of the P-cell of “particular (sub) species”. The latter is not totally unlike in the paper *you* appear to be a co-author, see your Fig. 3:

www.pnas.org/cgi/content/full/97/7/3336

but in reverse, what physiological *OR* pathological genomic causes may lie beneath an exception. (What FractoGene could help with interpretation of your data goes way beyond the limits of a blog).

Contrary to your superficial notes, exceptions both in the positive and negative domain are most significant. The positive excesses will substantiate not only the proposed explanation by PROCESS but also actual species to pin down the culprit cell(s) for excessive reverberate iteration (onion, salamandra). Negative excesses may indicate unduly “stuck” (pathological) recursion. When considering that such cell(s) may or may not be best found for PC-s, the above program is obviously of substantial size, since it may span from P-cells of vertebrates to cells of plants (onion). Since the full protocol entails morphology, fractal modeling, bioinformatics, physiology, pathology and genomics, as mentioned earlier, the entire project is best suited for a “Center of PostGenetics” (similar to the quoted new Ctr at Duke).

There is much more to planning a protocol (especially in competition with an ongoing one…), thus to protect interests my preference is direct communication - unless one enjoys posturing under pretexts of a (not so) hidden agenda.

pellionisz_at_junkdna.com

Comment #192690

Posted by demallien on August 5, 2007 11:43 PM (e)

Andras, you’re waffling. Andrea’s question was very fair, and very pertinent to the discussion. Until you answer it, you have effectively proposed an unfalsifiable theory, with all possible results being acceptable. We don’t like those much around here.

So please, in a nice, succint, answer can you please respond to Andrea’s question? Or shall we lump you in with all the snake oil merchants that come through this site?

Comment #192897

Posted by Andras Pellionisz on August 6, 2007 11:39 AM (e)

“demallien”

You don’t seem to be a scientist. Do you think we in a “Kangaroo court” with the infamous “did you stop beating your wife, answer with YES/NO?”- types of “fair questions” by lawyers trying to nail true scientists? Scientists accept all experimental data – and define their role not to arbitrate the facts but explain them.

“demaillien”, what the heck do you mean by a “criticism of a scientific theory” for which “all possible results [are] acceptable”??? If a theory does not accept all experimental results (e.g. rejects proof of obvious non-randomness and by ignoring evidence continues to pretend that the vast majority of the DNA is “Junk”), in my eyes is not a theory, but a dogma. Count in this thread entries still denying role to “Junk DNA” beyond ENCODE evidence to the contrary. We have sadly witnessed what “kindergarten debates” ensue if e.g. this thread is based not on science but dogmatism in PT.

Non-scientists can enjoy the only thing they are good at; “name calling” in PT (in that case, I don’t belong here). Scientists of PT (who can be counted on the fingers of a badly injured single hand) face a colossal dilemma. Accept *all* experimental data (and explain them!) and go wherever they take us (regardless of hidden or not so hidden ideological agenda) - or trivialize science to make room for ideology (but in that case “scientists” will lose their credibility in science).

Dr. Bottaro should know better from *his* own pieces of evidence in science that “Junk DNA” not being “junk” leads all scientists to far more pertinent, better questions than what emanates from his leaning to trivialization in PT.

Dr. Bottaro readily acknowledged that the “Danio-test” (as a first cut) is “doable by a grad student in less than a week”. Why doesn’t he “just do it” but let others lead science studies?

I have two explanations, one should remain not declared. The other is that knowing his paper (cited above) I purposefully mentioned the FractoGem as a fractal defect in the intronic region of the X25 gene, as a cause of a well-known “Junk DNA disease” of Friedreich’ Spinocerebellar Ataxia.

Dr. Bottaro’s cited paper shows (his Fig. 3, bottom right corner of panel D) a gross dendritic aberration of a Purkinje cell in their paper on Ataxia Telangiectasia (another “Junk DNA disease”). Given the scientific importance of the topics (both FSA and AT), instead of leaning towards trivialization, IMHO Dr. Bottaro would have publicly (or, more likely, via private e-mail) wonder about the possibility if AT as a “Junk DNA disease” may be caused by a similar fractal defect as in the case of the Friedreich’ Spinocerebellar Ataxia - if he was serious.

Because an answer to the “so what about FractoGene” (applied to cerebellum, etc) question of Dr. Aryaman Salizi may, for any of us, be a life-or-death matter, see

www.junkdna.com/junkdna_diseases.html

(while the sheer fractal appearance of the dendritic arbor of the Purkinje cell is something that most people are justifiably unlikely to care about).

I have provided not a trivialized “one curve” but a more appropriate experimental protocol of *my theory* of “two curves” (with “rules” and “exceptions” according to customary curve-fitting). Too bad (for them) that non-scientists might not understand even the basics. Great for scientists who are already on their way towards novel and clear goals.

I am open.

pellionisz_at_junkdna.com

Comment #192977

Posted by Henry J on August 6, 2007 2:58 PM (e)

Well, speaking as another non-scientist, I don’t see how establishing that a stretch of DNA has a fractal pattern would establish that it also has some function. Fractal patterns as I understand them are caused by repetitive additions or insertions, which could be random (i.e., genetic drift). But I suppose I could be missing something.

(Of course, fractal by random addition could still (afaik) cause genetic disease, since for something to cause problems doesn’t necessarily require that it had a useful function prior to causing the problem.)

Henry

Comment #193051

Posted by Andras Pellionisz on August 6, 2007 5:54 PM (e)

Henry,

It is great to have bona fide non-scientists around, to explore how people think about “junk DNA”.

In principle, you are quite right to guess that “for something to cause problems doesn’t necessarily require that it had a useful function prior to causing the problem”.

I can answer using your earlier posting “…with more space there’s less detrimental effect of having unneeded stuff, so more junk accumulates” (to which somebody answered not to invite you to his garage).

Sure, you can have stuff crowding your garage that never served “useful function”. In practice, however, under Darwinian theory, you should then expect to drop out with your jeopardizing excess of junk (e.g. drop dead as you trip over stuff, or at least pay painful mortgage for space you can’t use); see Darwinian argument in 1987 by Malcolm J. Simons that compelled him to obtain his patents.

Since Malcolm is widely known to be affected by a “Junk DNA disease” himself, after having pinned down that “junk was anything but” he is motivated having already spent two decades to finding out the best approach to what might exactly be the function that Darwinian theory actually required.

Thus our collaborative work (e.g. “fugu paper”, etc.)

pellionisz_at_junkdna.com

Comment #193098

Posted by Henry J on August 6, 2007 8:36 PM (e)

Re “In practice, however, under Darwinian theory, you should then expect to drop out with your jeopardizing excess of junk […]”

Yeah, if reproducing the junk uses up a significant amount of resources, or if the junk interferes with some function - which apparently it sometimes does, but also apparently not all that often?

Presumably there’s a balance in there somewhere, natural selection removing actual junk, vs. insertions, duplications, and maybe other mutation types, adding it. I guess the question is where does one expect the equilibrium between those to be reached, and how quickly.

Henry

Comment #193107

Posted by Andras Pellionisz on August 6, 2007 9:12 PM (e)

Henry says (about the dropout of Junk required under Darwinian theory):

“Yeah, if reproducing the junk uses up a significant amount of resources, or if the junk interferes with some function - which apparently it sometimes does, but also apparently not all that often?

Presumably there’s a balance in there somewhere, natural selection removing actual junk, vs. insertions, duplications, and maybe other mutation types, adding it. I guess the question is where does one expect the equilibrium between those to be reached, and how quickly.”

[AJP] “How quickly”??? - How about not even in half a Billion years?

“Ultraconserved elements” are among the strongest arguments that if mother Nature did not drop out “junk” - they are likely to have function, e.g. to play key regulatory roles in vertebrate gene expression.

Just for one example, see the non-coding sequences conserved over half a Billion years (picture is worth a hundred word):

http://www.junkdna.com/2006.html#ancient_noncodi…

“We generated ~1.4x genome sequence coverage for a cartilaginous fish, the elephant shark (Callorhinchus milii), and compared this genome with the human genome to identify conserved noncoding elements (CNEs). The elephant shark sequence revealed twice as many CNEs as were identified by whole-genome comparisons between teleost fishes and human. The ancient vertebrate-specific CNEs in the elephant shark and human genomes are likely to play key regulatory roles in vertebrate gene expression”

Don’t blame me for such a finding and interpretation. The last 3 of the 12 authors were:

J. Craig Venter, Robert L. Strausberg, Sydney Brenner [yes, the same Sydney Brenner…]

pellionisz_at_junkdna.com

Comment #193135

Posted by Henry J on August 6, 2007 10:13 PM (e)

Re “[AJP] “How quickly”??? - How about not even in half a Billion years?”

That was how quickly would the two opposing effects reach equilibrium. Not how quickly natural selection would it wipe out unnecessary DNA sequences; if various effects are continually generating more such sequences, it won’t.

I don’t doubt that there’s some function in sequences for which function was not previously known; as far as I know, nobody expects that all functional sequences would have been identified already.

Henry

Comment #193180

Posted by Andras Pellionisz on August 7, 2007 12:08 AM (e)

Henry said:

“I don’t doubt that there’s some function in sequences for which function was not previously known; as far as I know, nobody expects that all functional sequences would have been identified already”

Perfectly agreed. We rest our case.

Henry seems to be a very good (“fast converging to the facts”) case where even a “non-scientist” is likely to be convinced by hard evidence, that e.g. himself or a loved one, if suffering from a “junk DNA disease” should be helped by fast accelerated R&D in this field - regardless of ideology.

pellionisz_at_junkdna.com

Comment #193183

Posted by demallien on August 7, 2007 12:10 AM (e)

Andras,
Again, rather than answering the relatively simple question that Andrea has put to you, you chose to waffle and blither. Not a good sign.

What I don’t get is that you have come here to try and convince us by argument. We’re all rather more inclined to the scientific way of doing things here. You know, hypothesis, experiment, conclusion. I would expect that any scientist when faced with disbelief of his/her theory, would simply go out and do the necessary experiments to show that the theory is true (or false, if the doubters were right). You on the other hand try to convince people by badly expressed argument. That dog won’t hunt.

So, Mr Arrogant, go away, do some work, and publish the results. We might be more convinced by your stories afterwards.

Anyway, I don’t get what your point is. Although I am no biologist, I use genetic algorithms for my work, and have studied my Kimura and Kauffman, more so than you by all evidence. I certainly don’t know where anyone would get the idea that “junk” DNA had no purpose (ps, I thought that scientists had decided “junk DNA” was no longer the preferred expression). Genetic drift in particular would be impossible without it, and yet Kimura has shown the importance of this mechanism to evolution.

Furthermore, if rather than being an arrogant know-it-all, you had instead done some basic research on the various positions of commentators on this blog, you would know that we often regret the existence of the term “junk DNA”. You see, each time someone discovers some function in “junk DNA”, the creationists go wild, claiming, just as you do, that this disproves Darwinian evolution. And each time we have to explain that “junk DNA” just meant that the DNA in question doesn’t code for proteins, not that it can’t have any function whatsoever.

Please Andras, fell free to pull you head out of your arse, and go and do some work so that you can at least clearly respond to some of the more obvious question marks that hang over your theory. Until then, I for one shall be filing your word salads under the heading “snake oil merchant”.

Comment #193490

Posted by Andras Pellionisz on August 7, 2007 3:24 PM (e)

Anonymous “demallien” wrote (readers will note that he/she is the last remaining “name-caller” comfortably hiding behind anonymity):

“…if … you had … done some basic research on the various positions of commentators on this blog, you would know that we often regret the existence of the term “junk DNA”..”

[AJP] It did not escape my attention that “Junk DNA” as a scientific term, that finally collapsed with ENCODE, will ruin all those who used it as a shield of mud-throwers. Many are still stuck underneath the rubble and keep exercising a kindergarten behavior - perhaps because of the trauma. “Demaillien”, don’t you realize that people are dying of “junk DNA diseases” while you still engage in hardly anything better than “name calling” at the level of a 5-year old child? Have you got any decency left? Why don’t you have the guts to say “yes, not only I regret the existence of the term “Junk DNA” but I am sorry that I am still in the way of those who rush to help those suffering from “Junk DNA diseases””?

Anonymous “demallien” says:

“I don’t get what your point is. Although I am no biologist, I use genetic algorithms for my work… I certainly don’t know where anyone would get the idea that “junk” DNA had no purpose (ps, I thought that scientists had decided “junk DNA” was no longer the preferred expression).”

[AJP] Now we are talking. (See, you could do a whole lot better than childish name-calling).

I am - in addition to a “PostGenetics Evangelist” here on PT - also one who pioneered Neural Networks (in an earlier paradigm-shift; you may have still been in the real kindergarten when I already did quite a bit of R&D, now turning to its 5th decade.. why don’t you check out the accomplishments of those that *you* criticize?)

Thus, I know quite well that workers of “Genetic Algorithms” are very well in tune with, and shall profit from, my efforts towards “Algorithmic Design to DNA approach”. “Genetic Algorithms” (yes, there are “fractal genetic algorithms“) together with Neural Networks will do wonders on the scorched land of what used to be “Junk DNA” - the 98.7% of human genome. Why don’t you discover the great opportunity (“don’t bite my finger, look where I am pointing”)???

I am proposing that all those under the shattered remnants of “Junk DNA notion” could escape to “Algorithmic Design of DNA”. It is something that even *you* can better use than to be stuck with those still crying “Junk DNA” and throwing mud on those who actually help getting over your problem.

Since you are “no biologist” it does not surprise me that you are ignorant not only of my accomplishments, but apparently never even read Dr. Ohno’s 3.5 page short abstract “So much junk in the human DNA” (1972) originating the concept that we have just buried. Kindly take the time to read the “Obituary of Junk DNA” at

http://www.junkdna.com/#obituary_of_junk_dna

Comment #193584

Posted by Torbjörn Larsson, OM on August 7, 2007 8:41 PM (e)

Andras Pellionisz wrote:

Scientists accept all experimental data – and define their role not to arbitrate the facts but explain them…. Scientists of PT … “scientists” will lose their credibility in science

Your attempts to high-jack all sorts of scientists as being representative of biology is revealing of your motives, as is your attempts to turn away the discussion from moving beyond untested suggestions of correlations.

The biologists among us know the facts, and we want to use them to arbitrate the explanation (theory). You have had room to explain yourself at length, but when Andrea Bottaro challenge your theory to give a simple prediction you feel interrogated. You seem to feel it is about your oh so important to guard research, while it could as well be tests with known data.

You even feel so threatened that you unfairly label Bottaro’s question as unscientific when it is repeated by non-scientists. (Again, the intentional confusion - you mean not knowledgeable biologist.)

The impression you give is that your theory can’t answer simple questions that data should explain. If that is the impression you want to make here, fine. Just don’t go around in the process and throw around silly and erroneous characterizations of other scientists and sciences.

(Oh, and stop jumping on laymen members of the blog discussion - this blog is for all interested, and not acknowledging that makes your efforts seem silly there as well.)

Comment #193661

Posted by Andras Pellionisz on August 7, 2007 11:09 PM (e)

Lay people will remember:

1) Junk DNA as non-functional stuff is history
2) Anyone of us can get sick or die because of “Junk DNA” glitches
3) Those clinging to the notion of useless Junk (scientists or not) don’t do us good service – and badmouthing is an outright disqualification
4) There are algorithmic approaches to explain function beyond 1.3% (“beyond genes”)
5) “Simple tests” for a leading one can be done in 1 week by a grad student (zebrafish PC)
6) Testing and refining competitive approaches will take significant resources and time and thus intellectual property is, and increasingly will be, a key factor

Specialists in the field already know:

1) Designing competitive research protocol is not a blog issue. Peer-reviewed science publications are appropriate public means, while already ongoing and developing collaborations are arranged directly
2) PostGenetics Centers are emerging (declared by name or not). Challenges are interdisciplinary and collective efforts are a must
3) The PostModern era of Genomics is disruptive, its birth is painful and entropy of the emergence is high. Pioneering, by definition, takes a lot of flak - what else is new?

Comment #193686

Posted by demallien on August 7, 2007 11:56 PM (e)

Andras wrote:

Lay people will remember:

1) Junk DNA as non-functional stuff is history
2) Anyone of us can get sick or die because of “Junk DNA” glitches
3) Those clinging to the notion of useless Junk (scientists or not) don’t do us good service – and badmouthing is an outright disqualification
4) There are algorithmic approaches to explain function beyond 1.3% (“beyond genes”)
5) “Simple tests” for a leading one can be done in 1 week by a grad student (zebrafish PC)
6) Testing and refining competitive approaches will take significant resources and time and thus intellectual property is, and increasingly will be, a key factor

And arrogant PhDs that are full of themselves will remember that science doesn’t care about titles, it cares about good ideas. I can’t help wondering if Andras would have rejected Einstein’s work out of hand - after all, what would a “lay person” working in a patent office know abut physics, right? On the other hand, as Andras has apparently discovered [snicker], a PhD won’t protect bad ideas from criticism. This is as it should be.

Specialists in the field already know:

1) Designing competitive research protocol is not a blog issue. Peer-reviewed science publications are appropriate public means, while already ongoing and developing collaborations are arranged directly
2) PostGenetics Centers are emerging (declared by name or not). Challenges are interdisciplinary and collective efforts are a must
3) The PostModern era of Genomics is disruptive, its birth is painful and entropy of the emergence is high. Pioneering, by definition, takes a lot of flak - what else is new

So why are you here boring and insulting us Andras? If blogs aren’t the appropriate forum, feel free to go elsewhere.

I note, in passing, still no data to back up the claims. Still no courage to predict what those experiments would show. Snake. Oil. Merchant…

By the way, could you please, for the love of FSM, stop repeating the strawman that science thinks that “junk DNA” has no purpose. It hasn’t been true since Kimura, which was when? 1960s? No-one here thinks that junk DNA has no purpose, no-one of a scientific inclination has thought that for a very long time, so give it up already. You won’t convince us, because we’re already convinced by the data.

Speaking of data, when are you planning on giving us some. Or even just an answer to Andea’s question would be nice. Should be easy for an expert like you, come on, amaze all of us dumb “lay people” with your PhD brilliance…

Comment #193966

Posted by Andras Pellionisz on August 8, 2007 3:56 PM (e)

Anonymous “demallien” and others still engaging in name-calling (with their hideous behavior nothing to lose) may wish to see my point: “badmouthing is an outright disqualification”.

Better yet, heed the warning by the owner of this thread:


Posted by Andrea Bottaro on July 20, 2007 9:33 PM (e)

People, this thread is depressing. Either you try to lift the tone above kindergarten-level name-calling, or I’ll just close it. It is sad that trolls can so easily derail a discussion here. They must be having a ball at our expense.

This thread fulfilled its role, anyway, since “Junk DNA as a scientific term is dead”. Long live PostGenetics; algorithmic design approaches and competitive concepts, let’s go ahead and do something for those suffering from “Junk DNA diseases”. The 60 (named) Founders and members from 34 Countries of International PostGenetics Society is a much better company with a positive agenda:

http://www.postgenetics.org

pellionisz_at_junkdna.com

Comment #194176

Posted by Torbjörn Larsson, OM on August 9, 2007 5:32 AM (e)

Syntax Error: mismatched tag 'blockquot'

Comment #194179

Posted by Torbjörn Larsson, OM on August 9, 2007 5:35 AM (e)

Andras Pellionisz wrote:

hideous behavior

Excuse me? I thought you were a PhD, and as far as I can see people have adressed you with the fair and hard dog-eat-dog style that we scientists are used to.

But so far, we are still only trying to measure up to your behavior. We haven’t yet reached the ability to overstep characterisation based on facts into fantasy.

Comment #194259

Posted by Andras Pellionisz on August 9, 2007 12:27 PM (e)

I used “hideous” according to its definition in the Merriam-Webster dictionary: “morally offensive”.

“Anonymous name-calling” (latest by “demallien”) in itself clearly falls into such category, IMHO. Those attempting to anonymously impugn the integrity of others backfires as it is only a reflection on those without merit to their “debates”. Kindergarten style is acceptable in a kindergarten but it depressed even the blog thread owner. Name-calling IMHO should be discouraged, (I credit this PT thread that it has been, not only by me), and is particularly objectionable when applied anonymously and in the interest of blocking or hindering efforts to help those uncounted millions suffering from “Junk DNA diseases”. Some of them may prove to be less forgiving than others.

pellionisz_at_junkdna.com

Comment #194323

Posted by Andrea Bottaro on August 9, 2007 4:44 PM (e)

Sorry for not keeping track of the thread, the real world intruded.

Dr. Pellionisz:
it is obvious, and too bad, that you are unwilling to subject your hypothesis to meaningful testing. I do see why, however, since there is already considerable data out there that does not conform to your predictions. In addition to the data and links provided above by Aryaman Shalizi in a comment above, I will just point out to another interesting tidbit, in the paper by TG Smith et al, “Quantitative Phylogenetic Constancy of Cerebellar Purkinje Cell Morphological Complexity”, J Comp Neurol 331:402-406, 1993. It reports the quantitative analysis of Purkinje cell fractality in a number of placentates, one marsupial and two bird species, showing that fractal complexity is essentially identical in these species. C-values varies in these critters by about 3-fold. I found this paper particularly informative because it used objective quantification of the parameters in question, as opposed to just showing examples of supposedly representative P-cells (which of course raises the issue of observer bias, statistical significance, etc).

Anyway, to be entirely frank, in addition to your unscientifically secretive and prickly attitude, and your tendency to misrepresent existing evidence (I see you are still mischaracterizing the significance of the ENCORE findings, even after we have gone through them point-by-point), it is clear that your hypothesis, devoid as it is of a mechanistic basis and of significant predictive powers with regard to the existing evidence, has a tough hill to climb before it is taken seriously, so I wish you good luck with those endeavors.

Oh, one more thing. You stated:

Dr. Bottaro’s cited paper shows (his Fig. 3, bottom right corner of panel D) a gross dendritic aberration of a Purkinje cell in their paper on Ataxia Telangiectasia (another “Junk DNA disease”). Given the scientific importance of the topics (both FSA and AT), instead of leaning towards trivialization, IMHO Dr. Bottaro would have publicly (or, more likely, via private e-mail) wonder about the possibility if AT as a “Junk DNA disease” may be caused by a similar fractal defect as in the case of the Friedreich’ Spinocerebellar Ataxia - if he was serious.

I am serious, and I don’t need to wonder: I can actually go to the existing database of AT mutations, and check them out myself (as can you, by the way, but apparently don’t). As far as I can see, all known mutations in the ATM gene affect protein expression or structure, causing amino acid substitutions or truncations.

I will leave the thread open until the weekend, in case you want to reply, but I agree with you that it has fulfilled its role. I am particularly pleased that you now agree that a strict interpretation of Darwinian theory would predict that “junk DNA” should not exist:

In practice, however, under Darwinian theory, you should then expect to drop out with your jeopardizing excess of junk

This was of course the very point of my original post: that the claim by Casey Luskin and other ID advocates that Darwinian theory is somehow directly responsible for the idea of “junk DNA” is sheer nonsense, historically and scientifically. At least we have clarified this point to everyone’s satisfaction. I hope you will send an e-mail to Luskin in this regard.

Comment #194447

Posted by Torbjörn Larsson, OM on August 10, 2007 7:32 AM (e)

Andras Pellionisz:

Andras Pellionisz wrote:

“Anonymous name-calling” (latest by “demallien”)

I can’t find it. He calls you arrogant, which is about observable behavior, and he calls your product “snake oil”, which isn’t about your person.

Comment #194666

Posted by Andras Pellionisz on August 10, 2007 5:22 PM (e)

Dr. Bottaro:

I agree that your depressing thread, though I did what I could to lift it, served out its useful purpose

1) With ENCODE, “Junk DNA” is out, dead as a doornail. You are simply wrong to have said “*all* that anyone can conclude from the ENCODE data is the bare fact that more of the genome undergoes transcription than we suspected”. This insults not only all who took part in the 11-Country effort (for 4 years), but also flabbergasts those who now may wonder “is that *all* we spent $50 M tax-dollars for?”

2) Algorithmic Design approaches to DNA are in.

(Blog-alternatives were notified of these predicted outcome with my posting that eventually was made room here; Comment #188856)

I further agree that anything mathematical has a tough hill to climb with non-scientists, and even with non-mathematically minded biologists. I encountered in PT just a single person who knows a related field “Genetic Algorithms”, and even he/she preferred anonymous name-calling over actual science.

Your comments (as a scientist, but apparently short on mathematics) on the cited TG Smith et al. (1993) paper reveal your lack of understanding even basics of fractals.

You confuse “fractal dimension” with “fractal complexity”.

They are *not* the same at all. For instance, the Koch-curve can have and increasing “level 1”, “level 2” … “level n” complexity (ad infinitum), yet its “fractal dimension” is preserved through all levels (1.26, see an exemplary link below).

When looking at the Purkinje cells in my fractal model at different stages (my Fig. 3. B, C, D, E in the “fugu paper”) those familiar with fractals know that their fractal dimension is preserved. This is a core concept to fractals; scale-free self-similarity (“pattern in a pattern”), based on the invariance of fractal dimension in the small or in the big. The TG Smith (1993) paper says exactly that (no more) for Purkinje neurons by a sampling of species (Dr. Shalizi did even less, he only guestimated 5 out 8 genome-sizes). It is too bad that TG Smith et al. having spotted a fractal property did not follow-up on towards any “fractal model” of one or more P-cells (though I published mine in 1989). I don’t blame them, however, the first “fractal wave” (from 1989 – to 1996) was likewise butchered (see refs. 15-16 in the “fugu paper”) as the “Operon-regulation” by Jacob & Monod in 1961 was derailed (in spite of their Nobel in 1965) by the deliberate framing of Ohno (in 1972). People often mistake “kindness for weakness” and “assertiveness for arrogance”, but masses at this time will rise for millions dying of “junk DNA diseases” and make this new wave break through. Clearly, fractal modeling was beyond TG Smith et al., and is apparently beyond you or Dr. Shalizi – but I went with Dr. Simons on record with peer-reviewed journal publication and I even outlined a program here that takes a collective effort for a PostGenetics Center).

To give you something to grab regarding fractal dimension, for biologists a good place to start towards “appreciation of basics of fractals” is e.g. the independent site of:

http://www.vanderbilt.edu/AnS/psychology/cogsci/…

Dr. Bottaro, with your present ignorance you will have to climb, however, mountains of mathematics before anything you touch upon fractals or FractoGene can be taken seriously, so I wish you good luck with the endeavor of catching up with the mathematical necessities to pursue PostModern Genomics.

[AB] “you are unwilling to subject your hypothesis to meaningful testing”.

[AJP] This is total nonsense. On the contrary, you and PT will remain on record that “it takes less than a week for a grad student” to come up with the zebrafish-test of FractoGene, yet PT is apparently unwilling to spend even a week of effort if evidence for Algorithmic Design is not in their perceived ideological interest. (Although I tried to help, since “random” and “junk” will lead PT nowhere - while it may still be time to embrace Algorithmic Design). We published with Malcolm Simons a peer-reviewed paper open to the whole World, with the declared invitation to rally experimentalists; “comparison are expected to blossom as a new branch of research”. In a provocative manner, we even placed unmistakable “question marks” to point where to look; and one question mark has been answered within two months (guinea pig genome size, right on target). You may label it “secretive” that I don’t give away in a blog progress reports that my colleagues and I actively cooperate with are doing, or that I don’t throw away my IP for blogs, but I think it would be less than smart to do that; you may not even be honestly asking.

Oh, one more thing.

Most fortunately, FractoGene (and in general, more-and-more mathematically minded approaches in PostModern Genomics) will be appreciated not by those who are ignorant of even the basics of mathematics.

Research will be judged by those who suffer “Junk DNA diseases”.

Yes, let’s take Ataxia Telangiectasia (ATM), in which you found Purkinje neurons truncated in their dendritic arborization. Thus one should, IMHO, wonder if ATM intronic mutation could be identified as a fractal defect of a regulatory mechanism. (Although I am quite familar with tabulations “under development” for genomic mutations, I just don’t think that staring at them, without some coherent conceptual framework of how the full genome works, will in itself result in actually helping patients).

Apparently, you may not have looked Vorechovský et al (1996) in www.junkdna.com/junkdna_disease.html

“We describe the first ATM mutation in the splice junction found in the 5’ splice site of intron 17, leading to exon skipping”

I submit to you (more so to learned parents of kids affected by this syndrome) that an intronic fractal defect, derailing regulation, might really be of the interest of those who are really serious.

Who are “really serious”? People affected with “Junk DNA diseases” and their loved ones! They will soon be outraged en masse that Genomics and Medicine before ENCODE was “barking up the wrong tree” (protein synthesis with Crick’s Central Dogma) – and R&D were not paying enough attention for non-genic(regulatory) mechanisms, such as fractal structures and their defects that FractoGem Miner can help identify.

It has been and will be interesting to chalk up giants of genomics one-by-one (who earlier went on record as “Ohno followers”) lately turning from the wasteland of “Junk-yard” to the riches of “Regulation Research” (Collins, Venter, Brenner, to name just a few). It will be increasingly embarrassing for the remaining hold-outs (Dawkins, some non-scientists in PT, and “also ran”-s) to turn their coats.

How this whole debate about Pellionisz’ algorithmic approach will ring in readers’ mind, mesmerized Post-ENCODE “what’s next”?

“Hell – he may be right”. “What’s in it for me?”

pellionisz_at_junkdna.com

Comment #194680

Posted by Andrea Bottaro on August 10, 2007 5:46 PM (e)

Dr. Pellionisz:

thanks for your reply. I guess the record of past comments is there for everyone interested to wade through and assess independently, so I’ll gladly let you have the last word.

This thread is now closed to further comments.