Uncommon Despair

Posted 22 April 2007 by PvM

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.

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.
— Cordova

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

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).
— T Ryan Gregory

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:

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).
— Ryan Nichols

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?)

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.
— Dembski

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.
— Campana

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

brad daly · 22 April 2007

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_.

PvM · 22 April 2007

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.

Hawks · 23 April 2007

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).

Andrew Lee · 23 April 2007

"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?

TR Gregory · 23 April 2007

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 -- some 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; BiÃ©mont and Vieira 2006). The upshot is that some non-coding DNA is most certainly functional -- but 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/2007/04/word-about-junk-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.

ERV · 23 April 2007

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.

raven · 23 April 2007

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 Â± 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?

chunkdz · 23 April 2007

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.

Unsympathetic reader · 23 April 2007

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.

PvM · 23 April 2007

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

Unsympathetic reader · 23 April 2007

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.

fnxtr · 23 April 2007

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).

PvM · 23 April 2007

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'...

Les Lane · 23 April 2007

It's hardly surprising that those who read the Bible literally will read the word "junk" literally.

chunkdz · 23 April 2007

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.

PvM · 23 April 2007

...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'?

Unsympathetic reader · 23 April 2007

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.

John · 23 April 2007

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.

Unsympathetic reader · 23 April 2007

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.

raven · 23 April 2007

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. jens.mayer@uniklinik-saarland.de 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!

TR Gregory · 23 April 2007

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/2007/04/questions-about-junk-dna.html

raven · 23 April 2007

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.

Philip Cunningham · 23 April 2007

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.

Smokey · 23 April 2007

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.

ERV · 23 April 2007

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!

Raging Bee · 23 April 2007

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.

minimalist · 23 April 2007

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

philip cunningham · 23 April 2007

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

CJO · 23 April 2007

Nope.
It's Poe's Law.

Lazy Day · 23 April 2007

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.

Philip Cunningham · 23 April 2007

Sorry for my grammar Lazy, When is the ID court?

Raging Bee · 23 April 2007

One more thing, Philip: if you want to brag about the "predictive power" of theism, please remember that theists have, at various times, used Bible quotes to "prove" that:

a) the Earth is flat;
b) the Earth stands still;
c) disease is caused by God's will (or demons), not by small invisible things called germs;
d) slavery was the "natural state" of the African race;
e) AIDS is God's punishment of gays for being gay.

Also, you don't cite any actual specific predictions of theism. Are you even serious?

philip cunningam · 23 April 2007

Excuse my texas grammar, I will clean it up. When is court?

dhogaza · 23 April 2007

1. Materialism did not predict the big bang, Yet Theism always said the universe was created

Apparently this sentence was cut off when it was posted. It ends in "about six thousand years ago".

CJO · 23 April 2007

SUBPOENA:
Philip Cunningham, you are ordered to appear in ID court, Feb. 29th, 2009, on either the Brooklyn Bridge or some prime real estate in Florida, we're not sure yet.
PS Bring your bible!

Philip Cunningham · 23 April 2007

Theism would predict that the DNA code has a high level of integrity. Materialism has presupposed that a huge portion of the DNA will be useless. ID proponents predict that in the future we will find that most if not all of the code will be found to have purpose. I remind you that man is still in his infant stage of understanding the DNA code. I remember reading a quantum physicists state that it would take man a billion-trillion CDs to store the information, in the limited mathematical language man now uses, to give the proper locations for how all the molecules are stored in just one human body. This gives some indication to the level of complexity that we are dealing with in the DNA.

raven · 23 April 2007

Phillip: Predictions of scientific materialism compared to predictions of theism...Well let's see how they compare.

Hmmmm, about those creo predictions. The creo creed states that all terrestrial animals got on the Big Boat. Presumably they got off. 99% of them are now extinct. Including all the nonavian dinosaurs. Where are our dinosaurs! We miss our dinosaurs. What is the theist explanation? One theory (of mine) is that it was the result of poor post deluge planning (like the Iraq invasion) and/or incompetent dinosaur husbandry. The materialist explanation is well known. There was no Big Boat holding kangaroos and everything else terrestrial. The dinosaurs died out 65 million years ago almost certainly due to bad luck and a large asteroid impact.

Viscount · 23 April 2007

"a) the Earth is flat;
b) the Earth stands still;
c) disease is caused by God's will (or demons), not by small invisible things called germs;
d) slavery was the "natural state" of the African race;
e) AIDS is God's punishment of gays for being gay."

f) Lightning is caused by gods chucking spears at the ground
g) Bats are birds
h) The moon and sun were formed when Raven stole some light out of a box and flew around, dropping bits of it everywhere
i) pi = 3
j) Spiders are descendants of Arachne, who was turned into a spider for her weaving-related hubris
k) Snakes used to have legs

Viscount · 23 April 2007

Actually that last one isn't far off, but it also predicted that snakes (and donkeys!) could talk, so there you go.

Ryan Nichols · 23 April 2007

Thanks for quoting from my paper on the vacuity of IDT in your post! Reading through your post and the comments, I was reminded of a neglected irony regarding IDT and 'junk DNA', which I didn't mention in my original work on IDT. I refer to Dembski's use of his explanatory filter. The EF offers a probabilistic test for whether something/system/organism is explicable by appeal to natural laws + chance + evolution. Setting aside well-documented flaws with Dembski's use of the probability calculus, consider what the EF would say about 'junk DNA'.

Dembski claims, on the one hand, that IDT would account for the presence of that DNA by appeal to intelligent causes. In other words, what appears to be mere junk would in fact, on further IDT analysis, appear to be the creation of intelligence. However, Dembski never actually applies his explanatory filter to the data surrounding 'junk DNA.' In fact, based on the probability bounds that Dembski sets, and based upon his other examples of the use of the explanatory filter, my hunch is that the explanatory filter would not yield a result that 'junk DNA' is even 'designed' in the first place.

If I am correct about this point, the controversy about the epistemology of the causes of 'junk DNA' surprisingly becomes a stumbling block for the ID Theorist. Appeal to 'junk DNA' does not constitute a telling example against the Darwinian. Naturally, the Darwinian will insist that there are highly plausible explanations of 'junk DNA' from within the realms of natural selection, random mutation and evolutionary genetics. But in addition, the failure of 'junk DNA' to be awarded 'designed' status a la the explanatory filter stands as a wonderful example of the internal inconsistencies plauging ID Theory as well as its inapplicability to actual biological explanation.

Unsympathetic reader · 23 April 2007

Philip Cunningham: "I remember reading a quantum physicists state that it would take man a billion-trillion CDs to store the information, in the limited mathematical language man now uses, to give the proper locations for how all the molecules are stored in just one human body.

You'd also need about the same amount of storage to specify the location of molecules in 70kg of warm water... In practically any shape of container.

Philip Cunningham · 23 April 2007

Ryan, The filter of Dembski is used to determine if a specific molecular "machine" is designed. Yet you criticize it for not being able to explain junk DNA. Nobody really has any idea what is occurring in the "junk" DNA regions. How can you criticize something that nobody really has a good grasp on yet? As well, for the specific molecular "machines" that Dembski's filter is applied to, it presents a compelling mathematical standard that chance has a extremely hard time explaining.

philip cunningam · 23 April 2007

Unsypathetic,
Yet the water won't die if molecules are not properly placed.

normdoering · 23 April 2007

I'd like to see the term "junk DNA" getting junked. I don't like the pejorative nature of the word "junk." You've got to be embarrassed when important functions are found in something you called junk.

Call it "Unknown DNA" until you know for sure. In which case when you do find strings of DNA that are never used you should eventually be able to give them a more "historical" label, like "Vestigial DNA" and "Invader DNA" (from viruses and such).

Lazy Day · 23 April 2007

The next "ID is not religion" trial will start up right after you convince your local school board to insert ID into the science curriculum.

Philip Cunningham (from prediction #6): "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." Philip Cunningham (from comment #171551): "Theism would predict that the DNA code has a high level of integrity."

Which is it?

Philip Cunningham (from comment #171551): "ID proponents predict that in the future we will find that most if not all of the code will be found to have purpose."

LOL! At first, I thought this was just more of your poor grammar - but it is actually a typical example of ID "science". "ID proponents predict that in the future..." - The non-specific, unfalsifiable prediction of the future. A corner stone of ID. "...we [IDists] will find [by reading an ID friendly blog] that most if not all of the code will be found to have purpose [by hard-working scientists who had no need of the God-is-a-complex-craftsman hypothesis]."

Steve Reuland · 23 April 2007

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

As late as 2007, molecular biologists were of the opinion that most "junk DNA" is in fact useless. Or at least, if it has a function it is non-obvious and as of yet still undiscovered. One thing that IDists don't appear to understand is that the issue is not one of junk DNA being functional vs. non-functional. As of yet we have seen some very small amount of junk DNA proven to have a function of sorts, and this number will probably rise, but the vast majority of it still has no known function. Most of it probably never will. ID advocates however pretend as if all junk DNA has been found to be functional (most likely, they just don't know any better), and then go on to congratulate themselves for correctly making a prediction that is neither correct nor predicted.

philip cunningham · 23 April 2007

In ID, The amount of DNA code that serves no function whatsoever is presumed to be nil. Yet establishing a complete 100% functionality for the DNA could be impossible, due to man's limited ability to understand the complexity of the amount of information being handled in the DNA. Yet there may be a threshold of functionality that could be established that would rule out the materialistic presumption of a high level of non-functional DNA. Yet as I stated before, we are still in our infant stage as far as understanding the complexity of the DNA code

jkc · 23 April 2007

Lazy Day: Philip's grammar is the least of his problems. He can't even spell his own name consistently (see comments 171540 and 171566).

Anyway, Mr. Cunning-whatever, can you please provide chapter and verse (so to speak) as to where theism predicts the big bang, sub-atomic particles, relativity, universal constants, DNA, and the Cambrian explosion? These predictions are not part of the theism I hold to nor any that I've ever heard of. Saying that theism proposes that God created the universe is a far cry from making these predictions.

Oh, and while you're at it...can you also tell us when Bill Gates became an expert on DNA?

Steve Reuland · 23 April 2007

In ID, The amount of DNA code that serves no function whatsoever is presumed to be nil.
— philip cunningham

Well then, I guess we can dispense with that crazy ID idea. I didn't think much of it to begin with, but it's good to see that it's incompatible with the evidence.

Yet establishing a complete 100% functionality for the DNA could be impossible, due to man's limited ability to understand the complexity of the amount of information being handled in the DNA.

Oh darn. So it turns out that the ID "prediction" isn't testable after all. I suppose they will go on thinking that all of the genome is functional no matter what the data actually say.

Yet there may be a threshold of functionality that could be established that would rule out the materialistic presumption of a high level of non-functional DNA.

What "presumption" are you talking about? Prior to the advent of genomics, it was broadly assumed that the entire genome would be functional. It came as quite a surprise when that turned out not to be the case.

tacitus · 23 April 2007

In ID, The amount of DNA code that serves no function whatsoever is presumed to be nil.

Why? What is so contrary to ID about DNA regions that serves no function? Why couldn't a designer have created DNA with junk regions? Perhaps it was a necessary result of the way DNA was initially constructed/designed? IDists continually argue that ID cannot say anything about the nature of the designer, so who are we to say that a designer must have created DNA with zero non-functioning parts?

This is an excellent example of why ID has no predictive power whatsoever.

Hawks · 23 April 2007

Philip cunningham wrote:
In ID, The amount of DNA code that serves no function whatsoever is presumed to be nil.

The sad part of this statement is that even some "prominent" ID proponents think that there is something to it. The only way you can presume this is true,is if you also presume that the designer would not put any non-functional DNA in organisms. But to do that you would have to say something about the intentions of the designer. But guess what, ID "theory" explicitly and intentionally says NOTHING about the designer.

Why is it that ID supporters don't even understand their own "theory"?

raven · 23 April 2007

Philip cunningham wrote: In ID, The amount of DNA code that serves no function whatsoever is presumed to be nil.

Well at least this is nonfuzzy enough to be comprehensible. We already know enough to think this isn't close to being so. 1. Already posted above this thread, summary.

"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." 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.

2. Pseudogenes, more fossils. 3. Comparison of human, chimp, and macaque genome sequences indicates that much of the noncoding DNA is rapidly evolving, indicating few if any sequence constraints. 4. At least the function of noncoding can be tested using present technology. Sequencing closely related genomes is one way. Identifying functions is another. One can always make knockouts and empirically test what phenotype presence or absence of given noncoding DNA yields, the disreputable scientific method that only got us from the caves to the 21st century. 5. Also posted above, genome sizes differ widely in mammals and birds implying that much of it is dispensable if lower than average or not particularly deleterious if present in higher amounts, i.e neutral. The available evidence which is considerable and piling up fast indicates that some noncoding is functional and much of it is apparently genome parasites and stuff that is just there and of little utility. And implies that Cthulhu and the flying spaghetti monster are lazy and haphazard designers. PS What if we were just a high school science project for a budding Designer. That could explain a lot. Just waiting for the Haphazard but trying real hard and learning a lot-Designer theory to be taught in biology classes. LOL

silverspoon · 23 April 2007

<=Philip Cunningham wrote:"1.Materialism did not predict the big bang, Yet Theism always said the universe was created.">

This is fascinating. Theism predicts what happened during the first 10âˆ’33 seconds of the universe (that duration of time we haven't cracked yet), and that a creator (some spiritual being) is responsible for that period of time.

Just one question for Philip Cunningham. How did theism come to that conclusion? Surely he has a mathematical model which supports his theory? I'll be waiting.

Philip Cunningham · 23 April 2007

Since this thread is about DNA I want to stay on topic so...
There are about....
Three-billion letters of code on six feet of DNA. The DNA contains the "complete parts list" of the trillions upon trillions of proteins that are in your body, plus, it contains the blueprint of how all these countless trillions of proteins go together, plus it contains the self-assembly instructions that somehow tells all these countless proteins how to put themselves together in the proper way. According to Bill Gates, the DNA code is written in some type of super-code that is far, far more advanced than any computer program ever written by man. If you were to write out that super-code, you could fill a three-thousand volume encyclopedia (a million letters per encyclopedia) ! If you were to read the code aloud, at a rate of three letters per second for twenty-four hours per day (about one-hundred-million letters a year), it would take you over thirty years to read it. The capacity of a DNA molecule to store information is so efficient that all the information needed to specify an organism as complex as man weighs less than a few thousand-millionths of a gram. The information needed to specify the design of all species of organisms that have ever existed (a number estimated to be one billion) could easily fit into a teaspoon with plenty of room left over for every book ever written on the face of earth. For comparison sake, if mere man were to write out the proper locations of all those proteins in just one human body, in the limited mathematical language he now uses, it would take a bundle of CD-ROM disks greater than the size of the moon, or a billion-trillion computer hard drives, and that's just the proper locations for the protein molecules in one human body, that billion-trillion computer hard-drives would not contain a single word of instruction telling those protein molecules how to self assemble themselves.

To say such amazing complexity does not at least hint at design is just plain foolishness, would not you agree.

David Stanton · 23 April 2007

Phillip,

Your prediction was that there would be almost no nonfunctional DNA in the human genome. Others have already pointed out that endogenous retroviruses represent a significant fraction of the human genome, are well understood and have no real function. Your hypothesis is falsified. Thanks for at least making a concrete prediction.

As for your claim about photosynthetic organisms being found in ancient strata, so what? Were they eukaryotes? Were they found with any eukaryotes in that strata? Were there any of the other organisms you yourself pointed out didn't evolve until the "cambrian explosion"? How long did it take for vertebrates to appear in the fossil record? How long for primates and humans to appear? The fact is that the order and timing of appearance of major groups as seen in the fossil record is exactly what is predicted according to modern evolutionary theory and not at all what one would predict if "God did it".

By the way, "theism" (whatever you mean by that) doesn't make any predictions and "materialism" (whatever you mean by that) doesn't make any predictions. Philosophies are not living organisms. They do not think or predict in any way.

JohnK · 23 April 2007

Philip Cunningham: establishing a complete 100% functionality for the DNA could be impossible, due to man's limited ability to understand the complexity of the amount of information being handled in the DNA.

Unfortunately for you, the reverse is not true since knockout experiments can eliminate stretches of codons with no effect.

Yet as I stated before, we are still in our infant stage as far as understanding the complexity of the DNA code

Perhaps you could apply your vast knowledge of the subject to critiquing: Halligan, D.L., Keightley, P.D., Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison, Genome Research 2006 July; 16(7): 875---884. About ~20% of the genome of the model species D. melanogaster (1/20th the size of humans) is protein-coding genes, more than 60% of the genome appears to be functional non-protein-coding DNA involved in gene expression control, leaving almost 20% non-functional.

snaxalotl · 23 April 2007

you tragic materialist scum

the Bible says blah blah blah blah

which vaguely sounds like some modern scientific idea, which is now therefore:

predicted by the Bible

Philip Cunningham · 23 April 2007

About ~20% of the genome of the species D. melanogaster (1/20th the size of humans) is protein-coding genes, more than 60% of the genome appears to be functional non-protein-coding DNA involved in gene expression control, leaving almost 20% non-functional.

Now that it a pretty bold statement; 20% is non-functional. It may have enviromental reaction information. Or it may have a use in some other function we have not thought of yet. I think it is very premature to say that 20% of the DNA is totally non-functional when we have just barely begun to understand the DNA. As for the knockout of genes; It reminds me of the time materialists claimed the appendix had no function. Yet the appendix has been found to have essential function after all.

Hawks · 23 April 2007

Philip cunnungham wrote:
"To say such amazing complexity does not at least hint at design is just plain foolishness, would not you agree."

I would agree. But I would also say that even hinting that such complexity was intelligently designed is plain foolishness.

Raging Bee · 23 April 2007

Philip blithered:

If we don't know -- and can't know -- what function all that DNA serves, then how can we know whether ID's presumption is true?

And while we're on the subject of the predictive power of "poof-goddidit" "explanations," let's do a comparison in the criminal justice field: "materialism" gave us fingerprinting, profiling, criminal psychology, DNA testing, and lots of useful procedures and protocols for crime-scene investigation. "Theism," by contrast, gave us wild stories of alleged witches shagging Satan and using magic to cause people to do bad things. What's your comment on that comparison, Philip?

Raging Bee · 23 April 2007

I think it is very premature to say that 20% of the DNA is totally non-functional when we have just barely begun to understand the DNA.

Has anyone actually said that? Or are you just misrepresenting concepts and ideas you don't understand?

creeky belly · 23 April 2007

1. Materialism did not predict the big bang, Yet Theism always said the universe was created. Cosmology predicted inflation 20 years before the Cosmic Microwave Background was found, and Einstein described inflation when studying general relativity, at no point was creation implied or utilized
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. Wave properties of matter are on a small distance scale, which we do not experience in our everyday life. A materialistic theory predicted and described this as well from the wave equations of Schroedinger (the structure of electron orbitals, tunneling, interference, photoelectric effect).
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. These were deduced from Maxwell's equations, by applying a materialistic theory (electrodynamics) to relative motion
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. Materialistic theories predicted these constants exist. How do we know that the inverse of the square root of the permitivity of free space(constant) times the permeability of free space(constant) would be another constant, the speed of light? Not from Theism.

Tex · 24 April 2007

In angiosperms (flowering plants) the size of the genome ranges from about 0.10 picograms (1/30 of the human genome) to 127 picograms (about 40 times larger than the human genome.
The small values come from Arabidopsis and other small weeds, the large values from plants in the lilly family. This range is larger than that cited by Raven in comment 171481 for animals.

The lillies have over 1,000X more DNA than weeds and more than 40X the DNA in humans. Lillies are nowhere near 1,000X more complex than Arabidopsis, so almost all of this extra DNA (over 99.9% of the genome)must be utter rubbish.

Check the genome sizes for yourself here:

http://www.rbgkew.org.uk/cvalues/CvalServlet?querytype=2

David Utidjian · 24 April 2007

Tex,

Hah! The Amoeba dubia has that beat at a genome size of 6.7Ã—10^11 or about 200 times larger than the human genome.

Thus the tiny amoeba is FAR more complex than us mere humans.

-DU-

Frank J · 24 April 2007

Philip:

I understand that you have a problem with "materialism," and no problem with a "theory" that "explains" everything, thus explains nothing. What I'm really curious about is, according to your version of the "theory," how many years has life existed on Earth? An order of magnitude will suffice. Also, do you think that humans are biologically related to dogs? dogwoods? both? neither? Note that none of these questions require acceptance of "Darwinism" to agree with the consensus of mainstream science.

Philip Cunningham · 24 April 2007

Reply to Frank J.'s questions of the age of earth and the relationship to other species to man. I do indeed think the age of the universe is 13.7 billion years old. Yet, since Theism presupposes a primary cause (God) that has always existed in a timeless eternity, I have no problem accepting the age of the universe as being that old. Now to the animals.
Even with the fossil record as crushing to the evolutionary theory as it is, evolutions greatest stumbling block is the absolute inability of natural methods to account for the generation of meaningful information in the DNA. (Generation of meaningful information in DNA by natural means would be a violation of entropy, regardless of what naturalists say). For even though it is suggested that evolution is true, when we look at the 98.8% similarity between the DNA of a Chimpanzee and the DNA of a Human, that similarity is not good enough to be considered "conclusive" scientific proof. Our DNA is 92% similar to mice. Does that make us 92% mouse? Our DNA is 44% similar to a fruit fly; are we therefore 44% fruit fly? Our DNA is 18% similar to the weed thale cress; does that make us 18% thale cress? Of course not! We must dig deeper to find the integrity of mutation rates in DNA to see if the change is possible at all. Which we, through the miracle of science, can now do. The primary thing that is crushing to the evolutionary theory is this fact. Of the random mutations that do occur, and have manifested traits in organisms that can be measured, at least 99.999% of these mutations to the DNA have been found to produce traits in organisms that are harmful and/or fatal to the life-form having the mutation! Professional evolutionary biologists are hard-pressed to cite even one clear-cut example of evolution through a beneficial mutation to the DNA. These following quotes make this point clear.

"It is entirely in line with the accidental nature of naturally occurring mutations that extensive tests have agreed in showing the vast majority of them to be detrimental to the organisms in its job of surviving and reproducing, just as changes accidentally introduced into any artificial mechanism are predominantly harmful to its useful operation " H.J. Muller (Received a Nobel Prize for his work on mutations to DNA)

"But there is no evidence that DNA mutations can provide the sorts of variation needed for evolution... There is no evidence for beneficial mutations at the level of macroevolution, but there is also no evidence at the level of what is commonly regarded as microevolution." Jonathan Wells (PhD. Molecular Biology)

"We see the apparent inability of mutations to truly contribute to the origin of new structures. The theory of gene duplication in its present form is unable to account for the origin of new genetic information" Ray Bohlin, (PhD. in molecular and cell biology)

"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)

"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)

Man has over 3 billion letters of DNA code, which according to Bill Gates, the founder of Microsoft, far, far surpasses, in complexity, any computer program ever written by man. Even if there was just a 1% difference of DNA between chimps and humans, that would still be 30 million base pairs of DNA difference. 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. Since, it is an established fact that at least 99,999 in 100,000 of any mutations to DNA will be harmful and/or fatal, then it is also an established fact that there is at least a 99,999^30,000,000 to one chance that the monkey will fail to reach man by evolutionary processes. The monkey will hit a dead end of harmful/fatal mutations that will kill him or severely mutilate him before killing him. The poor monkey barely even gets out of the evolutionary starting gate before he is crushed by blind chance. This would still be true even if the entire universe were populated with nothing but monkeys to begin with! This number (99,999^30,000,000), is Impossible for blind chance to overcome! If that was not bad enough for the naturalists, mathematician William Dembski PhD. has worked out the foundational math that shows the mutation/natural selection scenario to be impossible EVEN IF the harmful/fatal rate for mutation to the DNA were only 50%. The naturalist stamps his feet again and says that symbiotic gene transfer, cross-breeding (yes, they desperately suggest cross-breeding as a solution), gene duplication and multiplication of chromosomes, alternative splicing etc .. etc .. are the reasons for the changes in DNA between humans and apes. They say these things with utmost confidence without even batting an eye. Incredibly, this is done in spite of exhaustive experimental evidence to the contrary.

"The six feet of DNA coiled inside every one of our body's one hundred trillion cells contains a four-letter chemical alphabet that spells out precise assembly instructions for all the proteins from which our bodies are made . . . No hypothesis has come close to explaining how information got into biological matter by naturalistic means." (Lee Strobel PhD.)

"If pressed about man's ancestry, I would have to unequivocally say that all we have is a huge question mark. To date, there has been nothing found to truthfully purport as a transitional species to man, including Lucy, since 1470 was as old and probably older. If further pressed, I would have to state that there is more evidence to suggest an abrupt arrival of man rather than a gradual process of evolving". Richard Leakey, world's foremost paleo-anthropologist, in a PBS documentary, 1990.

Raging Bee · 24 April 2007

Even with the fossil record as crushing to the evolutionary theory as it is...

Dream on, fool. This is nothing but a bald assertion, with absolutely no basis in observable reality.

...evolutions greatest stumbling block is the absolute inability of natural methods to account for the generation of meaningful information in the DNA.

Define "information," and specify exactly how it can be quantified. If you can't do that, then you can't possibly say whether or not a given event "generates" "information."

(Generation of meaningful information in DNA by natural means would be a violation of entropy, regardless of what naturalists say).

Still flogging the "entropy" argument? That was refuted decades ago! You're WAY behind the curve, even by creationist standards. (What about an acorn that grows into a bloody huge oak tree? Does that "violate entropy" too? What about water crystalizing into ice?)

Also, since you've completely refused to respond to our questions about the "predictive power" of "theism" (I typed "predictive poser" by mistake there, which may be a fortuitous Freudian slip), I'll conclude that you've lost that argument too.

David Stanton · 24 April 2007

Phillip,

Once again the tired old creationist assertation that probability rules out this or that. The power of evolution lies in random mutations and cumulative selection and thus is entirely capable of producing humans from the common ancestor of chimps and humans. Your calculations are inappropriate and meaningless. How do you explain the shared mistakes in human and primate genomes? Why do many species have exactly the same endogenous retroviruses inserted in exactly the same ppositions in exactly the same genes? Did God copy the mistakes?

As for the assertation that "there are no beneficial mutations", where have I heard that one before? Perhaps you should take a look at the discussion thread on the evoution of antibiotic resistance in bacteria. Not only do beneficial mutations occur naturally, but they can be induced in the laboratory as well. Not even creationists generally dispute this any more. Even Egnor calimed that brain tumors should be beneficial and he is a world-class neurosurgeon. Maybe you didn't get the memo.

All of your tired old nonsense has been addressed in the Talk Otrigins archives. I suggest you increase your knowledge.

Philip Cunningham · 24 April 2007

Response to criticisms;

1. What about the y acorn that turns into a oak tree; Water crystalyzing into ice?

Thats your proof for a violation of entropy?; Geez, My grandmother could see that the information was already there!

2 Antibiotic Resistance as proof of a violation of entropy.

Many times naturalists will offer "conclusive" proof for evolution by showing bacteria that have become resistant to a certain antibiotic such as penicillin. When penicillin was first discovered, all the gram positive cocci were susceptible to it. Now 40% of the bacteria Strep pneumo are resistant. Yet, the mutation to DNA that makes Strep pneumo resistant to penicillin results in the loss of a protein function for the bacteria (called, in the usual utilitarian manner, penicillin-binding-protein). A mutation occurred in the DNA leading to a bacterial protein that cannot interact with the antibiotic and the bacteria survive. Although they survive well in this environment, it has come at a cost. The altered protein is less efficient in performing its normal function. In an environment without antibiotics, the non-mutant bacteria are more likely to survive because the mutant bacteria cannot compete as well. So as you can see, the bacteria did adapt, but it came at a loss of function in a protein of the bacteria, loss of genetic information in the DNA of the bacteria, and it also lessened the bacteria's overall fitness for survival. Scientifically, it is better to say that the bacteria devolved in accordance with entropy, instead of evolved against the second laws primary tenet of entropy. As well, all other observed adaptations of bacteria to "new" environments have been proven to be either the result of such entropy or a complex adaptation of preexisting genetic information that somehow knew how to adjust to the new environment. For naturalists to "conclusively prove" evolution they would have to clearly demonstrate a gain in genetic information. Naturalists have not done so, nor will they ever, for it would violate entropy.

For over two billion years cyano-bacteria ted the fossil record in colonies called stromatalites. Contrary to what naturalistic thought would expect, these very first cyano-bacteria colonies scientists find in the fossil record are shown to have been preparing the earth for more advanced life to appear, from the very start of their existence, by "detoxifying' the earth of sulfur, and other "toxic" elements, and slowly building up the necessary oxygen for future life to exist on earth. Interestingly, the percentage of oxygen that slowly built up in the atmosphere is now the exact percentage it needs to be to be of maximum biological utility for oxygen breathing life-forms to exist (21%). This necessary percentage of oxygen in the atmosphere is maintained by an impressive amount of complex feedback that gives us further reason to believe the earth is extremely unique in its ability to support complex life in this universe. If the oxygen were only a few percentage lower, oxygen breathing life-forms would become severely hampered in their ability to metabolize energy; if a few percentage higher, there would be uncontrollable outbreaks of fire across the land. This falls right in line with the anthropic hypothesis and has no explanation from any theory based on blind chance as to why the very first bacterial life found in the fossil record would suddenly, from the very start of their appearance on earth, start working to prepare the earth for future life to appear. Nor can naturalism explain why, once the bacteria had prepared the earth for higher life forms, they continue to steadfastly maintain the proper balanced conditions that are of maximum benefit for higher life-forms.

CJO · 24 April 2007

Nor can naturalism explain why, once the bacteria had prepared the earth for higher life forms, they continue to steadfastly maintain the proper balanced conditions that are of maximum benefit for higher life-forms.

Like syphillis? Or the bubonic plague? Steadfast, they are. "Proper balanced conditions," for "higher life-forms"? mmmm, no. Someone's testing out their Creationism Generator beta-version or something. Whoever you are, when the bugs get worked out, I want a copy!

Frank J · 24 April 2007

Philip:

I asked about the age of life on Earth and you gave me the age of the universe. IIRC someone at the Kansas Kangaroo Court tried to pull that fast one too. So please try again.

As for the "?" about common ancestry, there too you didn't really answer the question, so I'll rephrase it for clarity. Please pick a "best tentative guess" as to whether thet "?" lies closer to modern humans being related to: (1) dogs and not dogwoods, (2) dogwoods and not dogs, (3) both, (4) neither. Also, if it's not (3), do you have any plans to challenge Michael Behe directly? That's his position, so if your's is strictly strictly scientific, one would think that you'd prefer to debate someone who doesn't have a prior commitment to "materialism," correct?

This time please try to answer the questions without adding your superfluous objections to "Darwinism," "materialism," etc.

raven · 24 April 2007

There are dozens of examples of mutations resulting in new information useful or necessary for survival in organisms. The three most common single agent disease killers in the world, TB, malaria, HIV/AIDS, all have major problems with drug resistance that kill millions. Most involve changes in existing proteins but that is how evolution acts. By coopting existing genes to perform new functions. Fins become legs, arms, wings, and then, even fins again as in a dolphin. One recent example is abstracted below. Adult lactose tolerance has recently evolved in humans, not once but twice. We even know how down to the genetic level.

Nat Genet. 2007 Jan;39(1):31-40. Epub 2006 Dec 10. Convergent adaptation of human lactase persistence in Africa and Europe.Tishkoff SA, Reed FA, Ranciaro A, Voight BF, Babbitt CC, Silverman JS, Powell K, Mortensen HM, Hirbo JB, Osman M, Ibrahim M, Omar SA, Lema G, Nyambo TB, Ghori J, Bumpstead S, Pritchard JK, Wray GA, Deloukas P. Department of Biology, University of Maryland, College Park, Maryland 20742, USA. A SNP in the gene encoding lactase (LCT) (C/T-13910) is associated with the ability to digest milk as adults (lactase persistence) in Europeans, but the genetic basis of lactase persistence in Africans was previously unknown. We conducted a genotype-phenotype association study in 470 Tanzanians, Kenyans and Sudanese and identified three SNPs (G/C-14010, T/G-13915 and C/G-13907) that are associated with lactase persistence and that have derived alleles that significantly enhance transcription from the LCT promoter in vitro. These SNPs originated on different haplotype backgrounds from the European C/T-13910 SNP and from each other. Genotyping across a 3-Mb region demonstrated haplotype homozygosity extending >2.0 Mb on chromosomes carrying C-14010, consistent with a selective sweep over the past approximately 7,000 years. These data provide a marked example of convergent evolution due to strong selective pressure resulting from shared cultural traits-animal domestication and adult milk consumption.

David Stanton · 24 April 2007

So "devolving" doesn't count because it doesn't "add information"? First you claim there are no beneficial mutations, now you try to explain them away. Which is it? If the mutations conferring anitbiotic resistance decrease survivability in certain environments and would only be selectively maintained in certain environments under strong selection, then it should be possible to look at the DNA and determine the conditions under which the organism were selected. That seems to be "information" in any meaningful sense of the word. By the way, do the multiple types of globin genes count as "information"? They evolved through gene duplication and divergence, adding new functions. You can tell which lineage vertebrates belong to by simply looking at the globin genes they possess. We know when the duplication events occurred and in which lineages. Does that count as "devolving"? Does that count as "information"?

As to your cyanobacteria scenario, that was exactly the point I was trying to make. A real "intelligent designer" who could produce cyanobacteria from scratch would hardly have to wait for billions of years in order for the planet to become habitable for other types of life forms. Why not just put oxygen into the atmosphere to begin with? Why not just "design" organisms that didn't need oxygen? Seems to me the "anthropic principle" would "predict" that the earth should have been perfect for humans from the beginning. Once again, creationism "predicts" exactly what science has shown to be true.

Guess I have to repeat my other question. Did God copy the mistakes? That would be grounds for expulsion from some institutions.

Raging Bee · 24 April 2007

1. What about the y acorn that turns into a oak tree; Water crystalyzing into ice?

Thats your proof for a violation of entropy?; Geez, My grandmother could see that the information was already there!

In what form, exactly? Did your grandmother tell you how to detect, count and quantify this not-always-apparent "information?"

Also, if the "information" in ice is present in liquid water, before it freezes, why can't the "information" in a beneficial mutation also be present before the mutation?

You still haven't defined "information," therefore your "theory" is still nothing but vapor-ware.

JohnK · 24 April 2007

Why are we trying to have a discussion with someone who has just claimed apologist Lee Strobel has a PhD and is effectively some sort of genetic authority, and that the human appendix has an "essential function"?

CJO · 24 April 2007

We're not. We're just helping some mischievious programmer beta-test their creo-bot.

As I said before: When it's de-bugged, I WANT A COPY!!!

Philip Cunningham · 24 April 2007

Now this is interesting Raven!

Convergent adaptation of human lactase persistence in Africa and Europe.Tishkoff SA, Reed FA, Ranciaro A, Voight BF, Babbitt CC, Silverman JS, Powell K, Mortensen HM, Hirbo JB, Osman M, Ibrahim M, Omar SA, Lema G, Nyambo TB, Ghori J, Bumpstead S, Pritchard JK, Wray GA, Deloukas P.
Department of Biology, University of Maryland, College Park, Maryland 20742, USA.

A SNP in the gene encoding lactase (LCT) (C/T-13910) is associated with the ability to digest milk as s (lactase persistence) in Europeans, but the genetic basis of lactase persistence in Africans was previously unknown. We conducted a genotype-phenotype association study in 470 Tanzanians, Kenyans and Sudanese and identified three SNPs (G/C-14010, T/G-13915 and C/G-13907) that are associated with lactase persistence and that have derived alleles that significantly enhance transcription from the LCT promoter in vitro. These SNPs originated on different haplotype backgrounds from the European C/T-13910 SNP and from each other. Genotyping across a 3-Mb region demonstrated haplotype homozygosity extending >2.0 Mb on chromosomes carrying C-14010, consistent with a selective sweep over the past approximately 7,000 years. These data provide a marked example of convergent evolution due to strong selective pressure resulting from shared cultural traits-animal domestication and milk consumption.

Now me being curious, Raven, I have to ask: Where is the information coming from? Three point mutations in Africans that are apparently different from the Europeans are enabling the digestion of milk into hood. Now this is all fine and well. Just how did these totally random mutations, as required by neo-darwinism, know exactly which adjustments to make in the genome to enable the extension of this already existing ability to digest milk. They claim homozygosity for the rest of the genome they looked at. So apparently this is an extreme example of some kind of fantastic luck that enabled this convergent adaptation of milk digestion into hood! Wow, with that kind of fantastic luck I'd by my ticket to Vegas right now! Or, how about a much more likely scenario, There is a preexisting biological feedback loop somewhere in the immense complexity of genome that searched for, and somehow found the proper response in the genome that would enable this ability to be extended. Thats the only two choices, It is either a fantastic roll of the dice, as required by darwinism, or it is a complex adaptation of preexisting genetic information. Since I believe what hard math tells me, I choose to believe it was the complex adaptation of preexisting information. I see no conclusive proof for a violation of entropy since many questions remained unanswered.

hoary puccoon · 24 April 2007

I find it tragic that someone would use his highly-evolved brain to waste everyone's time and drag a discussion around in circles. It's sometimes hard for people grasp the concept that evolution truly has no goal. But if you want proof of that, Philip Cunningham is it.

Ric · 24 April 2007

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.

Don't make me laugh. All of your theistic "predictions" are just the result of shoehorning vague, poetic language to fit scientific conclusions after the fact. Plus, many of your "predictions" (for example, "Yet Theism would of [sic] naturally expected this level of complexity in the DNA code.") are just pulled out of thin air. One could just as easily say that theism predicts simplicity as the essence of perfection (which it has done in the past, at least until scientists begin to find that DNA was so complex.) I'm unimpressed. P.S. "Materialism" doesn't predict anything.

Raging Bee · 24 April 2007

Or, how about a much more likely scenario, There is a preexisting biological feedback loop somewhere in the immense complexity of genome that searched for, and somehow found the proper response in the genome that would enable this ability to be extended.

Describe how, and where, this "feedback loop" would work? And where, exactly, is the "proper response" physically stored prior to its discovery ("somehow") by this "feedback loop?" (Do you even know what a "feedback loop" really is? I've never herd of a feedback loop searching for, and finding, information.)

David Stanton · 24 April 2007

Phillip,

Your "question" has already been answered. Random mutation, coupled with cumulative selection is sufficient to produce the observed result. As was already pointed out, this is where the information comes from. You fall back on the age old cry of "directed mutation". We have been through this all before. Got any evidence for this claim? Got a plausible mechanism for how this could happen? If the "super code" of the genome is already so complex, how much more complex a system where every possible beneficial mutation is already "known" and can be produced as needed! Why not just make optimal organisms in the first place? Your scenario is completely unnecessary.

I pointed out that your cyanobacteria scenario was complete nonsense. You did not respond. I assume you agree with me. I asked another question twice already. Did God copy the mistakes? I will not ask again. Nor will I respond to anything else you care to write until you do respond to the question. I suggest others adopt the same attitude.

By the way, the thread topic was "junk DNA". You didn't respond to my questions about retroviral transposons or globin genes either.

Richard Simons · 24 April 2007

Philip Cunningham said

Many times naturalists will offer "conclusive" proof for evolution by showing bacteria that have become resistant to a certain antibiotic such as penicillin.

Rubbish. First of all, naturalists do not study bacterial resistance to antibiotics. Secondly, give me five citations to claims by scientists to provide conclusive proof for evolution. I would be very surprised if you could find them.

Generation of meaningful information in DNA by natural means would be a violation of entropy . . .

Twaddle. If this were true, physicists would be creating a stink about it.

Even with the fossil record as crushing to the evolutionary theory as it is, . . .

Poppycock. There is nothing in the fossil record that contradicts the theory of evolution.

Our DNA is 18% similar to the weed thale cress; does that make us 18% thale cress?

No-one says it does. However, it does indicate that we could share something like 18% of our biochemistry with thale cress. Virtually all the references you have given have been to old sources, physicists and computer specialists and people who have openly said that if anything contradicted their understanding of Genesis they would ignore it. Doesn't that give you even the smallest hint that you might not be on the right track?

Science Avenger · 24 April 2007

Philip Cunningham said: Our DNA is 92% similar to mice. Does that make us 92% mouse? Our DNA is 44% similar to a fruit fly; are we therefore 44% fruit fly? Our DNA is 18% similar to the weed thale cress; does that make us 18% thale cress? Of course not!

Now wait a minute. The statement needs some clarity to get exact, but why exactly do you say "of course we are not 92% mouse"? If we started listing mouse and human traits, we'd get a pretty long list. Two eyes, two ears, one nose, one mouth, two forelimbs, two hindlimbs, one anus, hair, one heart, lungs, fingers, toes, etc. Just what would constitute 92% mouse to you? This creationist way of looking at things boggles my mind the most. How can anyone look at their cat, as I am looking at mine right now, and NOT see the relationship? They can see evidence of motor design in a flaggelum but they can't see evidence of kinship with a cat? Give me a friggin break.

Chris Harrison · 24 April 2007

Hold on, you guys only have one anus?

Sorry for the interruption, creationists like Phillip just become incredibly boring after the 600th time.

neo-anti-luddite · 24 April 2007

Phillip Cunningham wrote: Our DNA is 92% similar to mice. Does that make us 92% mouse? Our DNA is 44% similar to a fruit fly; are we therefore 44% fruit fly? Our DNA is 18% similar to the weed thale cress; does that make us 18% thale cress? Of course not!

Why is it humans who would be "92% mouse" rather than mice who would be 92% human? Break free of the anthropocentric hegemony! Were mice not made by God?

Henry J · 24 April 2007

What would "violation of entropy" even mean?

Henry

David Stanton · 24 April 2007

Henry,

I'm not sure what "violation of entropy" means, but I'm pretty sure that "digestion of milk into hood" would also "violate entropy".

Philip Cunningahm · 24 April 2007

Sequence Similarity Alone Does NOT Prove Common Ancestry

As Francis Collins, head of the project which mapped the human genome, has written of DNA sequence similarities, "This evidence alone does not, of course, prove a common ancestor" because an intelligent cause can reuse successful design principles. We know this because we are intelligent agents ourselves, and we do this all the time. We take instructions we have written for one thing and use them for another. The similarity is not the result of a blind mechanism but rather the result of our intelligent activity.

Why do many species have exactly the same endogenous retroviruses inserted in exactly the same ppositions in exactly the same genes?

Now this is an interesting question; Since, as I stated before, we are still in our infant stage in our understanding of the DNA code. I would have to think it is a rather bold and premature assertion on your part to say that the genome does not use the information in the endogenous retrovirus for some purpose we have not yet deduced. To boldly state otherwise is to claim complete knowledge of the genome. If you have managed complete knowledge of the genome sir, You are in line for multiple Noble Prizes, big villas, lots of gold and a white french poodle named fluffy.

What is a violation of entropy?
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. Abiogenesis (life originating from matter) would be a blatant violation of this law. As well, Evolution needs to clearly demonstrate a gain in genetic information to conclusively prove it is true. This breakthrough would violate entropy and probably make the scientist who clearly illustrated it very famous.

The milk drinking mutation in africans,, This mutation is clear entropy. The information in the genome that disabled the milk drinking enzymne in older africans was lost so the africans could continue to drink milk.

Richard Simons · 24 April 2007

Philip Cunningahm, Cunningam or Cunningham, (whatever you call yourself),

Sequence Similarity Alone Does NOT Prove Common Ancestry

And who said it did? Besides, there is not just mere similarity, there is a nested hierarchy of features of organisms.

an intelligent cause can reuse successful design principles.

The avian excretory system is particularly suitable for conserving water. So why did the intelligent cause not reuse the successful design in desert mammals? It would, of course, violate the nested hierarchy but surely an intelligent cause would not be limited by that.

Why do many species have exactly the same endogenous retroviruses inserted in exactly the same positions in exactly the same genes? Now this is an interesting question;

And one that you avoided answering.

This mutation is clear entropy.

What on earth do you mean by this guff? BTW: There was no need to give a simplistic definition of entropy. The problem is (at least in part) that you are using the word in a strange way, like saying that a 2-mile bridge span is a violation of length. While the sun shines, the whole entropy argument is, in any case, irrelevant. You seem to believe that any mutation results in a loss of 'information'. So a bacterial population that mutates to become resistant to an antibiotic loses information. Then when it mutates again and loses its resistance to the antibiotic it loses more information. So the final population, although it is indistinguishable from the first, actually has less information in it. Do I have that correct?

David Stanton · 24 April 2007

Philip,

Thanks for responding to my question. So, your answer is that God did it and we are just too stupid to figure out why. God put exactly the same mistakes in human and chimp genomes that predispose us to exactly the same diseases. Man, she definately seems to lack imagination.

The conclusion that SINES have no function comes from our knowledge about them, not our ignorance. They are not even functional transposons. They can't even transpose without the aid of other transposons. They are too short to code for functional proteins by themselves. They insert randomly into the genome where they cause insertional mutagenesis which can cause disease and even death. There is no known function for these sequences and it is hard to even imagine what possible function they could ever have.

Of course all this is beside the point. You are the one who claimed they, and every other sequence in the human genome, has a function. You are the one who must provide evidence for this claim. What is your evidence? Or were you just making stuff up?

As for the famous Second Law of Thermodynamics, please state exactly how random mutation and selection violates this law? Why is it so impossible to accept that three nucleotide substitutions could arise by random processes and then be selected on? What could possibly prevent them from eventually arising by chance alone? By the way, you can't use a probability calculation here unless you can demonstate (1) exactly how many mutations could produce the exact same phenotypic effect (hint, the answer is undoubtedly many more than three) and (2) how many meiosis events have occurred in human history.

Still waiting for an explanation as to why God needed billions of years to make a little oxygen. Maybe she had a failure of imagination on that one as well.

creeky belly · 25 April 2007

What is a violation of entropy? 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. Abiogenesis (life originating from matter) would be a blatant violation of this law. As well, Evolution needs to clearly demonstrate a gain in genetic information to conclusively prove it is true. This breakthrough would violate entropy and probably make the scientist who clearly illustrated it very famous.
— Philip Cunningham

The second law of thermodynamics actually states: In a closed system, the change in entropy with respect to time is greater than or equal to zero. The earth is not a closed system (It gains external energy from the sun on the order of 1000 Watts per square meter or 1000 Joules a second per square meter, and internal energy from radioactive decay), therefore the second law does not apply, QED. Even within a closed system you can have localized decreased entropy, for example: Let's say system 'A' and 'B' are thermally coupled in a closed system: 'A' has 4 states, 'B' has 8, so there are a total of 32 states. The total entropy is the logarithm of the number of states, or log(32). When the system is allowed to come to thermal equilibrium, 'A' has 6 states and 'B' has 6 states, or 36 total states. This means that 'B' will have necessarily decreased entropy in order to come to thermal equilibrium; from log(8) to log(6). Notice the total entropy (for 'A' and 'B') increased from log(32) to log(36). This experiment has been empirically verified, and is essential to understand how engines and chemical reactions operate (to name a few uses). If you're going to use physics laws, you need to know when and why they are applicable. This is a definite case of "I'll use entropy in an information theory context at the same time I'm using it in a thermodynamic context". It doesn't logically follow, and neither do your arguments.

Frank J · 25 April 2007

As Francis Collins, head of the project which mapped the human genome, has written of DNA sequence similarities, "This evidence alone does not, of course, prove a common ancestor" because an intelligent cause can reuse successful design principles.
— Philip Cunningham

Collins, and Richard Leakey who you mentioned earlier in a similar context, both agree that, when all the evidence is taken together, common ancestry is the only reasonable explanation of how that "common design" is actuated. I hope you are not pretending that they deny common descent, or worse, that they are adopting the "don't ask, don't tell" approach that you seem to prefer. That approach is especially pathetic because a few people, like Schwabe and Senapathy, have actually attempted to support independent abiogenesis as a specific alternative to common descent, while the ID scammers can't even call it by name. I'm still waiting for the answers to my questions.

Frank J · 25 April 2007

You "Darwinists" just don't understand ID. ;-)

raven · 25 April 2007

Philip: Which [ENTROPY], in simple terms, means things tend to fall apart, they never tend to put themselves together.

Oh really? As another poster pointed out, what happens when you plant an acorn? An oak tree is much larger and more dynamic and metabolicly active than an acorn. Or a human zygote. I wouldn't call an adult human a "zygote that tended to fall apart." Both of these violate the tendency to fall apart, second law of thermodynamics. They don't of course and neither does evolution or abiogenesis. The earth is not a closed system, being close to a rather large fusion reactor called the sun. Energy can and does reverse entropy LOCALLY in an open system which is why you are alive right now. This was all figured out decades ago and repeating very old fallacies is pointless. Quote mining Collins and Leakey wasn't intellectually honest. This is a fundie christian thing I guess, they do it constantly. Must be an exception to the ten commandments. Thou shalt not lie except when attempting to suppress science and head back to the dark ages. I'll have to check my copy and update it. The rest of your points are equally muddled but since you are starting from a premise and stuffing facts in to fit, not going to explain anymore. No one cares what you and your sectarian coreligionists believe. It is your perogative to believe whatever you want. The USA is open and people believe all sorts of stuff, druids, wiccans, the Greek and Norse gods, UFOs, elvis, Velikovsky, Marxism, bigfoot, flying spaghetti monster and so on. What we, meaning scientists, the public, and the constitution object to is one subculture trying to impose its religious views on children in biology classes.

Philip Cunningam · 25 April 2007

Probability and Complexity of Protein genesis presents impossibilities for Materialism

It is easily demonstrated mathematically that the universe does not even begin to come close to being old enough, nor large enough, to ally generate even one precisely sequenced protein that would be required for the simplest living bacteria. This would still be true even if amino acids had a tendency to chemically bond with each other, which they don't despite over fifty years of experimentation trying to get amino acids to bond naturally. The staggering impossibility found for the universe ever generating a specifically sequenced 100 amino acid protein by would still be true even if the entire universe were nothing but groups of amino acids, and we tried a trillion unique combinations per second for all those amino acid groups for 30 billion years! Even a child knows you cannot put any piece of a puzzle anywhere in a puzzle. You must have the required piece in the required place! The simplest forms of life ever found on earth are exceedingly far more complicated jigsaw puzzles than any of the puzzles man has ever made. Yet to believe a naturalistic theory we would have to believe that this tremendously complex puzzle of millions of precisely shaped, and placed, protein molecules "just happened" to overcome the impossible hurdles of chemical bonding and probability and put itself together into the sheer wonder of immense complexity that we find in the cell. Naturalists have absolutely no answers for how this complexity arose in the first living cell unless, of course, you can take their imagination as hard evidence. Yet the "real" evidence scientists have found overwhelmingly supports the anthropic hypothesis once again. It should be remembered that naturalism postulated a very simple "first cell". Yet the simplest cell scientists have been able to find, or to even realistically theorize about, is vastly more complex than any machine man has ever made through concerted effort !!

Instead of us just looking at the probability of a single protein molecule occurring (a solar system packed full of blind men solving the Rubiks Cube simultaneously), let's also look at the complexity that goes into crafting the shape of just one of the proteins, out of the millions of proteins, that would be in that very first cyano-bacterium found on earth. Complexity will give us a better indication if a protein molecule is, indeed, the handi-work of an infinitely powerful Creator.
In the year 2000 IBM announced the development of a new super-computer, called Blue Gene, that is 500 times faster than any supercomputer built up until that time. It took 4-5 years to build. Blue Gene stands about six feet high, and occupies a floor space of 40 feet by 40 feet. It cost $100 million to build. It was built specifically to better enable computer simulations of molecular biology. The computer performs one quadrillion (one million billion) computations per second. Despite its speed, it is estimated it will take one entire year for it to analyze the mechanism by which JUST ONE "simple" protein will fold onto itself from its one-dimensional starting point to its final three-dimensional shape. In real life, the protein folds into its final shape in a fraction of a second! The computer would have to operate at least 33 million times faster to accomplish what the protein does in a fraction of a second. That is the complexity found for JUST ONE "simple" protein. It is estimated, on the total number of known life forms on earth, that there are some 50 billion different types of unique proteins today. It is very possible the domain of the protein world may hold many trillions more completely distinct and different types of proteins. The simplest bacterium known to man has millions of protein molecules divided into several hundred distinct types of proteins. These millions of precisely shaped protein molecules are interwoven into the final structure of the bacterium. Many times specific proteins in a distinct protein type will have very specific modifications to a few of the amino acids, in their sequence, in order for them to more precisely accomplish their specific function or functions in the overall parent structure of their protein type. To think naturalists can account for such complexity by saying it "happened by chance" should be the definition of "absurd" we find in dictionaries. As well, proteins have been proven to quickly lose their function in the cell with random point mutations.

"Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially... These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its 'new duties'. It is at this point it will be destroyed --- along with the organism carrying it." Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering)

David Stanton · 25 April 2007

Once again Philip ignores all criticism and falls back on "I just can't imagine how something so improbable could ever occur." What part of random mutation and cumulative selection didn't he understand? What part of Second Law of Thermodynamics is not a valid argument didn't he understand? Why has he repeatedly falied to answer questions? Why does he think that quote mining will work with people who obviously know better? His God seems very small to me.

Here is an example of the argument used here:

"Mr. Gates, you wanted to see me."

"Yes I did Phil. There is a problem with this program you wrote. It seems to have hundreds of thousands of defective viruses inserted into it. Some at critical points that significantly reduce efficiency. Why did you put all that useless junk into your program? You know it will only make the program worse and worse over time."

"But Mr. Gates sir, I put those viruses in intentionally. I know it is hard to see, but they really do something very important. I guess you just don't understand how important they really are."

"Oh really. Then tell me, why are they inserted in exactly the same places in your program and this program written by me two years ago. I know I didn't put them in when I wrote the program. They are the result of a virus that contaminated our files when a hacker got into our system. They really make the program a lot worse, but I can't seem to get rid of them because they keep copyng themselves. No Phil, you copied most of this program and tried to pass it off as your own work. You're fired."

Ric · 25 April 2007

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

GuyeFaux · 25 April 2007

It is easily demonstrated mathematically...

Then please do so.

Raging Bee · 25 April 2007

Philip: your blatant misrepresentation of the second law of thermodynamics -- easily pointed out by creeky belly in post #171839 above -- proves that you are both extremely ignorant and shamelessly dishonest. Your fancy words and quote-mining have no credibility whatsoever, and you are in no position to lecture anyone else about what we know and don't know.

Even most creationists -- including Dr. Egnor -- have enough sense of shame not to use the "entropy" argument anymore; that's how transparently bogus it is. If evolution REALLY violates such a basic law of physics, then where's the physicist claiming a Nobel prize for pointing this out? (Physicists gave us the atom-bomb, so don't try to tell us they're being intimidated by the "Darwinist establishment.") If you're going to mindlessly paste fancy-sounding text and call it argument, you'll have to do a better job than that.

Did someone say "Uncommon Despair?"

It is easily demonstrated mathematically...

So demonstrate it already. We're waiting...

Glen Davidson · 25 April 2007

Mostly my eyes glaze over when looking at the PRATTs that Philip and other drones cut and paste, so I haven't bothered much with this thread. But I noticed this in another poster's writings (and his comments were good), and thought I'd add a bit about it as well:

Philip: Which [ENTROPY], in simple terms, means things tend to fall apart, they never tend to put themselves together.

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? I especially like the mineral crystals and how they'd be considered "complex" (a complete misuse of the term) by Dembski, and how a cube of pyrite would count as specified complexity with his "explanatory filter"---except for the fact that it isn't "specified". Indeed, one of the reasons that fossils were onced thought to be "forms" in the earth is that mineral "forms" appear there which would not be readily understood by the ancients as having been spontaneously ordered. Of course Dembski konws that the order of crystals isn't "specified", the trouble is that apart from knowing the specifics of crystal formation, his "filter" would have absolutely no way of determining that this is the case. Which gives us the analogous value of the EF in biology. Nil. His filter only works when we already know if the "complexity" is specified, and does not work when it is not known---and when we actually have evidence that biology is not specified (no rational design in it) it properly (by Dembski's rules) would have to rule out biological complexity as having not been specified. We live in an earth that was ordered by "natural processes", which is fortunate because life could not exist in the primordial nebula. The trouble for the various sorts of creationists is that this ordering (and the building of complexity off from spontaneous ordering) didn't quit with "physical processes", rather it eventually began to feed upon itself in reproducing biological entities. Indeed, it is incumbent upon any denier of evolution to explain how evolution could be prevented, including at the abiogenetic stage. Glen D http://tinyurl.com/35s39o

David Stanton · 25 April 2007

Ric,

I sure looks to me as if Philip is just cutting and pasting from various diatribes and manifestos. That might explain why he has repeatedly failed to answer questions and address issues of substance. Of course there is an easy way to tell for sure. Just look for the same errors in this sentence in other versions:

"It is easily demonstrated mathematically that the universe does not even begin to come close to being old enough, nor large enough, to ally generate even one precisely sequenced protein that would be required for the simplest living bacteria."

So far, Philip has failed to:

(1) Give his estimate for the age of the earth
(2) Give any potential function for SINES
(3) Give any definition for information
(4) Respond to questions about globin genes
(5) Provide a plausible mechanism for directed mutations

Frank J · 25 April 2007

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

Yes, and sources that I suspect he knows are peddling nonsense. He knows how to play the game.

Frank J · 25 April 2007

So far, Philip has failed to: (1) Give his estimate for the age of the earth
— David Stanton

Actually I asked for the age of life on Earth. Some in the big tent are conceding old Earth but not necessarily old life. I don't think it has much to do with their personal belief or uncertainty, but a means to not alienate rank & file YECs, at least those who don't as too many questions. Speaking of which, don't forget (6) which is to give a best guess about common descent. There's probably no topic that better shows how IDers know that they're just playing games. If they really thought that the evidence challenged common descent, as opposed to their cariacure of "Darwinism," they'd challenge Behe directly. Of course Behe - who probably personally accepts all of evolution - surely wishes he hadn't gone on record conceding common descent before it became politically incorrect to do so.

Richard Simons · 25 April 2007

What interests me about someone like PC is that he obviously thinks that hundreds of thousands of physicists are so ignorant of biology that not one realizes that the theory of evolution 'violates' a basic physical law and that every last biologist is completely ignorant of basic physics. The arrogance is astounding.

Alternatively, everyone is involved in a vast conspiracy (why? What would be in it for me that is also a motive for Christians, Jews, Buddhists, atheists and the rest?)

Henry J · 25 April 2007

Physicists gave us the atom-bomb, so don't try to tell us they're being intimidated by the "Darwinist establishment."

Then why did they invent all that radiometric dating stuff when "Darwinists" needed it? :D

How do stars coalesce, produce complex and ordered magnetic phenomena, and eventually create shells of different materials inside?

Ah, but that's because a huge dust cloud fell apart! Ya see. :D

If they really thought that the evidence challenged common descent, as opposed to their caricature of "Darwinism," they'd challenge Behe directly.

I dunno - if they really thought they had evidence that way, Behe would probably have thought that, too, and said that instead of what he did say. Henry Btw, "Behe" isn't in the spell checker. ;)

argystokes · 25 April 2007

Philip,

The discussions at the Pandas Thumb tend to be transient. If you are interested in a lengthy discussion, may I suggest that it be moved to After the Bar Closes, the forum associated with this blog? I'm sure the forum moderator would be happy to set up a thread for you.

http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?act=SF;f=14

Gunthernacus · 25 April 2007

chunkdz wrote: As late as 1998, Dawkins was predicting that junk DNA is useless...and that this prediction seems to fit with his blind, pitiless, indifferent mechanism.

Evolution is blind, ID has foresight - okay, that's fair. Evolution is pitiless, ID is pitiful - that's at least half right; ID is quite pitiful. But, indifferent? Are you saying that the Designer-about-which-nothing-can-be-known is compassionate? Caring? Concerned? If not, in what way would you characterize the "ID mechanism" that separates it from the "indifference" of unguided evolution?

trrll · 25 April 2007

The term "junk DNA" since its inception has been used to refer specifically to DNA that has no current function whatsoever. The identification of noncoding DNA with junk DNA is therefore an error, since it was known long before the term "junk DNA" was coined, that some noncoding DNA serves a regulatory function.

Natural selection does indeed predict that some amount of junk DNA will exist, based upon evidence that DNA sequences can be duplicated and inserted elsewhere in the genome, and that the likelihood of this occurring is influenced by DNA sequence. It makes no explicit prediction as to what fraction of noncoding DNA will turn out to be junk, other than it will depend upon the strength of selection for a small genome (probably weak in large animals) and the frequency of deletion mutations.

Other evidence--namely large differences in DNA content of species that are closely related morphologically and evolutionarily--leads to the prediction that in some species a substantial fraction of the genome is junk. So far, this seems to be holding up quite well, despite the discovery of additional regulatory sequences in noncoding DNA.

Hence, discovery of regulatory sequences in nocoding DNA is by no means a problem to natural selection, or even unexpected. The notion that evolutionary theory predicts that all noncoding DNA is functionless "junk" is a straw man fabricated by ID zealots. Given that this has been pointed out repeatedly by geneticists, the claim that the discovery of additional noncoding regulatory sequences represents some kind of challenge to evolution cannot at this point in time be seen as anything other blatant dishonesty.

On the other hand, it is difficult to imagine why a designed genome that does not have to evolve should contain any true junk DNA that is entirely without function. I find it notable, therefore, that ID advocates do not seem to have the courage to make the stronger prediction that all noncoding DNA has a biological function, which requires only the assumption that the hypothetical designer is at least somewhat rational.

secondclass · 25 April 2007

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

Plagiarizing would be a better word. He has copied at least the following passage without attribution:

Sequence Similarity Alone Does NOT Prove Common Ancestry As Francis Collins, head of the project which mapped the human genome, has written of DNA sequence similarities, "This evidence alone does not, of course, prove a common ancestor" because an intelligent cause can reuse successful design principles. We know this because we are intelligent agents ourselves, and we do this all the time. We take instructions we have written for one thing and use them for another. The similarity is not the result of a blind mechanism but rather the result of our intelligent activity.

secondclass · 25 April 2007

Thats your proof for a violation of entropy?; Geez, My grandmother could see that the information was already there!
— Philip

Does your grandmother talk about "entropy" and "information" without being able to define them, as you do?

Philip Cunningham · 25 April 2007

Darn, So many criticisms so little time, Oh Well.. I'll respond to this following one..

These examples you point out, all exibit a pattern of information that is inherent in the material itself. That is to say that no further information input was required to make the material do what it naturally does. That is what differentiates living matter from non living matter. 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 ...

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

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

As a side note...The whole philosophy of materialism, upon which evolution is built, is suspect in my view because of scientists inability to find 90% of the universe...the infamous dark matter.. Hmmmm ,can't seem to find 90% of the material that is suppose to be there...And then I hear stuff like...Oh we know its there because we can infer it we just can't directly detect it...HMMMM,, can't find 90% of the stuff that is the basis of your materialistic philosophy? I don't know about you guys but it makes me wonder if materialism is all that it is cooked up to be.

There universe is full of many mysteries and wonders...for someone to place all their money on a totally materialistic explanation for everything in life and in the universe seems like a very foolish bet to me. It just seems a bit to easy if you know what I mean.

I believe this may be my last blog on this thread since it is getting old. Take Care.

PvM · 25 April 2007

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."

Cool, so much for the idea that intelligent design can explain the information in nature. Of course, in order to explain the information in the DNA, one has to only explain the transfer of information from the environment to the genome. In other words, exactly what science has shown can explain the origin of information in DNA. And yet ID keeps ignoring these facts. How sad, how scientifically vacuous. How ID.

creeky belly · 25 April 2007

As a side note...The whole philosophy of materialism, upon which evolution is built, is suspect in my view because of scientists inability to find 90% of the universe...the infamous dark matter.. Hmmmm ,can't seem to find 90% of the material that is suppose to be there...And then I hear stuff like...Oh we know its there because we can infer it we just can't directly detect it...HMMMM,, can't find 90% of the stuff that is the basis of your materialistic philosophy? I don't know about you guys but it makes me wonder if materialism is all that it is cooked up to be.
— Philip Cunningham

Technically speaking only about 20% of the universe is dark matter, about 60% is supposed to be dark energy (which is thought to be a vacuum energy). Since dark matter does not couple with electromagnetic radiation you can't actually "see" that it's there, in the same way that you can't "see" an electron. It does, however, interact gravitationally, and was in fact observed recently when two galaxies collided. By examining the x-ray emission, the analysis confirmed a large quantity of dark matter existed in the galaxies. I know it might be tough to accept that you don't have clue about what's going on in science these days, but that's ok, it's your prerogative (It helps having more than a fifth grader's understanding of cosmology). It's not like the scientific community cares that you can't accept reality.

trrll · 25 April 2007

As a side note...The whole philosophy of materialism, upon which evolution is built, is suspect in my view because of scientists inability to find 90% of the universe...the infamous dark matter.. Hmmmm ,can't seem to find 90% of the material that is suppose to be there...And then I hear stuff like...Oh we know its there because we can infer it we just can't directly detect it...HMMMM,, can't find 90% of the stuff that is the basis of your materialistic philosophy? I don't know about you guys but it makes me wonder if materialism is all that it is cooked up to be.

Wow. This truly reaches some sort of a pinnacle of ignorance. You have it almost completely backwards. No, dark matter doesn't represent some failure to detect something that is "supposed" to be there--the only way that we know it is there is because we have detected it by its gravitational effect. What we don't know is exactly what it is made of. There actually are a number of possibilities suggested by physical theory. The challenge is in coming up with an experiments to determine whether one of these known possibilities is correct, or whether the theory needs to be revised.

David Stanton · 26 April 2007

Philip,

Thanks for once again ignoring all my questions. But not to worry, if you ever do grace us with your presence again we'll all be waiting to ask the same questions all over again. And by the way, we will never be satisfied with quote mining, cutting and pasting nonsense to obscure the issues and inappropriate calculations. You are perfectly free to believe anything you want, but if you want to convince anyone else of anything you need to have some evidence and some sound reasoning. Good luck.

Just one more thing. You wouldn't by chance be the realpc would you? He seems to have disappeared lately. I wonder why.

raven · 26 April 2007

Philip Cunningham wrote: As a side note...The whole philosophy of materialism, upon which evolution is built, is suspect in my view because of scientists inability to find 90% of the universe...the infamous dark matter..

Philip, you have followed the creo script to a T. Are you somebody's AI software program or what? Materialism has brought us electricity, running water, a life span almost twice what it was, modern technology such as cars, computer, the internet etc..Religious fanaticism has brought us basket cases like Iraq where they have been fighting over and butchering each other on a fine point of theology for 1400 years.Unlike xtianity which managed to halt the 400 year catholic protestant butchery a whole 5 years ago in Northern Ireland. The dark ages still exist and you are free to move to any of a number of medieval trash heaps.

can't find 90% of the stuff that is the basis of your materialistic philosophy?

I don't know what dark matter or energy is either. So what? It doesn't have anything to do directly with evolution or the age of the earth. You have fallen into the trap of the god of the gaps. Science asks questions and search for the answers, the truth. Things we didn't know become things we know, repeat. We didn't know the human genome sequence a decade ago, now we do. A feat BTW, not produced by sniping at knowledge workers but by hard work by many talented and hard working scientists.So what happens when scientists discover the nature of dark matter and dark energy? Humans are good at solving problems like this, part of what makes us humans is curiosity and determination.This means that god doesn't exist then? Foolish theology

I don't know about you guys but it makes me wonder if materialism is all that it is cooked up to be.

Try living in an anti-materialism state for a while. There are a few left. Afghanistan and Somalia are the most advanced examples. They are very, very religious. They also have short, miserable lives. BTW, they are also BYOAK, bring your own AK47. For some reason anti-materialist states with high numbers of fanatics have a high rate of violence. I'm at least done here. I don't think you are even a real christian fundie. Just a troll with lots of time and some personality problems.

raven · 26 April 2007

Dave Stanton: Just one more thing. You wouldn't by chance be the realpc would you? He seems to have disappeared lately. I wonder why.

Quite likely. Or a clone that you wouldn't be able to tell the difference. Notice how he keeps changing the subject when one of his cut and pastes fails. This was a thread about junk DNA and now it is about dark matter. Pure troll and not to be taken seriously.

hoary puccoon · 26 April 2007

If there's a chance we can get back to the original topic, I'd like to address Cordova's claim that "Darwinism" predicts junk DNA. Charles Darwin never made any such prediction. He knew nothing about discrete inheritance, never heard the word 'gene,' and wrote The Origin of Species ten years before DNA was discovered-- which happened 75 years before it was discovered to be the genetic material, and 84 years before its structure was worked out. 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.) In fact, the entire history of evolutionary biology is littered with surprises coming out of the blue, from atomic energy to plate tectonics to the Hox genes. What has been so extraordinary about the theory of evolution is how well it has fit in with later discoveries nobody could have predicted. (Dinosaurs have feathers?? Bacteria have sex???)
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. In order to get the public to understand just how unfair creationists attacks are, it's the kind of bias that needs to be pointed out again and again.
(But, in this case, the thread was derailed first. Hmm. Have Sal Cordova and Philip Cunningham ever been photographed together?)

Raging Bee · 26 April 2007

Yeah, this sounds like realpc allright. His General Theory of Unspecified Complexity and Stuff still needs work...

Henry J · 26 April 2007

Re "But, indifferent? Are you saying that the Designer-about-which-nothing-can-be-known is compassionate?"

Compassionate? With some of the stuff in nature, if it was designed/engineered, that designer/engineer was not merely indifferent, but actively sadistic. And that's the view of God that the I.D. argument directly implies. And that makes me wonder what the heck I.D. pushers are actually trying to convince people of.

Henry

Glen Davidson · 26 April 2007

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

Glen Davidson · 26 April 2007

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

Frank J · 26 April 2007

Philip, you have followed the creo script to a T
— raven

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.

Moses · 26 April 2007

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.

trrll · 26 April 2007

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.

Science Avenger · 26 April 2007

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.

Philip Cunningham · 26 April 2007

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!

Torbjörn Larsson · 26 April 2007

ID lacks predictive power beyond 'Darwinism does not explain X'.

This explains what PvM means when he claims that ID only predicts negatives. But it seems 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 being wrong (predict creation) does not contradict evolution (could still be correct elsewhere; 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 is compliant with both ID and evolution. I find PvM insistence that ID makes predictions confusing when scientists mostly agree that it is entirely sterile. Also confusing is that there seems to be a lack of consistence:
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.

Sir_Toejam · 26 April 2007
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*

Torbjörn Larsson · 26 April 2007
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:
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.

PvM · 26 April 2007
So here ID is also claimed to predict CSI?!
Detect... Not predict.

Sir_Toejam · 26 April 2007
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.

PvM · 26 April 2007
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.

stevaroni · 26 April 2007
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.

Frank J · 27 April 2007
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.

Raging Bee · 27 April 2007
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?!

David Stanton · 27 April 2007
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.

David B. Benson · 27 April 2007
Since Phillip does the Gish Gallop so well, you'll have to wait until eternity...

Henry J · 27 April 2007
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

Raging Bee · 30 April 2007
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.

slpage · 30 April 2007
Lee Strobel is a hack journalist, he does not have a PhD.