FractoGene

I have a specific and a general comment to make: "As far as I can see, Dr. Pellionisz’s speculations do not attempt to explain nonfunctional pseudogenes" "Nonfunctional pseudogenes" are a nonsense that *DOES* need to be explained, by algorithmic and quantitatively predictive scientific theory, where the predictions can be experimentally supported or refuted. Therefore, they certainly fall into the domain of theoretical (and then, experimental) investigation. ("Pseudogene" is defined as a non-functional *gene*. However, while not (apparently) "protein coding" how can anyone be sure that they can not have some (albeit perhaps not yet fully understood) function? Rigoutsos' "pyknon"-s (see http://www.pyknon.com) are, similarly all over the DNA, in the human the found 128,000 short repetitive sequences are not at all restrained to either the "protein coding" or "non-coding" regions. The apparent fractality of the DNA, since fractals are absolutely deterministic, inevitably calls for explanation. Yes, recursive fractal algorithms are both extremely powerful and extremely common in Nature - it is outright foolhardy to continue to ignore "Junk" DNA anymore (these days, hardly anyone ignores this exploding subject, anyway). My general comment is, that ID definitely scored big by correctly predicting (for the right reasons or not) that "Junk" DNA had a function - while most Darwinists (with few exceptions) stuck with the untenable (frankly, quite ridiculous) notion that 98.7% of human DNA was "Junk". Having worked with NASA, I find it (not at all :-) difficult to comprehend that on one hand they are probing Mars (clearly, Extra Terrestrial) for "signs of life", yet on the other they have problems accepting that e.g. a fractal compression of hereditary information passed from ET to our planet is scientifically impossible to exclude as a possibility. (NASA missed the Mars TWICE by confusing metric and non-metric distance measurements...) The debate, however, should not be fought in the turf of belief, IMHO. Since anyone believes whatever he/she wants to believe - thus the debate might be endless. Meanwhile, hundreds of millions are dying with "non-coding DNA diseases" (see http://www.junkdna.com/junkdna_diseases.html) - while "Junk" DNA is not getting (outside of PostGenetics, http://www.postgenetics.org) the "priority number one" that it deserves. ID scored big on "Junk" DNA - "don't negotiate past the deal". There will be no debate by anyone diagnosed with any of the potentially up to 150,000 "junk DNA diseases". "How much is needed, how to make up quickest for decades lost???" Dr. Pellionisz pellionisz@junkdna.com Pellionisz

> That’s the whole point of ID — to move “mind stuff” _into_ the > natural science. Right now, natural science has to pretend that > “mind” doesn’t exist in order to work. The genius of the ID > program is to include mind in science without forcing a false > reductionism to mind. That may be fine for a long term objective. But ID doesn't have a _scientific model_ of the "mind stuff" either. Until such model exists (which can predict something that makes empirical difference), postulating "mind" as designer is counter-productive to ID acceptance as a legitimate scientific theory. The best ID can do at present is to offer a model of a hardware & software implementation of the "intelligent agency". The only plausible candidate (which already has mathematical models and empirical basis) is the implementation through adaptable/itelligent networks, from cellular biochemical reaction network up to social and ecosystem networks. Biochemical networks & their algorithms http://groups.google.com/group/talk.origins/msg/623400a8de95db21 Algorithmic formulation of ID & intelligent networks (links) http://groups.google.com/group/talk.origins/msg/505e0620c272c339 Trying to push "mind" as the designer long before it is ready as a scientific & mathematical model is precisely the reason ID is being rejected by the natural science. Much more productive approach is to offer the model of the "intelligent agency" in terms of the _present_ natural science. Once that is accepted, the intelligently guided, purposeful evolution and origin of life become perfectly plausible and acceptable theory for the present natural science, obsoleting the neo-Darwinist random, aimless and pointless evolution. The "mind stuff" aspect would remain temporarily within the philosophical and theological implications of ID. Insisting on passing these aspects, which no one really understands, anyway, as a science at this stage is the key impediment to ID's acceptance as a legitimate _present-day_ theory. We all understand, of course, that ID is more harmonious with the "mind stuff" being eventually part of natural science than neo-Darwinism or 19th century materialism. Unfortunately, there is nothing in the present natural science of matter-energy indicating 'what is it like to be such and such arrangement of atoms & fields' that make up you. There isn't even a hint that anything of the sort is needed, let alone any model where "mind stuff" makes any empirical difference. nightlight

The bottom line is simple. ID theorists predicted that most DNA would have real function, whereas NDE has found value in the fact that there is significant discarded -- without function -- the waste product of the RM+NS process. As it is becoming clear that much (most?) the "non-coding" DNA (DNA which does not define proteins) does involve itself in the phenotype of an organism, so it is ID that clearly wins this point. Let me also just remind that (if I understand correctly) Gould was somewhat concerned to discover that some coding DNA coded for more than one protein. This, if I understand, concerned him deeply, I believe that he suggested that a significant amount of such discovery would be the death nell to RM+NS. I also understand that we now know that the average piece of coding DNA codes for 5 proteins. At this point I think that Gould is no longer a neo-Darwinist. How say ye? Is my understanding on this topic correct? bFast

"the realm of mind stuff is presently outside of natural science" That's the whole point of ID -- to move "mind stuff" _into_ the natural science. Right now, natural science has to pretend that "mind" doesn't exist in order to work. The genius of the ID program is to include mind in science without forcing a false reductionism to mind. johnnyb

The lengths these people go through to deny the ovbious is quite stunning. Saxe saxe17

"I wouldn't be surprised if DNA uses recursive mathematics for generating its complexity (plants do this for their structure at a macro level)." Recursion (self-referential algorithms and self-calling functions) is an extremely powerful tool in computer science. The AI (artificial intelligence) techniques used in chess- and checkers-playing computer programs are based upon this concept. This is the basis of what we call a "tree search." The immune system apparently uses a search/trial-and-error technique in order to devise antibodies to pathogens. The immune system also maintains a database of previously-seen pathogenic agents and how to defeat them. This is what immunization is all about. As an ID research proposal I would suggest pursuing what we have learned from AI research to see if human-designed algorithms are reflected in biology, especially when it comes to the immune system: 1) Iterative Deepening: Make initial, shallow, inexpensive searches, and increase the depth and expense of the searches iteratively. 2) Investigative Ordering: Order results from 1) to waste as little time as possible during deeper searches. 3) Maintain short-term memory to rapidly access solutions to the most-recently-seen problems. (We use RAM-based hash tables in chess and checkers programs for this purpose.) 4) Maintain long-term memory for catastrophic themes that tend to recur on a regular basis. (We use non-volatile, disk-based endgame databases in chess and checkers programs for this purpose.) This is just a brief overview of the most basic techniques used in AI game-playing computer programs. There's a whole lot more really cool stuff. Isn't it amazing how random mutation and natural selection created chess-playing computer programs? :-) GilDodgen

The biochemical reaction networks will automatically create fractal structure by virtue of internal modeling of their environment and self. That is the same phenomenon familiar from the networks of neurons, such as human brain, where we create internal model of our environment, which includes self-actor (model space counterpart of 'self') and of other networks (other humans, which have corresponding actors in the model space). After certain level of refinement of the the internal model via learning (which takes children 5-7 years to master), the actors at higher modeling resolution gain their own internal model (since that is a more accurate model of that actor than an unaware or random acting actor), which in turn contains all 'smaller' actors. Further refinements create a recursively nested structure similar to a ring of reflecting spheres, where each sphere has a small image of the entire ring and all other spheres, and within each of these little image spheres, there is an even smaller ring of spheres,... For more on this (and references) see couple talk.origins posts: Biochemical networks & their algorithms http://groups.google.com/group/talk.origins/msg/623400a8de95db21 Algorithmic formulation of ID & intelligent networks (links) http://groups.google.com/group/talk.origins/msg/505e0620c272c339 In my view, ID will only become acceptable as a legitimate scientific theory if one can show how is this "intelligence" (or at least the relevant part of it), which is being offered as the explanation, _implemented_ in the realm of matter-energy (the realm of mind stuff is presently outside of natural science). Regarding the cellular biology, this implementation is given as a cellular biochemical network. The most immediate intelligence behind evolution is implemented in the matter-energy realm as the ecosystem network, which contains all numerous other networks (such as species, gene pools, organisms & cellular level networks) as subnetworks. The alternatives, such hinting at mind stuff, falls outside of the present natural science, hence no explanation resting on such speculative foundation can be acceptable to the natural science. The genuine model of mind stuff (which can answer, at least in principle, "what is it like to be such and such arrangement of atoms" that makes you) within natural science is much too far in the future to be useful as any kind of basis for ID as a legitimate discipline within the present natural science. In short, ID needs to walk first before running, and run first before flying. Its present (and transient) setbacks are due to trying to fly from the crawl. nightlight

Actually the pseudogenes was junk DNS IHO was against evolution. Why would NS keep pseudogenes (junk) around for millions of years unchanged while making major changes. Ex. Man and chimp has a lot identical pseudogenes yet the human brain made great advancements which mutations in this area can do a lot of damage. Smidlee

Salvador, Miller's comment refers to nonfunctional pseudogenes, not to junk DNA in general. As far as I can see, Dr. Pellionisz's speculations do not attempt to explain nonfunctional pseudogenes. Where is the egg that Miller is supposedly wiping from his face? zapatero

Correction: I think Miller isn't done wiping the egg off his face. :=) scordova

The theory of intelligent design cannot explain the presence of nonfunctional pseudogenes unless it is willing to allow that the designer made serious errors, wasing millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, in contrast, can easily explain them as nothing more than failed experiments in a random process of gene duplicaitons that persist in the genome as evolutionary remnants. Ken Miller, 1996 criticizing Michael Behe see page 224, Darwin's Black Box

I think Miller is done wiping the egg off his face. :=) Salvador scordova