Uncommon Despair

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On UcD, Salvador Cordova, makes the common and fallacious argument that ID somehow predicted function in ‘junk DNA’. In fact, there is no logical foundation for this claim as ID lacks predictive power beyond ‘Darwinism does not explain X’. At most Sal can claim that people who are also proponents of ID have ‘predicted’ function for Junk DNA. But as such they are not much different from scientists who have predicted function for Junk DNA as well. Where they differ is in what motivated them to reach such a conclusion.

Cordova Wrote:

ID theory has provided positive inspiration toward scientific inquiry and participating in the reversal of “the greatest mistake in the history molecular biology”, a mistake inspired by Darwinist dogma.

ID has contributed little either in predicting or establishing function in ‘Junk DNA’ but it also seems to be basing its claims on further ignorance about the origin and evolution of the term Junk DNA (which originated from the ideas of proponents of neutral evolution and was originally limited to refer to pseudogenes). While it should not come as a surprise that ID attempts to ride on the coat tails of real science, such an attempt can be quickly countered.

Nevertheless, even in his enthusiasm, Sal seems to have downgraded ID’s contribution to ‘positive inspiration’. Even ID proponents seem to shy away from making claims that ID is scientifically fertile and are willing to settle for ‘inspirational’.

Already in 1998 Should Scientists Scrap the Notion of Junk DNA? Bob Kuska describes how science had come to realize the many treasures in ‘junk DNA”.

(Journal of the National Cancer Institute, Volume 90, Number 14 Pp. 1032-1033)

and Bring in Da Noise, Bring in Da Junk–the Semantics of Junk DNA

The term ‘Junk DNA’ is somehow unfortunately chosen as it has led quite a few creationists like Sal astray into believing that ‘Junk DNA’ cannot have function or that it was inspired by Darwinian dogma.

Let’s explore this in some more detail. More generally, the term junk DNA refers to ‘non coding’ DNA, that is DNA which is not directly expressed as proteins. In other words, Junk DNA denotes parts of the DNA for which no function has (yet) been identified. Since science has established that there exist strongly conserved regions of DNA with no identifiable function, it has concluded that this may point to a yet unknown function of Junk DNA.

The term Junk DNA can be traced back to an article by Ohno titled “, “So Much ‘Junk’ DNA in Our Genome.”, published in 1972. What many have forgotten is that Ohno was commenting on a particular form of ‘junk’ namely pseudogenes and the term “Junk DNA” slowly took on a different meaning to include all non-coding sequences (sequences that do not produce proteins).

See for instance: B. Kuska, Should Scientists Scrap the Notion of Junk DNA? JNCI Journal of the National Cancer Institute 1998 90(14):1032-1033

Recent findings by scientists have shown that the use of the term Junk to describe non-coding DNA has been unfortunate as evidence has been found that shows that some of the non-coding DNA indeed has function (as many had already suspected based on Darwinian arguments). For instance, there are regulatory elements which regulate the actually gene expression, which reside in non-coding parts of the genome.

The literature seems to understand that Junk DNA does not mean ‘without function’.

Note that the term “junk DNA” is not a term of art. It may simply mean DNA whilst they have a function - do not code for protein at all. It may also mean DNA sequences that appear to have no function at all.

Source: An Introduction to Genetic Engineering, Life Sciences and the Law By George Wei 2002 SUP

At Genomicron, T Ryan Gregory provides us with an exquisite overview of Junk DNA

T Ryan Gregory Wrote:

To satisfy this expectation, creationist authors (borrowing, of course, from the work of molecular biologists, as they do no such research themselves) simply equivocate the various types of non-coding DNA, and mistakenly suggest that functions discovered for a few examples of some types of non-coding sequences indicate functions for all (see Max 2002 for a cogent rebuttal to these creationist confusions).

Now remember that ID can at most observe that there exists DNA for which no function has been found and allow our ignorance to lead to a design conclusion. However, ID lacks the predictive capability to make a claim that Junk DNA has a function. On the other hands, science, facing the hard tasks of reducing our ignorance through research, hypothesis building has reduced our ignorance about Junk DNA by finding how some ‘Junk DNA’ serves a function after all.

Wikipedia identifies much research in this area and despite the claims by some ID proponents that ID somehow inspired or predicted Junk DNA, the ‘shocking’ reality is that ID was mostly absent from the scene.

Why ID is scientifically without much value

So why is ID doomed to remain scientifically irrelevant? For the simple reason that it cannot compete with ‘we don’t know’. In other words, at best, ID can be ‘we don’t know’, at worst it becomes a gap theory where our ignorance is replaced with a term ‘intelligent design’.

That this is the case is not hard to understand. ID is based on the observation or at least argument that a particular feature cannot (yet) be explained by science. Since ID however does not provide any independent hypothesis to explain the feature, it cannot compete with the ‘we don’t know’ hypothesis. In other words, at best, ID is an argument from ignorance: We don’t know, thus designed. ID proponents tend to shroud this by using unnecessary terminology such as complexity (which basically means the same as ‘we don’t know’) and specification (which basically means nothing more that ‘it has a function’). Worse, once science has identified an explanation for the system, and ‘design’ quickly disappears.

Ryan Nichols, author of “ The Vacuity of Intelligent Design Theory” noticed how ID proponents are often unaware of the limited thesis proposed by Dembski:

Ryan Nichols Wrote:

Before I proceed, however, I note that Dembski makes an important concession to his critics. He refuses to make the second assumption noted above. When the EF implies that certain systems are intelligently designed, Dembski does not think it follows that there is some intelligent designer or other. He says that, “even though in practice inferring design is the first step in identifying an intelligent agent, taken by itself design does not require that such an agent be posited. The notion of design that emerges from the design inference must not be confused with intelligent agency” (TDI, 227, my emphasis).

Source: Ryan Nichols, Scientific content, testability, and the vacuity of Intelligent Design theory, The American Catholic Philosophical Quarterly, 2003 ,vol. 77 ,no 4 ,pp. 591 - 611

Nichols continues to describe why ID is also doomed to remain scientifically vacuous.

Proponents of Intelligent Design theory seek to ground a scientific research program that appeals to teleology within the context of biological explanation. As such, Intelligent Design theory must contain principles to guide researchers. I argue for a disjunction: either Dembski’s ID theory lacks content, or it succumbs to the methodological problems associated with creation science-problems that Dembski explicitly attempts to avoid. The only concept of a designer permitted by Dembski’s Explanatory Filter is too weak to give the sorts of explanations which we are entitled to expect from those sciences, such as archeology, that use effect-to-cause reasoning. The new spin put upon ID theory-that it is best construed as a ‘metascientific hypothesis’-fails for roughly the same reason.

See also one of my earlier postings showing why ID is doomed to remain scientifically irrelevant.

The reason ID fails is simple, it lacks any predictive power beyond ‘X cannot be explained by Y’. In case of Junk DNA, there is simply no logical foundation for ID’s claim that ‘Junk DNA’ needs to have function, unless one presumes capabilities, or aspects of the designer. But ID is clear that it is unable to address these issues and that these issues are separate from ID.

Now, historically, the reason why ID can claim that it made successful predictions is because contrary to its claims, it did make presumptions about its designer and argued that God would not be wasteful. So now ID is faced with an interesting conundrum, either it admits that it was the assumptions about their God not being wasteful which lead to this ‘prediction’, or accept that it lacks any scientific foundation for its claims. Of course, either way, there is no good scientific reason to presume that God would not be wasteful, or God would surely not have created antelopes and cheetash :-)

So how did ID make this ‘prediction’ ? For this we need to understand the history of this prediction, which, to noone’s surprise, can be found in creationist arguments.

See ‘Junk’ DNA: evolutionary discards or God’s tools?

It’s time to put to rest yet another “confusion by design”

As I pointed out elsewhere almost a year ago:

The idea that Junk DNA has function has no roots in ID unless it relies on the premise of a Christian God and even then the argument has no predictive value since creationists argue on one hand that God designed all life and that thus design was initially perfect, leading to the conclusion of no ‘junk DNA’ or Junk DNA will have function. Or they argue that Junk DNA can be explained by the Fall, leading to a deterioration of the genome. Since ID provides no logical link between its scientific premises and its prediction about Junk DNA, the conclusion is inescapable, its prediction is guided by theology not science.

In other words ID cannot make predictions about “Junk DNA” which follow from their premise. All it can do is detect complex specified information and since junk DNA has no specified function yet, it cannot make any such predictions. Unless there is another premise which guides ID such as the efficiency of the Designer or the Designer’s Creation being perfect in the sense of no superfluous systems or DNA which has no function. So either ID is vacuous scientifically or it makes predictions which follow from particular assumptions about the Designer. The latter one is contrary to ID’s approach and thus has to be rejected, unless one links ID to its historical and metaphysical roots.

Source

On UcD Campana observes in response to Dembski fishing for evidence that Junk DNA was inspired by Darwinism (how hard is it to do the necessary research I wonder?)

Dembski Wrote:

I suspect that the “junk DNA” hypothesis was originally made on explicitly Darwinian grounds. Can someone provide chapter and verse? Clearly, in the absence of the Darwinian interpretation, the default assumption would have been that repetitive nucleotide sequences must have some unknown function.

Campana Wrote:

I just got my hands on Ohno’s paper. It seems like the link provided by Pellionisz pretty well summarizes what is going on here. Ohno was looking for function, and the paper does seem something like a lament. However, this only appears to negate Bill’s postulate that “the ‘junk DNA’ hypothesis was originally made on explicitly Darwinian grounds.”

By using the term “junk DNA”, Ohno was offering terminology to summarize one proposal for the role of repetitive DNA.

The Ohno paper is one of a number of papers in a collection, and another interesting paper in the anthology, by R.J. Britten, offers an overview of early 70’s perspectives on the origin/purpose of the repetitive DNA. Britten reveals that, “Whether the repeated DNA in its now widely interspersed state is simply spacer between genes or carries out an active role is the subject of intensive current investigation.” On the next page, Britten offers 9 possible roles of repetitive DNA, including only one the possibility that it was “2. CARRIED ALONG (Parasitic or garbage).” By using the term “junk DNA”, Ohno was offering terminology to summarize the “CARRIED ALONG” proposal for the role of repetitive DNA.

Based on this Britten quote above, and a brief review of all of the hits on PubMed for “junk dna,” it seems that scientists have been looking for functions in the “junk” all along. As Bill suspected, the default scientific position has been to look for function, as well it should.

So will ID and Dembski continue to repeat its claims? We shall see. If history is a predictor of the future then we may expect more…

My thanks go out to my dear friend and YEC’er Salvador “Darwinian TE (Theistic Evolution) just doesn’t cut it scientifically” Cordova and Uncle William “Bill” Dembski without whom this useful tutorial would not have been possible.

141 Comments

Isn’t there some conjecture, based in the Selfish Gene theory, that some “junk DNA” is viral DNA that’s been “benignly” inserted into various genomes over the course of biological history and thereafter replicated by the various genomes’ organisms? Matt Ridley discusses this in _Genome_.

There are many explanations for “Junk DNA”, and selfish DNA is one explanation. However there are many other mechanisms that can contribute to non-coding DNA. Of course non coding means, non coding for protein which does not mean that it does not have any function at all.

And, of course, we can go back much further in time before 1998 to find examples of publications that find functionality for “junk DNA”. See, for example,

Zuckerkandl. “A general function of noncoding polynucleotide sequences”, Molecular Biology Reports. Volume 7, Numbers 1-3 / May, 1981.

PvM wrote: “Of course non coding means, non coding for protein which does not mean that it does not have any function at all.”

From my understanding, there always the possibility that even non coding DNA actually does code for protein. It is a matter of convention rather than an actual knowledge about transcription/translation of a DNA sequence when deciding whether or not an ORF should be deemed coding (this is often decided by the length of the ORF).

“Since science has established that there exist strongly conserved regions of DNA with no identifiable function, it has concluded that this may point to a yet unknown function of Junk DNA.”

Pardon my humanities major-ignorance, but… what on earth is going through IDist’s minds when they read a sentence like the above as some sort of vindication of their position, when as I understand it the entire notion of a “conserved sequence” is of a piece with the hypothesis of common descent, both in its existence and in the methodologies by which one is discovered?

Thanks for the nod. In response to there being proposed functions in the literature, I will quote from my Genomicron post.

Those who complain about a supposed unilateral neglect of potential functions for non-coding DNA simply have been reading the wrong literature. In fact, quite a lengthy list of proposed functions for non-coding DNA could be compiled (for an early version, see Bostock 1971). Examples include buffering against mutations (e.g., Comings 1972; Patrushev and Minkevich 2006) or retroviruses (e.g., Bremmerman 1987) or fluctuations in intracellular solute concentrations (Vinogradov 1998), serving as binding sites for regulatory molecules (Zuckerkandl 1981), facilitating recombination (e.g., Comings 1972; Gall 1981; Comeron 2001), inhibiting recombination (Zuckerkandl and Hennig 1995), influencing gene expression (Britten and Davidson 1969; Georgiev 1969; Nowak 1994; Zuckerkandl and Hennig 1995; Zuckerkandl 1997), increasing evolutionary flexibility (e.g., Britten and Davidson 1969, 1971; Jain 1980; reviewed critically in Doolittle 1982), maintaining chromosome structure and behaviour (e.g., Walker et al. 1969; Yunis and Yasmineh 1971; Bennett 1982; Zuckerkandl and Hennig 1995), coordingating genome function (Shapiro and von Sternberg 2005), and providing multiple copies of genes to be recruited when needed (Roels 1966).

Does non-coding DNA have a function? Some of it does, to be sure. Some of it is involved in chromosome structure and cell division (e.g., telomeres, centromeres). Some of it is undoubtedly regulatory in nature. Some of it is involved in alternative splicing (Kondrashov et al. 2003). A fair portion of it in various genomes shows signs of being evolutionarily conserved, which may imply function (Bejerano et al. 2004; Andolfatto 2005; Kondrashov 2005; Woolfe et al. 2005; Halligan and Keightley 2006). On the other hand, the largest fraction is comprised of transposable elements Рsome of which become co-opted by the host genome, some of which play major role in generating genomic variation, some of which may be involved in cellular stress response, and yet others of which remain detrimental to host fitness (Kidwell and Lisch 2001; Bi̩mont and Vieira 2006). The upshot is that some non-coding DNA is most certainly functional Рbut when it is, this usually makes sense only in an evolutionary context, particularly through processes like co-option. More broadly, those who would attribute a universal function for non-coding DNA must bear the following in mind: any proposed function for all non-coding DNA must explain why an onion or a grasshopper needs five times more of it than anyone reading this sentence.

http://genomicron.blogspot.com/2007[…]unk-dna.html

I plan to post more in the series on noncoding DNA, but it’s dependent on finding the time. For now, the above-mentioned posting has a fair bit of background on Ohno’s concept of “junk DNA” and the modern incarnation of the term. And yes, most of the functions being identified for noncoding DNA are dependent an evolutionary framework, including the concept of co-option which is usually rejected outright by IDers because, when applied in a different context, it solves the irreducible complexity issue.

Ive got a series of posts up on this topic– ‘ID vs ERVs’.

Im up to seven, and Ive got another 30 pages of Sternberg to get through. Ugh.

From www.genomesize.com Human is 3.5 pg/cell

Number of mammals: 438 Smallest mammalian genome size: 1.73pg, Miniopterus schreibersi, Bent-winged bat Largest mammalian genome size: 8.40pg, Tympanoctomys barrerae, Red viscacha rat Mean for mammals: 3.47pg ± 0.04

Avian genome sizes tend to be smaller.

I’ve no doubt that much noncoding DNA is functional, introns, regulatory regions, etc..As shown by phylogenetic conservation.

Some of it is clearly probably just genome parasites and adventitious accumulations. This is implied by the fact that genome sizes vary widely even within mammals and between mammals and avians. Not seeing how or why the the actual functional genome varies all that much between say mammals. Does the red rat really have twice as many genes as a human? Or a bat half as many?

You failed to attribute Sal’s quote (“the greatest mistake in the history molecular biology”) to John S. Mattick, Director of the Institute for Molecular Bioscience at the University of Queesnland in Brisbane Australia.

You also failed to point out that Sal referenced Andreas Pellionisz for the quote:

“Most Darwinists erroneously predicted that 98.7% of the DNA was devoid of function (“junk”), while the ID/ET theory correctly predicted some yet to be decoded function of junkDNA.”

It is not Sal Cordova who says that Darwinism made a failed prediction, it is the Darwinists themselves. Sal just reported it.

The issue is predictive power. If Darwinism can only predict things after the fact, then it has no predictive power to speak of.

However, the notion of junk DNA having function is perfectly in line with a design paradigm.

Cordova had all this explained to him in great detail on numerous occasions in the past. You think anything ever gets through that numb skull?

And in any case… Because ID “biology” can best be classified as an amalgam of design PLUS natural mechanisms, I don’t see why an IDer wouldn’t expect some truly functionless genomic sequences to arise. They will arise naturally, even in designs that start off “perfect”. Even Behe accepts that.

However, the notion of junk DNA having function is perfectly in line with a design paradigm.

Anything is in line with a design paradigm since it can explain anything and thus nothing. Scientifically vacuous in other words

chunkdz, FYI: It’s Andras not Andreas.

It’s not clear whether he is a world-renowned DNA researcher. Certainly his self-promotional materials would suggest that but the rest of the record remains quite uncertain. His background is mathematical modeling of neurophysiology.

If anything, his fascination and subsequent mis-use of the term “junkDNA” doesn’t help matters.

The ID robots never did any work to explain just what the non-coding regions are for. Yet they will continue to argue that just because their assumption was based on theology doesn’t make it wrong (It just makes it non-science).

What is truly ironic is that these new findings show how evolution has far more opportunities than even the strongest skeptics would have imagined… In other words, the moment we lift the veil of our ignorance we find how RNA networks and evolvability enhance our understanding how evolution works.

In the mean time ID is still polishing off ‘poof’…

It’s hardly surprising that those who read the Bible literally will read the word “junk” literally.

As late as 1998, Dawkins was predicting that junk DNA is useless.

Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA. … Can we measure the information capacity of that portion of the genome which is actually used? We can at least estimate it. In the case of the human genome it is about 2% - considerably less than the proportion of my hard disc that I have ever used since I bought it.” - Richard Dawkins, “The Information Challenge.” the skeptic. 18,4. Autumn 1998.

…and that this prediction seems to fit with his blind, pitiless, indifferent mechanism. Does this mean that if conversely they were to find 100% functionality in the human genome that this would support a purposeful design inference? Interestingly, it seems that some of Dawkins’ “junk tandem repeat DNA” is actually proving to be quite functional after all.

…and that this prediction seems to fit with his blind, pitiless, indifferent mechanism. Does this mean that if conversely they were to find 100% functionality in the human genome that this would support a purposeful design inference? Interestingly, it seems that some of Dawkins’ “junk tandem repeat DNA” is actually proving to be quite functional after all.

Anything would support a design inference, except actual knowledge. As far as irony is concerned, I truly could not care less about Dawkins and his claims. Remember though that it was the ignorance of ID proponents about the use and the predictions of junk DNA which led them astray. If they relied too much on the popular science by Dawkins rather than on the scientific literature, then fine, I can understand their confusion. Seems that ID has too much of a fixation on Dawkins and not enough on the science of evolution.

Science has moved on my friend and ID has yet to catch up. Same problem applies to many ID ‘arguments’ such as Meyer’s claims about the Cambrian etc.

So we agree that Junk DNA was not neccessarily a Darwinian prediction and that it were scientists not IDers who found the predicted functions hiding in the ‘junk’?

Umm… Dawkins didn’t “predict” that 98% of the human genome was junk. He incorrectly inferred it. For that matter I don’t think “Darwinists” predicted that 98% of a genome would be composed of completely useless sequence. I think most biologists were somewhat surprised when the level of non-translated DNA was found to be so high. Sequence homology without selection or recent ancestry would be something “Darwinists” wouldn’t expect.

As for “junk tandem repeat DNA”: Well, some of that can definitely be deleted, transposed or rearranged with no discernable effect. Is that a prediction of ID? That some sequences arise that are “junk” is simply basic biology.

Chunkdz wrote: “As late as 1998, Dawkins was predicting that junk DNA is useless.”

Baloney. You seem to have trouble reading. The claim you quote isn’t remotely close to being categorical:

Dawkins: “Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.…”

He’s writing about only two subclasses, and specified them, so you simply lie and claim that he was talking about the entire category.

“…and that this prediction seems to fit with his blind, pitiless, indifferent mechanism. Does this mean that if conversely they were to find 100% functionality in the human genome that this would support a purposeful design inference?”

Only if that’s what you hypothesized the mechanism of the purposeful design to be. Oh, but you lack the confidence, integrity, and honesty to make a real, testable prediction.

“Interestingly, it seems that some of Dawkins’ “junk tandem repeat DNA” is actually proving to be quite functional after all.”

Some? EXACTLY how much, chunkdz? MET predicts WHICH “junk” DNA is most likely to have function, and that’s where real scientists look, while sophists like you pretend that this tiny minority is representative of the entire category.

FWIW: The idea that 100% of the human genome has a proximate function is an assertion that can be found in the YEC literature. Biologists would be surprised if that was the case, given what we currently understand of the biochemical mechanisms behind DNA replication and modification. And wouldn’t you know it, 100% of the human genome is not conserved or necessary.

Genomics. 2002 Sep;80(3):331-43. Links The human endogenous retrovirus family HERV-K(HML-3).Mayer J, Meese EU. Human Genetics, Medical Faculty, University of Saar, Homburg, Germany. [Enable javascript to see this email address.]

A substantial amount of the human genome is composed of human endogenous retroviruses (HERVs). Manifold HERV families have been identified, among them several so-called HERV-K(HML) families. Although the HERV-K(HML-2) family has been studied in detail, other HERV-K families are not as well characterized. We describe here the HERV-K HML-3 family in more detail. We estimate that there are about 140 proviral loci or remains of such per haploid genome. Most loci are severely mutated. Proviruses displaying larger deletions in gag and pol are common. A multiple alignment of 73 HERV-K(HML-3) sequences displays several potentially important differences compared with the HERVK9I sequence in Repbase. A consensus sequence with open reading frames for all retroviral genes was generated, for which intact dUTPase motifs and env gene variants with different coding capacities are observed. Phylogenetic analysis shows near-monophyly with distinction of two closely related subgroups. Proviruses formed about 36 million years ago. However, no continuous activity through primate evolution is indicated.

Speaking of ID predictions, a nontrivial amount of the human genome is composed of defective retroviruses. These are relicts, nonfunctional as viruses, and ancient by common descent, being found in apes and old world monkeys. These are the molecular equivalent of broken toys found in an old basement. Or genomic fossils.

1. This IMO, is evidence for sloppy design. Either the flying spaghetti monster is a lazy and haphazard worker or just maybe it doesn’t exist. If one is going to know the designer through his products, it is hard to escape the conclusion that he isn’t very good at it.

2. Getting back to the real world, these relicts would seem to be DNA without any real function, noncoding DNA of neutral significance. If memory serves me, it is thought by some that a few sequences have been coopted to serve functions subsequently. A good example of chance and necessity working with what is available.

I’ll note in passing that this virus has recently been recreated in vitro, the phoenix retrovirus. There is now no doubt that it was an ancient retrovirus. Can the IDers create life like molecular biologists can? Hah!

Outside of the ID debate (my blog is intended to be about science outreach only), I will be putting together a post about “Junk DNA Q&A”, so please let me know your questions if you would like to see them included.

http://genomicron.blogspot.com/2007[…]unk-dna.html

This whole noncoding functional versus nonfunctional is a little too simplistic.

Theory 1. It is junk DNA, no use.

Theory 2. Noncoding is all functional.

There is of course at least another option.

Theory 3. Some noncoding is functional, some is not doing anything notable.

Comparison with the chimp and macaque genomic sequences goes a long way towards showing that Theory 3 is correct. As well as a huge amount of other data. Fortunately, not being IDers, scientists can design experiments and test each and every segment if they want to by knockouts, genome comparisons, and so on.

Hmmm, Predictions of scientific materialism compared to predictions of theism…Well let’s see how they compare.

1. Materialism did not predict the big bang, Yet Theism always said the universe was created. 2. Materialism did not predict a sub-atomic (quantum) world that blatantly defies our concepts of time and space, Yet Theism always said the universe is the craftsmanship of God who is not limited by time or space. 3. Materialism did not predict the fact that time, as we understand it, comes to a complete stop at the speed of light, as revealed by Einstein’s theory of relativity, Yet Theism always said that God exists in a timeless eternity. 4. Materialism did not predict the stunning precision for the underlying universal constants, for the universe, found in the Anthropic Principle, Yet Theism always said God laid the foundation of the universe, so the stunning clockwork precision found for the various universal constants is not at all unexpected for Theism. 5. Materialism did not predict the fact that the DNA code is, according to Bill Gates, far, far more advanced than any computer code ever written by man, Yet Theism would of naturally expected this level of complexity in the DNA code. 6. Materialism presumed a extremely beneficial and flexible mutation rate for DNA, which is not the case at all. Yet Theism would have naturally presumed such a high if not, what very well may be, complete negative mutation rate to an organism’s DNA. 7. Materialism presumed a very simple first life form. Yet the simplest life ever found on Earth is, according to Geneticist Michael Denton PhD., far more complex than any machine man has made through concerted effort. Theism would of naturally expected this. 8. Materialism predicted that it took a very long time for life to develop on earth, Yet we find evidence for photo-synthetic life in the oldest sedimentary rocks ever found on earth (Sarah Simpson, Scientific American, 2003). Theism would have expected this sudden appearance of life on earth. 9. Materialism predicted the gradual unfolding of life to be self-evident in the fossil record, The Cambrian Explosion, by itself, destroys this myth. Theism would of expected such sudden appearance of the many different fossils in the Cambrian explosion.

Yep, your right! We shouldn’t dare question the predictive power of something that has been so accurate.

raven: “This whole noncoding functional versus nonfunctional is a little too simplistic.”

Yes, but you aren’t helping things by muddying the categories. No molecular biologist is claiming that the category “noncoding” is the same as the category “junk.”

“…Theory 3. Some noncoding is functional, some is not doing anything notable.”

This needs to go further. MET predicts which noncoding DNA is most likely to have a function, too.

chunkdz said:

*snip of Dawkins quote and Pellionisz comment*

Well you didnt read my posts, chunkdz. Im going to run off and cry now.

LOL!

Materialism did not predict the fact that time, as we understand it, comes to a complete stop at the speed of light, as revealed by Einstein’s theory of relativity…

You just contradicted yourself, Philip; in fact, you pretty much discredited your whole argument. “Einstein’s theory of relativity” is a materialistic theory, not a theistic one.

Is it sad that I can’t tell whether Philip Cunningham’s post was serious or a satire?

I beg to differ, Materialism presumed time and distance to be constant which was shatter by relativity. Theism always had a tenet of a timeless dimension

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Philip Cunningham…

Those are some great predictions; please bring them to the next “ID is not religion” trial.

Normally, I feel that grammar corrections are a waste of time, so when you wrote:

“Yep, your right!” - I forgave.

However: “Theism would of naturally expected this.” and “Theism would of expected such sudden appearance of the many different fossils in the Cambrian explosion.”

Yikes! “Would of”?!? The contraction for “would have” is “would’ve”. Please clean that up before you submit it to the court.

Yes, and how do planets form? How do stars coalesce, produce complex and ordered magnetic phenomena, and eventually create shells of different materials inside? How do masers exist near some stars? How do collated beams of matter produce narrow beams of radiation coming from exploded stars (pulsars)? Snowflakes become intricately ordered in what manner? How do dendritic gold and silver form, and become exquisitely and beautifully patterned arrangements of matter when previously they had just been dissolved in hot water? How are Platonic solids formed in the ground by pyrite and gold (rarely) crystals? How do ordered channel networks form from mere runoff of precipitated water?

These examples you point out, all exibit a pattern of information that is inherent in the material itself.

And how much thinking did it take to come up with that answer? I’ll tell you, it was none. You’ve droned that pathetic mantra over and over again (true, I’ve followed the thread little, but that theme recurs so constantly I could hardly have missed it), without explaining, without dealing with any details, and without acknowledging the differences between the sorts of ordering which occur.

You only have this stock, uncomprehending “answer”, you have absolutely no means of discussing how clouds of gas collapse upon themselves, produce intricate and varied magnetic patterns, actually produce the gold, iron, and sulfur (gold and pyrite) out of hydrogen and helium, and sometimes end up with magnetic forces collimating jets of gas and producing narrow beams of photons.

Because you have no capacity for doing anything but quoting, you again cut and paste, committing your usual fallacy of argumentum ad verecundiam.

That is to say that no further information input was required to make the material do what it naturally does.

Unfortunately, you don’t know that, and you have no support for that contention. Indeed, I mentioned any number of phenomena which interact with their environments (hint, this involves information exchanges which influence further developments in the various interacting systems) to produce self-ordering, and of course you simply deny science with your decidedly non-knowledgeable response.

What is more, once upon a time you wrote this:

Entropy is the primary tenet of the second law of thermodynamics.(one of the most validated laws in science) Which, in simple terms, means things tend to fall apart, they never tend to put themselves together.

Very simple, and very inaccurate. And it was what I was primarily responding to in the first half (or so) of my post. My examples, as well as those of others, completely demolish that claim, while you shift the goalposts to argue something else in “reply”.

That is what differentiates living matter from non living matter.

So life violates SLOT? Are you really that incapable of discussing science?

A completely separate type of information is readily apparent in the DNA code that is not a part of nor a resultant product of the material that it is encoded on. Thus this quote …

“There is no known law of nature, no known process and no known sequence of events which can cause information to originate by itself in matter.” Werner Gitt, “In the Beginning was Information”, 1997, p. 106. (Dr. Gitt was the Director at the German Federal Institute of Physics and Technology)

Non-sequitur (even if the Gitt was stupid enough to believe as you do), as information has had to increase throughout cosmic evolution, as well as in biological evolution. Nevertheless, his name “Gitt” is well given, as the claim is completely bogus. Information increases with entropy. You’ve been given the sources as well, if you’re Charlie Wagner as you seem, and either way there’s hardly any excuse for you to be pig-ignorant when you pretend to be knowledgeable enough to discuss these things with people who really do know science.

That is the main question that is revelent to the debate over life’s origin. Where is this non-inherent information coming from?

Why don’t you take a course, and find out rather than reveling in your ignorance?

Thus this quote..

“But in all the reading I’ve done in the life-sciences literature, I’ve never found a mutation that added information… All point mutations that have been studied on the molecular level turn out to reduce the genetic information and not increase it.” Lee Spetner (Ph.D. Physics — MIT)

Oh good, another fallacious appeal to authority, using someone who isn’t even qualified to speak expertly about biology (that is, proper authorities may be appealed to, but do not carry the main argument in any intellectual discussion), and he’s an anti-evolutionist to boot. Just your caliber, “Philip”, everything wrong, no competence in dealing with the issues, and not even a very intelligent use of your fallacy.

Thus if information is not self generating from the matter or from some natural law then it must come from some outside source.

Information unavoidably increases with entropy increases. It’s because your premises (like your whole range of argumentation) are faulty that you “reach” your faulty conclusion.

Those are the only options there are for the orgination of this information in the DNA code! I’ve seen naturalists try to pass off all sorts of mutations to DNA as a gain in information and they have all come up short upon closer inspection. This is the number one and main question upon which the whole theory of evolution rises or falls! Where is the information coming from?

Only a true ignoramus would have a problem with that. Obviously you have no worthwhile knowledge of evolution.

The whole philosophy of materialism, upon which evolution is built

Complete nonsense. Evolution, like all science, is built upon empiricism. “Material” and “matter” are understood according to empirical science, rather than vice versa. True, “materialism” is often conflated with “physicalism”, but that still leaves “physical” and “material” in question, not providing answers nor any actual guidance to the practice of science.

There are various philosophies of realism (which recently took a hit via quantum experimentation), non-realism, and phenomenalism. Those are more the philosophies that serious scientists espouse, not some amorphous and largely meaningless “materialism” (many scientists do consider themselves to be materialists or physicalists, but these people are generally fairly naive about philosophy).

I realize that you creationists/IDists have to believe that “materialism” is the basis of evolution, you’re just comletely wrong about that (for, as I noted, even as “physicalism” the concept of “materialism” is still at best incomplete). So there you are, the ID/creationist basis for criticizing evolution is what is biased, fallacious, ignorant, and dishonest—and your side can’t even characterize evolutionary science accurately, let alone come up with meaningful arguments against what it fails to grasp.

Glen D http://tinyurl.com/35s39o

One other note relative to the “entroy argument:: Someone, I don’t know who, wrote that even the IDists have given up using the SLOT argument.

I think that many or most did steer clear of such an ignorant PRATT, but recently Genville Sewell’s misunderstanding (more bluntly, misrepresentation) of it has become more popular with IDists, probably because they’ve lost on so many other fronts.

Indeed, Philip seems to be mirroring Sewell’s rambling and incompetent discussion of SLOT on UD and elsewhere. It’s all fine for me, because the more UD and the other IDists branch off into other pseudosciences, the less likely that anyone knowledgeable will ever make the mistake of thinking that ID is science, or even a possible science.

Glen D http://tinyurl.com/35s39o

raven Wrote:

Philip, you have followed the creo script to a T

Actually the “don’t ask, don’t tell” ID script. Classic creationists, and less politically correct IDers (like Behe 10 years ago) would have had no problem answering my simple questions. PC (very appropriate initials!) ignored one question 3 times, and the other twice - if you count his initial answer to the wrong question.

Comment #171885

Posted by Ric on April 25, 2007 9:19 AM (e)

Anyone else think Phil Cunningham is just blindly copying and pasting from creationist sources?

MEEEEEE!!!!

I think, after reading his work (especially on the highly-discredited and abandoned 2nd Law arguments) that he’s just got the “creationist arguing faith” and is doing the early religious-giddy phase of slaying dragons. After he’s been made a fool of long enough, he’ll either see he’s been sorely used by his masters and have a confidence break or, having consistently lost, he’ll declare victory and hang out the rest of the boys in the club.

hoary puccoon:

Furthermore, I believe Francis Crick claimed that junk DNA was ‘a complete surprise.’(The early molecular biologists worked mainly with bacteriophages and E coli, which don’t have much extraneous DNA.)

If Francis Crick said this, I’m surprised. While the existence of introns can reasonably be said to be a surprise, selfish DNA is certainly predictable from natural selection. Crick (with Orgel) definitely did say this:

Natural selection ‘within’ the geneome will favor the indefinite spreading of selfish preferred replicators. Natural selection between genotypes provides a balancing force that attempts to maintain the total amount of selfish DNA at an equilibrium (steady state) level—organisms whose genes contain an excessive proportion of selfish DNA would be at a metabolic disadvantage relative to organisms with less selfish DNA.… It is hard to get beyond generalities of this kind. To do so we would, at least, need to know how much selective disadvantage results from the presence of a given amount of useless DNA.

— L.E. Orgel & F.H.C. Crick, “Selfish DNA: the ultimate parasite,” Nature 284(1980)604

The picture Cordova paints of evolutionary biologists sitting back and working out ‘predictions’ from ‘Darwinism,’ —for all the world like medieval theologians figuring out how many angels could dance on the head of a pin— is the kind of sneaky bias creationists build into their arguments.

On the contrary, working out predictions from a scientific theory is exactly what scientists do, just as in the example by Crick above. In the case noted, the available information was inadequate to make more than a general prediction, but Orgel & Crick were at least able to determine what sort of additional information would be required to make such a prediction. Such predictions provide an invaluable guide to the design of experiments, and even incorrect predictions frequently stimulate scientific progress. The distinction between scientific predictions and the sort of medieval theology you describe is that scientists are always seeking to derive predictions that they can test experimentally, providing a self-correcting mechanism that is crucial to preventing the accumulation of scientific error.

The biggest objection that scientists have to ID/Creationism is not its supernaturalism, but rather its inability to make testable predictions, because a theory that makes no testable predictions is scientifically sterile, and tends to be a roadblock to scientific progress. Whereas a scientist will make his theory as detailed as he can in order to test it–because in science an incorrect theory that can be tested and shown to be wrong is superior to a correct theory that cannot be tested–ID/Creationists keep their doctrine as vague as possible, refusing to hypothesize as to the nature, motivations, intelligence, or competence of their supposed designer, because their true interest is in protecting their doctrine from being disproved rather in than advancing scientific knowledge.

In case it matters, I vote Mr. C. be directed to answer the questions and comments of his interlocutors directly, in his own words, without massive cutting and pasting, or be booted as a troll. He is simply wasting space.

As far as a Theistic philosophy making predictions in science, I want to point out a comment I just read in this May’s issue of Readers Digest. It is called “Boy Genius”. It is a story about Albert Einstein as he was growing up and when he got to America. On page 156 it tells of him talking to a Dutch diplomat at a reception for the National Academy of Sciences. Einstein says to the Diplomat”I’ve just developed a new theory of eternity.”

Now I want to make this point crystal clear. Materialism, Naturalism, Physicalism ,Realism or whatever you want to call the philosophy over science at that time did not make this prediction. Only Theism predicted the reality of an eternity.

That is a concrete prediction!

Syntax Error: mismatched tag at line 31, column 201, byte 1886 at /usr/local/lib/perl5/site_perl/5.12.3/mach/XML/Parser.pm line 187

I want to point out a comment I just read in this May’s issue of Readers Digest.

now why doesn’t it surprise me you’re a fan of reader’s digest?

*yawn*

PvM Wrote:

ID lacks predictive power beyond ‘Darwinism does not explain X’.

This explains what PvM means when he says that ID only predicts negatives.

But it is wrong; ID predicts nothing. (Without specifying the properties and processes of the designer.)

Let us start with facts used to support theories: 1. Same facts can support several theories. For example, r^2 dependence of Newton gravity and GR point sources.

2. Converse facts does not support other theories. Creationism being wrong (no observed creation) does not support evolution.

And go on to predictions used to test theories: 3. Several theories can predict same facts. (So no distinguishing test.) For example, r^2 dependence of Newton gravity and GR point sources.

4. Converse theories does not need to predict facts that test other theories. Creationism (predict creation) does not contradict evolution (could still be correct in between; creation facts need to be established).

But specifically here, from ID there is no predictions at all without a specified designer. EF isn’t predictive. IC has several definitions, isn’t derivable from ID, and is compliant with both ID and evolution. (In fact, predicted by the later.) SC or CSI aren’t defined, isn’t derivable from ID, and would be compliant with both ID and evolution.

I find the insistence that ID makes predictions confusing when scientists mostly agree that ID is entirely sterile. Also confusing is that there seems to be a lack of consistence:

PvM Wrote:

All it can do is detect complex specified information

So here ID is also claimed to predict CSI?! Unfortunately this isn’t true, since there is no consistent and working definition of CSI. And as for IC, it is arguable if it is derivable from ID itself.

So here ID is also claimed to predict CSI?!

Detect… Not predict.

Detect… Not predict.

no, it doesn’t even do that.

since WD’s filter is unusable, ID is not a workable theory, and no work has ever been done to even formulate ID into something that can measurably independently detect ANYTHING, it’s just a lame duck.

the only “detection” is simple observer bias on the part of the inventors of the concept to begin with.

might as well say ID is a “cuteness” detector; has about the same meaning.

no, it doesn’t even do that.

since WD’s filter is unusable, ID is not a workable theory, and no work has ever been done to even formulate ID into something that can measurably independently detect ANYTHING, it’s just a lame duck.

I’d agree with you that WD’s filter is unusable since we lack the data to calculate probabilities for most scenarios relevant to evolution. You are right that other than for some examples involving card games, ID has failed to provide much of a relevant example.

Not that WD has tried. And boy has he tried.

My quote in context

All it can do is detect complex specified information and since junk DNA has no specified function yet, it cannot make any such predictions.

Since ID relies on CSI and since S cannot even be addressed due to lack of specification, ID cannot predict that DNA would have function based on ID’s premises.

Phillip writes…

It is easily shown, mathematically, for it to be fantastically impossible for evolution to ever occur between chimps and man, or chimps and anything else for that matter.

Please do so.

Oh, and please put your answer in standard information theory terms, and show your work.

I’ll wait.

Stevaroni:

Anyone can spin (or cut & paste) bogus calculations showing the “impossibility” for “evolution to ever occur between chimps and man, or chimps and anything else for that matter.” Even assuming he means speciation (another word that anti-evolution activists tend to avoid in favor of more ambiguous terminology), note that he hasn’t even said what he think might have happened instead of speciation from a common ancestor. And I asked 3 times. So I think that he also owes us at least comparison calculations, however bogus, of the probability of independent abiogenesis of two or more lineages of similar eukaryotes, to pick the most commonly implied formal alternative to “speciation by genetic variation and selection.” Otherwise it’s nothing but the same old bait & switch.

Philip’s last post is so stunningly, laughably silly as to make Larry Farfromsane look insightful by comparison…

I want to point out a comment I just read in this May’s issue of Readers Digest…

Is this story corroborated by an independent source, like, say, the Weekly World News?

…It is called “Boy Genius”. It is a story about Albert Einstein as he was growing up and when he got to America. On page 156 it tells of him talking to a Dutch diplomat at a reception for the National Academy of Sciences. Einstein says to the Diplomat”I’ve just developed a new theory of eternity.”

Did either Einstein, or Reader’s Digest, describe in any detail what that theory was? I’ve heard of Einstein’s theory of relativity, but never of his “theory of eternity.”

Now I want to make this point crystal clear. Materialism, Naturalism, Physicalism ,Realism or whatever you want to call the philosophy over science at that time did not make this prediction. Only Theism predicted the reality of an eternity.

No, a PERSON made a STATEMENT. How do you support your assertion that “theism” is responsible for this wonderful (unspecified) insight? Was Einstein a priest or minister at the time? I see “crystal clear” is not your strong suit.

That is a concrete prediction!

Really?! What did it concretely predict?!

Raging Bee,

You missed the point completely. The topic of this thread was junk DNA, so obviously Einstein’s “Theory of Eternity” is … Wait a minute, what was that “theory” again? Oh, never mind.

Still waiting for Philip to answer my questions as well.

Since Phillip does the Gish Gallop so well, you’ll have to wait until eternity

Re “Since Phillip does the Gish Gallop so well, you’ll have to wait until eternity…”

And until then, he’ll just be horsing around, so just say neigh.

Henry

Guess what, Phil: a friend of mine just did some casual research, and found that Einstein’s “theory of eternity” was just a joke about long boring speeches:

On April 25, Einstein paid a visit to the White House to meet with President Warren G. Harding. Afterward he attended a reception at the National Academy of Sciences, where he listened to long, boring speeches. As the evening droned on, he turned to a Dutch diplomat and said, “I’ve just developed a new theory of eternity.”

And your desperate attempt to use a joke as “proof” of ID makes the joke even funnier. “Uncommon Despair” indeed.

I guess that shouldn’t be a surprise, given that so many conspiracy-theories start out as jokes and get picked up by people too ignorant and self-important to understand the concept of humor.

Lee Strobel is a hack journalist, he does not have a PhD.

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This page contains a single entry by PvM published on April 22, 2007 5:47 PM.

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