Home » The Design of Life » ID’s “predictive prowess”

ID’s “predictive prowess”

A producer from one of the national talking heads programs is discussing with FTE’s PR firm whether to interview me or Jonathan Wells regarding our new book THE DESIGN OF LIFE. The producer has some reservations about interviewing us:

Hi [snip],

As I’m sure you know, one of the main claims any scientific theory can make is predictive prowess. In other words, if a theory is true, then other things should also be verifiable experimentally, or by research. Before we make a call on your clients, can you or they provide any samples of things that intelligent design theory has predicted, which researchers have later determined to be true?

Thanks.

[snip]

I have my own list of answers, but I’d like to hear those of this group.

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220 Responses to ID’s “predictive prowess”

  1. ID predicts that neo-Darwinists will get so upset at a group of people following the evidence where it leads and unraveling their shaky theory that they will accuse ID of being a new brand of Creationism and not science.

    :)

    Sorry…..

  2. Here’s a few:

    1) Origin of life: Intelligent design can predict that science will never be able to explain how this complex life arose (homochirality). This prediction has been confirmed every year for decades.

    2) History of life: Life is shown too complex to develop slowly over time. Life will appear rapidly and remain in stasis. This has been confirmed countless times, i.e. the big bangs of life.

    3) Irreducibly complex living forms exist.

    4) Molecular machines.

    5) Evolutionary convergence.

  3. That after “billions and billions” of generations of any particular biological entity no new morphology will occur due to random mutations and natural selection.

  4. Intelligent Design Theory predicts that the trademark evidences of design typically recognized by normal humans will be both ubiquitous and compelling – so much so that opponents will have to obtusely warn their disciples against acceptance of the obvious (as Francis Crick has done: “Biologists must constantly keep in mind that what they see was not designed, but rather evolved”).

    In simpler words: if things are intelligently designed, they should appear so. They do.

  5. ID predicts that many, if not all, innovative technology achievements of human kind (read agency) will have direct parallels in, or derivation from, biological systems.ID predicts that the information content (CSI) of living systems will decline, not increase, over time.ID predicts that the input of random, non-specific information into a functional or nonfunctional system will ever only degrade or inhibit that system in all but a few trivial and insignificant ways.

  6. Well so much for formatting by the preview.

    To note [off-topic] the WordPress plugin Ajax Comment Preview provides an exact format preview.

  7. The obvious one is that “junk” DNA is not junk.

  8. To expand on the comments of edj,

    The single most important prediction of Intelligent Design is that, although there might be the occasional degeneration of either macroscopic or microscopic structure, most structures should serve a purpose. Thus most organs should not be vestigial, and most DNA should not be “junk DNA”. There were those bold enough to say this when there appeared to be evidence to the contrary.

    As time has gone on, it appears that the ID position has been vindicated compared to the position that most DNA would prove to be purely selfish, or that we should expect to find multiple examples of organs that were useful to our evolutionary ancestors but not to us.

    This is an instance where not only is design theory making falsifiable predictions that appear to be corroborated, but where the Blind Watchmaker hypothesis can be legitimately considered a “science stopper”.

  9. Peter,

    Did ID really predict the big bangs of life?

    Does gradualism, even if it were supported by the fossil evidence, prove that evolution is undirected, requiring no intellegence? That’s the claim of Dawkins, for instance. But must ID show an absence of gradualism? Doens’t Behe show that gradualism is no help in explaining non-telic origins of IC?

  10. I was thinking the same thing as edj, to me that is the most compelling example!

  11. ID would predict

    1) Fx of Junk DNA
    2) Fx for the appendix
    3) That prokaryotes did not evolve from eukaryotes due to constraint issues:
    http://www.sciencemag.org/cgi/...../5776/1011
    4) That Human chromosome 2 and primate genome argument is not viable due to design constraints.
    5) Genomes of “primitive” creatures like the Jellyfish can be more advanced then many contemporary species.
    6) OOL (there’s gotta be stuff here)

  12. - Polyfunctional DNA encoding is one I believe DaveScot made.

    - Creature variation limited to either pre-existing (“built in”) or superficial changes, vindicated by Behe’s EoE work on the malarial parasite.

  13. I guess I must be the exception among ID advocates. I think we are doing ourselves a great disservice by focusing on the design while ignoring the designer. I think this shows a lack of faith in the ID community. Sorry, that’s how I feel. We are engaged in a nasty war (don’t kid yourselves) against an entrenched and determined enemy. And we are the attackers. The way I see it, we cannot win this war the way we’re going about it. The enemy owns the territory. They have impregnable fortresses and giants in their midst. They own the educational system and they own the media. Unlimited propaganda and unmitigated deceit are their weapons of mass destruction. Sure, many of us have shown great personal courage but that’s not going to cut it. We won’t stand a chance if we think we can fight this war on our own. The enemy will crush us like bugs.

    In my opinion, the most important falsifiable prediction of the ID hypothesis is the existence of a designer or a group of designers. If you truly believed in the existence of a designer, don’t you think that, given his vast intellect (nobody is going to design complex life forms by being stupid), he would have anticipated this battle a long ago and would have left us the means to fight it and win it? Where is your faith?

    If you want to know how I think we can engage the enemy in open warfare and kick some ass, take a look at my blog.

    PS. Dr. Dembski, you are being set up for a fall, in my opinion. I would decline the offer if I were you. Now is not the time. One man’s opinion.

  14. I don’t think some of those are really predictions of ID — for example, is irreducible complexity predicted by ID, or is it just something that most likely requires ID?

    I’d like to disagree with the “talking head” about the idea that a theory about things that happened in the distant past necessarily must have predictive value, to be science. Does the idea that the universe started 15 billion years ago with a big explosion have predictive value, or is it just the most direct inference from the observed redshifts of distant objects?

    If ID is compatible with the evidence, and no other theory of how life got to its present state is, then ID wins scientifically (at least for now) whether it has predictive value or not.

    Or to put it another way: If the correct explanation of where life came from (whatever that may be) happens to have no predictive value, does that make it scientifically impossible to answer the question of where life came from? Predictive value, while certainly preferable to none, is not an absolute requirement of a scientific explanation.

  15. How does Tom Cruise get past this kind of vetting?

  16. DarelRex, in 14, mentions I’d like to disagree with the “talking head” about the idea that a theory about things that happened in the distant past necessarily must have predictive value, to be science.

    I’ll agree with this. But, even if it isn’t a prediction about what happened, there is a need for the explanation to be internally consistent with the other claims of science (or to be strong enough to displace them).

    My point is that the internal consistency is demonstrated by correlation to other predictions that were played out. The method, at least for science is: Observe an event, conjecture an explanation, deduce a prediction from the explanation, test the prediction, validate or debunk the conjecture. (From wiki, on Scientific Method.)

    I would hope that the predictions of ID are of the type that can be tested – like some of the claims about probabilities that aren’t so extreme or obvious.

  17. 17
    Unlettered and Ordinary

    Greetings!
    I do not know what predictions need to be made. Design is everywhere in nature and it is not hiding. Not only is it functional but is looks good as well. Intelligent Design is really self explanatory, nature is intelligently designed and it is this design in nature that requires an explanation. This is not a new paradigm to science. Before and after Darwin many of the great science giants searched the design in nature and with results that changed the world. They were not seeking to explain away God but uncover his handy work. Nothing we humans have ever designed and manufactured even comes close to what is found in nature.

    One predictions I have for ID is that nature holds the keys to advanced technology for us humans to unlock. In every living thing at lease one technological advancement waiting to be discovered. Properly understood and utilized, all the organisms that make up our eco-systems will propel human intellect to places we cannot imagine.

    If that is not Intellegent design then all engineers and artists are all frauds.

    I further predict that the tech found in the organisms is there specifically for human intellect and use.

    This is really a rule for science, but why not nature. I look at it this way, if I were a being whose intellect towers infinitely over every other being, but to whom were my children, I would design nature to teach and amuse them, to inspire and instill a sense of awe in them. The design I would have put in nature would be specifically for them and comprehensible to them.

  18. (1) As already mentioned, “junk-DNA” would completely undermine ID if it turned out to really be “junk”. But, of course it isn’t.

    (2) A fair-level of “front-loading” would be expected. When they find genes for the expression of digits in sea anemones (sea squirts?), this throws Darwinism for a loop, but is almost an expectation for ID.

    (3) A complicated level/levels of regulation. If “junk-DNA” is not junk—as ID fully expected—then, concomitantly, it should have a function. The most likely function is that of regulation. When you consider that the ratio of non-coding to coding DNA is 48 to 1, then you must also expect an incredible level of regulation.

    (4) Since we’re dealing with “information”, ID would expect “error-correction” for DNA (let’s remember that the Darwinists would be hoping for the opposite—gotta have lots of variation, you know).

    (5) Again, because we’re dealing with “information systems”, one would expect high levels of redundancy built into the genome.

    (6) Lots of environmental triggers: if you’re designing life that must deal with huge temperature and climatic changes, then there must be a way for the genome and the environment to interact.

  19. 19
    Unlettered and Ordinary

    Greeting again!

    Science requires that nature be intelligently design so it can be intelligently investigated. This is a prerequisite for science that is all to often forgotten. If nature was not intelligently designed then no matter how much we investigated it, we would find it incomprehensible. It is precisely because it is designed that we can understand it.

  20. (7) Using the analogy of a computer program, one would expect what I call “subroutines”, or, put another way, various parts of the genome that are used for a variety of purposes in an “on-demand” basis. These “subroutines” would be part of the “regulatory” system of the genome.

  21. (8) Just as a computer must “compile” a program, there must be some kind of chromosomal system that associates the various “parts of the program” in a deterministic way. That is, the right parts have to be in the right place, and connected to one another in a ‘logical’ way.

  22. Taking ID broadly, it predicts signs of intelligence. After that, you can make a bunch of lower-level predictions. Front-loading, DNA, molecular machines, etc.

  23. Help me out here. What does Darwinism predict?

  24. “Help me out here. What does Darwinism predict?”

    That some atheists may become intellectually fulfilled.

  25. BarryA wrote:

    Help me out here. What does Darwinism predict?

    The way I understand it, Darwinian theory predicts gradual evolution, common descent and that all species can be classified so as to form a gapless family tree.

    The sudden appearance of huge numbers of fully-formed species in the fossil record soundly falsifies the gradual evolution hypothesis. Killed at the starting gate.

  26. Barry A (23):

    To give you just one example – evolutionary theory was used to predict where and in what rock strata the Tiktaalik fossil would be found. That is why the researchers went to the time, expense and inconvenience of looking in northern Canada.

    I think William Demski’s prospective interviewers are looking for that kind of prediction for ID. But I haven’t seen anything that specific coming from it yet.

  27. we don’t just see a discontinuous tree, we see a discontinuous bush. There’s a lack of clear cut phylogeny. What used to be clear cut (remember the horse sequence?) eventually gets messier. The prediction is that evolutionists will eventually throw out the rest of their favorite examples and appeal to “sister branches” and convergence

    We see all the phyla appear front loaded in the beginning and no new phyla emerge as time progresses. For example, ~500 vertebrate fish (Haikouichthys) were found in the early Cambrian in China.
    D. G. Shu et al., “Head and Backbone of the Early Cambrian Vertebrate Haikouichthys,” Nature, Vol. 421, 30 January 2003, pp. 527, 529.

    What about finding a vertebrate in the ediacara?
    http://www.abc.net.au/science/.....984724.htm
    and a year later http://www.abc.net.au/worldtod.....266616.htm
    “NANCE HAXTON: That fossil, only six centimetres long, is now believed to be the oldest vertebrate fossil on earth at 560 million years old. It ultimately proves that the origin of all complex life goes back much further than previously imagined. Shaped like a tadpole, the creature had muscles, a head, a fin on its back, but most importantly a backbone.”

    If OOL was a natural process we would expect multiple origins over time. A natural OOL could not predict biologic universals. Totally expected if they were the result of common design.

    We should find that most observed cases of microevolution are really rigged and not the result of rm/ns. Spetner gives a whole list in chapter 7 in his book Not by Chance.

    He didn’t put antibiotic resistance in his list but perhaps we now can. Look in DoL page 296 note 36: “In fact, a strict Darwinian explanation for antibiotic resistance seems to be more the exception than the rule. In times of environmental stress, bacteria go into a programmed defense that constitutes a targeted search for gene combinations that will enable at least a few of the bacteria’s descendants to survive (the genetic changes here are therefore not random mutations as understood within neo-Darwinism)…”

    We can predict we’ll find a mechanism for these directed mutations triggered by an environmental cue.

  28. 28

    Following on from the comment about nature being the key to advanced technology (indeed it already has) I feel that one often overlooked prediction of ID could be the key to a wonderful breakthrough. It’s a little complicated but bear with me. We know that ID predicts a line between micro and macro evolution which is uncrossable. This therefore means that elements of the DNA code are being protected from change. Now there are several, very real ways in which this can be done – evolutionists, of course, simply assume that nothing is happening so they don’t bother to research these – but I reckon that the coolest of these is the notion of molecular shielding. There are several ways that DNA nucleotides can be damaged – radiation is the most infamous one, but chemical damage does it too. If molecular shielding exists to protect nucleotides from macroevolution, then it must be capable of not only deflecting radiation, but also has a physical component to prevent unwanted chemistry. It’s a perfect forcefield on an atomic scale. The possibilities if we could get access to this power are amazing… we’re looking at totally real forcefields capable of stopping both matter and radiation. The US military would kill for stuff like that. Even better, because it is nano scale to begin with, it can have more mundane, practical function in materials; wire shielding, radiation suits, overalls.

  29. Clarence

    Just one example of an ID prediction:

    The ID front-loaded genome hypothesis predicts that a mechanism exists for preserving unexpressed genomic information for geologic periods of time.

    In a recent experment 1.5 million base pairs of non-coding DNA containing over a thousand highly conserved sequences between mice and men were deleted from the mouse. There was no detectable difference between the GM mice and their unaltered parents. The experimenters were stunned. They expected to find all kinds of problems in the GM mice which they could then use to infer the function of the conserved sequences in humans and possibly get a handle on a large number of genetic defects in humans.

    That result put a huge gaping rent in the chance and necessity theory. Natural selection can’t act on unexpressed genomic content. If natural selection didn’t conserve those sequences over 180 million years of divergent evolution between mice and men what the heck did preserve it? That question was shrugged off. The researchers were interested in ways to isolate and identify the function of DNA in humans and were not at all interested in DNA with no evident function. So instead of trying to figure out what worked to preserve that DNA they instead abandoned the mouse genome and started comparing sequences highly conserved between men and fish, men and reptiles, and men and amphibians. The scientific establishment at large seems to have little interest in testing the chance & necessity hypothesis. Isn’t that just precious?

    Being a proponent of ID by way of ancient front loading of the genome I was very pleased to see the results of this experiment but hardly surprised by it. I’d been expecting this result. I also expect to see genomic information coding for phenotypic features that were never expressed by the ancestors of the organism. Tantalyzing bits and pieces are being found. Stuff like genes that code for quadriped limbs in radially symetric organisms is one that comes to mind.

    And just for the record, the Tiktaalik prediction speaks only to evolution by common descent not evolution by chance & necessity. Try again. ID does not dispute common descent. It disputes evolution by chance & necessity.

  30. Clarence,

    The whole history of Darwinism is that evolutionists have gone looking for a particular fossil and they always find it. (Of course, later on they’re shown to be hoaxes.) But that’s because you can interpret any piece of fossil you find in any way you please. In Henry Gee’s book, “Deep Time”, he makes this very point.

    What does Tiktaalik represent? It represents some kind of aquatic form that has digits. But sea anemones have the gene for forming digits. So what is the point of Tiktaalik? Has Darwinism “proved” that the “environment” brought about the gene for digits? I hardly think so. It very likely demonstrates prediction #6 in my earlier post, #18–that is, there should be plenty of environmental triggers. So your adventurers went to a specific type of environment and found a particular type of fossil. Whose prediction does it fulfill?

  31. DaveScot (29),

    I’d agree that front-loading would be a good prediction for ID. I think my question to that would be, when did the front-loading occur? If it was front-loaded at or near the origin of life then ID would need to explain why the fossil record shows increasing complexity over time, rather than having complex features crop up all over the fossil record, even at the early stages, which is what one might expect from front-loadinng.

    To give an example: there have been occurences of chickens being stimulated to produce teeth (“hen’s teeth”). Those teeth were reptilian in nature, as might be expected from an evolutionary origin. They did not produce mammalian teeth. So the question for front-loading advocates is, if front-loading is true then we can predict that chickens can be stimulated to produce mammalian teeth (because the genes, being front-loaded, are already there).

    That is a clear and specific prediction. Surely a research programme could work on that?

    On your comment:

    “ID does not dispute common descent.”

    I think this is one of the things the ID Movement needs to clarify. Some (e.g. your good self, Mike Behe) don’t dispute it. Others (William Dembski, for example) seem to. Why the disagreement? How will William Dembski answer that in his interview?

    PaV, I simply don’t agree with your comment that a fossil can be interpreted any way you please. Like the rest of science, inetrpretations of fossils are peer reviewed and criticised by the expert community and a consensus opinion emerges once there is sufficient data. If you have an explanation that fits the evidence then the community will concur; if you don’t then your opinion is just your own and essentially of no sscinetific relevance. To say that most fossils Darwinists search for are hoaxes in simply untrue – there are quite literaly millions of fossils in museums, and the number of “hoaxes” would amount to a handful. In a few hours I can find literally hundreds, possibly thousands of fossils on beaches a couple of hours drive from me – are you seriously saying that these are hoaxes?

    I think you miss the point about the search for Tiktaalik. According to evolutionary theory there ought to have been transitional species between fish and the earliest land-dwellers. Given that the fossil record shows and absence of land-dwellers in earlier strata and the appearance of land-dwellers in later strata, it follows logically that the transitionals should have fossils represented in strata intermediate between them.

    Also, one would expect the transitionals to appear in strata derived from a river or shallow water where they could transition to land. By combining these time and environment limitations the researchers could find the most suitable strata in which to search for the transitionals. And they succeeded – a big plus for evolutionary theory.

    Converesely, I see Tiktaalik as a negative for ID. If the designer has designed fish, and then wants to design something for the land, why bother with a transitional? Why not just design land-dwellers and cut out the middle-man (or middle-fish, if you like). That is what ID needs to explain: if ID is true then why Tiktaalik?

  32. DaveScot,

    “And just for the record, the Tiktaalik prediction speaks only to evolution by common descent not evolution by chance & necessity. Try again. ID does not dispute common descent.”

    So you are saying that the dna for all creatures for all history existed in the first life form? If not then there are some gaps. How do you explain these gaps?

  33. one problem with the front loading hypothesis is that it also seems to imply gradualism, but unlike Darwinism this would be pre-programmed like the gradual development of an embryo.

  34. ari-freedom: “one problem with the front loading hypothesis is that it also seems to imply gradualism”

    What’s wrong with that?

  35. Davescot 29:

    Why isn’t lateral sequence transfer in the recent past a plausible explanation?

  36. I think the easiest prediction for ID is to follow up on Behe’s ideas from the Edge of Evolution. Namely, there is a limit to what natural processes can do and we expect to find that in the world around us.

    For example, in the future when the genomes are mapped for all mammals and there exists mappings of multiple variants within each species, what will be found in these gene pools. It would then be possible to look at the gene pools not only of the species but of the genera and families.

    NDE would predict new variations increasing over time at the species level and thus the gene pools of the genera and families would exhibit greater variation over time but ID would predict less variation over time at the species level as the main cause for species formation is loss of information, not gain of information.

    Of course there will be both but if the gain of information is small and trivial in terms of implications for evolutionary biology then ID is vindicated and NDE falsified as a generator of novelty. The basic NDE prediction is that novelty will appear at the species level and eventually lead to new families and orders. But if the evolutionary tree is getting thiner at the edges and not thicker then ID is vindicated and NDE falsified.

    There is research going on today that is investigating this which is why I say there is much ID research proceeding in biological laboratories even if it is not designated as such. Every time a biologist maps a genome of a species or multiple members of a species, he/she is doing ID research.

  37. DaveScot wrote:

    Being a proponent of ID by way of ancient front loading of the genome I was very pleased to see the results of this experiment but hardly surprised by it. I’d been expecting this result. I also expect to see genomic information coding for phenotypic features that were never expressed by the ancestors of the organism.

    Dave, let me see if I get this right. Are you saying that ID predicts that all the information needed for an organism to adapt to its environment via natural selection is pre-programmed from the beginning and is not the result of random mutations (as per Darwinian evolution theory)?

  38. 33 mike1962
    because that’s not what the fossil record is telling us

  39. 39

    In response to post 14
    ID predicts that there are characteristics that, when those characteristics emerge and the origins are known, are the result of design. IC and SC are two of those characteristics (there could be more). Humans make cars which exhibit IC and cars are a product of design. This can be falisfied. For instance, if one can show that IC and SC can emerge independently of design (and independently of already existing IC and SC structures) that would falsify the notion that IC and SC reliably signal design. If it can be shown that there are no characteristics that reliably signal design, that would falsify the notion that design can be reliably detected.

  40. ari-freedom: “one problem with the front loading hypothesis is that it also seems to imply gradualism”

    What’s wrong with that?

    I’m not an expert in these matters but may I venture that it only implies micro-gradualism (variations in the phenotype), that is, starting from a fully formed genome? Please, correct me if I’m wrong.

  41. 41

    Once we show that there are characteristics that reliably signal design, we should then try to examine whether or not life and the universe exhibit those characteristics.

  42. 42

    So basically, ID research would attempt to look for what characteristics reliably signal design and then it would try to determine (look into, research) if life and the universe exhibit those characteristics.

  43. ID predicts that when M & NS operate, they will be characterized more as trench warfare (breaking things) than as an arms race (making things).

  44. One of the problems with making predictions is that the evidence for ID based on analogous systems in engineering just keeps rolling in at such a rapid pace. But what if that evidence hadn’t been discovered yet?

    Here would be some predictions most of which would be post hoc but some may yet to be discovered. These are based entirely on what one would expect from an intelligently designed system from an engineering perspective.
    A robust specificationSpecification integrity controlsManufacturing facilities with quality controlOptimized materialsMaterials selection schemesDimensional tolerance controlSequenced assembly instructionsAssembly control and error checking systems
    Coordinated transport systems for materials and wasteBuild-in testFeedback and feedforward systemsError checking and correctionModularity and reusability in componentsSignalling between functional modulesFault sensing systems and responseParallel processingRecursive systems
    Contrained redesign capabilitiesInternal acceptance testing of new designsControlled failureCoordination with outside systems (ecological awareness)Built-in learning

  45. Looks like the ul and li tags don’t work like they do in the preview. Here’s the list again:

    *A robust specification
    *Specification integrity controls
    *Manufacturing facilities with quality control
    *Optimized materials
    *Materials selection schemes
    *Dimensional tolerance control
    *Sequenced assembly instructions
    *Assembly control and error checking systems
    *Coordinated transport systems for materials and waste
    *Build-in test
    *Feedback and feedforward systems
    *Error checking and correction
    *Modularity and reusability in components
    *Signalling between functional modules
    *Fault sensing systems and response
    *Parallel processing
    *Recursive systems
    *Contrained redesign capabilities
    *Internal acceptance testing of new designs
    *Controlled failure
    *Coordination with outside systems(ecological awareness)
    *Built-in learning

  46. front loading as an alternative to rm/ns to explain observed cases of microevolution makes sense. Limited descent makes sense (for example, lions and tigers probably had a common ancestor as they can produce hybrid ligers)

    But bacteria turning into people through front loading? Pardon my Yiddish, but that sounds a bit “farfetched.”

  47. OK. Here are some predictions that I believe a proponent of ID and/or front-loading could make.

    (1) Optimality of DNA. If anything in nature was designed by a Higher Intelligence, DNA was. If something is intelligently designed for some purpose, then it should be optimal for that purpose. Of course, it can get a bit tricky if an entity is designed for many different purposes which have conflicting requirements, necessitating some sort of engineering compromise. Nevertheless, one simple prediction that ID would make is that NO biologist will ever be able to build a genetic code which can do a BETTER job than DNA for ALL of the following purposes: regulating the development and functioning of organisms; transmitting genetic information faithfully from one generation to the next; and making minor adjustments (mutations) in response to environmental changes. If someone can design a molecule that excels DNA in one of these areas and equals it in the others, then ID is falsified.

    (2) Inexhaustibility of DNA as a research model. If DNA was designed by a Supernatural Intelligence, then one would expect it to be a perpetually fruitful research subject for scientists – especially computer scientists, and that these scientists will always be able to make refinements in computer coding and data storage by copying existing features of DNA molecules. If we ever reach a stage where scientists can say, “That’s it. We have nothing more to learn from DNA. We’ve now got data storage devices that incorporate all of its desirable features and more besides,” then ID will become obsolete as a hypothesis. Why? Because any Designer that’s dumber than Homo sapiens doesn’t deserve to be called a designer, that’s why.

    (3) The existence of active or dormant equivalents for each and every functional vertebrate gene in all phyla of metazoa (animals). We already know that genes for the expression of digits have been identified in sea anemones. However, even a fairly modest version of the front-loading hypothesis would also imply that sponges (which are animals) should have these genes too. A bolder version of the hypothesis (one front-loading event, at the dawn of life) would imply that plants and bacteria should have these genes as well.

    With regard to (1): an article in “Science Daily” (Fen. 9, 2007) at http://www.sciencedaily.com/re.....230116.htm refers to DNA as “nearly optimal for encoding signals of any length in parallel to sequences that code for proteins.” It reports that Dr. Uri Alon and his doctoral student Shalev Itzkovitz “showed that the real genetic code was superior to the vast majority of alternative genetic codes in terms of its ability to encode other information in protein-coding genes.” That sounds like DNA is good but not optimal. The researchers “also demonstrated that the real genetic code provides for the quickest incorporation of a stop signal–compared to most of the alternative genetic codes–in cases where protein synthesis has gone amiss.” My prediction here is that even IF alternative genetic code turns out to be better than DNA at BOTH of these things (encoding other information as well as incorporating a stop signal) then there should definitely be some other function of DNA (e.g. long-term transmission of genetic information) at which the alternative genetic code does not perform as well as the code we find in DNA. If, on the other hand, DNA turns out to be merely in the top 1%, say, of all possible designs, then this discovery would suggest that DNA in its present form somehow developed over the course of time from something less perfect, and that it stopped improving when it reached a local fitness peak.

    As regards prediction (2), things are looking good for ID, if an article in “Science Daily” (Feb. 23, 2007) and available online at http://www.sciencedaily.com/re.....034152.htm is anything to go by. “In a report scheduled for the April 9 issue of ACS’ Biotechnology Progress, a bi-monthly journal, Masaru Tomita and colleagues in Japan point out that DNA has been attracting attention as perhaps the ultimate in permanent data storage.

    “Data encoded in an organism’s DNA, and inherited by each new generation, could be safely archived for hundreds of thousands of years, the researchers state.”

    It sounds like DNA will be a pretty fruitful area for computing research, for the foreseeable future.

    (3) is perhaps the easiest prediction to test. Does anyone know of any confirming or disconfirming genetic data from sponges or from plants?

  48. peter

    So you are saying that the dna for all creatures for all history existed in the first life form?

    Not necessarily. One method used to insure the integrity of data is to store copies of it in different locations so if one is visited by catastrophe the others survive. If life here was seeded by an intelligence it wouldn’t be limited to a single first form. It would be limited by only what was able to survive. There could have been any number of them although on the young earth they’d be limited by the environment at the time. One organism doesn’t have to contain the entire database for everything that follows. It could also be a distributed database with different fractions of it of residing in organisms that didn’t reproduce sexually. Life may have begun here from hundreds or even thousands of cell lines. Extremophiles of all kinds would be a good starting point.

    If not then there are some gaps. How do you explain these gaps?

    There is also the possibility of multiple front loadings over the course of history although I tend to favor just one instance. Existing species can be easily modified with new information by highly transmissable, highly contagious viral vectors which in principle could cause some large and abrubt phenotype changes in a very small number of generations or even just one generation constrained only by physical limitations like a fish not being able to have mice hatch from its eggs.

    Keeping within the realm of the physically possible under the known laws of physics places some constraints on the whole matter. For instance, the source of the initial life would have be in causal contact with the earth. Barring faster than light travel that rules out most of the universe. Because of the immense energy required to accelerate a mass to a significant fraction of light speed and slow it down upon arrival it becomes more reasonable as the mass of the payload decreases. So you wouldn’t ship, metaphorically speaking, the San Diego Zoo here and have it soft-land. The same constraints would also limit being able to observe what was happening so to make appropriate adjustments or along the way.

    I haven’t read the book but I understand that Francis Crick and Leslie Orgel took these factors into account when they wrote Life Itself which was about what they called the theory of Directed Panspermia.

    To stay within the bounds of the physically possible, in other words to avoid resort to the supernatural, one needs a good understanding of what is physically possible for intelligent agents. I highly recommend K. Eric Drexler’s book Engines of Creation which was the seminal work in the emerging field of nanotechnology which devotes a good portion of the book to the limits of the physcially possible through intelligent agents with well developed nanotechnology.

  49. PaV @ 18 –

    (1) As already mentioned, “junk-DNA” would completely undermine ID if it turned out to really be “junk”. But, of course it isn’t.

    Just to clarify – what if some junk DNA had no function, but the rest did?

    (3) A complicated level/levels of regulation. If “junk-DNA” is not junk—as ID fully expected—then, concomitantly, it should have a function. The most likely function is that of regulation. When you consider that the ratio of non-coding to coding DNA is 48 to 1, then you must also expect an incredible level of regulation.

    Would that imply that organisms with more junk DNA would need more regulation, and hence be more complex? Would that be an ID prediction?

    Bob

  50. 50

    This is a fascinating discussion! I particularly like Venus Mousetrap’s prediction that a forcefield must be protecting DNA. Discovery of this field would completely vindicate ID – I would compare it to Eddington’s discovery of the bending of light-rays around the eclipsed sun, thereby corroborating general relativity. And, as VM says, it would have fantastic applications in industry. These are exciting days all right for ID! When have Darwinists ever improved our lives as much as ID one day will?

    Still, I’d like to hear Prof. Dembski’s list. He’s being a bit of tease – asking us mere laypeople to guess what ID predicts, when he, the leading ID scientist in the world keeps the real ID predictions close to his chest! And no girl likes being teased….

    So Dr Bill, no more flirting, let’s get to second base right now!

    Peace and kisses,
    Zoe.

  51. I’ve never seen a credible scientific justification for this:

    “junk-DNA” would completely undermine ID if it turned out to really be “junk”.

    It appears to be a theological argument presupposing a perfect designer whose perfect design can’t have or could never have acquired any functionless baggage over the course of its existence.

  52. Does the idea that the universe started 15 billion years ago with a big explosion have predictive value

    Absolutely. It predicted the cosmic microwave background radiation (CMBR) which was subsequently found and heralded as a confirmed prediction of the theory much like Einstein’s theory of relativity (or was it special relativity?) predicted that light would be bent by intense gravity fields and much later this was confirmed by the observation of stars very close to the disk of the sun during a solar eclipse.

  53. I really, really like Behe’s work on the evolution of P.falciparum viewed as a prediction of ID.

    However, if this is a confirmed prediction of ID it presupposes something that many IDists, particularly the devoutly religious, don’t want to accept – that the designer is no longer with us. If we don’t make that presumption then what was observed could be the result of a designer actively suppressing the evolution of P. falciparum. What’s good for the goose is good for the gander. If one posits an active intelligent agency with virtually limitless powers involved with the course of evolution then that designer can suppress change as easily as causing change to happen.

    That’s another reason why I prefer the front loading version which supposes one or just a few points in the history of life were design inputs were made. Then we can make the prediction that we won’t observe any significant creation of novel cell types, tissue types, organs, or body plans even when we observe a eukaryote such as P.falciparum having orders of magnitude more opportunities for mutation and selection to create complex novel structures than all the mammals that ever lived had available to them.

    This has been brought up a number of times by critics and a designer in absentia is the only reasonable response while still maintaining that lack of macro-evolution in the present world no matter how many replications or generations are involved is a prediction of ID. It’s a category-killer of a prediction in that case which has been confirmed in one well studied prolific eukaryote. It represents a test of both evolution by chance & necessity and evolution intelligent design. Chance & necessity’s predictions (in the laughable sense that it makes major predictions for the future trajectory of evolution when billions of trillions of replications under intense selection pressure are involved) failed miserably while the ID prediction was confirmed. Unless chance & evolution be completely useless in making predictions about the course and extent of evolutionary change it’s reasonable to say that it predicts something phenotypically novel and complex should emerge with that much opportunity to do what is claimed it did in the past.

  54. I don’t have the exact quote at hand but I don’t think Francis Crick intended panspermia to be taken too seriously. It was really intended as a “call to arms” to wake up the OOL community because he felt there were real problems they weren’t addressing.

    Carl Sagan spent a lot of time and effort debunking the idea of UFO’s even though his popularization of SETI as the inevitable result of evolution and “billions and billions” of earth like planets probably was responsible for the widespread belief we’ve been visited by aliens.

  55. However, if this is a confirmed prediction of ID it presupposes something that many IDists, particularly the devoutly religious, don’t want to accept – that the designer is no longer with us. If we don’t make that presumption then what was observed could be the result of a designer actively suppressing the evolution of P. falciparum.

    Just because the house is built doesn’t mean the builder goes away. He may be living in it even :-)

  56. tribune

    If the designer is still in the neighborhood still able to intervene then all bets are off. No matter what happens, evolution or lack thereof, it can be fobbed off as the intervention of a designer. It becomes a theory of everything, much like chance & necessity becomes when decoupled from statistical probability, and thus explains nothing. Right now the chance & necessity faithful are trying very hard to credibly explain why so little happened in all those opportunities for evolution that P. falciparum had in the last 50 years. If they shrug it off by saying “sometimes creative evolution happens fast with few opportunies for heritable change and sometimes it doesn’t happen at all with billions of trillions of opportunities” then chance & necessity becomes a theory of everything with no predictive power making it an absolutely useless historical narrative far removed from the practice of science.

  57. One other prediction illustrates the difficulty of making predictions.

    I have run into the argument a number of times that if a Creator (the propounders of this argument discount space aliens) wanted to re-use a part from one organism in another one, He would simply copy the relevant DNA where it was needed. On the other hand, the cytochrome C gene seems to have been copied with slight modifications from organism to organism, so that there is a branching tree effect.

    The branching tree isn’t quite as perfect as it is cracked up to be, and different proteins can give different branches. And how much variation can be allowed between different families, orders, classes, and phyla is not clear. Nor is it clear that the different forms of cytochrome C are not optimized to serve the purposes of the different organisms. To affirm the latter would take more knowledge about optimal organism function than we possess.

    However, one point is probably valid. If one designs an airplane and a car, certain designs will be taken over without significant modification, especially if the designer is the same, such as is apparently the case for the Saab. Why don’t we see this in nature?

    Those arguing this way have a point. Perhaps we do see here a prediction for intelligent design. Is is falsified?

    Actually, no. One frequently sees the same system re-used in a number of organisms. Histones and hox genes come to mind.

    But these examples are compatible with gene conservation and common descent. What is really striking is where common descent is not a reasonable explanation. What is really striking is when we have such things as bacterial rhodopsin showing up in rice. Nobody that I know of claims that the common ancestor of these had the gene. On the face of it, this would seem to falsify common descent.

    However, the immediate response is that this is “lateral gene transfer”; that the rice somehow got a bacterial gene inserted into its genome. So far it is a just-so story. We have no idea whether this can happen, or how easy it is. As examples of “lateral gene transfer” pile up, we should start asking questions about mechanism, and how easy it really is to get bacterial genes to go to the right place in the genome of another organism. Lateral gene transfer may be a fertile field for research by ID adherents.

    The breakdown of the final common ancestor to a network of shared genes is the NDE expression of a prediction that ID has been making for a long time.

  58. The religious perspective: G-d created man, creation was complete, He rested, generally assume order and degradation afterwards except for a few specified miracles to make a point.

    Life from aliens: more aliens could always try to seed earth with new lifeforms. Why assume they would stop trying?

  59. Dave

    No matter what happens, evolution or lack thereof, it can be fobbed off as the intervention of a designer.

    Or the non-intervention, which is a very important distinction and one of the pillars of Western Culture and science, itself.

    It becomes a theory of everything, much like chance & necessity

    Very good point. Darwinism, like theism, is not a science.

    becomes when decoupled from statistical probability, and thus explains nothing.

    Not objectively or measurably. But remember, anything extrapolated far enough becomes a matter of faith.

    Which is the wonderful thing about ID: it is not meant to be extrapolated any further than any other practical, useful science.

    Here’s criteria for design; object meets/doesn’t meet criteria; object is/may not be designed.

    A very simple program. And who is the designer? The program can’t address it.

  60. Paul Giem

    Functional genes can certainly show up as if by magic where intelligent agency is involved. We routinely transplant genes from one organism to another. One rather visible (pun intended) example that gets a lot of popular press is the insertion of a gene that codes for a luminescent protein that glows under ultra-violet light. It’s been inserted in things ranging from tobacco to fish to cats. Glow in the dark pets are coming soon to a petstore near you!

  61. Continuing from #21:

    (9) This is an expectation; not a prediction: Since Bateson showed that morphology can take on geometric proportions from one taxa to another, we should expect some kind of mathematical formulation to occur. To have a mathematical equation programmed right into the genome would be inefficient. So, something along these lines will probably be discovered at the level of a protein complex, or a protein complex interacting with miRNA and siRNA (my guess)

    (10) Again, an expectation; not a prediction: As progress is made in robotics wherein sophisticated programming allows for very life-like motions, a similarity between the signal processing scheme of animals and machines is likely to emerge.

  62. tribune7
    Still you need some basis for assuming non-intervention. Maybe we (or something else) are pre-programmed to turn into some super creature at some time in the future?

  63. ari

    Still you need some basis for assuming non-intervention.

    Well, yes. The idea that miracles must not be expected is one of the axioms of our culture. Other cultures do not hold this.

    And note that this axiom is not based on science but rather science is based on it.

  64. Clarence #31:

    “I simply don’t agree with your comment that a fossil can be interpreted any way you please. Like the rest of science, inetrpretations of fossils are peer reviewed and criticised by the expert community and a consensus opinion emerges once there is sufficient data.”

    This is a very naive view, Clarence. It’s not that simple.

    “I think you miss the point about the search for Tiktaalik. According to evolutionary theory there ought to have been transitional species between fish and the earliest land-dwellers.”

    Maybe you’ve missed the point that evolutionary theory—Darwinism—predicts all kinds of intermediate forms. Where are all the other millions of intermediate forms that the fossil record was predicted, by Darwin, to contain?

    Let me add: you missed my point about the possible environmental factors that effect the genome. IOW, how can you distinguish between a genome that has adapted itself to a particular environment, and a genome that has been “produced” by the same said environment? How do you confidently distinguish the one from the other?

    “Given that the fossil record shows and absence of land-dwellers in earlier strata and the appearance of land-dwellers in later strata, it follows logically that the transitionals should have fossils represented in strata intermediate between them.”

    Conversely, how do you know that it isn’t the case of a “land-dweller” adapting itself to an intermediate environment, rather than an aquatic form adapting itself to a more terrestial environment? Remember, it’s an intermediate. Now you can see why we need lots of ‘intermediate forms’ to untangle the mess.

    “Converesely, I see Tiktaalik as a negative for ID. If the designer has designed fish, and then wants to design something for the land, why bother with a transitional?”

    If He explained the answer, would you understand?

    More to the point: does every “design” have one, and only one, form to it? Isn’t it possible to “design” something in such a way that it takes on different forms in different circumstances?

  65. See Research ID

    Junk DNA

    Predictions of Intelligent Design

    Encourage readers to add to Predictions of ID etc.

  66. DaveScot wrote:

    If the designer is still in the neighborhood still able to intervene then all bets are off. No matter what happens, evolution or lack thereof, it can be fobbed off as the intervention of a designer.

    I’m not sure I understand this argument. What is the difference between the designer being present a long time ago to front-load a bunch of genomes (say during the Avalon explosion) and then be absent for 100 million years (for whatever reason) before returning to front-load a new set of genomes? Why would the new intervention either falsify the ID hypothesis or render it unfalsifiable? Maybe the designer was not absent between life form explosions. Maybe he had a reason to wait a 100 million years. After all, you did suggest the possibility of multiple front-loadings. I don’t get it.

  67. Bob O’H @ 49:

    “Just to clarify – what if some junk DNA had no function, but the rest did?”

    In Darwinian theory, when no conceivable idea exists for the necessary intermediates between form A and form B, we’re told/assured that “well, we don’t know what it’s function is, but someday we will.” It all looked like “junk” to Darwinists before. Now it’s obvious that it isn’t all “junk”. When you have some plants that have four copies of the genome, to know why that’s the case isn’t so obvious at times. I imagine we’ll find that some of the “junk” sure appears to be “junk”. According to Fred Hoyle, you would expect some “junk”—but this is from the man, of course, who demolished Darwinian theory in his book, “The Mathematics of Evolution.”
    Maybe there’s a reason for some “junk”. One of the predictions of ID that I listed included one about ‘redundancy’. Would that classify as “junk”?

    “Would that imply that organisms with more junk DNA would need more regulation, and hence be more complex? Would that be an ID prediction?”

    To a degree it would be a prediction.

    Let me ask you this: Would Darwinain theory “predict” that rice would have over 50,000 proteins in its genome while humans would only have about 30,000?

    PaV

  68. To have a mathematical equation programmed right into the genome would be inefficient. So, something along these lines will probably be discovered at the level of a protein complex, or a protein complex interacting with miRNA and siRNA (my guess)

    How would the structure of the proteins and RNAs be coded and inherited if not from the genome? Are you suggesting some other form of inheritance?

    Bob

  69. See Research ID continued:

    Empirical ID Research

    Gonzalez’ Lunar exploration prediction

    “In fact, we might predict that such evidence is available somewhere, if we search diligently enough. It was precisely this prediction that led one of us (Guillermo) to consider the value of lunar exploration for uncovering relatively well-preserved relics of Earthly life from this early period.”

    ——-
    Also:

    Intelligent Design is Empirically Testable and Makes Predictions

    By Jay Richards and Jonathan Witt
    at Evolution News & Views

    “Behe predicts that scientists will not uncover a continuously functional Darwinian pathway from a simple precursor to the bacterial flagellum and, moreover, any detailed evolutionary pathway that is articulated will presuppose other irreducibly complex systems.”

    Note particularly:

    NOTES:
    1. Philosophers of science now know that “prediction” is too narrow a criterion to describe all scientific theorizing. Empirical testability is the more appropriate criterion.

    2. “Empirical testability,” “falsifiability,” and “confirmability” aren’t synonyms. “Empirical testability” is the genus, of which falsification and confirmation are species. Something is empirically testable when it is either falsifiable, confirmable, or both. Moreover, something can be confirmable but not falsifiable, as with the Search for Extra-Terrestrial Intelligence (SETI) or the existence of a cosmic designer. Both of these claims are still empirically testable. Further, recent work in the philosophy of science has revealed the degree to which high level scientific theories tend to resist simple refutation. As a result, Karl Popper’s criterion of “falsifiability,” which most commentators seem to presuppose, was rejected by most philosophers of science decades ago as a litmus test for science. Nevertheless, it’s certainly a virtue of scientific proposals to be able to say what evidence would count against it.

  70. “Would that imply that organisms with more junk DNA would need more regulation, and hence be more complex? Would that be an ID prediction?”

    To a degree it would be a prediction.

    To what degree? I don’t understand your qualification.

    About the “what if only some junk DNA had function” question, I was asking whether some junk DNA being non-functional would (in your phrase) “completely undermine ID”. I’m still interested in knowing this.

    Bob

  71. Nevertheless, it’s certainly a virtue of scientific proposals to be able to say what evidence would count against it.

    I think this is what most Darwinists are looking for, a specific experiment that can potentially falsify the ID hypothesis. Unless ID theorists can specify such an experiment, I believe that ID will not be accepted as a science. The fact that ID can be confirmed (a sudden return of the designer to the scene would do it) does not carry much weight, in my opinion.

  72. 72

    OK, enough already!! Let’s all pipe down so that Prof. Dembski can get a word in here!!! I want to hear the actual list – not just everyone’s pie-in-the-sky speculations!

    Sheesh, some people just like hearing the sounds of their own voices ;-)

    Smiles,
    Zoe.

  73. The fossil record is evidence for rapid change followed by relative stasis.
    This suggests that DNA is capable of changing radically in a short period of time. Present research demonstrates that small changes can be guided by an externally directed intelligent force. We are already doing such experiments although our methods are crude. For example recently scientists have introduced genes into various animals to make them glow in the dark. I say crude because we are simply taking an existing gene from one animal and introducing it into another… or messing with a particular gene site. We had prior knowledge gained from research that this particular gene and position coded for something that glows.

    Radiation may be a better alternative to causing change. We know for example that fruit flies can be mutated when exposed to random X-ray radiation, none of the mutations are beneficial because the radiation is not specified.

    It is well known that we use radiation in the form of laser light, or radio waves to transmit information all the time in our modern world.

    Prediction:
    If the radiation was instantiated by an intelligent agent in the correct wavelength, proportion and sequence to the DNA molecule, changes could be directed to cause informational change and new survivable body plans could be made rapidly. Furthermore the specific information content required to be carried in the radiation will rule out natural cause as a possible source. A subsequent prediction would be that parts of DNA are designed as a receptor of information… “an antennae” which can receive new instructions.

  74. Yo, Plaything. Who put you in charge of this blog? LOL. Patience is a virtue, you know.

  75. Genomic Entropy
    Per “ID’s “predictive prowess”
    John C. Sanford concludes:

    “the genome is degenerating.”

    “All evidence points to human genetic degeneration”.

    Ch 10 Is the downward curve real?

    “Genetic Entropy & The Mystery of the Genome” (2005) Ivan Press, Elim Pub., Lima NY ISBN 1-59919-002-8

    Corollary: Genomic degeneration or entropy points back to intelligent design with original full function.

    “What is the mystery of the genome? Its very existence is its mystery. Information and complexity which surpass human understanding are programmed into a space smaller than an invisible speck of dust. Mutation/selection cannot even begin to explain this. It should be very clear that our genome could not have arisen spontaneously. The only reasonable alternative to a spontaneous genome is a genome which arose by design.”

    —————————–

    Summarizing and rephrasing Sanford’s book:

    1. All genetic evidence points to accumulating degradation of the genome.
    2. ID predicts that organisms comprise numerous complex functions with well tuned performance.
    3. Mutations degrade or destroy biologic functions, causing disorder, disease and death.
    4. Mutations with selection will progressively increase genetic mutational loads, increase the frequency of genetic diseases, reduce longevity, and eventually result in species death.
    5. Accumulating genomic entropy, declining longevity, and genetic diseases point back to designed organisms with non-degraded function.
  76. 76

    Yo, Plaything. Who put you in charge of this blog? LOL. Patience is a virtue, you know.

    This girl has never been big on patience… ;-)

    Flounces,
    Zoe.

  77. 77

    … or on virtue, now that I think about it LOL.

  78. DaveScot: Functional genes can certainly show up as if by magic where intelligent agency is involved.

    Is there a way to distinguish between human designer “magic” from other types of “magic”?

  79. 79

    Prediction: The fundamental laws of physics will be shown to preclude the possibility that life could arrise by any chance or probabilistic processes and thus REQUIRE the input of both energy and information from an intelligent agent who is in posession of both.

  80. “Converesely, I see Tiktaalik as a negative for ID. If the designer has designed fish, and then wants to design something for the land, why bother with a transitional?”

    I would expect designs to live in transitional environments. There are flying fish and mudskippers but I don’t think anyone claims they are turning into anything.

    However I think that this fish will turn out to be like the coelacanth, another lobe finned fish which was claimed to walk and hyped as the ancestor to tetrapods until it was actually discovered swimming in the ocean.

  81. btw…why are we only talking about biology?

  82. Accumulating genomic entropy, declining longevity, and genetic diseases point back to designed organisms with non-degraded function.

    DLH, thanks for the references. I was thinking that, assuming that genomic entropy is true, if the rate of degradation is known and if the average degree of degradation of a population sample can be obtained, it should be easy to calculate backwards to get an approximate creation time for a given organism. Kinda like carbon-14 dating in physics. We could then compare the date with the fossil record to see if they match. Just throwing stuff at the wall.

  83. 83
    EndoplasmicMessenger

    I think we can say that ID predicts that practices and techniques that are commonly used by human intelligence in designing and engineering machines, including computing machines, will be found in biological systems.

    An example of this are codes (e.g, ASCII, EBCDIC). Certainly a huge component of cells that Darwin (and any purely materialistic theory) did not (and cannot?) predict but that falls easily with the realm of ID is the Genetic Code.

  84. DarelRex (#14): “If ID is compatible with the evidence, and no other theory of how life got to its present state is, then ID wins scientifically (at least for now) whether it has predictive value or not.”

    I think this hits the nail on the head. ID has indeed made some predictions that have been fulfilled, but the demand by Darwinists that ID must have “predictive value” is a red herring. To use the SETI analogy, to observe that a signal from Tau Ceti has an intelligent signature (could not have been produced by any known natural mechanisms) has no predictive value other than that it would be a good idea to concentrate on this star for more signals, because this initial detection seems to indicate alien intelligence. The SETI astronomers wouldn’t reject this observation as unscientific.

  85. DaveScot (#54): “If we don’t make that presumption (that the designer is no longer with us) then what was observed could be the result of a designer actively suppressing the evolution of P. falciparum.”

    Not necessarily. The designer might merely intervene to inject new genetic information at certain points in time, and let RM & NS operate unmodified the rest of the time. This would not require any active suppressing of a natural mechanism, and not invoke front loading.

  86. Better late than never:

    Prediction:

    1) If the universe was the product of a common design then I would expect it to be governed by one (common) set of parameters.

    2) If the universe were designed for scientific discovery then I would expect a strong correlation between habitability and measurability.

    3) Also if the universe was designed for scientific discovery I would expect it to be comprehensible.

    Test:

    1) Try to determine if the same laws that apply every place on Earth also apply throughout the universe.

    2) Try to determine the correlation between habitability and measurability.

    3) Try to determine if the universe is comprehensible.

    Potential falsification:

    1) Observe that the universe is chaotic.

    2) A- Find a place that is not habitable but offers at least as good of a platform to make scientific discoveries as Earth or B- Find a place that is inhabited but offers a poor platform from which to make scientific discoveries.

    3) Observe that we cannot comprehend the universe, meaning A) what applies locally does not apply throughout or B) what applies in one scenario, even locally, cannot be used/ applied in any similar scenario, even locally.

    Confirmation:

    1) Tests conducted all over the globe, on the Moon and in space confirm that the same laws that apply here also apply throughout the universe.

    ”(S)pectroscopic observations of distant galaxies over a broad range of wavelengths verify that their atoms have the same properties as those measured in Earth laboratories. On the basis of such observations, astronomers and cosmologists feel justified in extrapolating the laws of physics from their tiny laboratories to the entire universe.” Page 323 “The Privileged Planet”

    2) All scientific data gathered to date confirm that habitability correlates with measurability.

    3) “The most incomprehensible thing about our universe is that it is comprehensible.” Albert Einstein

    Prediction:

    If living organisms were the result of intentional design then I would expect to see that living organisms are (and contain subsystems that are) irreducibly complex and/ or contain complex specified information. IOW I would expect to see an intricacy that is more than just a sum of chemical reactions (endothermic or exothermic).

    Further I would expect to see command & control- a hierarchy of command & control would be a possibility.

    Test:

    Try to deduce the minimal functionality that a living organism. Try to determine if that minimal functionality is irreducibly complex and/or contains complex specified information. Also check to see if any subsystems are irreducibly complex and/ or contain complex specified information.

    Potential falsification:

    Observe that living organisms arise from non-living matter via a mixture of commonly-found-in-nature chemicals. Observe that while some systems “appear” to be irreducibly complex it can be demonstrated that they can indeed arise via purely stochastic processes such as culled genetic accidents. Also demonstrate that the apparent command & control can also be explained by endothermic and/or exothermic reactions.

    Re-animation of dead organisms- this should be easy to do if living organisms were just chemical reactions.

    Confirmation:

    Living organisms are irreducibly complex and contain irreducibly complex subsystems. The information required to build and maintain a single-celled organism is both complex and specified.

    Command & control is observed in single-celled organisms- the bacterial flagellum not only has to be configured correctly, indicating command & control over the assembly process, but it also has to function, indicating command & control over functionality.

    Living organisms are dynamic systems which employ command & control/ regulation throughout.

    Conclusion (scientific inference)

    Both the universe and living organisms are the result of intention design.

    Any future research can either confirm or refute this premise, which, for the biological side, was summed up in Darwinism, Design and Public Education page 92:

    1. High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design.

    2. Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity.

    3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity.

    4. Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems

  87. Mapou

    if the rate of degradation is known and if the average degree of degradation of a population sample can be obtained, it should be easy to calculate

    An excellent observation.

    Clarifying, ID Predictions:
    1) The average human genomic mutational load will steadily increase.

    5b) The rate of increase in human genomic mutational load will provide a reliable basis for projecting back to a common ancestor.

    That is similar coalescent analysis that projects back. See “mitochondrial Eve”, “the most recent common ancestor” – projected to be less than 200,000 years ago.

    Ho and Larson in ”
    Molecular clocks: when timesare a-changin’” observe:

    “However, debate has arisen about the considerable disparities between molecular and palaeontological or archaeological dates, and about the remarkably high mutation rates inferred in pedigree studies.”

    This exposes the difficulties of fitting evolution to the data. This promises good prospects for ID to provide quantitative models with good predictions.

    The quantitative data on human mutation statistics is just now being obtained in the International HapMap project.

    PS Armando G.M. Neves et al. in “Applications of the Galton–Watson process to human DNA evolution and demography” show that “mitochondrial Eve” could occur with an exponentially growing population.

  88. Joseph, in 91, shows good style for this topic! (IMO, of course.)

    A prediction, at least a scientific prediction, is only as good as the paper it is written on. But providing predictions with proposed tests and a means to confirm or disconfirm the prediction, now that makes a good fit into the scientific process.

    Those steps of confirmation are just as important for ID to be a scientific theory as they are for any science.

    Kudos, joseph!

    As a side note (and not to detract from the good work), I want to suggest that to confirm ID, the prediction and test should specifically disconfirm contrasting claims of evolution or other sciences. Simultaneously supporting other sciences, or being neutral to the claims of other sciences is probably insufficient.

    For example, I don’t think evolution (or other sciences) make a prediction of the comprehensibility of the universe (see 91, first prediction sub 3). Finding that the universe is comprehensible may simply be a confirmation of comprehensibility, neither advancing ID over evolution, or retarding any other science.

  89. 89
    Unlettered and Ordinary

    Greetings!

    I may be just crazy but evolutionary predictions have not been accurate or precise, and are usually base on three underlying assumptions universal common dessent, random mutations and natural selection…

    Further, they go looking for the data through that framework which in reality in a flawed approach, which really explains their failure well.

    Where as with ID, we can use tried and proven design principles from programming to construction and engineering to make predictions about what we might find in nature.

    As well as tried and proven principles of efficiency and effectiveness, in product design and manufacturing.

    Let’s not abandon aesthetic principles for no good reason.

    My point is that ID is rich with actual design principles that actual Intelligent agents use frequently.

    These principles provide us with an excellent criteria for predictions that may be both accurate and precise without resorting to too much speculation. And all the principle I am talking about have been in use since long before me, and you and you and YOU.

    Everything can really be boiled down to a bunch of simple principles that govern the whole process. Both physics and chemistry can do it and do do it. Biology probably does it some where.

    I don’t count UCD, RM, or NS, because these infringe on the observations of reality. And the only reason people take them into account is because they have be taught to look for them. I don’t deny the actual processes we observe in nature, but the terms excluded are poor representation of what is actually observed.

    My point is if you are going to include these terms they need redefining to account for what is observed in nature, not the mis-interpreted and shallow definitions the darwinists use and are what are commonly understood to be by the public.

    And as I pointed out these are assumptions, and the only one that might be viable is NS.

    UCD is based on circumstantial evidence at best, and really can only be explained if ID is true and only if evolution was used. And the fossil record show a different picture completely contrary to UCD without using ID. The evidence is speaking, shhhhhhh, you might hear it. As for the evidence DNA might become the only evidence for UCD but only if ID is true and only if the functions for the non-coded DNA support that conclution. “IF”!

    RM is not viable and we all know it, it is really a divertion, and it requires a whole lot more “IF’S” than can really be given.

    NS requires Intelligent direction and this is done by us when breeding and the rules are different in nature. Nature balances environmental factors against an organisms adaptability, genetic constitution and flexability, and reproductive ability at the population level that results in the organisms average health and versatility.

    Whatever work is done in a lab is not a representation of real nature. However, the observations found in nature of speciation and hybridization shows that what we humans do with relative ease, nature does it too but not with the same efficiency or effectiveness or purpose.

    I guess what I mean is; in nature a rottweiler and a chihuahua don’t breed, the chihuahua is food for the rottweiler. But for some insane reason we could breed them relatively easily. The same rules don’t apply, and it is “assumed” that nature acts as an intelligent breeder.

  90. Q:

    As a side note (and not to detract from the good work), I want to suggest that to confirm ID, the prediction and test should specifically disconfirm contrasting claims of evolution or other sciences. Simultaneously supporting other sciences, or being neutral to the claims of other sciences is probably insufficient.

    I agree. Question is, can ID theory, as it stands, deliver?

  91. As ID continues to prove itself researchers will become more sensitive to the notion that some things were designed for a purpose
    and should not be tanpered with.
    [1] Researchers will abandon their reckless battle cry, “anything we can do it ought to do,” and replace it with the assertion, “we are moral stewards of the earth.” They will stop trying to clone human beings and focus their efforts on using science to promote the common good.

    [2} There will be a return to the “natural moral law” as the standard for jurisprudential wisdom.” When science finally confirms the wisdom of the ages and proves that all creatures are products of a thoughful design, society and culture will take the hint and think more seriously about objective morality.

    {3} The unnatural perception that science and religion should be radically separated will give way to the common sense fact that two disciplines are distinct but related. This will foster a much more fruitful environment for scientiic inquiry.

    In other words, ID will help promote the idea that science is less about using humanity and more about serving it.

  92. Pave (68)

    “This is a very naive view, Clarence. It’s not that simple.”

    I’m not saying it’s not messy often it is, even inefficient at times. But as a method for getting at what is going on in nature, it’s unparallelled. Remember it isan’t just the US doing this – it’s global. Europe, Asia (including China), Africa… you name it, wherever science is done, it’s done this way.

    “Maybe you’ve missed the point that evolutionary theory—Darwinism—predicts all kinds of intermediate forms. Where are all the other millions of intermediate forms that the fossil record was predicted, by Darwin, to contain?”

    There are many that have been discovered – human, whale, horse, to name the most obvious ones for which many intermediates have been discovered. Museums are awash with them. Go to a Natural History Museum and you will often see a collection of fossil skeletons showing the intermediate forms. I saw a good one on whales recently (can’t remember if it was in Washington or London).

    “Let me add: you missed my point about the possible environmental factors that effect the genome. IOW, how can you distinguish between a genome that has adapted itself to a particular environment, and a genome that has been “produced” by the same said environment? How do you confidently distinguish the one from the other?”

    I’m not entirely sure what you mean. Perhaps you can clarify the process by which the environment could affect the genome – that sounds like a form of Lamarckism to me, which has long been abandoned.

    “Conversely, how do you know that it isn’t the case of a “land-dweller” adapting itself to an intermediate environment, rather than an aquatic form adapting itself to a more terrestial environment? Remember, it’s an intermediate. Now you can see why we need lots of ‘intermediate forms’ to untangle the mess.”

    Er, no. If a land-dweller had evolved to give rise to organisms living in a transitional environment, then the logic would have been this: there should be land-dweller fossils in earlier strata. But there weren’t any – there were only acquatic forms in those strata. That is why the researchers were looking for a transitional form from the acquatic to land-dwelling forms, not the other way around. Do you see the logic there?

    Now, if you want to make the prediction that Tiktaalik arose from land-dweller forms, then fine -but it is up to you to seek out the evidence that those land-dweller forms existed in strata from earlier times than the Tiktaalik fossil.

    I would just add that I wouldn’t get to hung up about the term “intermediate”. In a sense, every species that ever existed was an intermediate, except for those that became extinct. Hopefully homo sapiens is one too.

    “If He explained the answer, would you understand?”

    Who is “He”? I do hope you haven’t prejudged who the alleged designer is! In any case, if there is a designer, I would expect the answer to be intelligible – certainly we seem to make great strides in understanding the rest of nature, so why not Tiktaalik?

    “More to the point: does every “design” have one, and only one, form to it? Isn’t it possible to “design” something in such a way that it takes on different forms in different circumstances?”

    I’m not sure that is relevant. One ccould argue that if something has a different form then it is a different design, regardless of whether the circumstances change.

  93. Clarence

    Here’s the thing about the fossil record. I consider it strong evidence of common descent and along with molecular homology in living organisms is enough to convince me beyond any reasonable doubt that all life descends from just several or fewer common ancestors beginning hundreds of millions or billions of years ago.

    The gaps are important because it tells us how much change occurred from one evolutionary step to the next. Darwin’s theory calls for a nearly infinitesimal range of tiny steps. We don’t see that in the array of organisms living today and we don’t see it in the fossil record. To be sure we do see steps laid down in the expected chronological order and this IMO is enough to make the case for common descent. It’s just not enough to make the case for Darwinian or neo-Darwinian theory.

    What we’re really focusing on is not the evidence for common descent but the evidence for the mechanism that caused the change between ancestors and their descendants. Our position is the steps are too big to bridge by chance mutation & natural selection. The math just doesn’t add up. The statistical probability, when bounded by the number of individual opportunities for change to occur, make the odds of evolution happening by chance & necessity far too small to be credible.

    In support of this claim that the odds are too small to be reasonable Mike Behe examined what evolution by chance & necessity was able to accomplish in a living eukaryote that was closely scrutinized as it replicated billions of trillions of times where each replication was one opportunity for random mutation to produce a heritable change. Keep in mind that billions of trillions of opportunities for heritable change in the genome is orders of magnitude more opportunities than mammals had as they evolved from reptiles.

    The result of all that observed replication was essentially nil with regard to any complex novelty. No change occurred that helped the organism better survive that exceeded two or three interdependent nucleotide changes. This is exactly what the probability assumptions underlying ID predicted would be the case and is compelling evidence that those assumptions are correct.

    Now, given that we have made a probability claim about what chance & necessity can accomplish in the way of generating novel, functional organic complexity and we have confirmed that the estimated probabilities are sound by correctly predicting what was actually observed over billions of trillions of chances, how can anyone possibly accept the notion that the same mechanism that failed to produce any significant phenotypical change under direct observation with billions of trillions of chances somehow, in the distant past when it wasn’t being observed, produced all the novel cell types, tissue types, organs, and body plans that distinguish mammals from reptiles? Not only were those new things somehow produced, they were produced in orders of magnitude fewer opportunities. It simply doesn’t follow that chance & necessity is anywhere near sufficient to have generated that much novelty with that number of chances.

  94. DaveScot,

    Thanks for a most interesting reply. I agree with your first paragraph entirely, and there’s a lot of food for thought in the rest.

    I agree with much of the second paragraph too – but given the sparsity of the fossil record, due to the low probablility of an organism being fossilised, we are never going to get the absolute record of life (i.e. organism 1 begat organism 2 begat organism 3 and organism 4 etc. etc.). It’s a bit like a giant “Join the Dots” picture – the full puzzle may have a million dots, you can only see a thousand or so, but nonethless those thousand dots still let you see that it’s a picture of an elephant.

    Just like in most court cases, there will never be absolute, slam-dunk, caught-red-handed evidence of evolution of the whole of life. My view, though, is that there is now so much evidence, from the fossil record and elsewhere, that it’s been demonstrated beyond a reasonable doubt.

    I appreciate you are focusing on the probablility of the mechanism and the gaps in the fossil record. I think you are right about the gaps, but I think the experience to-date suggest those gaps become less and less as more discoveries are made (although we will never have the complete picture). In that regard they are more likely to be apparent gaps rather than real reflections of the history of life.

    Mike Behe’s statistical approach is interesting, but I think the jury is still out on whether or not he is right. I note in particular the exchanges he has had with Ian Musgrave and Abbie Smith on other blogs, and his own resultant admission that his “Edge of Evolution” analysis of HIV wasn’t quite right (although he still maintains his general thrust). Also the transcript of his cross-examination by Eric Rothschild in the Kitzmiller trial at Dover also raised big questions about his statistical analysis of microbial evolution.

    These raise the question of what would be considered to be “complex novelty”, particular in relation to the phenotype. If that means we would expect whole new structures, like limbs, in microbes or viruses, then we will almost certainly never see “complex novelty” in our lifetime – I haven’t done the analysis but I would expect it would take a huge length of time (by human standards, but not geological ones). But if “complex novelty” includes genotype changes (as I would expect) then we would see it often. Indeed, I expect we see it everytime there’s a new flu outbreak or new form of HIV.

  95. StephenB, great post (96)

  96. DaveScot

    “Life may have begun here from hundreds or even thousands of cell lines. Extremophiles of all kinds would be a good starting point.”

    So there is then no evidence which proves universal common descent, although some common descent is possible.

    “Existing species can be easily modified with new information by highly transmissable, highly contagious viral vectors which in principle could cause some large and abrubt phenotype changes in a very small number of generations.”

    I am not a biologist, correct me if I am wrong, but new phenotypes require multiple simaltaneous changes to function. This method seems very unlikely to explain changes such has bi-pedalism which requires several anatomical changes at the same time, let alone the many millions of new species in history. Highly contagious viral vectors seems very speculative.

    “Try again. ID does not dispute common descent. It disputes evolution by chance & necessity.”

    It seems to me that this limited common descent, like evolution and healing, are all funtions which may affect a phenotype, but do not explain life’s history.

  97. ID predicts that reverse engineering will further scientific endeavors.

    ID predicts that some organisms may be viewed as protoypes, thus an absence of detailed evolutionary fossil record.

    ID predicts that significant evolution takes place in the mind of the Maker.

  98. the wonderer
    Good exploratory thinking on reverse engineering.

    Why “prototypes” in

    “ID predicts that some organisms may be viewed as protoypes, thus an absence of detailed evolutionary fossil record.”

    How about:

    “ID predicts distinct species with an absence of intermediary evolutionary fossil record”?

    Why appeal to “evolution” in:

    ID predicts that significant evolution takes place in the mind of the Maker.

    This is ambiguous in “microevolution” vs “macroevolution”

    Alternative:
    “ID predicts most differences between species are due to design by an Intelligent Designer,with little macroevolution”.

  99. We have to be careful to distinguish between predictions made by ID supporters and what ID theory actually predicts, which is that you won’t get specified complexity even after trillions of replications.
    Theories need a structure so that the prediction logically follows.

  100. In post #20, I wrote this:

    (7) Using the analogy of a computer program, one would expect what I call “subroutines”, or, put another way, various parts of the genome that are used for a variety of purposes in an “on-demand” basis. These “subroutines” would be part of the “regulatory” system of the genome.

    I’m happy to report that this prediction has been confirmed. See here.

  101. Speaking of chance and necessity, there is a news story today about the discovery of a giant fossilized South American rodent that weighed 1 ton. The explanation given by Darwinists is that the rodent grew to that size in order to defend itself against predators like sabertooth tigers. The reason given is that rodents are not fast runners. My question is, why grow big then? Why not evolve into a fast runner that can elude predators? And if change is random and both outcomes are equally beneficial to survival, why not do both? How does evolution decide which way to go?

  102. Mapon, there’s nothing like a good “just-so” story. Welcome to the head-scratchers. We all scratch our heads at these kinds of stories.

    If this rodent spent time in water like a hippopotamus, then maybe a mouse became a rat became a…… whale! It’s a whale of a story, I tell ya.

  103. Rodents of unusual size?

    until that rat reached a certain size it would only get slower as it grew and still not formidable against tigers.

  104. Genetic Times has a story about mice given bat-like forelimbs, not by switching genes, but by swapping the mouse Prx1 gene regulatory element with that of a bat.

    The article goes on to say, “this unprecedented finding demonstrates that evolution can be driven by changes in the patterns of gene expression, rather than solely by changes in the genes, themselves.”

    Isn’t this an example of frontloading? How do mice evolve functional genes millions of years before their actual use? Isn’t this an example of design whereby the designer creates multiple tentative prototypes but chooses only a subset for actual expression? Isn’t this kind of like the way an artist would draw multiple sketches of a subject before making a final decision?

  105. ari-freedom:

    until that rat reached a certain size it would only get slower as it grew and still not formidable against tigers.

    My thoughts exactly. Besides, why should the predators do nothing while the prey is evolving? They, too, should grow so as to compensate, no? Where are the fossilized remains of giant saber-tooth tigers?

  106. PaV: “It’s a whale of a story, I tell ya.”

    LOL, yep.

  107. For the non-Princess Bride fans, here is some context to ari-freedom (107):

    [after Westley rescues her from the lightning quicksand]
    Buttercup: We’ll never succeed. We may as well die here.
    Westley: No, no. We have already succeeded. I mean, what are the three terrors of the Fire Swamp? One, the flame spurt – no problem. There’s a popping sound preceding each; we can avoid that. Two, the lightning sand, which you were clever enough to discover what that looks like, so in the future we can avoid that too.
    Buttercup: Westley, what about the R.O.U.S.’s?
    Westley: Rodents Of Unusual Size? I don’t think they exist.
    [Immediately, an R.O.U.S. attacks him]

  108. Inconceivable!

  109. Clarence #97

    “There are many that have been discovered – human, whale, horse, to name the most obvious ones for which many intermediates have been discovered.”

    You’re new to the game. Go check out what Stephen J. Gould has to say about the supposed “horse” lineage.

    “I’m not entirely sure what you mean. Perhaps you can clarify the process by which the environment could affect the genome – that sounds like a form of Lamarckism to me, which has long been abandoned.”

    Ah, but you see, Lamarck is making a big comeback. They have discovered that RNA can be transmitted from one generation to the next, and the transmitted RNA can contain ‘information’ about how the next generation is to set up certain cell structures. Plants are known to impart information between generations using RNA also. This is cutting-edge stuff. Maybe old Darwin was too rough on Lamarck, the true author of ‘evolution’.

    “But there weren’t any – there were only acquatic forms in those strata. That is why the researchers were looking for a transitional form from the acquatic to land-dwelling forms, not the other way around. Do you see the logic there?”

    You mentioned earlier that there are ‘intermediate forms’ for the whale lineage. Tell me, does the lineage go from land-to-sea, or sea-to-land? Do you see the logic now?

  110. ari-freedom #107,

    I suspect their thinking has to do with the long canines the R.O.U.S. has. I love “just-so” stories—you can do so much with them.

  111. Mapou in 108 asks Isn’t this an example of frontloading? How do mice evolve functional genes millions of years before their actual use?

    That could be the right explanation. But, it might also be argued that it was a neutral mutation that occurred long ago, and just now found a fitness landscape in which it would be expressed.

    Is there a premise and test that could be suggested by ID which would allow people to clearly demonstrate whether it was a front-loaded feature from long ago, or a neutral mutation?

  112. It didn’t sound like the mouse sprouted bat wings, just that their limbs were longer after the gene ‘opened the floodgates’ on cartilage cell growth.

  113. Bob O’H #72:

    “How would the structure of the proteins and RNAs be coded and inherited if not from the genome? Are you suggesting some other form of inheritance?”

    Some algorithm is needed if the genome is to produce structures that exhibit patterns amenable to mathematical analysis. This algorithm will necessarily have to be iterated just as a cpu must iterate a set of equations in order to ‘draw’ patterns onto a printer. It would be inefficient in the highest degree to use the transcriptional properties of DNA as a substitute for this iterative process. Hence, it would be more logical/probable for some cluster of proteins to process this algorithm, possibly in conjunction with the intermittent interactions of a special kind of RNA. This processing will most likely happen at the quantum level and will thus be very hard to detect. So, we can almost expect that this property of living organisms—if it exists—will be one of the last ones to be discovered.

    #74:

    “About the “what if only some junk DNA had function” question, I was asking whether some junk DNA being non-functional would (in your phrase) “completely undermine ID”. I’m still interested in knowing this.”

    I think I know the line of your argument you want to go down, so, (and this is very cryptic, but I think you’re up to the task) I ask:

    If a Mercedes-Benz has a “Hillary Clinton for President” sticker on its rear window, does this mean it wasn’t designed?

    [I've decided this is entirely too cryptic. So, concisely, partial imperfection does not disqualify something from having been designed.]

    As to the 1-to-1 relationship between “junk-DNA” and ‘regulatory mechanisms’ in the genome that you’re asking about, in the above question I think you’ll see that there’s nothing to say, in an ‘a prior’ way, about what the degree of correlation might be (or necessarily has to be).

  114. ari-freedom #116:

    Yes, you’re right. But this means that the regulatory mechanism of the gene for limb elongation must work cooperatively with other genes, which are, in turn, regulated. This different regulatory section for limb elongation must then be part of a larger regulatory process. So you have a ‘subroutine’ operating inside of a larger ‘routine’. Based on information technology, this is something you would predict to be found happening.

  115. ari-freedom:

    It didn’t sound like the mouse sprouted bat wings, just that their limbs were longer after the gene ‘opened the floodgates’ on cartilage cell growth.

    Yes. Notice that the article makes a big deal about how “successive slight modifications” would ultimately result in the evolution of diverse limb morphologies, like a hand, wing, or fin” but fails to mention that a mouse that evolved long forelimbs without actually being able to fly would not survive long.

    Also, even if the mouse actually managed to evolve wings, this means that the sophisticated neural wiring needed to control those wings in flight and navigate would have to evolve simultaneously, a very tall order. A flying bat-whale of a story, if you ask me. LOL.

  116. PaV, the subroutine idea is brilliant.

  117. PaV –
    1. Thank you for the just so story about algorithms. How will you test this speculation?

    2. Whether junk DNA is designed or not is not of direct relevance to whether it has a function or not. I’m asking about whether you are claiming that it all has a function. Your comment seems to suggest that you’re saying that some junk DNA might not have a function.

    You then state that there’s nothing to say a priori about the correlation between regulation and junk DNA. If that is so, then I assume that you are saying that junk DNA could have another function. Do you have any suggestions or just so stories about what these other functions might be?

    Bob

  118. Q:

    That could be the right explanation. But, it might also be argued that it was a neutral mutation that occurred long ago, and just now found a fitness landscape in which it would be expressed.

    Interesting. The problem I have with this is that, since mutations are said to be random, there should be millions of mostly deleterious but unexpressed genes within complex genomes. By deleterious I mean that they should be unusable in any “fitness landscape”. Is this observed?

  119. (post #13 Mapou:) I think we are doing ourselves a great disservice by focusing on the design while ignoring the designer…
    They have impregnable fortresses and giants in their midst.

    Mapou, I agree with you completely. This impregnable fortress you speak of is just one Principality, a Power of Darkness. Tearing down this stronghold of the enemy will not occur except by spiritual means.

    Sword thrusts of Scientific Theory & Opinion will not win, only the Word of God which is sharper than any 2-edged sword (Hebrews 4:12).

    Perhaps the reason ID shies away from naming “The Designer” is because to Muslims it is Allah as revealed by Mohammad, Jesus Christ (who is the image of the invisible God, the firstborn of every creature) to the Christians, Gd to the Jews, and of course many others.

    To name “The Designer” would then start another round of religious debate of who is the true God.

  120. Mapau, in 122, mentions “The problem I have with this is that, since mutations are said to be random, there should be millions of mostly deleterious but unexpressed genes within complex genomes.”

    Except, that according to how natural selection is argued, those millions of deleterious mutations that are unusable in any fitness landscape would most likely be removed if they were ever expressed.

    I’m not sure what a “deleterious but unexpressed” gene is, unless you mean it is neutral for one environment, and deleterious for another. Does ID make a claim about such an event? It seems to be contrary to inferrable design principles.

  121. Mike Behe’s statistical approach is interesting, but I think the jury is still out on whether or not he is right. I note in particular the exchanges he has had with Ian Musgrave and Abbie Smith on other blogs, and his own resultant admission that his “Edge of Evolution” analysis of HIV wasn’t quite right (although he still maintains his general thrust).

    “Resultant admission”? He wasn’t aware of this information when writing the book. That’s it…where’s the “admission”? And if a revision to the book is released there’d be no issue with including this example since it would have no effect on the rest of the book.

    On page 138 of Dr. Behe’s Edge of evolution:

    As one study put it “Each and Every possible single-point mutation occurs between 10^4 and 10^5 times per day in an HIV-infected individual.” (HIV population dynamics in vivo Collin J.M., 1995). Every double point mutation, where two amino acids are changed simultaneously, in each person once a day. (This means a chloroquine-type resistance mutation-where two particular amino acids had to appear before there was a net beneficial effect-would occur in each aids patient every day. Not that’s mutational firepower!) In fact, just about every possible combination of up to six point mutations would be expected to have occurred in an HIV particle somewhere in the world in the past several decades-double the number that could occur in the slower mutating P. falciparum. In addition to all those point mutations, enormous numbers of insertions, deletions, duplications and other sorts of mutations would occur as well.
    An exactly what has all that evolution of HIV wrought? Very little. Athough news stories rightly emphsize the ability of HIV to quickly develop resistance, and although massive publicity makes HIV seem to the public to be an evolutionary powerhouse, on a functional biochemical level the virus has been a complete stick_in_the_mud. Over the years its DNA sequence has certainly changed. HIV has killed millions of people, fended off the human immune system, and become resistant to whatever humanity could throw at it. Yet through all that, there have been no significant basic biochemical changes in the virus at all…

    Smith herself briefly came onto UD. Short version is that assuming you accept the assumptions surrounding Smith’s hypothetical scenario (which many on UD did not) this example still falls in line with the main points of EoE. In fact, destructive modifications like passive leaky pores (a foreign protein degrading the integrity of HIV’s membrane) would provide yet another example for his trench warfare analogy. So why call it an “admission” when the example only strengthens the premise of the book?

    I made this point back then:

    1. A bundle of assumptions seems to be substituted for hard data. Reconstructing a speculative Darwinian pathway is not hard data. It would be best to stick to observed evolution known to have been caused by unguided Darwinian processes rather than perceived/inferred evolution.

    2. Behe only made an ESTIMATE for a generalized “edge of evolution” that can apply in all circumstances. I don’t see why this “edge” could be expanded a bit further under fortunate circumstances. Obviously I’m doubtful observation will expand this “edge” enough to save Darwinism but if there is a minor expansion everyone (especially Darwinists) needs to keep in mind that potentiality won’t hurt ID. So the current estimate need not be defended overly much by ID proponents. I for one will say right now that I think the estimate too low.

    When I say “estimate” I only mean that although everything was based upon real observations the derived edge/limit of evolution is not a hard limit in that under certain conditions Darwinian processes “might” be capable of a bit more. This is an assumption on my part, but as we gather more evidence over the years I’m assuming we’ll derive a more accurate “generalized” limit that may be slightly higher than what is currently given.

    I also would not want to be associated with people like Ms. Smith. Let’s just say that people who are respected over at PT like Abbie Smith have wished horrific deaths on public figures in “interesting” fashions…among other lovely statements.

  122. beancan5000:

    Sword thrusts of Scientific Theory & Opinion will not win, only the Word of God which is sharper than any 2-edged sword.

    Ain’t that the truth?

    To name “The Designer” would then start another round of religious debate of who is the true God.

    Yeah. There is also the legal and cultural tradition in western societies regarding the separation of church and state. To name a designer would make it inadmissible in public education. ID advocates seem to want to avoid this at all costs.

    Personally, being an unapologetic Christian, I have no qualms about Christianity becoming the victorious religion after all is said and done. If our God was the designer, then we should rely on him, period. We have nothing to fear.

    Given what I now know about the sophisticated use of metaphors in the Bible to hide scientific secrets, there is no question in my mind that we will win indeed this battle. And we will win decisively with great fanfare. However, we will not do so the way we’re currently going about it. In fact, I would say that we’ve been losing big time with our current strategy.

  123. 123

    It’s now two days since Professor Dembski alerted us to the list of predictions he has compiled. I’m beginning to think he never meant to share them with us! I’m enjoying this discussion – and impressed, as ever, by the knowledge people bring here. But many of the predictions are a little wooly, along the lines of “If naturalism is disproved/if God is back in control of things, then the following would ensue.” (As a pagan ID proponent, I have to say that if the gods are back on top, as I believe they are, some of you had better watch your butts – Zeus can get a little itchy with that thunderbolt :-) ).

    These predictions, while interesting, are not specific consequences of the ID-theory – consequences that might, for instance, immediately redirect the research of lab-scientists. This is what we need to know, and we need to hear it from someone who has worked deeply in the highly technical areas of ID. That person is Dr Dembski.

    So I don’t think I can be alone in wondering when Prof. Dembski is going to share this enormously important document with the world. Did Einstein hang back about the perihelion of Mercury, or the bending of light around the sun’s disk? No, he was quite up-front about these concrete predictions. The Prof. is being falsely modest if he thinks he’s one bit less of a revolutionary than Einstein! So let’s have those predictions.

    Peace – Zoe.

  124. The edge of evolution not specific enough? We should be able to design antibiotics that bacteria will never be able to evolve resistance to. This would save many lives.

  125. As for predictions, I made this comment here:

    “So you want other applications that would require acceptance of ID? How about designer drugs that take into account the limitations of Darwinian mechanisms predicted by ID?

    What one needs to know to do that:

    a) A drug and how the drug breaks the bacteria or virus
    b) All possible stepwise evolutionary pathways for developing resistance to that drug (potentially the most difficult aspect)
    c) How fast on average the drug kills the virus or bacteria
    d) Rate of replication/estimated limits of Darwinian mechanisms

    http://www.sciencemag.org/cgi/.....ct/1152725

    Short version is that they’ve identified the host proteins required by HIV. Perhaps Behe’s work could be applied to this line of research. How?

    Several hundred of these genes might make good drug targets, since they can reduce HIV infection without killing the host cell. Blocking 28 of these genes could even prevent the formation of functional viruses (obviously the preferred scenario). HIV is dependent on its host for the functionality of parts of the nuclear pore, RNA transcription machinery, Golgi complex, and controls for proteins on the cell surface.

    Now first note my previous comment where I quote Behe’s discussion of HIV. As parts of the host genome, these genes do not possess the replication rates nor the selective pressures that allow HIV to rapidly evolve around therapies. The virus could still evolve to be less dependent on these specific genes but, given the fundamental nature of the host proteins required to sustain life, this seems fairly unlikely. In fact, if there is a particular host gene that plays a critical function for HIV I say researchers should examine it to see what sort of modifications would be required for HIV to work around it. If they are beyond Behe’s edge then that should be the primary target for designer drugs.

    Still…as Behe pointed out in his book (in regards to malaria) this seems to be an indirect way to attacking the problem. Perhaps there is a way to modify the host’s immune system or something else. Using the trench warfare analogy, why not build a defensive fortified wall instead of blowing up a bridge?

  126. I wrote:

    The problem I have with this is that, since mutations are said to be random, there should be millions of mostly deleterious but unexpressed genes within complex genomes.

    Q replied:

    Except, that according to how natural selection is argued, those millions of deleterious mutations that are unusable in any fitness landscape would most likely be removed if they were ever expressed.

    Sorry, I can’t go along with that. I see no way for natural selection to get rid of bad unexpressed genes from a population. If such a gene suddenly became active in an individual, NS would only get rid of the individual with the expressed gene. The others would continue with their bad unexpressed genes unaffected.

    Q:

    I’m not sure what a “deleterious but unexpressed” gene is, unless you mean it is neutral for one environment, and deleterious for another. Does ID make a claim about such an event? It seems to be contrary to inferrable design principles.

    An example might be an unexpressed gene that would cause your brain to become disconnected from your spinal cord if it became active.

  127. Mapou in, 131, said “Sorry, I can’t go along with that. I see no way for natural selection to get rid of bad unexpressed genes from a population. “
    Thanks for adding to your previous comments. I can agree with your comment.

    Mapou also said “An example might be an unexpressed gene that would cause your brain to become disconnected from your spinal cord if it became active.”

    I know I don’t want my brain to disconnect from my spinal cord when it becomes active! I uses my brain at least a few times a day. :-) puns – the best form of low humor.

    Back on track: It sounds like an interesting investigation. If such genes are found, what predictions would ID make about those genes that would allow testable discrimination between front-loading and neutral mutations that occured long ago?

  128. Q, in my non-expert opinion, the existence of unexpressed genes falsifies Darwinian evolution. The reason is that, since NS can only discriminate against expressed genes, it cannot get rid of bad unexpressed genes from a population. It follows that, since random mutation is given as the primary mechanism of speciation, over millions of years, the number of bad unexpressed genes due to mutation should accumulate uncontrollably. Is this observed?

    Looking at it from the ID side in which RM seems to be given almost no evolutionary role, an intelligent designer would have no reason to keep bad genes around. This is true for the same reason that a software engineer has no desire to conserve bad code. Therefore, I believe that, in contrast to Darwinian evolution, ID predicts that very few bad unexpressed genes should exist in a complex genome. Note that I am speaking for myself. I am not yet well versed in the “official” ID theory to know what it actually says on the matter. I’m learning slowly, time permitting.

  129. I haven’t read all the comments, so if someone already said this…

    One prediction that stands out for is the prediction that if species are designed, then it is highly likely that we should see repeating design structure and functionality across the board, even when there are no “evolutionary relationships” between species. One example is vision. A designer once having figured out how to make vision possible and stable, would more then likely use that design or a variant of that design over and over because vision is extremely complex.

    Evolution cannot adequately explain why various species supposedly evolve similar organs and forms without any evolutionary relationship between the species. If mutation is the origin of novel organs and limbs etc, then why does mutation seem to create similar organs and limbs in species without any evolutionary relationship between them? Not only are we expected to believe that random mutation can build computer coded nanotechnology (far surpassing anything we can design, for example cold fusion in plants) as well as flight technology superior to anything we can design, swimming technology superior to anything we can design, and on and on, but we are also expected to believe that random mutation can build the same type of technology over and over.

  130. mentok,

    Good point. I believe Convergence is the general term, and yes, we see “theme and variation” in artistic and engineered works. It is hard to explain from a NDE perspective, but makes sense from a Design perspective.

  131. 131

    Mentok and Atom,

    See the section “Origin of the Carnivorous Plants” in the article:

    http://www.math.utep.edu/Facul.....s/carn.pdf

    for some examples of “convergence”.

  132. Also, don’t know if someone said this one…

    -Signature Information: We could expect an engineer to leave some form of signature or copyright notice on their creation (signing it, if you will.) As related to living things, this signature would need to be*:

    1) Robust: Since living things change/mutate, it would need to be able to survive such changes; this rules out superficial markings, as these are the easiest surfaces to change.

    2) Universal: It should be applicable to everything from DNA, stars, galaxies, the elements, bacteria, to elephants and humans. This rules out things such as banners or physical symbols/machinery.

    3) Non-linguistic or at least reasonably universally understandable: The signature should be understandable by most, ruling out a specific language.

    What could fit these requirements*? I argue that a mathematical relation could, as it could be encoded in everything from the periodic table to man to galaxies, it is robust (if the relationship is recursive or multi-leveled), and mathematics are the universal language. With this in mind, I think that Phi (also known as the Divine Ratio) is such a signature mark. It shows up EVERYWHERE in nature, as if nature has a reason to favor this particular ratio over others. It can be seen in the ratio of width to run length in DNA, in the spiral shape of galaxies, in the fibonnacci sequence, in the body proportions of man and animals, and lots of other places. It ties together all of nature with a single unity and is robust enough to still be recognized everywhere, even after eons of environmental change.

    So signature information as backed up by the ubiquitous Phi is one I think that serves as good evidence for ID. (Creationists, a proper subset of ID proponents, did predict this, even before the first century AD.)

    -Atom

    *These requirements are borrowed and modified from Walter ReMine, The Biotic Message. I have my own interpretation as to what the signature is, however. (He believes it to be Nested Hierarchy.)

  133. 133
    Unlettered and Ordinary

    Greetings!

    Atom: I thought of this too but you said it…

    The Signature of the designer is every where, The Golden ratio, The Fibonacci numbers, and PHI as you mentioned found in living things.

    I like the math in flowers, these are superb in mathematical design and aesthetic beauty. Definite Signature comming in loud and clear.

    I think this is not only a very good observation, it’s perfect, Mathematics in not only comprehensible, but it really only applies to intelligent agents capable of using it, such as ourselves. I know of no other organism that uses mathematics consciously, deliberately, and purposefully.

    For that matter, Are there any organisms that possess any of our many capabilities? I suppose that’s beside the point. We are more than a bit unnatural, artificial, and perhaphs supernatural, and opposed to nature, too which we find ourselves the lone exception.

    I would expect The Designer to leave his signature around just to let us know, completely aware we would find them and be mystified and delighted.

  134. Bob O’H #122:

    Yes, the algorithm idea is a “just-so” story. And, it’s falsifiable. But, I carefully pointed out that what is likely happening is something at the quantum level, along the lines of quantum-computing. Until such time as we are able to build sophisticated quantum-computers, I don’t think we’ll have the technology to begin to test for the kind of scenario I’m suggesting.

    As to the “junk-DNA”, it’s entirely possible that DNA without a known function might exist in genomes. I’ve already anticipated that you will turn around and say that if it’s possible for DNA not to have function, then in what way can you say that it is ‘designed’. Which gets us back to the Mercedes-Benz and Hillary Clinton.

    As to other possible ‘functions’ for “junk-DNA”, I’ve already mentioned one: redundancy. The other possibility is “excess capacity”; i.e., there are latent functions, latent potentialities that await ‘triggering’. You’ll note that one of the things that I listed as a prediction are environmental ‘triggers’. Entire regulatory circuits could be “dormant”, if you will, right now, and won’t begin to function within the genome unless some triggering sets it off. Just some thoughts.

  135. Atom #137:

    My mind goes along similar lines as yours.

  136. 136

    I’ve certainly come to the party late it seems, but I have some predictions of my own. I’ve posted them as a post as my blog.

    ID predictions

  137. Clarence #99:

    “Mike Behe’s statistical approach is interesting, but I think the jury is still out on whether or not he is right. I note in particular the exchanges he has had with Ian Musgrave and Abbie Smith on other blogs, and his own resultant admission that his “Edge of Evolution” analysis of HIV wasn’t quite right (although he still maintains his general thrust).”

    I’ve had personal correspondence with Dr. Behe about this. He has very graciously, IMO, accepted the vpu viroporin formation as an instance of protein-to-protein binding. I think he’s being entirely too magnaminous in doing so.

    But let’s point this out: if you’re going to change the zero to a 1 in the column showing the number of protein-to-protein bonds formed by HIV over the last 10^20 generations, then you must also change the 10^20 number also. The reason for this is that Dr. Behe was relying on evidence of HIV since the late 70′s, whereas the vpu viroporin ensemble developed in the late 1920′s. So, does the 10^20 become 10^30 or 10^40 replications? I don’t know what the number would be, but it would certainly be larger—and IT TOO would have to be changed. This, of course, doesn’t change the force of Dr. Behe’s argument one bit. It’s like telling someone who tells you that he needs to borrow $6,000,000,000, that he’s wrong, that he needs to borrow $6,000,000,000.25 It hardly changes the reality!

  138. Mentok, I like your thoughts on lateral functionality.

    Atom, the signature idea is very interesting but I have my doubts. If the designer really wanted to be found that easy, he would just show up in his shiny sky chariot and land on P.Z. Myers’ lawn. I think he’s the kind that likes to hide himself. I’m sure he left us plenty of clues but, in my opinion, the clues were meant only for the believers, not the deniers.

  139. I’ve already anticipated that you will turn around and say that if it’s possible for DNA not to have function, then in what way can you say that it is ‘designed’.

    No, I was going to suggest that if it was without function, then some people around here might think that it “would completely undermine ID”.

    Bob

  140. Mapou (102), you wrote:

    “Speaking of chance and necessity, there is a news story today about the discovery of a giant fossilized South American rodent that weighed 1 ton. The explanation given by Darwinists is that the rodent grew to that size in order to defend itself against predators like sabertooth tigers. The reason given is that rodents are not fast runners. My question is, why grow big then? Why not evolve into a fast runner that can elude predators? And if change is random and both outcomes are equally beneficial to survival, why not do both? How does evolution decide which way to go?”

    The answer to your question is that the there is actually no “decision” at all – merely an outcome. “Decision” inplies some conscious act, either on the part of the rodent or on the part of evolution. But there is no such consciousness, and no such decision.

    The probable explanation is that slightly larger rodents had a higher probability of surviving attacks by predators, hence had more chance to reproduce so that trait would have carried on for several generations until those particular rodents reached the size they did. It’s equally possible that other rodents DID escape by running faster than predators, in which case there would be other species of rodents which were fast runners.

    Elephants, for example, tend to be safe from lions because of their size (although oddly, some lions in Namibia have very recently taken to group attacks on young elephants) whereas gazelles rely on speed.

    This often leads to natural “arms races” in prey and predator evolution, which can result in extremes – hence the extreme size of elephants (and rodents, in the case mentioned), and the high speeds of both cheetahs and gazelles.

    There is no set path for evolution -the outcomes are often matters of luck and chance.

  141. the idea (and this follows more from ReMine’s message theory than Dembski/Behe) is that ID would expect different things than evolutionists. Evolutionists really wanted most of DNA to be junk so we would predict most DNA would not be junk. Or take IC for example. Evolutionists wanted everything reducibly complex and everything could certainly have been designed that way, but we would predict to find provable IC structures.

    If life was designed, it would be in a way to make it harder for evolutionists to come up with a simple coherent explanation.

  142. PaV (110):

    “You’re new to the game. Go check out what Stephen J. Gould has to say about the supposed “horse” lineage.”

    I did – what makes you think he doubted that horses evolved? Horse evolution, with intermediates, is well established – check this out: http://www.talkorigins.org/faq....._evol.html

    “Ah, but you see, Lamarck is making a big comeback.”

    With whom?

    “They have discovered that RNA can be transmitted from one generation to the next, and the transmitted RNA can contain ‘information’ about how the next generation is to set up certain cell structures. Plants are known to impart information between generations using RNA also. This is cutting-edge stuff.”

    Well, this is the first I’ve heard of it. Any references? I would appreciate an explanation of how (i.e. the mechanism) by which “the environment” managed to trigger the appropriate RNA changes to get passed from parent to offspring – i.e. how did the environmental influences on the phenotype get translated into the genotype.

    “You mentioned earlier that there are ‘intermediate forms’ for the whale lineage. Tell me, does the lineage go from land-to-sea, or sea-to-land? Do you see the logic now?”

    That’s a very easy one – the whale lineage clearly goes from land-to-sea. Check this out: http://www.talkorigins.org/features/whales/

    Do you see why this is? The land-dwelling forms, such as Ambulocetans, were found in strata dating to 50 million years ago, whereas the “true” whale forms such as Basilosaurus didn’t appear until much later – 35 to 40 million years ago. As the ancestral, land-dwelling forms were older than the acquatic forms the logic dictates that the transition was land-to-sea.

    That is the clear logic. I’m not sure what logic you are using, but if this is diffciult I’m happy to discuss further.

  143. 143

    DLH #100

    Prototype, as in engineers will try something out, then improve it. I suspect that many of the similarities in apes and humans may be viewed this way. (This may mess with some people’s theology) The change, does not come about physically, until it has come about in the mind of the engineer.

    RE: use of evolution, I meant neither micro- nor macro- but rather the type of change thru time that does not require intermediate physical forms, but rather mental constructs that then get made by an engineer. I am taking my thinking from the evolution of the automobile.

  144. Bob O’H,

    you said

    “No, I was going to suggest that if it was without function, then some people around here might think that it ‘would completely undermine ID.”

    I think that those who hold this here are few and far between and getting less over time. The modern synthesis is completely compatible with ID (in their books, Behe, Dembski and Wells accept it and use it to illustrate how it can change species over time.) In fact it makes good sense for a designer to have designed a system that can be modified by the processes described in the modern synthesis. Few remark that the system of life is exquisitely designed so that it can be modified through natural processes and as such makes life in this world richer as species adapt to changing environments through these naturalistic processes. And we see how it creates hell as genomes or cells get modified to create medical challenges that shorten life or creates misery.

    The modern synthesis predicts that many of the changes in a genome will lead to junk and thus some useless DNA accumulates over time while most will be culled out. So it is reasonable to expect “real” junk in the genomes. It is a question of how much. So the presence is not a threat to ID. And as more and more of the non coding DNA is found to have function, the stronger the ID position gets.

    Where ID parts with nearly all who ascribe to the modern synthesis is in its power to create complex functional novelty. That it creates changes that have some functional benefits is without doubt but the changes are not real novelty but slight changes to the genome that may have dramatic effects but alas are only simple changes. Many of the changes actually represent deterioration to the genome which has some current advantage but which represents long term problems for the organisms with these changes.

    Behe’s book, Edge of Evolution, was all about that and I personally believe when more and more genomes get mapped the results will support Behe’s conclusions that few species changes/differences are the result of complex functional novelty. In other words the modern synthesis can produce thousand of cichlid species but can it produce bats with wings and sonar navigating systems. The ones that have complex functional novelty will be a challenge to the robustness of the modern synthesis as the mechanism for the origin of all species.

    This may seem a diversion to your comment but actually flows from what ID accepts and finds reasonable. And as such is the basis for what ID will predict versus what those who hold only to the modern synthesis will predict. There should be much overlap but ID will have a whole set of possible predictions not possible within the modern synthesis because this theory is limited in what could be logically expected by additions to variation in a genome produced by naturalistic methods. But for most biological research today, there is very little that is not compatible with ID since many within ID accept the random variation/selection paradigm as operating to make minor changes to the genome (some of which have dramatic effects especially in the medical area.)

  145. 145

    hi everyone! this thread is really interesting and I’m sorry I’ve been away for a couple of days.

    I was very glad to see DaveScot agrees with me about dna being protected from mutations. People seem to be complaining in this thread that no-one is giving real predictions, but the limitations of microevolution really is testable – we HAVE the dna, after all. In this day of modern genetics there is no reason why scientists can’t test for dna protection – we couldn’t do it thirty years ago but we can now.

    I have come up with a list of potential ways to protect dna from mutation.

    - molecular forcefields (the most likely)
    - error-correction
    - natural selection of unwanted mutation (mutants die off)
    - retroamino introsposon (via pi bond)

    The problem with the error-correction hypothesis is that it raises the question of what guides the error-correction, and how that itself is coded. This is why I believe that the protection is intrinsic to the molecules, and not the dna.

    I didn’t mention it before, but dna protection also has obvious medical benefits, especially in the field of cancer. We know cancer is caused by mutations in the cell replication program – I’m sure all programmers here have accidentally caused an infinite loop in their code before. It also ties in with what PaV was saying about subroutines – it would be so easy to make a subroutine call itself repeatedly. dna protection, if we could manipulate it, could protect those areas of dna which are vulnerable.

  146. Venus Mousetrap
    something like this?
    http://news.nationalgeographic.....ction.html

  147. 147

    DaveScot said (comment #48) –

    There is also the possibility of multiple front loadings over the course of history although I tend to favor just one instance. Existing species can be easily modified with new information by highly transmissable, highly contagious viral vectors which in principle could cause some large and abrubt phenotype changes in a very small number of generations or even just one generation constrained only by physical limitations like a fish not being able to have mice hatch from its eggs.

    In the co-evolution of co-dependence where two kinds of organisms — e.g., bees (or other pollinators) and flowers — become dependent on each other for survival, the changes in both kinds of organisms would have to simultaneously occur in the same localities. The Darwinists have not even acknowledged that this co-evolution of co-dependence presents special difficulties that would not be present in evolutionary adaptation to widespread fixed physical features of the environment, e.g, water, land, air, and climate.

    On to a different subject –

    There are different kinds of “predictions” in science:

    (1) A positive prediction that something will be observed. Example: the theory of relativity’s prediction that starlight would be bent by the sun’s gravity in a coming eclipse. If this bending had not been observed, that would have been a big strike against the theory.

    (2) A prediction of a single possible occurrence (or maybe just a few possible occurrences). Example: It was predicted that a fossil like Tiktaalik might be found in a particular place, and such a fossil was found there. However, failure to find the fossil would not have been a big strike against Darwinism — such failure could just be attributed to bad luck.

    (3) A prediction of the likelihood of many occurrences. Example: Darwinism predicted that many transitional fossils would be found, but they have not been found. This is a big strike against Darwinism.

    (4) A finding that something that was not predicted is consistent with a theory. This is sometimes falsely called a “prediction,” but it is more like serendipity.

    I certainly disagree with the Darwinists’ claim that something must make predictions in order to be considered scientific.

  148. ari-freedom, thanks for that link. Wow! Self-repairing DNA? How did something like this evolve? Isn’t this a case of irreducible complexity?

    Venus, I was wondering along the same lines that, if every cell contains a copy of the genome, could there be a repair or quality control mechanism in the reproductive systems of animals that uses this redundancy to ensure that any DNA material passed to offsprings is of the highest quality?

    I mention this because, as a software engineer/designer, I know that various error-correction schemes are used during data copying and/or transmission. I tend to look at reproduction as a form of communication whereby information is transferred from one system to another. Therefore, I would suspect that one of the better places a designer would incorporate a quality control mechanism would be the reproductive system. Is this currently an area of study?

  149. this is another interesting example
    http://www.newscientist.com/article.ns?id=dn7185

  150. I believe ID makes some important predictions about humanity. I’m assuming here that the Designer is a Cosmic Designer as well as the Author of Life, and that the Designer planned the arrival of each and every race of intelligent beings in the cosmos. Here are my predictions. The last one is a short-term prediction:

    (1) The following scenarios will never happen: technologically advanced aliens wiping out the human race; the human race wiping out another alien race; an asteroid from space destroying humanity; and the human race wiping itself out. If an intelligent race were wiped out, this would render pointless the whole exercise of creating it. Therefore, presumably the Designer has set up the cosmos in such a way that either we are alone, or if other alien races exist, then we cannot find them, or if we do find them, then we cannot interfere with them.

    (2) For the same reasons, we can be confident that robots will never be able to take over the world, and that humans will never be able to create a “master race” of superior beings that could turn on us and destroy us.

    (3) We can likewise be confident that computers will never be able to read or control our thoughts, and that no race of aliens should be able to do this either. If this were possible, it would make moral agency impossible for the race that was being controlled.

    (4) Man-made global warming should either turn out to be a hoax, or to be a problem with a straightforward technical solution that won’t exhaust our resources. Reason: a Cosmic Designer must have foreseen the fact that human beings, in their efforts to stay warm, mass-produce artifacts, travel more quickly and make scientific advances, would make use of the Earth’s fossil fuel reserves. Presumably the Designer wanted us to make technological and scientific advances. If the use of fossil fuels resulted in humanity’s extinction (or for that matter, a mass extinction of species) then that would indicate a distinct lack of foresight on the Designer’s part. However, it may be the case that man-made global warming is real, but a technical solution is close at hand. IF the IPCC’s climate predictions are correct, then an ID proponent should expect a major technological breakthrough by 2020 at the latest in fighting global warming.

  151. vjtorley, [Off topic]

    I’ve been reading through your dissertation and so far it is very good! Almost book like! (If not book length, hehe.) I like your conservative approach.

    Atom

  152. Clarence(143):

    Horse evolution, with intermediates, is well established – check this out:

    Really. Check this out. You do believe in National Geographic, right? Here’s a quote:

    “Kathleen Hunt, a biologist at the University of Washington in Seattle, said the modern-day horse is ‘merely one twig on a once flourishing bush of equine species. We only have the illusion of straight-line evolution because Equus is the only twig that survived.’”

    I mention that RNA involvement is ‘cutting edge’. You reply:
    Well, this is the first I’ve heard of it.

    Well, that’s what makes it cutting edge. As to references, why not try a Google search?

    I would appreciate an explanation of how (i.e. the mechanism) by which “the environment” managed to trigger the appropriate RNA changes to get passed from parent to offspring – i.e. how did the environmental influences on the phenotype get translated into the genotype.

    Let me understand: I have to make the prediction, and then also explain the exact way the prediction will come about? I suppose that if I explained it now, and it was later discovered to be exactly as I predicted, then I would receive the Nobel Prize, right?

    That’s a very easy one – the whale lineage clearly goes from land-to-sea.

    And in post #97 you wrote:

    “That is why the researchers were looking for a transitional form from the acquatic to land-dwelling forms, not the other way around. Do you see the logic there?”

    Well, I’m sure that’s what they were looking for. The question is, what did they find? You’ve just admitted that land animals can become aquatic. Your sticking point earlier was that there were no land animals yet. But we’re dealing with geologic time, where the age of strata might not be known within a million or more years accuracy; and we’re dealing with a boundary between the Devonian and the Carbonferous. So, right at that boundary, are we dealing with an innovation that produced land-animals, one of which quickly went back to fish-like characteristics through a process of adaptation because of the environment; or, are we dealing with straight-line evolution produced by the same environment? Which is it? Can you tell me that unequivocally?

    Do you see the logic?

  153. Atom:

    Thank you. Glad you enjoyed reading the dissertation.

  154. PaV #138:

    Just to clarify things. If you want to build a pentameric structure with C5 symmetry from asymmetric (chiral) monomers as in the case of the Vpu viroporin channel you need to create two protein binding sites per subunit. Furthermore, these two binding sites have to appear simultaneously to yield the pentamer.

  155. jerry (145)[for the time being]

    The modern synthesis is completely compatible with ID (in their books, Behe, Dembski and Wells accept it and use it to illustrate how it can change species over time.)”

    Jerry, you’re failing to distinguish between the modern synthesis and what is termed ‘microevolution’. We can observe something like ‘microevolution’, which I prefer to call ‘adaptation’. But the Modern Synthesis, or neo-Darwinism, is a different critter.

    Your friend Allen MacNeill from Cornell says here that the “modern synthesis is dead.”

    And William Dembski himself started a thread here that was entitled: “Further Indications that neo-Darwinism is dead.”

    So, I would be a little careful who you have saying what.

    Here’s a question: a male donkey mates with a female horse to produce a mule. The mule is phenotypically different from both of its parents. It looks like an intermediate–just what Darwin was looking for. Now, are these phenotypic differences the result of: (a.) point mutations, (b.) genetic drift, (c.) gene transfer?

    If you answer (c.), then a follow-up question: why do you get a hinny and not a mule when you mate a male horse and female donkey? (That is, the same set of genes are available in both instances.)

    The only real answer to all of this lies in how chromosomes are pieced together during fertilization. This is roughly along the lines that Allen MacNeill is traveling. This is John Davison’s answer as well.

  156. 156
    Unlettered and Ordinary

    Greetings!

    I hope no one has forgotten about biomimetics.

    There must be tons of colaborative evidence in that field that conforms to ID, since the whole field is based on the premise of ID.

  157. 157

    PaV: actually according to what I know of ID theory, microevolution DOES lead to macroevolution IF you believe like evolutionists that DNA is fully open to change. But as we are discovering (like in those great links ari posted) DNA has protection built in, which is exactly what ID predicts because macroevolution cannot occur under the theory.

  158. PaV,

    We are into the same discussion we had before and you again want to impose your own definitions on modern day evolutionary biology while I want to work within what everyone in it is using. Because I think it works for ID. Constantly trashing the modern synthesis makes ID look like a bunch of cranks when it is so obvious that it does something. Concentrate on what it can do and what it cannot do. What was called the modern synthesis as defined in the late 1930′s and early 1940′s is not the same thing as it is today so don’t shoot down the old version. From Wikipedia, “Modern evolutionary synthesis is also referred to as the new synthesis, the modern synthesis, and the evolutionary synthesis.” One of the key components of the modern synthesis is that all evolution is gradual and this is the key element to challenge. Yes some evolutionary changes are gradual but the evidence does not support that all the evolutionary changes are gradual and this is what Provine and MacNeill are challenging.

    You can call the changes that happen, adaptation and I will call it the natural selection process because a subset of the gene pool is selected by environmental pressures. Yes it is adaptation but it also natural selection and yes it is also micro-evolution. And please do not go into the active versus passive nature of selection. We all know what it really means.

    The process of the modern synthesis is random variation plus selection/genetic drift/ or gene transfer. The second half of this does not create but only refines the gene pool. Behe, Dembski, Wells accept this but go on to discuss the modern synthesis’ limitations which all revolve around the creation of new variation which is very, very limited. We constantly see modifications of the gene pool (I know you will quote Provine to say there is no such thing as a gene pool). This is so obviously false as all we have to do is look at humans and see their different shapes, sizes, colors, abilities etc. There is no purple hair because it is not in the gene pool but maybe someday there will be a mutation and we will see someone with purple hair and our gene pool has expanded. Then when no one wants to mate with such an individual, the gene pool contracts.

    This refinement of the gene pools in terms of creating species variants is clearly said in everything I say so what’s the beef. There is also are lots of examples of where the gene pool gets expanded. I don’t use your terms but prefer to work within what is the terminology of evolutionary biology and don’t bow to your interpretation of Provine who I do not believe has said natural selection does not work because in the reference you gave to me before he discusses how it works. I believe he thinks it has been completely overblown and that I agree.

    MacNeill who is Provine’s associate clearly believes big time that natural selection works and how it affects the gene pool so why not go along with it and the others and then say it has limitations which MacNeill admits. He agreed with the limitations on the modern synthesis while he was here (primarily the gradual assumption) so we have an evolutionary biologist willing to have some agreement and saying the rest is speculation and they don’t have the models to account for real novelty in evolution. All on the variation side of the modern synthesis. He lists 47 types of variation creation and then admits they are not able to explain real novelty. Is there is any of this ID contests? No, so let’s join the conversation instead of being antagonistic all the time.

    You want to make arbitrary distinctions without a difference and I do not see where that gets us. Your example of mules, donkeys and horses is interesting but what does it change. I do not know what their mating problems are or why but the answers do not negate anything I propose nor do MacNeill or Davidson’s speculations on what is happening genetically with these animals. If it is proven that a rare process takes place with the mating of these animals then so what. It is just added to the list of things we know.

    I believe you are missing the whole point of the debate by bringing up a couple unusual examples which could very easily be folded into the modern synthesis and still be completely compatible with ID. These naturalistic processes will always be compatible with ID as long as they are true and because they are true they actually strengthen ID. They are absolutely nothing to be afraid of. Evolutionary biologist are 100% wedded to a naturalistic mechanism for variation creation and will change the definition of the modern synthesis to accommodate non gradual changes without blinking an eye. We can agree with their changes and still challenge the ability of their models to create real novelty. All within their paradigm. We are not out to destroy their paradigm, only modify it one or two key areas.

    I have read Behe’s book and Dembski and Well’s book and what I get out of both of them is that the modern synthesis works but is limited. What I got from reading Dembski elsewhere on the modern synthesis is that he is not against it philosophically but that it is not a comprehensive theory based on today understanding of biology. What he is against is the BWT or the Blind Watchmaker Thesis.

    I also take away from this that what most evolutionary biologist call evolution is nothing more than refinement of the gene pool to meet an environmental pressure and this is trivial but by joining them we can discuss it. But I believe that throwing non standard terminology and non relevant examples out all the time in a provocative way prevents an intelligent discussion.

    For example, a Darwinist come here and brings up the thousands of cichlids species and the 60,000 beetle species and then challenges ID to explain it. Our answer is no problem because ID agrees with the process that probably created all those cichlid and beetle species and they were probably not created by some unknown intelligence. Instead we say it is no big deal and probably represent trivial variation creation and natural selection and this makes sense from an intelligent design perspective because this process is good design basics. We then go on to explain to them what a big deal is and ask if they have any way to explain it and they will be left stuttering with such inanities as deep time or gene duplication or some other speculative process and we can counter with the Edge of Evolution etc. We are having a discussion within their framework and showing its limitations.

    I am sorry about this long post but I feel strongly that this is the way to go in the ID debate and if anyone has a better suggestion I would like to hear it.

  159. PaV (153)

    “Really. Check this out. You do believe in National Geographic, right? Here’s a quote:

    “Kathleen Hunt, a biologist at the University of Washington in Seattle, said the modern-day horse is ‘merely one twig on a once flourishing bush of equine species. We only have the illusion of straight-line evolution because Equus is the only twig that survived.’””

    I have to wonder if you understand what you read. It DOESN’T mean that horses didn’t evolve or that there were no horse intermediates – nothing you’ve posted even hints at that. What it DOES mean (and was made clear in the Talk Origins site I referenced earlier) is that horse evolution is much more complex than was earlier thought. Essentially there wasn’t a simple, straight-line evolution from the earliest equine forms to the modern day horse, there were a number of different branches of the horse family, most of which died out leaving only the modern-day horse family. I strongly advise you to read the Talk Origin website I posetd before.

    “I mention that RNA involvement is ‘cutting edge’. You reply:
    Well, this is the first I’ve heard of it.

    Well, that’s what makes it cutting edge. As to references, why not try a Google search?”

    Well, YOU are the one who made the assertion and it’s up to you to provide the evidence (or at the least the reference on which you are replying). If you think you can make assertions withpout provifing evidence then your assertions can also be dismissed without evidence.

    “Let me understand: I have to make the prediction, and then also explain the exact way the prediction will come about?”

    Not necessarily “exact”, but at least a rough indication would help. How else do you expect to make a prediction? Coming up with one out of thin air, as opposed to a well thought-out prediction based on scvientific principles, simply doesn’t cut it.

    “I suppose that if I explained it now, and it was later discovered to be exactly as I predicted, then I would receive the Nobel Prize, right?”

    If your work was original and added significantly to human knowledge then I’d be happy to see you get it.

    “Well, I’m sure that’s what they were looking for. The question is, what did they find? You’ve just admitted that land animals can become aquatic. Your sticking point earlier was that there were no land animals yet. But we’re dealing with geologic time, where the age of strata might not be known within a million or more years accuracy; and we’re dealing with a boundary between the Devonian and the Carbonferous. So, right at that boundary, are we dealing with an innovation that produced land-animals, one of which quickly went back to fish-like characteristics through a process of adaptation because of the environment; or, are we dealing with straight-line evolution produced by the same environment? Which is it? Can you tell me that unequivocally?”

    I think you need to read a basic text on the principles of geology and palaeontology, because either you are writing tongue in cheek or you need a basic primer in the subject. This is very clear and simple: I can unequivocally say that at the time Tiktaalik was living, the transition was from sea-to-land. This is because the whole history of the fossil record, from the formation of the earth to then, has no land-dweller forms in it. Consequently the transition must have been from sea-to-land.

    Now, if you are saying that there was a tiny, tiny inflexion in the fossil record where Tiktaalik was found, and actually an earlier species had transitioned from sea to land, and then migrated back to sea (God knows why because the land represented a great opportunity for new species to expand into without competition, whereas the sea was a highly competitive environment), all in a tiny patch of time and without leaving, as far as we can tell, any fossil evidence at all then that is a different matter. Nonetheless I can STILL say, unequivocally, that Tiktaalik was tarnsitioning from sea-to-land. That is because its primary oxygen gathering apparatus were gills whereas its lungs were rudimentary – see here: http://en.wikipedia.org/wiki/Tiktaalik

    If it had derived from a land-dweller it would, of necessity, have had true lungs and the gills would, as in modern land-dwellers, have been dispensed with as being an unnecessary and resource sapping expense.

    “Do you see the logic?”

    I did. And once the contrary evidence was apparent I saw right through it.

  160. Accepting part of their framework may make you a little popular but scientists are looking for one unified theory instead of 2. That was the biggest problem with Darwin’s Black Box. ID as an explanation for a couple of cases and NDT for everything else? If you accept NDT as so useful then why not just wait and have faith in Darwin?

    Edge is so important precisely because it does try to go after more of the whole enchilada. (“The Edge of Evolution makes the case that design is not just needed for the fanciest biological systems, but for almost all of them.”) But we still need to look at everything else: fossil record, OOL, embryology, Spetner’s NREH, altruism, etc.

    Everything that limits the scope of NDT helps the case for ID because otherwise evolutionists will stick with Darwin and just extrapolate.

  161. ari-freedom: Everything that limits the scope of NDT helps the case for ID because otherwise evolutionists will stick with Darwin and just extrapolate.

    Right. In my opinion, evolutionists (the atheists among them) have only one agenda: they want to destroy religion and the concept of God, especially the Christian God. To explain away the fallacies of NDT on earth, they would rather postulate that an alien race that evolved elsewhere came and messed with evolution rather than accept that God did it. Theirs is a hateful agenda directed at Christians more than anything else. If Christians did not believe in a God, evolutionists would not be atheists. It’s all politics and human nature. The reasons for the hatred are many but that’s a different story.

  162. Jerry,

    Yes, this is the same go-round as last time. And we don’t need to do that again. But I think you need to distinguish between so-called microevolution, which I prefer to call adaptation, and the modern synthesis. Population genetics, for the most part, looks to be a big waste of time; and, of course, the modern synthesis is based upon it. They talk about an ‘allele’. This hardly has any meaning. The whole of population genetics needs a more rigorous underpinning. Modern genomic assay techniques will likely give it the rigor it needs. But, of course, this will very likely only serve to highlight the ways in which what is considered “microevolution’ is a limited concept.

    Behe very easily compliments Darwin for the insight he provided biologists. He is willing to accept the formulation, RM+NS, as a meaningful biological reality.

    What do we see as a result of RM+NS? What does Behe see that impresses him? He sees bacteria that cannot live on galactose giving rise to a bacteria that can. He sees the malarial parasite developing resistance to chloroquine. But what does the bacteria do when it can’t find glucose? It starts mutating at a higher rate; and not only that, but in the exact area of its genome where it needs to change in order begin to metabolize galactose. Should we just say, “Oh, look at that. The bacteria just happened—all by chance—to mutate at a higher rate in the exact are needed”? Well, personally, I’m more than a little suspicious of such a thing happening by chance. In the case of the malarial parasite, yes, it changed; but the changes were not beneficial to the organism, but harmful. And in both instances, do we really want to call such minor changes “evolution”? Certainly “adaptation seems a more fitting word. I think Behe just graciously concedes ground to the Darwinistas. I find I cannot be that gracious.

    I have thalassemia. Analyze it according to population genetics. Have I really “evolved”? Freckles and red hair come from a mutation in the GC1R gene. Have the Irish “evolved”? These questions, if thought through, make the tenets of the modern synthesis look silly. I hope you make a genuine effort to think them through more carefully.

  163. PaV,

    You see I understand everything you say but I disagree on how to argue it. Not from the outside but from within.

    Once you are arguing from within you can take pop shots here and there and raise some doubts. There are two sides of the modern synthesis. Separate the two and then discuss each on its merits. I am not knowledgeable of all the side issues in genetics but leave that to the geneticists to fight out. How freckles appear is not an important issue. There is not much there for ID to care about except for two very important issues:

    1. the speed with which something can permeate a population,

    and

    2. the nature of the genomes of related species and whether they show any evidence of novelty or just devolution from a much larger gene pool. That is why I mentioned the thousands of cichlid and beetle species. The genetics of their origin would be another verification of Behe’s Edge of Evolution which right not rest on single cell organisms and viruses. There is not quite the reproductive events but the total is quite large and without any novelty would be a great next step for the Edge of Evolution. And things like this are currently being done within the framework of current evolutionary biology.

    If you are going to dismiss the modern synthesis wholesale then you better have a theory that embraces those elements of the modern synthesis that work. I just do not believe it is a complete house of cards. It has one major weakness and my point is to go after that and that alone. The evidence is on our side. But if you are going to say that nothing works then you will be the kook tilting at the windmills.

  164. Jerry wrote: If you are going to dismiss the modern synthesis wholesale then you better have a theory that embraces those elements of the modern synthesis that work. I just do not believe it is a complete house of cards. It has one major weakness and my point is to go after that and that alone. The evidence is on our side. But if you are going to say that nothing works then you will be the kook tilting at the windmills.

    I think I agree with this. If the modern synthesis was completely wrong, it would not have lasted this long, even among atheists. The great attraction of all bad theories and dogmas is that they are partially correct. This goes for all of science, not just evolutionary biology. Physics will turn out to be just as defective as evolutionary biology but that does not mean that it is all nonsense.

  165. 165

    Something that should certainly be on the list, from one of the leading ID experimenters and researchers in the world, Jonathan Wells. In a 2005 paper (“Do centrioles generate a polar ejection force?” Rivista di Biologia 98(1), 2005: 71-95), he makes the ID-based inference that centrioles are microscopic turbines:

    Centrioles consist of nine microtubule triplets arranged like the blades of a tiny turbine. Instead of viewing centrioles through the spectacles of molecular reductionism and neo-Darwinism, this hypothesis assumes that they are holistically designed to be turbines. Orthogonally oriented centriolar turbines could generate oscillations in spindle microtubules that resemble the motion produced by a laboratory vortexer. The result would be a microtubule-mediated ejection force tending to move chromosomes away from the spindle axis and the poles.

    From this ID hypothesis, several solid, testable predictions follow:

    A. It predicts that spindle microtubules in animal cells begin to oscillate at the beginning of prometaphase, and that those oscillations rapidly accelerate until metaphase.

    B. It predicts that the centriole contains a helical pump powered by dynein molecules located in the inner wall of its lumen.

    C. It predicts that the polar ejection force is regulated, at least in part, by intracellular calcium concentration.

    These are exactly the sort of solid, testable predictions that know-nothing critics of ID are always demanding — and we got ‘em! And in a peer-reviewed journal, no less!! Surely this must be on Prof. Dembski’s list — as I’m sure we’re going to be able to discover for ourselves soon (hint, hint, hint)!

    Peace, Zoe.

  166. Wells’s inferences do seem to lead to some solid ID predictions. Unfortunately, like with all ID predictions, Darwinism being non falsifiable is always claimed to make the same predictions. In other words, the claim is that Nature can act as a very accomplished design-mimic to the extent that the two can’t be distinguished from each other in the resulting biological system.

  167. Here are the principles that I am thinking about:
    1) life is cooperative, not competitive
    2) most observed genetic change is neutral or slightly degenerative and not selected for/against
    3) NREH as an explanation for microevolution, not rm/ns. organisms can adapt by mutating on purpose in response to an environmental cue. They could cripple functionality in order to get out of a jam.

    Pav gave an example
    “But what does the bacteria do when it can’t find glucose? It starts mutating at a higher rate; and not only that, but in the exact area of its genome where it needs to change in order begin to metabolize galactose.”

    Sounds like intentional crippling to me

    4) speciation can be sympatric (new species are created within a single population) and also a result of adaptive mutation

  168. jerry:

    Allen MacNeill, an evolutionary biologist at Cornell, says that the Modern Synthesis is dead. Isn’t that what I’m saying? Is MacNeill a kook?

    Since you likely haven’t studied population genetics much, you don’t know the flimsy nature of its foundation. All their talk about “alleles”, which is later translated into “genes”, is all nice talk. But that’s all it is. You have morphological changes that follow certain genetic laws: this is Mendelism, not Darwinism. In fact, Mendelism destroyed Darwinism. It took R.A. Fisher, and lots of in-breding and cross-breeding experiments, to salvage what eventually came to be know as the Modern Synthesis.

    As greater genetic detail has come about, this synthesis has been under attack. I find myself convinced that what passes for the modern synthesis is not anything at all like what is out there in nature. This is just now being discovered. On the link to MacNeill’s blog, you’ll find an article in which six different species of mice, on the same island, with the same climate have “evolved” from the native stock of mice brought over by the Portuguese 500 years ago. The original mice species had 40 chromosomes. Now there is only 1 species with 40, and all the others have between 22 and 30 chromosomes. It’s obvious that chromosomal fusion has occurred. From this fusion, new species have developed. But this has nothing to do with how population genetics is structured. These chromosomal rearrangements/fusions don’t seem to have added, or subtracted, any genetic material. It has simply been re-arranged. The species appear not to be able to form hybrids. Richard Goldschmidt, in 1940, said that this must be how different species arise. There is no “gradualism” involved here.

    Again, please separate the Modern Synthesis from so-called ‘microevolution’. We’ve entered a whole new era of genetics and population genetics. Most everything will have to be re-thought. The ultimate answer will likely turn out to be that there is an entire cellular mechanism that directs the way in which chromosomes are put together. Mendel stumbled on to some of its laws. But there is much more left to be discovered, and it will only be discovered as laboratory techniques become more and more sophisticated, as computers become more powerful and as search mechanisms follow suit, and as whole genome determinations become cheaper and quicker.

    But enough is known now by scientists like MacNeill to say good-bye to the ‘modern synthesis’. MacNeill talks about the ‘evolutionary synthesis’. We’ll just have to wait and see. Will it turn out to involve random processes? Very likely. Does that mean that Darwin was right? No. Does that mean that Design wasn’t involved? No. But, whatever it turns out to be, it won’t be what we now know as the ‘modern synthesis’.

  169. PaV,

    Nothing you have said changes my mind. Genetics is an interesting side show in the whole evolution debate and while all your examples are intriguing they have nothing to do with the evolution debate except to prove that whatever mechanisms for genetic change there are, does not produce novelty. So the mice are the same with different number of chromosomes. How does that affect the debate?

    This just makes the ID case easier as it is an example of new species with no new characteristics. Again supporting Behe’s Edge of Evolution. Rearrangements of the genome is interesting but in reality has nothing to do with the over all debate, which is the origin of novelty.

    The modern synthesis will be adjusted a little to accommodate your examples just as it has been adjusted several times since the 1940′s to accommodate new information. The basic premise on the genetic side is still the same, just with a lot more options on how species rearrange the chromosomes during reproduction. The real issue was and still is what is on the chromosomes as they are mixed during reproduction.

    So not every thing falls into the nice neat scheme of distributing genes for all reproduction events as people envisioned. Again this is interesting but changes nothing as far as I can see.

    One interesting effect is that if some reproductive anomaly created a variant with different number of chromosomes that cannot inter breed then in effect it created a founder effect without any geographical separation. It would be interesting to understand what happened to create enough of a population with the different number of chromosomes so they could inter breed.

    However, what is always the issue is the other side of the process and that is the origin of variation. That is the only real Achilles heal of the modern synthesis and the only place the debate should be taking place.

    I have seen nothing yet to change my mind on this. Unless someone can give an example where novelty was created by shuffling genes during reproduction by whatever means it happens. They may discover this some day and if it does happen, we all should sit up and pay close attention.

    If the modern synthesis is dead, it is not because of changes on the genetic side but on the variation side. If MacNeill makes his claim based on the genetics, then it is a false claim that won’t go very far. Evolutionary biology will just rewrite the specs for the modern synthesis a little.

    However, I had the impression that he was making it because of the lack of any evidence on the variation side which is why he brought up the 47 mechanisms of variation. He then said they have no models yet that would accommodate the origin of novelty. If only they would say that in the textbooks. They cannot re-write the specs on the variation side without a lot of consternation. Though many are trying such as Schwartz and Shapiro and others.

  170. magnan

    In other words, the claim is that Nature can act as a very accomplished design-mimic to the extent that the two can’t be distinguished from each other in the resulting biological system

    Not even close. Nature can’t plan ahead. It is reactive. Intelligence is proactive.

  171. jerry,

    Darwinism says that what is random, when extrapolated, results in what ‘appears’ to be ‘designed’. I say that what is designed , when extrapolated, results in what ‘appears’ to be ‘random’. Which side of this do you prefer?

  172. PaV,

    You said

    “Darwinism says that what is random, when extrapolated, results in what ‘appears’ to be ‘designed’. I say that what is designed , when extrapolated, results in what ‘appears’ to be ‘random’. Which side of this do you prefer?”

    I am not sure what this is supposed to mean in this debate you and I have been having because it reminds me of the theistic evolutionist’s position who claim that the whole process looks random but is really controlled by God. I have no problem with this philosophically but the evidence points elsewhere.

    Any way I believe what looks like it was designed, was designed. That is where I believe the evidence points. But again I do not know what this has to do with the variation/genetics discussion.

  173. PaV,

    Here is a quote from Allen MacNeill’s blog.

    “Creationists and supporters of Intelligent Design Theory (“IDers”) are fond of erecting a strawman in place of evolutionary theory, one that they can then dismantle and point to as “proof” that their “theories” are superior. Perhaps the most egregious such strawman is encapsulated in the phrase “RM & NS”. Short for “random mutation and natural selection”, RM & NS is held up by creationists and IDers as the core of evolutionary biology, and are then attacked as insufficient to explain the diversity of life and (in the case of some IDers) its origin and evolution as well.

    Evolutionary biologists know that this is a classical “strawman” argument, because we know that evolution is not simply reducible to “random mutation and natural selection” alone. Indeed, Darwin himself proposed that natural selection was the best explanation for the origin of adaptations, and that natural selection itself was an outcome that necessarily arises from three prerequisites:
    • variation (between individuals in populations),
    • inheritance (of traits from parents to offspring), and
    • fecundity (reproduction resulting in more offspring than necessary for replacement).

    Given these prerequisites, some individuals survive and reproduce more often than others, and hence their characteristics become more common in their populations over time.

    As I have already pointed out in an earlier post, the real creative factor in evolution isn’t natural selection per se, it’s the source(s) of variation that natural selection “preserves” from generation to generation. According to the creationists and IDers, the only source of such variation is “random mutations”, and so there simply isn’t enough variation to provide the raw material for evolutionary change.”

    It is interesting that MacNeill claims the ID people are promoting a strawman when in fact his post is the real strawman. MacNeill doesn’t post too often and this is from October. He then goes on to list the 47 means of variation creation. But when here admitted there were no models yet to explain the real novelty that appeared in the fossil record or in nature.

    So I say to Dr. MacNeill: We agree with you and anyone who says that evolutionists espouse rm + ns are promoting a strawman that doesn’t exists. The real paradigm is variation generation + reproductive processes is evolution and ID agrees with this 100%. It is just that no evidence exists that shows that naturalistic means can generate the necessary variation to produce the novelty we see in the natural world.

  174. jerry,

    We’re making predictions here. Let me take up the case of Darwin’s finces.

    I have stated before that there is no way that population genetics can explain the very rapid beak size changes that have taken place.

    Here’s something from a 2004 report in Science about the Galapagos finch beak development:

    We have identified variation in the level and timing of Bmp4 expression that correlates with variation in beak morphology in Darwin’s finch species. We are tempted to speculate that differences in the cis-regulatory elements of Bmp4 may underlie the distinct expression patterns, although alternatively they could be explained by differences in the timing or amounts of upstream inductive factors or differences in the transduction of such signals. Two such potential upstream signals are Sonic hedgehog (Shh) and Fibroblast growth factor 8 (Fgf8), which are expressed in the beak epithelium.

    Isn’t it clear that BMP4 is principally involved with the difference in beak sizes, and that other proteins coming from other genes are involved?

    Here’s my prediction:

    It will be found that some environmental/metabolic trigger is responsible for the changed regulatory processes leading to the different beak sizes. Further, based on the something Craig Ventner said in the transcript that Paul Nelson linked to, where Ventner is saying that they can manufacture DNA’s that are like different operating systems, and based on what I’ve said earlier in this thread about RNA, I believe that the environmental trigger will prove to be a RNA sequence that is passed onto the germ line and which is then translated into a protein that interferes with the regulatory/developmental program for the finches. (Interestingly, this process combines elements of Lamarck’s theory of “acquired characteristics” and Darwin’s theory of “panspermia”, and would thus provide a reason why both men came up with their different, and incomplete, understandings of evolution.)

    I’m more than willing to stand by this prediction.

    Now, tell me, how is variation + NS involved in such a process?

    As to NS: Provine has said that NS does nothing. Here’s an analogy. The Saturn rocket engine was developed to get man to the moon. Earlier rocket egnine designs didn’t provide sufficient thrust to lift the LEM into orbit. They weren’t good enough. They were tested and found insufficient. They wer rejected. They stopped being made. They “died off”. Now, should we say that the “moon” created the Saturn rocket engine? NS is no more than death. Does death create/produce/develop diversity of life?

    P.S. I’m a little burnt out on all this; how about you?

  175. PaV,

    Again you come up with an intriguing example which I do not think changes anything. Something has happened on the genetic side which is not clear. That does not destroy the paradigm just represents another modification of the genetic process that can easily be incorporated into future changes of the paradigm.

    I do not follow everything you are saying but essentially what you are saying is that some of the things that get expressed are not novelty but alternatives and these alternatives were in the gene pool or were part of the genome. And these differential expressions are not due to reproductive variations in the gene pool but to some environmental factor.

    Interesting but again it changes nothing. I might have the interpretation slightly wrong but I bet the correct interpretation still does not change anything because it is all on the genetic side.

    You said

    “NS is no more than death. Does death create/produce/develop diversity of life?”

    Two things:

    First, I am not sure I agree with this interpretation of natural selection and we have long discussions about just what natural selection is. Natural selection generally winnows the gene pool but this is not the same as death.

    Second, I constantly harp on the fact that the only things that creates novelty is variation and not natural selection. Natural selections only acts on what is in the gene pool of the population and presented to the environment and leads to differences in species variants based on environmental pressures. This is pretty clear in the real world. However, the process is limited in what will eventually appear and over time keeps winnowing down the gene pool and the possible alternatives available to the natural selection process. If somehow the gene pool expands and this expansion contains real novelty, then the natural selection process might lead to differential increases in this novelty in the gene pool if it affects differential reproduction and survival.

    How often do I have to say this. And by the way there are lots of predictions for ID here that are in sync with Behe’s Edge of Evolution premise. Behe has indicated that research that will support ID is research into organisms that have large reproduction events and no novelty.

    No, I am not burnt out on this because I believe this represents a major problem for many here and elsewhere who back ID. I happen to think that many who espouse ID do so with unclear ideas as to what is the total picture. Not that I understand everything but there are definitely naturalistic processes that clearly change things in the gene pools over time and to deny these processes makes ID people look like fools. Lets get rid of the foolish ideas that many ID people have and focus on the real issues.

    Also my address was to Bob O’H about junk DNA and trying to clarify his image of what ID proposes. You saw the post and renewed the debate from a couple weeks ago so I answered you as best I can.

    I will continue to bring up the points I make every time it seems appropriate. So far they get ignored and you are the only one who challenges what I am saying and as far as I can see your examples do not bring up anything that contradicts my basic premise. In fact your examples which are all interesting support my point of view that naturalistic processes affect what is in the gene pool and what gets expressed. For this I am appreciative but which I also find ironic since you keep fighting me.

  176. Second, I constantly harp on the fact that the only things that creates novelty is variation and not natural selection. . . . In fact your examples which are all interesting support my point of view that naturalistic processes affect what is in the gene pool and what gets expressed.

    Jerry, it appears where we differ is that when it comes to so-called microevolution you think that ‘genes’ are changing and I don’t. I agree that there are various means of variation. But how do we know that these are completely random. Why, for example, does recombination occur? Is it simply an accident of nature? I don’t see it that way. But, of course, it will be hard to prove whether these variations are ‘programmed’ or just mere serendipity. But, either way, we know that these mechanisms exist.

    But when it comes to changing ‘genes’ and ‘drifting gene pools’, I see it very differently. We don’t necessarily “see” this happening. Inference is more at play than true knowledge here. Instead, I see what ‘regulates’ the genes as changing, and changing through a combination of built-in genetic mechanisms and environmental triggers. Genes can deteriorate—which is normally what is seen in genetic defects—but it is usually just a single a.a. change. This is, yes, random; and, yes, it can have phenotypic consequences, but is simply a by-product of the overall mutation rate of eukaryotes. (If there are two a.a. changes in critical spots, viability is most likely lost.) When I pointed out that mutation rates of genomes all seem to be about one in one-tenth of the genome length of organisms, I mentioned this because it seems obvious to me that the mutation rate is “set” according to the length of the genome. To me this suggests two things: (1) design, (2) that a certain level of muation is needed at times for the overall survivability of species, which are called to adapt to many different environmental conditions.

    As to “junk-DNA” and Bob O’H, I’m the very person who pointed out on this blog that an experiment had been done wherein huge blocks of “conserved” junk-DNA had been excised in mice embryos, yet those embryos gave rise to perfectly normal mice. My point to Bob was that just because some “junk-DNA” doesn’t have function, you can’t go from there to concluding that all of nature is the result of randomness—not that I thought Bob was pushing that point. OTOH, the experiment I brought to the attention of this blog completely demolishes the idea of “selection pressure”. It was NS, and the “selection pressure” it exerted, that was touted as the driving force of conserved sequences, with the corollary that highly-conserved sequences must conserve some vital function. Yet, normal mice. The intelligent response to the experiment is the audible gasp that the biolgists gathered to learn about the experiment were heard to make. They understood that it completely undermined the modern synthesis (as does the Netural Theory). Logically, we should conclude that organisms have the power to ‘conserve’ when they want to, and to allow mutations when they want to. This speaks of organization and design—not random happenstances.

    But, all of this should get cleared up as science moves (chugs) along.

    Ciao!

    Oops! One more thing. In my last post I predicted RNA, in response to the environment, directly or indirectly, would be found to be passed on to the germ line of finches, which, in turn, would be expressed as a protein having an effect on subsequent devlopment. This all suggests that there is some kind of enzyme that permits proteins to be converted back to RNA, a reverse transcriptase for proteins. I wonder if anything like that has been found yet?

  177. PaV,

    You said

    “jerry, it appears where we differ is that when it comes to so-called micro-evolution you think that ‘genes’ are changing and I don’t. ”

    No, I don’t think the genes are necessarily changing. We are talking about the gene frequencies within a population’s gene pool and there is no reason there has to be different genes for micro evolution to take place, just different frequencies. You could have the same genes but with different population frequencies. Thus, you could have bigger, faster, stronger organisms on the average without adding any new genes to the gene pool and I would consider this micro evolution.

    It is also possible to have new genes or mutations to alleles such as in the anti-freeze gene in the Antarctic fish or something less significant such as one of your examples for a mutation that created freckles. Again, I would consider this micro evolution and trivial even though the freckle genes might have some hypothetical survival implication in some severe climate changes.

    You said

    “I agree that there are various means of variation. But how do we know that these are completely random. ”

    We don’t and I don’t assume they are but I also don’t know anything that says they are not random. If some are not random, then what type of variation is expected? It would be interesting to explore this. Post a thread on this and see where it leads. We need more threads like that.

    We will start to learn more about gene pools now that more than one entity of a population is having its genome mapped. This is happening big time for humans and we are seeing the human gene pool being developed. It will eventually happen for other species so we can see the extent of gene pools for various species. See

    http://www.sciencemag.org/cgi/...../5858/1842

    and

    https://www.23andme.com/

  178. —–Jerry writes, “So I say to Dr. MacNeill: We agree with you and anyone who says that evolutionists espouse rm + ns are promoting a strawman that doesn’t exists. The real paradigm is variation generation + reproductive processes is evolution and ID agrees with this 100%. It is just that no evidence exists that shows that naturalistic means can generate the necessary variation to produce the novelty we see in the natural world.”

    Jerry, have you read John Sanford’s book, “Genetic Entropy.” He contends that the “The Primary Axiom” for evolution is this: “man is merely the product of random mutations and natural selection. According to him, this is the monolithic view. Behe seems to put the emphasis on common descent, followed by RM+NS. In both cases, the traditional Darwinist model seems to loom large. How sure are you that MacNeill’s views are representative of the larger community?

  179. —-DaveScot has written an astoundingly terse and revealing pair of sentences—-”Not even close. Nature can’t plan ahead. It is reactive. Intelligence is proactive.”

  180. StephenB,

    I am sure that MacNeill’s expressed views are in the small minority and so is Provine’s. But I bet if there were no creationists or ID out there waiting to pounce on any dissent within the faithful, there would be many others who would express similar concerns. Occasionally we have a thread here about someone who questions Darwinian processes and we make a big deal of it. But they are few and far between.

    I look at common descent as not part of the paradigm but a conclusion to be accepted or rejected based on the evidence.

  181. you can’t question Darwinian processes without being pounced on by the Darwinists. Remember, “Science” says evolution is a fact and supporting ID is like denying the unambiguous reality of human caused global warming.

  182. [...] Comments ari-freedom: you can’t question Darwinian processes without being pounced on by the Darwinists. [...]

  183. Jerry: I think I can identify, at least in part, with one of your principles: We ought to reserve our heavy handed polemics for those who are impervious to reason. There are so few on the other side who will risk even the smallest deviation from the “no concession policy” that we ought to be gracious when it happens. As Margaret Thatcher once said about Gorbachev in the middle of the cold war, “I think I can do business with this man.” Somehow that overture helped create a climate that made the unthinkable thinkable. Reagan had set the stage beautifully be calling the Soviet Union “the evil empire.” But to have re-introduced that theme at such a delicate time would have destroyed all progress and changed history for the worse.

    In the heat of battle we sometimes forget that progress does happen sometimes. When someone on the other side shows courage and intellectual integrity, that last thing in the world we should be doing is to immediately demand more from them. Quite the contrary, we should pause and “try to do some business with them,” because that is what they are trying to do with us. Those are not the times to be interjecting irrelevant religious themes and harsh criticisms.

    At the same time, we must realize that one side is going to win and one side is going to lose. The so-called compromise position offered by Miller and company is not really a compromise. Realize that the term “Theistic Evolution” has been hijacked by neo-Darwinists to mean something that it doesn’t really mean. In its original conception T.E simply meant that God either guided or planted the seeds for a macro-evolutionary process, something that ID can accept with no problem. So we had this scenario: God reveals himself in scripture; God reveals himself in nature. Design is real.

    Today, the term theistic evolution, Miller style, means this: God reveals himself in scripture; God HIDES himself in nature. Design is illusory. From this perspective, God did not direct evolution at all, nor did he even set up the process. For Miller, everything is contingent and non-teleological—no programming allowed. That is nothing more than Darwinism with God as an irrelevant footnote. These biologists are positing a schizophrenic world view in which a purposeful, mindful God uses a purposeless, mindless process. This they call Theistic evolution even though it is no such thing. It is meant to mislead by evoking images of the old meaning while twisting the words to make them fit the Darwinist paradigm.

    In an attempt to defend the indefensible, they point to Aquinas, who once pointed out that God can create through contingency. But they twist his words to make it appear that God created “everything” through contingency, which is false. God may have created moon craters and snowflakes through contingency, but he created the DNA molecule through design. Indeed, these dishonest scientists try to use Aquinas, MR. DESIGN HIMSELF, as evidence against design. It doesn’t get any worse than that. I don’t know whether Cornelius Hunter sees through this charade or not, but it doesn’t matter. If he believes that Miller and Co are “Theistic Evolutionists,” that is a problem.

    So, all I am saying here is that I agree with your strategy for achieving some level of like-mindedness, whenever these opportunities arise. But I also must emphasize that we cannot compromise by integrating God with Darwin. God means design; Darwin means no design. There is no middle ground here and we cannot make intellectual compromises when there are none to be made. There will be no ties or stalemates in this battle; one side will go down.

  184. StephenB: So we had this scenario: God reveals himself in scripture; God reveals himself in nature. Design is real.

    I agree with you that the compromisers are really capitulating. However, Christian IDers really have a big problem. Did not Isaiah write “Truly, thou art a God that hideth thyself”? Sure, design is real but the enemy will never accept it. As a Christian, I believe that we need to reevaluate our strategy and change our approach to fighting this war. God must have anticipated this and I reject any notion that that he abandoned us. I am positive that he left us the means to win. We need to find God’s help in the one place where the enemy won’t look, in the scriptures. That’s how we’ll be victorious.

  185. —–Mapou, “I agree with you that the compromisers are really capitulating. However, Christian IDers really have a big problem. Did not Isaiah write “Truly, thou art a God that hideth thyself”? Sure, design is real but the enemy will never accept it. As a Christian, I believe that we need to reevaluate our strategy and change our approach to fighting this war. God must have anticipated this and I reject any notion that that he abandoned us. I am positive that he left us the means to win. We need to find God’s help in the one place where the enemy won’t look, in the scriptures. That’s how we’ll be victorious.”

    Mapou, Let’s make a few intellectual distinctions:

    [1} The Bible declares that God manifests himself in nature and that those who would deny it are without excuse. The passages in Isaiah refer to God's hidden "personality" which would not become evident until the coming of the Messiah. Morally and relationally, God did hide himself from man after the fall. God's "existence," however, is written in nature.

    [2] I am not suggesting that we should “use Scripture” to win the battle. We should do the science, plain and simple. Where we get the help is a totally different question. That you would conflate these two issues gives me pause. I only raise the issue about Scripture to point out that Miller-style Darwinists, who claim that their Darwinism is compatible with Christianity, are either being illogical or dinengenuous. If they were really serious about their Christianity, they would accept one of its most basic truths—nature is designed.

    [3] We will win the battle by proving, promoting, and defending the integrity of the design inference, and by proving that SCIENCE DOES NOT NEED RELIGION to find design in nature. Christians, of course, should pray that all of God’s truths will someday be acknowledged, both those revealed in Scripture and those revealed in nature. While prayer is a nobler thing that science, it cannot be used as a legitimate substitute. The two realms are compatible but distinct. Each can speak to the same truth from a different perspective, just as faith can believe in a truth that science can often verify. Still, the verification must be done through the use OF UNAIDED REASON in a consistently rigorous way. OTHERWISE, IT HAS NO VALUE. To confuse one’s religious beliief with the science of intelligent design is to do violence to both.

  186. StephenB,

    I never advocate compromise in a debate on truth. But what I see in the ID debate is bad science by many on the ID side and reflexively so. And we will never win the debate with bad science amongst those who are interested in learning and observing the debate.

    I believe truth will win out and that is the reason that I constantly harp on what I consider some fundamental errors that many make here. This site has been a constant source of learning for me and I assume others and I like it to get even better in the future. But it is also a constant source of bad reasoning and science by well intentioned commenters. I would like to reduce the latter and increase the former.

  187. jerry (177):

    Again, I would consider this micro evolution and trivial even though the freckle genes might have some hypothetical survival implication in some severe climate changes.

    Why even call freckles ‘microevolution’? One of the great problems in this debate is the equivocal nature of the word ‘evolution’. The accepted general idea of evolution is that when speaking about evolution it is assumed that evolution contains a ‘progressive’ component to it. What is ‘progressive’ about freckles? You suggest that it might be helpful in a certain situation. Well, that’s adaptation, not evolution. You’ll find that the word ‘change’ can easily be substituted for the word ‘evolution’. The next time you read an article, or even a book, where they use the word evolution, just substitute the word ‘change” for ‘evolution’ and see whether or not it affects the meaning. I bet it won’t. Why not talk about ‘evolution’ when we’re talking about a progressive type of evolution that walks us through the known fossil record and its progression of new forms, and ‘adaptive change’ when we’re talking about these kinds of trivial changes that are probably no more than artifacts arising from a mutational rate set to something other than zero?

    As to population genetics, what you seem to be missing is that when geneticists talk about changing gene frequencies, this is all assumed, not proven. The way that phenotypic changes have been measured historically is by visually examining specimens. When working with bacteria, this is a different matter. But then think about some of the experiments that are bandied about—do they represent a change from one ‘gene’ to another, or do they simply represent a change in a ‘switch’ that precedes the gene and is part of the regulatory process for that gene? IOW, I don’t think gene frequencies change at all; expression changes. Think of sickle-cell anemia, does it occur because the gene for hemoglobin disappears, or is it simply a single a.a. error? Well, of course, it’s the latter. What’s that got to do with “gene frequency”?

    Remember jerry that you can’t rely on scientists to tell you how little they know because they’re so absorbed with trying to add to what little they know. Again, I could be totally wrong. But my intuition tells me otherwise, and my intuition has proven quite will over the years. Quicker, faster, genomic sequencing, coupled with greater sophistication in compartative genomics ought to give us the answer. I bet I turn out to be right about this. (Let’s also add here that according to Sanford’s ‘genetic entropy’ argument, it’s quite possible for genes to be ‘lost’ or disabled, but that is a different matter. And, of course, we’re talking about degradation and not about anything progressive in nature.)

  188. jerry, (186)

    But it is also a constant source of bad reasoning and science by well intentioned commenters.

    Who exactly is the judge of whether something is ‘good’ sicence or ‘bad’ science? I’m curious.

    Let me state, unequivocally, that the change in beak size of Darwin’s finches has absolutley nothing to do with the modern synthesis, nothing to do with drifting gene pools, nothing to do with ‘changing gene frequencies’, and everything to do with environmental triggers.

    OTOH, Jerry, I think you buy the microevolution/modern synthesis/variation+NS story “hook, line and sinker.’ One of us is very right; one of us is very wrong. Now, do you want to dogmatically state, ahead of time, that you’re correct and that I’m wrong? Frankly, UD seems like an unlikely place for someone who wants to assert, unequivocally, that they know the modern synthesis to be true, and, consequently, this must be incorporated into the ID position.

  189. PaV,

    I will refuse to respond to anything you say after this comment till you get right what I say. You constantly distort what I say to fit a template you have so why bother answering your posts.

    The best distortions are

    “I think you buy the microevolution/modern synthesis/variation+NS story “hook, line and sinker.’”

    “UD seems like an unlikely place for someone who wants to assert, unequivocally, that they know the modern synthesis to be true, and, consequently, this must be incorporated into the ID position.”

    How can you say that after all my posts? These are the silly comments you make all the time that are complete distortions so why bother responding anymore.

    I will say it point blank that if someone does not accept parts of the modern synthesis and I have outlined which parts they are, then they got their head screwed on wrong and are making ID look foolish.

  190. jerry,

    Could you please, straightforwardly, say which parts of the modern synthesis must we accept? I’m guessing common descent. And, I’m guessing NS. Is that right?

  191. I’m also confused. The whole point of Spetner’s NREH was to replace the NDT for examples of MICROevolution. (he doesn’t even claim to pretend to have a theory for macroevolution since that was never observed)

    And the front loaders need the NREH before we can even talk about expanding it to explain universal common descent

  192. PaV,

    I do not consider common descent as essential to accept one way or the other. In fact I do not really consider it part of the basic evolution debate. It is something that follows or does not follow from the empirical evidence. It is a conclusion that one can accept or not accept based on the data. I hope this is clear enough.

    Also when I do discuss common descent, I distinguish between what some call universal common descent and what I call limited common descent. For the latter some species could descend from a closely related ancestor but not from an original single celled organism. Take this hypothetical example; cows and goats may be descended from a common ancestor but this does not mean they are necessarily descended from the first mammal directly or from lizards and amphibians before them. Since I consider the origin of species that have functional differences a mystery, I really have no concrete basis to assert or deny common descent.

    So as far as am concerned one can take or leave common descent in the evolution debate. I believe this is Dembski’s position also. I don’t find it a necessary one way or the other but something to be proven or falsified based on the evidence. Now, I have opinions but they are not essential one way or the other to what I call the real debate.

    If you want to dispute any of this, then I have no idea what could be disputed since I am essentially saying I don’t know for sure and don’t find it essential for the debate.

    I will answer the next part, which is the essential part, in the next post.

  193. jerry,

    I like your “limited common descent”. It sounds, pretty much, like my thoughts on the subject—and,… it’s pithy!

  194. PaV,

    Here is what I believe about the modern synthesis and it is long but written relatively quickly so may not be entirely coherent.

    1) The modern synthesis was developed by evolutionary biologists in the 1930′s and 1940′s to take care of problems with Darwin’s original ideas. That should not be controversial.

    2) It has changed over time to accommodate new information, the most dramatic being the discovery of DNA and the genome. But other changes have taken place besides these which are also accepted as part of the basic paradigm. This should not be a point of dispute. For example, genetics is a huge field and has several different theories associated with it. All are part of the modern synthesis and some are speculative.

    3) There are two separate but broad basic processes that are part of the modern synthesis paradigm. (By the way I use modern synthesis since most evolutionary biologists consider the term neo Darwinism inappropriate and out dated despite the wide use of it here.)

    These two basic processes are a) the creation of variation in the genomes of gametes in multi-cellular organisms and b) the subsequent expression of these genomes of the gametes in the population of the organisms after mating through principles of genetics. First a gamete or gametes gets changed through some variation creation event to produce something that is not in any of the members of the population and then second, the genomes of a new off spring are changed to reflect this new change to the genome that is in some of the gametes.

    These are two independent processes. At least I believe they are but am willing to discuss why they are not. I am not interested in single celled organisms for this discussion though I realize it is an important topic area. So I am keeping it to multi-cellular animals for this discussion. So far I hope it is non-controversial since I am just making the same demarcation that Behe has made.

    4) Somehow a gene pool is created and I use the Wikipedia definition of gene pool. Here it is

    “In population genetics, a gene pool is the complete set of unique alleles in a species or population. A large gene pool indicates extensive genetic diversity, which is associated with robust populations that can survive bouts of intense selection. Meanwhile, low genetic diversity (see inbreeding and population bottlenecks) can cause reduced biological fitness and an increased chance of extinction.”

    If you or anyone want to deny such a thing as a gene pool exists, then I suggest a thread be started and we can have a discussion. To me it is a no brainer and while I am sure there is lots to learn, it is easy enough to look at humans and all the variation that exist in their physical features and capabilities. Today there is a constant mapping of individual human’s genomes or parts of them to validate this concept. We may never get the complete human gene pool but a large subset is now being developed. I posted links on this above.

    5) I also believe that the gene pool is constantly being modified over time by variation events to gametes. These variation events are of several different types. For now I will accept Allen MacNeill’s 47 mechanisms and do not feel capable of disputing any of them. But as I will say below, it does not make any essential difference because there is no evidence they ever created anything of consequence.

    6) How the gene pool grows and contracts depends mostly on the second process which can include lots of sub processes we do not fully understand. This I usually refer to as the genetic side of the modern synthesis. In other words how do the genomes of the gamete cells get expressed in the gene pool and what frequency does each allele (or other genetic demarcation you want to use) have in the population and how does this change over time. (Behe uses Darwin’s term, natural selection, in the Edge of Evolution to designate this process but I bet if asked he would admit that this second basic process is not a single process but considerably more complicated.)

    7) Now here is one of the key things I do not accept in the modern synthesis, namely, that the gene pool gets modified gradually over time in such a way that when gametes combine they eventually produce a novel complex functionality that did not exist before. In other words I deny that there is any evidence that suggests that macro-evolution takes place over time because of small variation events in the genomes of gametes that then lead to small changes in the gene pool and eventually lead to large functional changes in members of the population. Gradual processes happens but there is no evidence of anything of consequence for evolution ever resulting from it. Since this assumption of the modern synthesis lacks any empirical evidence, it is discarded from my paradigm. But since there is good empirical evidence that the other parts of the paradigm have validity, then there is no reason to discard them.

    So I assert that small changes do take place but that there is no evidence that these small changes lead to anything but trivial changes to the genome. Can I be more clear. You are welcome to disagree with any of my statements above but the statements I have laid out are no threat to ID in any way and falsifying them does not necessarily strengthen ID. As I will outline below, I believe accepting them strengthens ID immensely and makes it a more acceptable paradigm to the scientific community.

    We must accept that sometimes these small changes to the genome lead to dramatic consequences in the natural world. Namely, genomes will be altered to allow some organisms to live in an environment where the genomes of their ancestors would not have been able to survive. And more than likely these organisms will be somewhat morphologically different but not necessarily so. This process by which some offspring with certain allele patterns are more likely to survive is our famous friend, natural selection. But again I assert that there is no evidence to support that the changes to the genomes will be nothing but trivial in terms of evolutionary biology.

    Again I want to emphasize that trivial changes can have dramatic effects, especially in terms of disease and medical issues and maybe in some cases, survival in certain environments. I also am willing to listen to various theories on how the gene pool gets modified that are different from natural selection, genetic drift and gene flow. I am sure that genetics can adjust to accommodate other mechanisms. It is not a big deal.

    So if you have any objections to the above comments, limit it to multi-celled animals because at the moment that is all I am interested in. If you have any questions or dispute any of this, please ask simple questions as opposed to putting thoughts into my mouth. Maybe I haven’t expressed it clearly enough. I find nothing of what I say that contradicts Behe, Dembski or Wells so it may be a question of semantics. I have read Behe’s book in the last year and just got finished Dembski and Well’s book.

    Now here on is my purely speculative ideas and treat is as one person’s speculation. After thinking about this process of variation and modification of the gene pool by genetic processes for a couple years now, I believe it was designed to work this way. It is a way of modifying populations so they can thrive and survive in different environments without direct intervention and that to me is fantastic design. So I believe it is possible that the DNA/RNA/protein system of life was designed as such so it could be modified to be flexible in changing environments. To me it is beautiful design but it is limited and these limitations are probably part of the design.

    So I propose a thread for the future, namely that the variation and genetic processes of the modern synthesis is beautiful design to allow for the flowering of life on the planet. However, the original gene pool for the various segments of life may have to be created for this to happen because natural processes will never lead to any gene pool that is robust enough to accommodate the changes necessary. So most of the life on the planet is devolution after these original gene pools are established. Again speculation to be verified, falsified or modified by future research. That is why I say that the investigation of genomes is ID research because I believe it will support Behe’s proposition that there is no novelty within all these genomes despite tens of millions of years of evolution or maybe devolution and zillions of reproductive events.

    What could be more devastating for the Darwinist then for ID to first appropriate most of their pet theory and then use it to show that all these species of birds, fish, mammals, beetles etc. are nothing but devolution of a gene pool long gone. There is no or little evolution in birds; there is no or little evolution in fish; there is no or little evolution in carnivora despite 10′s of millions of years for each and zillions of reproductive events. It would be absolutely crushing for the Darwinists. But here we are on this site reflexively denigrating the methods that are before our eyes that could enable us to humiliate the Darwinists.

    Long live variation plus natural selection and its variants. These are the tools to vanquish the Darwinists. Here is my proposed ID paradigm

    1) ID => evolution with novelty

    2) variation + natural selection => devolution =>
    richness of life => extinction

    Most of the action is in 2) but 2) could not happen if not for 1).

    Again all speculative but to me it makes more sense that anything else I have heard.

  195. jerry,

    you wrote this:

    After thinking about this process of variation and modification of the gene pool by genetic processes for a couple years now, I believe it was designed to work this way. It is a way of modifying populations so they can thrive and survive in different environments without direct intervention and that to me is fantastic design

    What I highlighted is exactly what I’ve been trying to hammer away at with you. So we’re on the same page on this afterall. Yes, it is a ‘speculative’ view, but it sure seems to make a lot of sense.

    Where I disagree—and this is surely ‘speculative’ too—is that I don’t think, as population genetics would tell you, that genes are “eliminated” and “fixed”. Again, intuitively, I think the genes are always there in the genome and in the population. Random changes can occur to these genes, either in the coding region or in the regulatory region surrounding the coding sequence, resulting in differing phenotypic expression.

    So I propose a thread for the future, namely that the variation and genetic processes of the modern synthesis is beautiful design to allow for the flowering of life on the planet.

    I wouldn’t word things just this way, but, that said, what you write summarizes my view quite closely. Asa Gray pretty much had this view.

    Thanks for taking the time to write out your views. Your full of surprises—pleasant ones, of course.

    It would be absolutely crushing for the Darwinists. But here we are on this site reflexively denigrating the methods that are before our eyes that could enable us to humiliate the Darwinists.

    Again, where I see things differently is that I believe their ideas on what you’re calling ‘devolution’ is wrong as well, not that the unfurling of the information that becomes present in the major taxa doesn’t involve random processes; hence, I think the humiliation will ultimately be deeper.

    But I must say, I’m quite pleasantly surprised to see that there is very little distance between our views.

    Pace.

  196. So, almost 200 responses later, can anyone provide anything that satisfies Dr. Dembski’s original request for:

    any samples of things that intelligent design theory has predicted, which researchers have later determined to be true?

    There are many examples above of predictions, but I didn’t see any that have been confirmed by researchers.

  197. congregate:

    What about “junk-DNA”?

    And, if something has already been confirmed, how could it then be a prediction?

    I predict that the sun is hot.

  198. PaV- What about junk DNA? Excellent question. What about it?

    The general sense here at UD seems to be that the intelligent design theory predicts that there will be no such thing as junk DNA. But I don’t understand how that follows from the theory. What part of the theory exactly that would compel that conclusion?

    If the theory says that the designer(s) wouldn’t put junk in the genome, isn’t that saying something about the designer? What evidence do we have to tell us what the designer(s) would or wouldn’t do?

  199. congregate:

    Based on ID principles, you would expect “junk-DNA” to have function, contrary to what was the consensus among Darinists.

    As to “junk” having no function, let’s remember that Darwinists thought that tonsils were junk, that the appendix was junk, etc. Then function was found.

  200. 200

    PaV said: Based on ID principles, you would expect “junk-DNA” to have function, contrary to what was the consensus among Darinists [the study of Samatha husbands?].

    But isn’t waste an inevitable by-product of any design endeavor we are familiar with? Isn’t there “junk-dna” for your computer lying around a lab somewhere in Silicon Valley? Would we expect human waste to have some crucial undiscovered function? OK I guess it does, but only in an indirect way.

  201. 201

    Also, what about previous revisions of software that are kept around even though they haven’t been used in years. In that case, its the opposite principle – not trashing something when it isn’t all that expensive to preserve.

  202. JunkYard: Also, what about previous revisions of software that are kept around even though they haven’t been used in years. In that case, its the opposite principle – not trashing something when it isn’t all that expensive to preserve.

    Interesting. As a software engineer, I don’t remember ever intentionally leaving junk code in my released programs. That would be a dangerous practice, in my opinion. Why would anyone want to leave unused code in an application?

  203. Interesting. As a software engineer, I don’t remember ever intentionally leaving junk code in my released programs. That would be a dangerous practice, in my opinion. Why would anyone want to leave unused code in an application?

    I don’t know about you, but in my attempts to write complex code, I certainly ended up with some routines here or there that in the end were not called up or even properly debugged.

  204. 204

    Mapou:

    Your program is full of junk, unless its absolutely optimal in terms of speed and space usage. But aside from that, I think all programs have a certain percentage of dead code, which is doing nothing but sitting in memory. So before release you make sure that every single subroutine is actually being referenced somewhere, and if it isn’t you yank it out. To what end?

  205. Junkyard, my code may be full of junk but not intentionally. It’s only because I am not that smart. Junk DNA is too obvious for an intelligent designer to overlook, in my opinion. Remember that we’re not talking about any designer here. If you can design and create complex life, I would say that you are a little bit smarter than average.

  206. 206

    That dead code may be completely obsolete, but not just random data. But if you have a statically allocated array of 100K and only 50K is ever used, then you will have a 50K long string of randomness in your actual code.

  207. 207

    Was the war against slavery a work of God? How messy was that process?

  208. Junkyard, my code may be full of junk but not intentionally. It’s only because I am not that smart. Junk DNA is too obvious for an intelligent designer to overlook, in my opinion.

    Does that mean you (and I) are not ‘intelligent designers’? How do you know how much smarter the intelligent designer of life as we know it was? That is exactly the point JunkyardTornado was making… you have to come up with very specific assumptions about the intelligent designer to conclude that there should or should not be non-functional DNA in organisms.

    Here your assumption appear to be: ‘designer is smarter than you, me and JunkyardTornado’ and ‘designer does not like junk’.

    Btw: what do you think does it mean that there are some organisms that are apparently full of junk DNA (e.g. humans) and others that contain virtually none (e.g. S. cerevisiae)?

  209. hrun0815: Here your assumption appear to be: ‘designer is smarter than you, me and JunkyardTornado’ and ‘designer does not like junk’.

    Absolutely. Was there ever any doubt? I don’t mean to be flippant but when was the last time you or I designed something even remotely as comnplex as a brain or a liver that worked?

  210. Absolutely. Was there ever any doubt? I don’t mean to be flippant but when was the last time you or I designed something even remotely as comnplex as a brain or a liver that worked?

    I don’t know when was the last time. Probably a couple of weeks ago. I failed.

    But that does not mean that there is necessarily a vaster power needed to design something that complex. For example, regular humans have designed chips that can greatly outperform brains at certain tasks. The complete distributed internet may have a similar level of complexity as the brain. Who knows. It’s hard to measure. But to me your assumptions are not self evident.

  211. PaV- What are the ID principles that lead us to expect that junk DNA would have a function?

  212. hrun0815: Btw: what do you think does it mean that there are some organisms that are apparently full of junk DNA (e.g. humans) and others that contain virtually none (e.g. S. cerevisiae)

    Well, I was hoping someone else would post a reply to your question since I’m not an expert in these matters. I can only repeat what I’ve been hearing lately, and it’s all over the place. Junk DNA is turning out not be junk after all. They apparently have essential regulatory functions. I guess a Darwinist’s junk is an IDer’s treasure. LOL.

  213. congregate: (211):

    Efficiency. Occam’s Razor.

  214. Most of the so called “junk DNA” may necessarily have to encode many levels of additional information (in addition to protein specifications in the “coding” DNA) in order to actually build higher multicellular organisms. If this is true, little or no true “junk DNA” would be a necessity of biological organization and would not be special predictions of either ID or Darwinism. But as it has been pointed out a number of times here, if most of the “junk” DNA is information intensive at many levels, RV + NS has been given further great difficulties in explaining it.

    Then why are there not another billion or more truly extraneous junk base pairs in addition to the present 3 billion in the genome? Maybe it gets too disadvantageous in cellular terms, like in the energy costs in chromosome duplication.

    Of course Darwinism has actually predicted the presence of a lot of true junk in the genome, but no problem since it can’t be falsified and one prediction we can be sure of is that a good Darwinian story will be concocted to explain the mostly absence of junk. Most likely something involving a selective advantage of efficiency in the cell cycle.

    No or little “junk DNA” would be predicted by ID assuming desire for efficiency or elegance are characteristics of the designer. But as I mentioned, little or no true junk in the genome may be a necessity not a choice.

  215. PaV-
    As I understand it Occam’s Razor is a general principle for choosing between alternatives, rather than a principle that derives from the idea that some things are too complicated to arise naturally. Can you clarify for me how it is an ID principle?

    As magnan suggests, efficiency would be an ID principle if desire for efficiency is a characteristic of the designer. But it’s hard to measure efficiency when you don’t know what all the factors to be taken into account are. A designed biological system might be efficient for using resources but inefficient for developing diversity. How do we measure efficiency in general? Do the standard examples of bad design represent inefficiencies that argue against design?

  216. congregate:

    Can you clarify for me how it is an ID principle?

    How does one clarify the obvious, pray tell?

    Only rascals seek evasion from truth through equivocation.

  217. PaV-
    Let me try to clarify what this rascal’s understanding is. As I understand it, Occam’s Razor (OR) is a method for choosing between two competing explanations. If two explanations are equally good at explaining some observation, OR says to go with the one that is the simplest. I don’t see that as an “ID Principle”, I think it is a standard scientific rule of thumb.

    You may say that Occam’s Razor says to pick ID over mainstream evolution, but I don’t think you can use OR to predict an absence of junk DNA under ID.

  218. congregate:

    This is likely my last response to you. You take a position to “efficiency” that is equivocal. You feel as though we need to know the designer in order to know whether the designer is efficient, or has that as a goal. We wouldn’t be talking about design and designers unless we already had experience of both. Your experience of design, I’m sure, makes it obvious that efficiency is a value. So, this can be simply presupposed. So, let’s not waste time on semantics.

  219. PaV-
    How can that be your last response, you haven’t responded yet?

    How is Occam’s Razor an ID principle?

    You take a position to “efficiency” that is unrealistically simplistic. What is the efficiency that a designer would value? A two door small car is more efficient for taking me to work; a pickup truck is more efficient for carrying large loads of building materials.

    Are art paintings “designed”? Are they all characterized by efficient use of materials?

    If ID predicts no junk DNA because junk DNA is inefficient, what does ID say about the recurrent laryngeal nerve, which goes from the brain to the throat looping around the aortic arch, adding about twenty feet of nerve fiber in a giraffe? That seems inefficient to me. Maybe there is a question for ID research, what is too inefficient to be produced by a designer?

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