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DNA researcher, Andras Pellionisz gives favorable review to a shredding of Dawkins and TalkOrigins

DNA researcher Andras Pellionisz has found unwitting friends in the ID community. He observed that while Darwinists like Richard Dawkins are dismissive of his field of scientific research, ID proponents are surprisingly enthusiastic about his work and that of his colleagues. We have thus found here at Uncommon Descent a friend from quarters I would have never guessed in Dr. Pellionisz and his colleagues.

Pellionisz lamented here that it is the ID proponents who show more interest than people like Dawkins in the highly important areas of research within biology [and imho, evolutionary biology is not a highly important field of research, SYSTEMS Biology is]. Pellionisz then added:

the issue of “Junk” DNA itself is much more vital for human kind, since hundreds of millions are dying of “Junk DNA diseases” while the urgency of plunging into active research is overlooked because on ANY ideological grounds.

Those looking at

http://www.junkdna.com/junkdna_diseases.html

will realize that for those to whom SCIENCE of “junk” DNA is still not the “mainstream” are socially guilty because of putting priority on ideology over survival.

Hundreds of millions of patients don’t appreciate delay of medicine by ideology.

It appears elements within the anti-Design community are institutionally biased against the important research Dr. Pellionisz and his colleagues are performing on behalf of science. And it is the ID community that is far more friendly to this important work than the communtiy of evolutionary biologists.

Pellionisz gives a favorable review of a pro-ID article. The article is: How Scientific Evidence is Changing the Tide of the Evolution vs. Intelligent Design Debate by Wade Schaer.

Dr. Pellionisz gives his review at junkdna.com

From the Shauer’s Article:

Richard Dawkins writes:

And there’s lots more DNA that doesn’t even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, “tandem repeats”, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself.

Panda’s Thumb also finds it important to argue for “Junk DNA”
….

Tandem Repeats are a class of repetitive DNA unique in every individual, which is why they are used in DNA forensic evidence, etc. … Talk Origins also has this to say about Tandem Repeats: “scientists view tandem repeat sequences as resulting from accidental DNA duplications.”

Now let’s look at what the scientific evidence is telling us about Tandem Repeats:

They Silence and Activate Genes

Tandem repeat sequences are frequently associated with gene silencing phenomena.

This region contains the major and minor promoters of the Tsix gene, which runs antisense to Xist, and the

DXPas34 tandem repeat lying close to the Tsix major promoter.

Our results identify a function for DXPas34 in murine XCI and demonstrate the critical role of Tsix transcription in preventing XCI in differentiating male ES cells and in normal functioning of the counting pathway.

Transfection studies in mouse mesenchymal C3H10T1/2 cells showed that it is the tandem repeat of the C/EBP binding site in PPARgamma2 promoter region that regulates dexamethasone-mediated PPARgamma2 gene activation.

These observations establish that a dinucleotide tandem repeat sequence, capable of self-association, forms part of a cell-specific silencer element in a mammalian gene.

They [tandem repeats] Determine the Length of a Dog’s Nose

Breeds with collie-like noses had more of a particular tandem repeat, while those with pug-like faces had more of a different tandem. And when the researchers compared bull terrier DNA, they found that terriers have one more repeat unit than they did in the 1950s, which could explain why the nose used to be droopier, the researchers note.

They [tandem repeats] Determine a Cow’s Milk Fat Percentage

In addition to this, another polymorphism in the 5′-regulatory region of this gene, the DGAT1 variable number of tandem repeat (VNTR), also showed a strong association with milk fat percentage.

These research finding show that, far from being junk, Tandem Repeats have important functional roles in the genome. More interestingly, the unique copy number in individuals seems not to be caused by random mutations, but rather by a built-in program that occurs during the combination of male and female DNA. While children will tend to inherit Tandem Repeat numbers similar to those of their parents, this variable component makes every child unique. The fact that Tandem Repeats are so well correlated to racial classifications shows that they have a role in determining what each individual looks like. Tandem repeats appear to be the major factor in what determines the size of your nose, the amount of body fat you have, your height, skin color, etc.

Transposons/Retrotransposons

Here’s what Talk Origins says about Transposons:
In many ways, transposons are very similar to viruses. However, they lack genes for viral coat proteins, cannot cross cellular boundaries, and thus they replicate only in the genome of their host. They can be thought of as intragenomic parasites.…finding the same transposon in the same chromosomal location in two different organisms is strong direct evidence of common ancestry, since they insert fairly randomly and generally cannot be transmitted except by inheritance….

So is there evidence that Transposons have function?

They [transposons] are Necessary for Embryonic Development

The research, published in the October issue of Developmental Cell, suggests that retrotransposons may not be just the “junk DNA” once thought, but rather appear to be a large repository of start sites for initiating gene expression. Therefore, more than one third of the mouse and human genomes, previously thought to be nonfunctional, may play some role in the regulation of gene expression and promotion of genetic diversity. Dr. Barbara B. Knowles and colleagues from The Jackson Laboratory in Bar Harbor, Maine, found that distinct retrotransposon types are unexpectedly active in mouse eggs, and others are activated in early embryos. Surprisingly, by acting as alternative promoters, retrotransposon-derived controlling elements drive the coordinated expression of multiple mouse genes. The researchers think that expression of retrotransposons during very early stages may contribute to the reprogramming of the mammalian embryonic genome, a prerequisite for normal development.

They [Transposons] Format the Genome File System…

Generic repeated signals in the DNA format expression of coding sequence files and organize additional functions essential for genome replication and accurate transmission to progeny cells. Retroelements comprise a major fraction of many genomes and contain a surprising diversity of functional signals.

That is just the beginning. Now let’s examine specific classes of Transposons mentioned in the two Talk Origins Articles.

SINE/Alu Sequences

The Talk Origins view of SINEs/Alu:

…current evidence suggests that only a very few Alu sequences are active sources of transcripts; perhaps transcription from most copies is inhibited by the chromosomal environment of the insertion

Further, the excellent health of individuals who lack particular Alu insertions supports the view that these insertions do not serve any important function in human physiology.

What does the recent scientific evidence say about SINEs/Alu?

Alu can turn a single gene into multiple proteins

Through a process called alternative splicing, humans create multiple versions of a gene and, consequently ,multiple proteins. It’s a way of constructing a new protein, while keeping a backup copy of the original version.For example, the researchers found that the ADAR2 enzyme contains 40 amino acids in its active site that arederived from an Alu element. The addition changes the activity of the enzyme.

“The excitement about the exonization of Alu is the ability to explain what is unique in our genome,” Ast says. The mouse genome contains 2.5 billion nucleotides, the human genome around 3 billion. “The quarter of a billion nucleotides, [or] the difference between human and mouse, is mostly [due to] retrotransposable elements like Alu,” he says.

They [Alu] affect Micro-RNA processing

Although Alu was originally thought to represent ‘junk’ having no biological functions, the presence of Alu sequences within protein-coding genes can affect the processing of mRNAs at multiple levels

Highly Conserved Vertebrate SINEs with unknown function

Extensive conservation of V-SINEs can, however, be more easily explained by the hypothesis that the central conserved domain may somehow “earn its keep” in the genome.

The observed conservation strongly indicates that the central domain of these transposable elements have been exapted, i.e., have become a functional component of the mammalian genomes.

The close copies of the ultraconserved element scattered around vertebrate genomes have changed less than would be expected over evolutionary time, indicating that they are functionally important. But relatively few of the copies contain parts that code for proteins, which suggests they [ultraconserved elements] instead are helping to regulate when genes are turned on and off.

“Thus, AmnSINE1 appears to be the best example of a transposable element of which a significant fraction of the copies have acquired genomic functionality.”

So many SINES have been shown to be FUNCTIONAL, counter to the Talk Origins claims. Alu sequences are unique to primates and seems to be particularly active in the human brain.

LINES

Talk Origins has this to say of LINES:
LINEs thus have several properties expected of “selfish” DNA sequences that can spread in the host DNA simply because they encode their own machinery for spreading.

In other words, they don’t serve a purpose other than to copy themselves, according to Talk Origins.

Here’s what some recent scientific evidence says about LINES:

Human LINE-1 sequences being investigated for function

Long interspersed elements (LINE-1, L1s) are the only active autonomous retrotransposons in mammals, covering as much as 18% of their genomes. L1s’ activity results in a great repertoire of actions, such as gene disruption, transcriptional regulation, alternative splicing, creation of exons and gene coding regions and amplification of the processed pseudogenes and the Alu SINE family.

A LINE-2 sequence which functions as a potent T-cell-specific silencer

In summary, we have identified a LINE-2 fragment named ALF that is a potent T-cell-specific silencer. We also show that agonists that down-regulate ALF-containing genes in T cells induce a factor that binds to a sequence within ALF. These findings are in contrast to other reports associating enhancer or promoter activities with repetitive elements (16,17), because ALF has the potential to function as a cell-type-specific silencer. We favour the hypothesis that this is not an arbitrary activity, and that ALF contributes to gene regulation in vivo.

LINE-1 sequences modify RNA expression

Because L1 is an abundant and broadly distributed mobile element, the inhibition of transcriptional elongation by L1 might profoundly affect expression of endogenous human genes. We propose a model in which L1 affects gene expression genome-wide by acting as a ‘molecular rheostat’ of target genes. Bioinformatic data are consistent with the hypothesis that L1 can serve as an evolutionary fine-tuner of the human transcriptome.

LINE-1 may have a role in DNA Repair

Thus, our results suggest that LINE-1s can integrate into DNA lesions, resulting in retrotransposon-mediated DNA repair in mammalian cells.

Extrapolating these findings to the 600,000 copies of L1 in the genome, we predict that the amount of DNA transduced by L1 represents ~1% of the genome, a fraction comparable with that occupied by exons. So again, there are plenty of examples now of functional LINES.

Endogenous Retroviruses and LTR retrotransposons

Talk Origins has this to say of Endogenous Retroviruses:
Endogenous retroviruses are molecular remnants of a past parasitic viral infection. Occasionally, copies of a retrovirus genome are found in its host’s genome, and these retroviral gene copies are called endogenous retroviral sequences. Essentially all of these endogenous retroviruses contain mutations that would disrupt the function of their genes, as would be expected if they inserted millions of years ago with no selective pressure to maintain the function of the genes.

Here’s what some recent scientific evidence says about Endogenous Retroviruses:

They [Endogenous Retroviruses] show up expressed in many cell tissues

Human tissues that lack HERV transcription could not be found, confirming that human endogenous retroviruses are permanent components of the human transcriptome. Distinct activity patterns may reflect the characteristics of the regulatory machinery in these cells, e.g., cell type-dependent occurrence of transcriptional regulatory factors.

They [Endogenous Retroviruses] are required for placental development?

In particular, a class of endogenous retroviruses, known as endogenous retroviruses related to Jaagsiekte sheep retrovirus or enJSRVs, are critical during the early phase of pregnancy when the placenta begins to develop.

They [Endogeneous Retroviruses] impact gene expression

Indeed, the LTR is the dominant promoter in the colon, indicating that this ancient retroviral element has a major impact on gene expression

EBR LTR promotes a significant proportion of the total EBR transcripts, and transient transfection results indicate that the LTR acts as a strong promoter and enhancer in a placental cell line. They are highly conserved between the mouse and distantly related species…. On account of their abundance, LTR retrotransposons are believed to hold major significance for genome structure and function.…High sequence similarity between several LTR retrotransposons identified in this study and those found in distantly-related species suggests that horizontal transfer has been a significant factor in the evolution of mouse LTR retrotransposons.

Did they cause the human/chimp split or are they simply one more indicator that humans are unique?

The discovery that human-specific retroviruses emerged at the same time other researchers believe humans and chimps diverged was startling.…McDonald said it is increasingly clear that organisms need the viral elements and that their apparent continual backdoor assaults on normal genes may, in truth, be more like a vast, sophisticated chess game on an enormously complex board. Admittedly, most of the scientists involved in the above studies of Endogenous Retroviruses still assume that they were parasites that somehow were incorporated into the genome with functional roles. However, since many of these perform similar functions in different species, one cannot prove common descent based upon the idea that shared retroviruses are shared errors.

Pseudogenes

Both the Talk Origins and Panda’s Thumb websites spend a lot of time on Pseudogenes.

I did not cite the full article here, but I encourage the serious readers to read Shauer’s article, Pellionisz review, and visit Pellioisz website.

I wish to thank Dr. Pellionisz for alerting me us to this wonderful compilation by Wade Schauer.

To quote a line from a famous movie, “I think this is the beginning of a beautiful friendship…”

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40 Responses to DNA researcher, Andras Pellionisz gives favorable review to a shredding of Dawkins and TalkOrigins

  1. By the way, does any one here save TalkOrigin’s articles. We may want to preserve some of their articles for posterity before they withdraw them in embarrassment….

  2. You’ll have to excuse me my science is more of the mind and spirit than body.

    I’ve read a bit about Junk DNA but am not altogether that familiar with it. From what I am reading, it’s best to not term it “Junk”, then? They do play a role in characteristics then?

  3. “…We may want to preserve some of their articles for posterity …”

    You do know about the WayBack Machine, right?

    http://www.archive.org/index.php

  4. I’ve read a bit about Junk DNA but am not altogether that familiar with it. From what I am reading, it’s best to not term it “Junk”, then? They do play a role in characteristics then?

    It was once supposed that 98% of the human genome was junk. To the Darwinists this was evidence of bad design, and further more, they said “junk” in the genome is more consistent with a mindless, wasteful evolutionary processes than intelligent design.

    One prominent researcher wrote me an unsolicited e-mail and said I should disbelieve the design hypothesis because of the “pathetic architecture of the human genome”. He was apparently referring to the “junkDNA”.

    These scientific developments appear to refute the “junkDNA” arguments.

    Also, and this is far more technical, in order to rescue evolutionary theory they had to invoke junkDNA to solve a problem posed by geneticist Motoo Kimura. Kimura realized the overwhelming majority of the molecules in organisms are not subject to natural selection, nor could they ever have been…

    Therefore, it became evident that finding large amounts of functionality in the 3.5 giga base pairs of our genome and in the genomes of other creatures would signify that there exists very many designs in nature that cannot be theoretically accounted for by Natural Selection. That amount of base-pairs is too many for natural selection to create one-base-pair at a time given the number of possible individuals within each species.

    That is why there is strong institutional bias against the work of Dr. Pellionisz and others. The new findings fly in the face of everything they have been asserting for decades. Pellioniz work which can improve medical research can also be used to bash evolutionary biology.

  5. I apologize if I sound stupid asking this. So there is a purpose for Junk DNA right? It’s hard to find an answer.

    Also would you say that DNA / the genetic code is of optimum design?

  6. Salvador,
    You might find this archive useful:

    http://web.archive.org/web/*/talkorigins.org

    It’s the/an internet “WayBack” machine. It goes back to 1997 for TalkOrigins. I don’t know how frequently they update or to what extent. But there is some semblance of the website preserved for us in the digital strata. ;)

    JGuy
    ps. I’m claim coinage of that term.

  7. digital strata, that is.

  8. A5:
    I apologize if I sound stupid asking this. So there is a purpose for Junk DNA right? It’s hard to find an answer.

    Scientists have found that some sequences of DNA that do not code for an amino acid sequence or any RNAs do have an effect on embryonic developement.

    At least one scientist (Shapiro?) has inferred much of the DNA we don’t know about could possibly hold some “system architecture”- possibly like an OS

    A5:
    Also would you say that DNA / the genetic code is of optimum design?

    It would be hard to say until we fully understand it. It would be like giving my 4 year old a print out of a C++ program I just wrote and asking her what she thinks about it.

  9. I apologize if I sound stupid asking this. So there is a purpose for Junk DNA right? It’s hard to
    find an answer.

    The answer is yes for more and more of it. It used to be that 98% of the human genome was labeled junk. At one time the evolutionary community was wiliing to lablel only 2% as useful, and the rest as junk. The word “junk” also expresses the prejudice they had for the Intelligent Designer’s work. :-) They could have chosen a less inflammatory word, but this symbolizes their attitude that it had not design or function….

    That 2% number has grown steadlity. Sanford last year said we could probably account for 38%. It seems now there is every reason to expect the number could go toward 100%.

    JunkDNA therefore is not junk, but the name persists, and frankly I’m in favor of keeping to leave a permanent reminder to the world of what the evolutionary biologist nearly did to the progress of scientific understanding….

    Also would you say that DNA / the genetic code is of optimum design?

    It is hard to say unless one knows what one is optimizing. For example, a car can be optimized for speed but not for fuel efficiency and vice-versa.

    The one dimension I would safely say it is very optimized for is information storage. A human being and all of organs, capilaries, nerves, systems, etc. , ability to self-heal, stored in one zygote? Amazing!

  10. “…a certain amount of hubris* was required for anyone to call any part of the genome ‘junk’”

    Francis Collins

  11. “It was once supposed that 98% of the human genome was junk. To the Darwinists this was evidence of bad design, and further more, they said “junk” in the genome is more consistent with a mindless, wasteful evolutionary processes than intelligent design.

    One prominent researcher wrote me an unsolicited e-mail and said I should disbelieve the design hypothesis because of the “pathetic architecture of the human genome”. He was apparently referring to the “junkDNA”. ”

    I guess we might as well concede they are correct and then note that the genome is not wasteful and that they already concede that this would be a hallmark of design, and that the architecture is not “pathetic” but careful and conservative, and again, that this is evidence likewise of design just as they originally said.

    I think much should be made of these new discoveries because they are tacit admissions of design by the ateleologists when they claim their absence is proof of no design. They will try to wriggle out of such conclusions but if they are pressed on it, at least those looking on from the sidelines will understand and see the point even if the fundies refuse to see reason.

  12. From and empirical and theoretical standpoint let me point out, these developments combined with the work of Kimura and elaborated by ReMine and Standford (and Designer-willing many more) have shown that Natrual Selection can’t be the source of these designs.

    To illustrate, consider that you have a mouse-like creature, how much functional change to it’s genome can you expect on average over time per generation? Not much. Evolution has a limited amount of parts it can add even under favorable situations. If 3.5 giga base pairs of DNA are mostly functional, there is simply not enough time and resources to build such a fabulous structure.

    In addition to that, there are serious rumblings that DNA could be only a fraction of the real information storage of the cell. A FRACTION! ID-friendly researcher James Shapiro (he is not formally an ID proponent) is doing exciting work on this topic. It may be, the whole cell, and not just the DNA is a wonderfully recursive memory storage device where almost every molecule counts for something!

  13. Scordova, I like how you write. You and Joseph should write more articles.

  14. Thank you a5b01zerobone.

    Let me add, since it may be on the mind of some, how the Kimura-ReMine-Sanford issue relates to the work of Michael Behe.

    The issues I’m discussing in terms of speed limits are making the exceedingly generous assumption that Michael Behe’s irreducible complexity does not also pose a serious problem. That is to say, the grinding out of these numbers assumes Behe is dead wrong for starters. Of course, if Behe is right or even half-right, it makes the problems all the worse.

    On top of that, the barriers to natural selection’s succes that I’ve enumberated with Kimura-ReMine-Sanford and Behe don’t even account for yet another barrier which I described in U-Paradox.

    At some point, one has to wonder what it will take for some die-hards to see the light….

  15. “At some point, one has to wonder what it will take for some die-hards to see the light….”

    Have you read Thomas Kuhn ? Don’t expect them too. Just wait for them to die off.

  16. Salvador,

    Thanks for posting the Schauer article and Dr. Pellionisz’s comments. Can’t stand PDF(anyone else?), but I’d read Schauer’s article several days ago and was impressed by the amount of observational evidence he’d gathered against the JunkDNA myth. Was hoping to see it published here.

    One of the articles if I remember correctly has a scientist estimating up to 60% is functionality for “junkdna.” Just a guess, but is devestating to the predictions of the faithful on Dawkins side if true.

    It is a great honor to see Dr Pellionisz’s commentary in keeping an open mind when searching for truth. Ideology or a personal beliefs should not be an automatic denunciation of one’s scientific position.

    Related to Dr. Pellionisz’s work is an article I read sometime ago about compression and storage algorithms studied by a team in Australia. I’d posted it here once before. They found that the hexagonal shape increased efficiency ratios just thru software simulations, but were limited in actual physical testing.

    Found the article!

    Fractal Image Compression on a Pseudo Spiral Architecture,
    http://64.233.167.104/search?q.....=firefox-a

    He’s probably already aware or way ahead of these findings.

    I had actually worked out by hand a spiral pattern out of curiosity for different reasons regarding a dual purpose numbering role for scaling up/down sequences and patterns. Essentially, what is found is a numerical stairway relationship which works out in DNA too. It is way to cool.

    We’re close to mimicking these spiral patterns in the storage platters of circular disk with multiple r/w heads for decades now since the 70s.

    So Bill Gates, IBM and others are onto something for a reason. Spiral architecture is a future storage medium. The advantage of a spiral system is storage capacity, cooling efficiency for funneling/displacing heat, reducing noise(umm yes, in the eye and in water) and for intelligent purposes, a reverse factorization method for quick search routines of linear sequences(jumping or leaping across one side of the double helix).

    A seemingly unrelated thought. This is partly why we see the repeated patterns in tornados, hurricanes, galaxies and dna. It is actually all related due to a basic set of laws yet to be discovered taking into account thermodynamics and other factors for information storage and exchange.

    If you think about the simplicity of a circular relationship you realize that fluidity rest on smooth structures which are also keen to take advantage of turbulence. Why are the filaments of the flagellum not attached directly to the back like our boats? The reason is it achieves a high rpm due to the design of taking into account the flow of fluid around the structure itself and utilizing it(think of a ramjet). Notice how they produce a spiral propeller system that takes advantage of the flow. A propeller at the dead flow backend does not do this.

    At this time, note another Aussie who is designing spiral propellers(still limited to inboard backend) that are much more efficient, quiet systems, already patented.

    I am not saying all spiral patterns we see in nature are equally related. That is an over generalization. But, science is overlooking the obvious. Something very fundamental in the design advantages that God’s nature is shouting out to us.

    Well, way out of my league. It is a real honor to have someone like Dr. Pellionsz posting here. I had looked at the fractal concepts before especially with compression and storage related media. Will definitely get a closer look at his work.

  17. “…elaborated by ReMine and Standford (and Designer-willing many more) have shown that Natural Selection can’t be the source of these designs.”

    Speaking of ReMine, his book, “The Biotic Message” is, IMHO, fabulous. He has a talent for exposing faulty logic. I’m surprised I don’t see it mentioned more often. And as far as this discussion goes, really what *is* it going to take for people to wake up and realize what we are seeing is incredible design? There’s just no other valid explanation for it. Lately, there’s been so much politically motivated hype about “stem cells” not being researched like they should be. In the end, what has 150 years of Darwin cost us?

  18. Shaner,
    I second the kudos on the book – “The Biotic Message”. It’s one of the better books out on the topic matter. Helpful in exposing the murk. I recall that Mung also gave what seemed some of his highest regards for this book – in the ARN book review forum.

  19. Michaels wrote: “Why are the filaments of the flagellum not attached directly to the back like our boats? The reason is it achieves a high rpm due to the design of taking into account the flow of fluid around the structure itself and utilizing it(think of a ramjet). Notice how they produce a spiral propeller system that takes advantage of the flow. A propeller at the dead flow backend does not do this.”

    That’s interesting. Even though I do not see the full concept yet. It does remind me of something I’ve learned from swimming. And I’m not certain it applies, but I’d like to throw this out for you to ponder..maybe you can make more with it… In competitive or combat swimming, there is a certain lesson you learn about swimming effieintly. The saying is “Be a propellor, not a paddle wheel.” .. That is, if your swimming, you don’t want to be a paddle wheel and push the same water you alrady set into motion away/behind you… you want to push the water that is relatively slower compared to your body – rather than chase the water moving behind you which will provide less inertia/resistance to push against… so one must slightly propellor (spiral) his/her hands through the water to push on the still water. This is a measurably more efficient means to swim through the water.

    Hope that was new, helpful or interesting to ya.. Don’t wanna be banned for being boring ;) Just kidding Dave et al.

  20. Scordova
    wrote:”If 3.5 giga base pairs of DNA are mostly functional, there is simply not enough time and resources to build such a fabulous structure.”

    JGuy: What of the guys like Kenneth Miller who will repeatedly repeat Gene repetition (ie. gene duplications).
    [BTW: For some reason, at times when I think of Kenneth Miller’s continue call’s for gene duplications, I can’t help but recall Steve Ballmer on stage.. see the video:
    http://video.google.com/videop.....038;hl=en.

    “In addition to that, there are serious rumblings that DNA could be only a fraction of the real information storage of the cell. A FRACTION! ID-friendly researcher James Shapiro (he is not formally an ID proponent) is doing exciting work on this topic. It may be, the whole cell, and not just the DNA is a wonderfully recursive memory storage device where almost every molecule counts for something!”

    That sounds exciting. Jonathan Wells also eluded to this in his contribution chapter to the book “Signs of Intelligence”.

    ps. Did you seet the TalkOrigins archive I sent you above?

  21. Shanner,

    I agree. ReMine does a wonderful job in exposing pretty much the major evolutionary illusions. Just like you, I am surprised that his book is not as widely “proclaimed” at least as Denton’s book “Evolution: A Theory In Crisis”.

  22. Mats,
    The probable reason, I’d guess, that ReMine’s book is not as widely proclaimed as Denton’s is because in ‘The Biotic Message’, ReMine not only deconstructs to revveal the illusion of evolution, but he goes further to propose an alternate scientific theory that materialist don’t want to acknowledge – ie. a theory that has scientific characteristics and is compatible with both ID theory & special creation.

    JGuy

  23. ..whereas Denton ‘only’ critiques Evolution to reveal that it’s nature is devoid of any realistic explanatory power.

    Though, still not something materialist fancy to contend with.

  24. [OFF TOPIC - sorry ]

    But…

    What would be the evolutionists explanation for what drives this father to do what he is doing?

    http://www.youtube.com/watch?v=f4B-r8KJhlE

  25. A5:
    You and Joseph should write more articles.

    Intelligent Reasoning

    JoeG, that’s me! I have also gone by “ID’s bulldog” and “John Paul” (John Lennon/ Paul Mc).

    I don’t think I would be a good fit here because I want a fight- a knock-down, fists flying, UFC style donnybrook- and let NS decide.

    Why? Because our opposition doesn’t understand anything else…

  26. Given the enthusiasm towards ReMine’s book, I think perhaps next week or so I’ll highlight it in a separate thread.

    Unlike Denton’s book, Biotic Message Theory is formulated to lead to empirically and theoretically testable results. That is why it takes Denton and other ID material one step further.

    Biotic Message theory then leads to one of the final frontiers of ID theory, namely, the search for Steganography which is directly related to the work of Pellionisz. I mention why ID theorists should be quite enthusiastic about searching for a Rosetta stone in reams of Junk DNA here: How IDers can win the war.

    The key to understanding biology may be through looking can be in places we least expect. For example, the study of junkDNA and bacteria led to important breakthoughs in immortalizing DNA, and this can lead to very important cures for skin burns and cancer. The ease by which this discovery was made is startling!!!!

    It is as if the physical artifacts were architected like a message which gives the observer clues how to decode it. That is by design. JunkDNA has a design that will make it amenable to computer analysis and linguistic analysis. It is not so cryptic that the machines of man will fail to understand it. That was not the intent of the Intelligent Designer. It was not His intent to conceal His designs such that they cannot be discovered. Paraphrasing the proverb of one ancient writer:

    “It is the glory of the Intelligent Designer to conceal a matter, it is the glory of Kings to search it out.”

    The Intelligent Designer has placed a Biotic Message in all of biology for us to read and learn from. Like our Privileged Planet, the universe of living things is friendly to scientific discovery for a reason.

  27. I just posted the followingHERE:

    The most incomprehensible thing about the universe is that it is comprehensible.- Albert Einstein

    Which is unusual given that most of the greatest minds that came before him knew why this was:

    In the book Mathematics: The Loss of Certainty by Morris Kline, Kline states that these scientist-mathematicians (Newton, Kepler, & Galileo) believed that “God had designed the universe, and it was to be expected that all phenomena of nature would follow one master plan. One mind designing a universe would almost surely have employed one set of basic principles to govern all related phenomenon.”

    The point being is we should be able to extend this comprehension to biology, ie living organisms. IOW we should be able to decipher any genetic code to understand what it is that makes an organism what it is.

    Knowing how something develops does not tell us what makes it what it is.

    The scientist enjoys a privilege denied the theologian. To any question, even one central to his theories, he may reply “I’m sorry but I do not know.” This is the only honest answer to the question posed by the title of this chapter. We are fully aware of what makes a flower red rather than white, what it is that prevents a dwarf from growing taller, or what goes wrong in a paraplegic or a thalassemic. But the mystery of species eludes us, and we have made no progress beyond what we already have long known, namely, that a kitty is born because its mother was a she-cat that mated with a tom, and that a fly emerges as a fly larva from a fly egg.–geneticist Giuseppe Sermonti

    IDists would proceed with the deciphering as anyone who tries to decipher or understand a ciphered or foreign code- that it is from an intelligent source and therefore can be understood.

    So the ID research question would be-

    How do we comprehend the genetic code(s) such that we will know why a fly is not a horse?

  28. When I was a kid, waaaaaaaaay back in the middle of the 20th century, doctors were yanking out tonsils left an right, in the assumption that if medical science was unable to identify an organ’s function, the organ must be useless. Only within the past few decades did doctors come to suspect the arrogance of such an assumption, when the relationship was discovered between tonsils and the body’s ability to fight off disease.

    I see a similar sort of arrogance in most discussions of “junk” DNA. We are still in the infancy of genetic science, yet we readily assume that if we can’t associate a particular DNA sequence with a particular correlating function, it must have no value within the greater context of the overall genetic code.

    I think it is quite likely that in the coming years, as we come to understand the genetic code better, the references to “junk” DNA will wane considerably.

  29. So the ID research question would be-

    How do we comprehend the genetic code(s)

    The beginning of the answer is comparative sequencing. Up until now we have presumed the existence of various phyla and orders…species was the haphazard result of mindless process. The Biotic Message + the ID Steganography Quest hypothesizes that the almost every molecule of difference is optimized to help us decode biology, i.e. the role and functionality of each molecule of DNA.

    Recall the story of the Rosetta stone, it is a model of comparative sequencing for pro-ID
    biologists today:

    Rosetta Stone

    The Rosetta Stone, a black basalt slab bearing an inscription that was the key to the deciphering of Egyptian hieroglyphics and thus to the foundation of modern Egyptology, was unearthed in July 1799 by Napoleon’s army in Rosetta (Rashid), Egypt, which is located in the western delta of the Nile.

    Its measurements are – 3ft 9in, long and 2ft. 41/2 in wide – (114x72x28cm).

    It contains three inscriptions that represent a single text in three different variants of script, a decree of the priests of Memphis in honour of Ptolemaios V. (196b.c.). Because the inscription appears in three scripts, hieroglyphic, (script of the official and religious texts), demotic, andGreek, scholars were able to decipher the hieroglyphic and demotic (everyday Egyptian script) – versions by comparing them with the Greek version.

    There could be money fame and glory for the pro-ID biologists who succeed in the grand quest to find Biology’s rosetta stone. In fact, there are probably many such stones in biology to help us decode and understand the structure of biology.

  30. If I may offer some observations, the idea of searching for “conserved” sequences via compartive statistical methods is consistent with how we are uncovering steganography in biology.

    Darwinists attribute the conservation to Natural Selection, but the neutralists (like Kimura) point out that there are insufficient population resources to maintain such large regions of “conservation”. Thus we have here designs not attributable to natural selection. Design would be the best explanation, imho.

  31. Sal:
    There could be money fame and glory for the pro-ID biologists who succeed in the grand quest to find Biology’s rosetta stone. In fact, there are probably many such stones in biology to help us decode and understand the structure of biology.

    Would they be finding the stone(s) or creating them, for future research to confirm/ refute and expand upon/ alter?

    Denton tells us that although genes may infuence developement it does not determine it. With this biological “Rosetta stone” in hand either that search will be over or it will take a new direction. And either option is scientifically exciting.

  32. With this biological “Rosetta stone” in hand either that search will be over or it will take a new direction. And either option is scientifically exciting.

    Indeed, and as I pointed out with the case of geron and the prevalent use of searching for “conserved” sequencing, we already have hints such an approach is operationally useful, medically beneficial, and potentially profitable (to be honest I made about $400 on Geron stock before I sold all my shares)…..

    But I don’t thing we have even touched the tip of the iceberg. One simple example. At first we observed the translation of DNA into a protein, kind of a nice sequential, start-to-finish read and write. Apparently no big deal. Then we saw that in some cases that the same strand of DNA could be tranlated backward into yet another meaningful protein. Then we saw the same process with frame shifting!!!

    The level and compactness of information is astounding. Even today we know there exists not just one layer of coding but layers and layers and layers. I seem to recall Sanford saying it appears that not just one level of coding exists for DNA but maybe 12 have been so far discovered.

    This brute force search for “conserved” sequences needs to be taken to the next level. There needs to be a bio-informatic search for (to paraphrase Francis Collins words), “the Hidden Language of God” which can only be decoded by comparative observations…

    We will learn about ourselves by studying as many pieces of biology out there as we can get our hands on.

  33. 33
    sagebrush gardener

    Which philosophy of origins is the “science-stopper” again?

    As someone said, all good research is ID research.

  34. On Michael7′ comment on fractal compression:

    1. The better reference is:

    http://crpit.com/confpapers/CRPITV38Wang.pdf

    2. The paper says (the mathematically obvious): “In short, for fractal image compression an image is represented by fractals rather than pixels” – and goes on to show that the trivial “pixels” (squares) are not nearly as natural nor effective as hexagonal pixels in a helical architecture.

    My decades of research can be summed up that “biology (neurobiology and genomics) is geometrical – and nature’s geometries are at the least non-Cartesian, and demonstrably non-Euclidean (in case of neurons and the genome, fractal)”.

    One does not have to get overly mathematical to grasp the message for us.

    Looking at e.g. a “Mandelbrot Set” (see

    http://www.junkdna.com

    frontpage) of course in one sense, “there are pixels”. Do they design the pattern, or merely express them – that is the question.

    One can envision that the Mandelbrot Set picture emerges by putting random dots on a two-dimensional array – and let “fall out” those that don’t fit (“don’t look nice”).

    This is not what is happening. There is a mathematical design to the seemingly maddeningly complex (and beautiful) pattern to emerge. It is an equation, simple and elegant:

    Z=Z^2+C

    (Admittedly, Z is not a real, but a so-called “complex number”…)

    Mandelbrot was lucky, since given his equation (a generalization of Gaston Julia’s similar equation for real numbers), he had early access to IBM’s massive computing power.

    If you iterate the above equation, starting with an arbitrary “Z” (a point on the two-dimensional array), the equation yield a further point, and so on.

    Thus, an increasingly complex (fractal) pattern emerges.

    It is not at all “random”, it is totally deterministic.

    All information is in the equation Z=Z^2+C

    The “information compression power” of fractals is astounding – and nature uses fractal geometry everywhere.

    FracoGene holds that the fractality of the DNA governs the fractal growth or living organisms (physiological or pathological).

    Pellionisz_at_junkdna.com

  35. Jguy,

    Haha, interesting info, didn’t think about that scenario :)

  36. “The level and compactness of information is astounding. Even today we know there exists not just one layer of coding but layers and layers and layers. I seem to recall Sanford saying it appears that not just one level of coding exists for DNA but maybe 12 have been so far discovered.”

    Wow. This would make a great topic for a blog entry. I ‘d like to learn more about this. Doesn’t this go beyond even the probability bound for something like an IC system arising thru random processes?

  37. Is Mandelbrot an intelligent designer?

    Earlier blog-entries stated/questioned:

    „The level and compactness of information is astounding. Even today we know there exists not just one layer of coding but layers and layers and layers. I seem to recall Sanford saying it appears that not just one level of coding exists for DNA but maybe 12 have been so far discovered.

    This brute force search for “conserved” sequences needs to be taken to the next level. There needs to be a bio-informatic search for (to paraphrase Francis Collins words), “the Hidden Language of God” which can only be decoded by comparative observations…

    Wow. This would make a great topic for a blog entry. I ‘d like to learn more about this. Doesn’t this go beyond even the probability bound for something like an IC system arising thru random processes?”

    Comments from A. Pellionisz:

    The question of 98.7% of (human) DNA is not that much of philosophy (even less, of ideology). The abandonement of the “Junk” DNA issue is scientific.

    Indeed, the question is mathematical; concerns the geometry of biological growth. In this reagard, in their Time Magazine debate, Francis Collins “wins” the debate for me (over Richard Dawkins) since F.C. looks for the “divine science” (of mathematics – not exactly a point of strength for R.D.) when the precisely stated question of F.C. is:

    “Is mathematics, along with DNA, another language of God?” (p. 63)

    In the science of biology, life is growth (physiological and pathological). In a growth process, when we are talking about “Layers and layers”, we are talking of what? “Level of coding?” An “IC system”??

    Looking at a broccoli or cabbage (especially the Romanesco http://www.lps.ens.fr/~douady/.....nesco.html ), the layers of a cabbage (many more than 12) one doubts very much that their growth occurs under an the guidance of an external “information control system”. Not only there isn’t a need for “different levels of coding” e.g. for each layer of a cabbage, each leaf on a tree, or each brain neuron in our brain – but there is no room in the relatively tiny DNA to contain all that information. Remember, the DNA of a human fits on a DVD, the smallest genome leaves plenty of room for music on a floppy disk.
    If there is no external “layered controller” how does biological growth occur?

    It is coded from the inside (with the code in the DNA). Mandelbrot could just walk from lecture-room-to-lecture-room and “seed” the entire field of fractals with “the Mandelbrot DNA”, the equation of Z=Z^2+C and the well-known Mandelbrot Set sprung up in zillions of copies. There is a great diversity from its original rendering; either by the number of recursive iterations used, or by slightly tweaking the “code”.
    The code in the DNA, though my research now shows evidence that it is fractal (its self-similar repetitions e.g. in FractoGem-s,

    http://www.fractogem.com

    are plain to see), is not comprised (and certainly will not be, for some time) as succintly as e=mc^2 or Z=Z^2+C.

    Yet, if the Universe is, mind-boggling as it astounds us, known to be governed by “divine mathematics”- are we to say that life (biological growth) can not be?

    Mandelbrot’ design is pretty intelligent. We have yet to see one comparable from a chimp…

    pellionisz_at_junkdna.com

  38. “Junk DNA” as a scientific term, would have lived 35 years on the 30th of June. Dr. Ohno introduced the term in 1972, and the notion is dead by the release of the first comprehensive results of US government (NIH) sponsored ENCODE.

    The “portal to junk DNA” at

    http://www.junkdna.com

    had to endure a 10-15 times larger peak of load compared to the daily average, and subsequently had to be switched to a more protected, higher capacity server. (New DNS is propagating and the site is already reachable by some). The “portal” reports on ENCODE. Pls. let your friends know about the “overload problem” and new availability at the same http://www.junkdna.com domain. In case of problems, email pellionisz_at_yahoo.com

  39. [...] I expect he will be delighted by the work of Solexa. Here is the latest from Dr. Pellionisz comment 87430 These icons link to social bookmarking sites where readers can share and discover new web [...]

  40. […] for several years before getting separated from it. I have promoted the work of another ET-ID fan, Dr. Andras Pellionisz. And last but not least, UD’s very own Rob Sheldon offered his hypothesis that comets […]

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