Processes of Molecular Machines Continue To Amaze

Papers on biochemistry and biophysics vastly exceed all other topics in science. Major discoveries are being made about how these cellular factories work while evolutionary explanations are used as a passing reference or not mentioned at all which is quite refreshing!  These carefully  and very advanced built structures speak of design from a mind (God’s in particular) rather than an unthinking process.

Authors in a paper published in Structure

“DNA polymerases are spectacular molecular machines that can accurately copy genetic material with error rates on the order of 1 in 105 bases incorporated, not including the contributions of proofreading exonucleases.”

On the next paper, we find a pretty amazing  journey through several motions when transfer-RNAs and messenger-RNAs traverse the ribosome protein-assembly factory with their amino-acid cargos and genetic data readouts.

The paper reveals details on how the L1 stalks of the ribosome bend, rotate and uncouple – undergoing at least four distinct stalk positions while each tRNA ratchets through the assembly tunnel.  For example, “the L1 stalk domain closes and the 30S subunit undergoes a counterclockwise, ratchet-like rotation” with respect to another domain of the factory.

This is not simple.  “Subunit ratcheting is a complex set of motions that entails the remodeling of numerous bridging contacts found at the subunit interface that are involved in substrate positioning,” they said. What scientists have learned so far about molecular machines makes the type of chemistry we learned in school very inadequate for understanding the machinery of the cell. For example, interactions between molecules are not simply matters of matching electrons with protons.

Here is another recent discovery where a molecular machine can detect a stretching force when a load is applied…In a paper published in PNAS

“Some myosin-Is are proposed to act as force sensors, dynamically modulating their motile properties in response to changes in tension.”  Why do cells need force sensors?  “Tension sensing by myosin motors is important for numerous cellular processes, including control of force and energy utilization in contracting muscles, transport of cellular cargos, detection of auditory stimuli, and control of cell shape.”

The paper had little to say about evolution other than saying it just “evolved.” Biophysics is an area of great scientific study and also it’s where evolution is a useless explanation. On the other hand in Psalm 19:1, “The heavens declare the glory of God; and the firmament sheweth his handywork.” Do you really think evolution created proof reading of errors in the cell so it can survive?  Evolution requires flexibility in nature and simplicity, but we don’t observe this. Indeed nature shows it being engineered or designed by intelligence.

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26 thoughts on “Processes of Molecular Machines Continue To Amaze

  1. More examples of irreducible complexity. Supposedly this was all “demolished” by Judge John E. Jones III, former chairman of the Pennsylvania Liquor Control Board. Instead what we find is that the paper simply claims “it evolved”. The detailed evolutionary paths showing functional intermediate forms gradually building myosin motors which control energy and muscle force, “transport of cellular cargos, detection of auditory stimuli, and control of cell shape” are non existent.

  2. CbyD: “More examples of irreducible complexity. Supposedly this was all ‘demolished’ by Judge John E. Jones III, former chairman of the Pennsylvania Liquor Control Board.”

    No. It was demolished by a number of expert witnesses whose evidence could not be controverted ny any of the intelligent-design witnesses. Judge Jones admitted later that he went into the trial with an inclination toward the ID side.[1]

    The most laughable part was when Michael Behe was presented with 59 reviewed papers and books establishing evolutionary paths for the “irreduciably complex” adaptive immune system, and all he could asy was “It’s not good enough.”[2] he did not even attempt to controvert any of the references.

    An interesting story came out of the trial. Lauri Lebo was a local news reporter assigned to cover the Kitzmiller case. Her father owned a fundamentalist radio station in Dover, and the whole family were staunch biblical literalists. Lauri was so impressed with the evolutionary explanations of Kenneth Miller and Kevin Padian[3] that she rolled over entirely—even at the expense of her father’s enmity until his death several years later.[4]

    Exposure to actual evidence can do that. So never take off your dark glasses and earplugs.

    ==============
    [1] William Dembski rejoiced in Uncommon Descent about the choice of Jones to hear the trial—before the trial, of course. During the trial, he ran off just before his deposition, leaving his attorneys in the lurch.. After the trial, he changed his tune.

    [2] The original concept of irreducibble complexity—he called it “interlocking complexity”— was introduced in 1918 by Herman Muller, who proposed it as evidence for evolution. Had Behe done his research, instead of merelty plagiarizing Henry Morris, he would have seen the danger signals.

    [3] Judge Jones called it “the biology course that everyone wishes he could have taken.”

    [4] Her book, “The Devil in Dover,” concentrates on the effects of the trial on the people involved.

  3. In the Dover case, Judge Jones wrote, “We find that while ID arguments may be true, . . . ID is not science.” (p.64.). The Judge is wrong on operational science verses historical science. What evolutionists tried to refute about design or ID is they claim the debate deals with a supernatural origin because it has parts. A metaphysical approach which evolution theorists do without a supernatural conclusion. ID argues that a not-yet complete machine which have no function is therefore invisible to natural selection! In other words, non-functioning “machine parts” which haven’t been produced yet cannot be detected by Darwinian selection. Thats the difference between a “reduced” element vs irreducible complexity.

    On the other hand, evolutionists argue especially on subjects like protein transport… “Certainly, other simple systems that could serve as precursors to vesicular transport should be possible.” That statement is metaphysics not science. The judge ruled on the basis that he believed natural origins can only be science even though ID may be true to him. A similar statement is also found below…

    Dr. Scott Todd, of Kansas University speaks about this very thing in nature magazine, he states and I quote…”Even if all the data point to an intelligent designer, such an hypothesis is excluded from science because it is not naturalistic.”

    Again, that is a metaphysical statement not science…

  4. Science by legal decree.

    Evolution — the only scientific theory protected by law.

    Let’s ignore the irreducible complexity clearly indicated in the article posted here and continue to misrepresent Michael Behe’s views.

    ID argues that a not-yet complete machine which have no function is therefore invisible to natural selection!

    That is correct and should be obvious to anyone. 16 years after the publication of Darwin’s Black Box and Darwinists are still trying to convince us that molecular machines are built through mutations and natural selection. And they’re still trying to refute Michael Behe.

    Judge Jones – great defender of evolutionary theory. A very convincing case given by evolutionists, yet again!!!

  5. CbyD: “Science by legal decree.”

    No. The Kitzmiller opinion did not decide that evolution is a “protected” or even a correct theory, as you yourself noted. The judge only decided that intelligent design is religion,[1] not science. Then he applied the settled law (Lemon v. Kurtzman) to prohibit the teaching of religion as science in a public school.

    Four years later, the Discovery Institute is still trying to pick up some scraps from Kitamiller.[2] They, at least , consider it a major defeat. and put some effort into avoiding what was shaping up to be a repeat (Selman v. Cobb County).

    ================
    [1] Actually, that ID is a form of creationism, which everyone knows (Edwards v. Aguillard, McLean v. Arkansas, Assn. Christian Schools v. Stearns) is not science.

    [2] To me, as a lawyer with a technical background, it is comical to note that some of the arguments Casey Luskin makes to the faithful are absent from the two law-review articles he wrote. The faithful may swallow them whole, but he knows that lawyers would just laugh. And some of the arguments made to the general public are never made when the DI tries to impress scientists. The uneducated public may be impressed, but scientists would just laugh. Different strokes for different folks, as they say.

  6. Michael in ipsissima verba: “The Judge is wrong on operational science verses [sic] historical science.

    Well, Michael, Judge Jones did not define, or even mention,”operational” science or “historical” science.” So it’s moot whether he was wrong with respect to them. He only decided that intelligent design is a subset of creationism, which is religion under previous decisions.

    As you[1] and judge Jones noted, “truth” is not a prt of the decision.

    ==================
    [1] Which I wrongly attributed to CbyD. Should I apologize to both of you, or just to him? Think about the implications before you answer.

  7. Michael in i.v.: ‘Dr. Scott Todd, of Kansas University speaks about this very thing in nature magazine, he states and I quote…”

    As you well know, quotes from creationists are not worth the electrons they’re written on, without a full citation.

  8. No need to apologize to me, Olorin (“implications” or not). You did already say ‘sorry’ and that is appreciated.

    As for the argument that “Judge Jones did not decide what is or isn’t science, he only said that ID is not science” … it seems like a stretch to me.

    But I conclude also that this issue is bigger than any of us here. I also think that Judge Jones is a bit player who will end up as an embarrassment over time. The worst strategy pro-evolutionists can take is to hold him up as a hero or even as an authority. But why should I give my opponents good advice? :-)

    All the best to you and Michael.

  9. CbyD, Judge Jones will probably never have another case like Kitzmiller in his whole career, and his career may well end at the steps of DC SD PA.

    So he’s a bit player. Not many of us get to be more than that. But he did his bit well. I’ve been analyzing judicial opinions for almost half a century, and that one is lucidly written. He gave each side as much time and as many witnesses as they wished. 40 days is a huge trial for this kind of case; Jones must have known it would have an impact far beyond its precedentail value. And it has.

    Embarrassment? I think not. For the reasons above.

    Before Kitzmiller, Bill Dembski loudly demanded to confront “evolutionists” in court, with the ability to cross-examine them and demolish their positions. He had his chance in Dover, but the demolishment by cross-exam went the other way. And Dembski himself absquatulated when faced with it. (As Thaxton did in the Aguillard case.)

    Since Kitzmiller, the DI has sought to avoid confrontations in court. Whether that’s boon or boondoggle for either camp remains to be seen.

    Charis kai eirene

  10. Michael’s source: “This is not simple….. . What scientists have learned so far about molecular machines makes the type of chemistry we learned in school very inadequate for understanding the machinery of the cell. For example, interactions between molecules are not simply matters of matching electrons with protons.”

    And the more we understand about how it works and how it came to be, the more mind-bogglingly stupendous it seems.

    Unfortunately, those who believe that it came about fully formed as an after-dinner magic show are blinded to the true awesomeness of it all.

    Understanding, not ignorance, brings appreciation..

  11. Michael’s source: “Biophysics is an area of great scientific study and also it’s where evolution is a useless explanation. On the other hand in Psalm 19:1, “The heavens declare the glory of God; and the firmament sheweth his handywork.””

    In the past few months, evolutionary research has led to a new class of “taste modulators” that reduce the need for sugar and artificial sweeteners. Evolution of the 4-chambered heart has led to an understanding of the cause of many infant heart defects. Investigations into the origin of multicellularity has led to a new class of antibiotics—ones which may avoid the problem of drug resistance altogether.

    When you find out what scientific advances Psalm 19:1 has led to in the past 2,500 years, please let us all in on the secret.

  12. And the more we understand about how it works and how it came to be, the more mind-bogglingly stupendous it seems.

    Unfortunately, those who believe that it came about fully formed as an after-dinner magic show are blinded to the true awesomeness of it all.

    Understanding, not ignorance, brings appreciation..

    While I agree in concept and I like your words, I think this contradicts and confuses your perspective and worldview.

    If it seems “mind-bogglingly stupendous” then that is different than something which is ordinary, the usual, expected, predicted … way of things. (If it was predicted, then there should be no surprise. But it wasn’t predicted — thus it is mind-boggling. If it wasn’t predicted, then what does that say about the theory?)

    If molecular machines were created “fully formed” (side note — most ID researchers do not argue that position) then that would not be as truely awesome as gravity causing rocks to roll down a hill?

    The more we understand, the more we will express our appreciation to the power of gravity and thank it for what it does?

    So, I think you’ve walked into a conundrum. I can’t follow the reasoning, myself. It’s a contradiction, as I see it.

    The logical, consistent, evolutionary-materialist response would be like this …

    “Evolution happens. So what. Those might look like complex, functional, highly-ordered and precise machines but they’re the products of known natural laws. Mutations can create these things all the time. Rain falls from the clouds to the earth. Gravity does that. Myosin motors sense and respond to forces and dynamically regulate tension, transport cellular cargos, detect auditory stimuli, and control cell shape. Mutations just do that. Nothing to be surprised at here at all.”

    So the good thing, as I see it, is that you express the humane (as opposed to the nihilistic) insight that these motors are, indeed, awesome and we should respond with appreciation. But I think you should connect those insights to the bigger picture. Why mindboggling if predicted? Why awesome if mundane and ordinary? Where do we direct our appreciation?

    I will add that we are very far from understanding the origins of these molecular machines. The Darwinian view simply doesn’t work. There are no evolutionary paths with intermediate forms that explain these structures.

    Thus we have extended evolutionary synthesis and non-Darwinian evolution (self-organization) filling the gap. And this will be very much what front-loaded ID theory has been arguing for the past couple of decades.

  13. CbyD, our perspectives must truly differ. My take on the creationist viewpoint seems to be the same as your take on the naturalistic one.

    CbyD fakes a naturalistic perspective: ““Evolution happens. So what. Those might look like complex, functional, highly-ordered and precise machines but they’re the products of known natural laws. Mutations can create these things all the time. Rain falls from the clouds to the earth. Gravity does that. Myosin motors sense and respond to forces and dynamically regulate tension, transport cellular cargos, detect auditory stimuli, and control cell shape. Mutations just do that. Nothing to be surprised at here at all.”

    Olorin takes the naturalistic perspective: “I wonder how evolution could have produced taste buds according to the current theory that each unit senses all the taste sensations. It couldn’t. Maybe the theory is wrong. Let’s go find out. Wow! If you dig down to the cell level, each cell does do a differwent tatse. A new understanding! What can I do with that understanding? Suppose I could find compounds that enhance each one separately, to ‘modulate’ the tastes that natural foods produce. Isn’t that exciting!”[1]

    Or, as one researcher put it: “The most exciting words in zcience are not ‘I’ve found it!’ but rather, ‘Hm. That’s strange….'” Science by definition is not “ordinary, the usual, expected, predicted … way of things.” Confirmation of a prediction is comforting, but certainly not awesome.

    CbyD takes the creationist perspective: “these motors are, indeed, awesome and we should respond with appreciation.”

    Olorin fakes a creationist perspective:
    Olorin: “The sky is very beautiful tonight.
    CbyD: “Yes. God made it; isn’t it awesome?”
    Olorin: “But why is it blue, not green or brindled?
    CbyD: “Because God made it that way,”
    Olorin: “Why did God make it that way, and not some other way?”
    CbyD: “Because that was God’s will.”

    Now THAT is boring. Beautiful, perhaps. Awesome, no.

    So, CbyD, I think you have it entirely backward. True awe comes from understanding, not from gazing at something with “appreciation.”

    I read the Bible the same way. It’s not enough to read the words and “appreciate” them in a literal way. I study books and take courses on interpretation, philosophy, history, archeology to try to winkle out the deeper meanings, to gain an understanding.[2] Why did John raise Lazarus at the end of Jesus’ ministry, rather than near the beginning, as the synoptics do? A clear literal conflict. But there was a reason. A reason that you will never know by mere “appreciation” of the words, but that elicits awe when understood.

    I’m being hard on you. On purpose. I want you to consider another viewpoint, even if you do not adopt it.

    And now I’m off to continue trekking through Stepehn Meyer’s “Signature in the Cell.” What? You thought I only read books that affirm evolution?

    =============

    [1] This example is the story of Charles Zuker, at U. Cal. San Diego (Scientific American, Aug. 2008, pp.96-99.

    [2] Historians consider biblical literalism a form of the “Whiggism fallacy.” Whiggists see words only from the perspective of the milieu in which they live, and not from the point of view of the original writers and readers.

    Here’s a small example: The rain falls upon the just and upon the unjust.” What does that mean?

  14. CbyD, our perspectives must truly differ.

    Yes, I think so. My reply was for Upson Downes and perhaps in your perspective you thought it was directed to you. :-)

    In any case, I have a chance to read your thoughts about this matter now.

    I notice that you decided to fabricate my thoughts (putting words in my mouth?) and pretend that you know what I would say in a dialogue.

    I’d call that very boring — certainly, when you take both parts of the discussion there’s not much value in my giving a response.

    I’m glad to consider another viewpoint, but I don’t think you addressed my ideas sufficiently.

    1st — the theory requires predictions. The theory is supported when the predictions come true. It is weakened when we are surprised (mind-boggled) with the results.

    2nd — You introduce God and your approach to the Bible for some unexplained reason. I will gladly review your theological concepts if you’d like to direct me to a site where I can review them. Other than that, it’s completely irrelevant because I said nothing about the Bible, Christianity or Judiasm.

    3rd — You argue as if I said that understanding does not contribute to appreciation. But I didn’t say that, so there was no reason for that argument. More importantly — its the fact that you guys (unless you’re the same) don’t understand the origin and development of molecular machines that you call it “mind-boggling”. So, perhaps a bit of discussion on what that term means would be of interest. It’s mind-boggling because of the profound complexity and order that we see — and again, science does not understand it. It’s a mystery how it performs these functions. There are no detailed evolutionary paths given for its origin and development (we only just discovered what these things do — claims of having an understanding of their evolutionary paths are simply absurd).

    You’ll see much better argumentation than this in Signature in the Cell, and I’m glad you’re reading that.

    Best regards

  15. Olorin – I was hasty with that reply and a bit snippy with some of the comments also. Your comments deserved a better response – sorry.
    I’ll just look at one point that I missed:

    Here’s a small example: The rain falls upon the just and upon the unjust.” What does that mean?

    I guess there could be come kind of literalist interpretation (and literalism is a method of interpretation, in spite of the fact that literalists claim that they are not interpreting) which would render the quote meaningless. So, I’m not sure why you picked that.

    I would offer, however, from an evolutionary perspective the quote should be meaningless.

    When citing the “just and the unjust” this proposes that there are these two classifications — or more simply, that there is “justice” and there are people who live justly.
    But evolution renders that meaningless. Nature does not command or forbid any human behavior. Human beings, as an evolutionary development from material nature (matter and energy) are not “just” or “unjust” — they’re just beings evolving over time.

    So, this quote declares that there are just and unjust — and Jesus’ hearers knew what he was talking about.

    I’m interested in your view of that quote — or what you were looking for there.

    I’ll also grant one score for your side also regarding the term “appreciation”. It could be used merely to mean “respect”. In that case, we can respect a challenge when we see it. In another meaning, appreciation refers to some thanks to be given. So, using the first term renders my point wrong or meaningless.

    But I maintain that the universe elicits our awe because it is “stupendously mind-boggling”. It is not that because we understand it but because we don’t (and probably never will).

    At the same time, our understanding of trivial things could cause us to lose any appreciation for them we might have had.

    Again, thanks for a more open-minded response than I expected — to such a degree that I was replying to a stereotype vs what you actually said!

  16. First, CbyD, ytou probably realize by now that Upson Diownes is a Soc Puppette for Olorin.

    Here’s one sentence that perhaps expresses best our different perspectives:

    CbyD: “But I maintain that the universe elicits our awe because it is “stupendously mind-boggling”. It is not that because we understand it but because we don’t (and probably never will).”

    For us (Olorin, Upson Downes, and Socrates Puppette), the universe is stupendously mind-boggling only if there is at least a chance that we can understand it. You find awe in unsolvable mystery, which I find not awesome at all. The awe is that God lets us figure it out.

    As to the dialogs, notice that your dialog on creation & mine on science were called “takes,” while mine on creation & yours on science were “fakes.” Also remember that Galileo used the dialog format to present his arguments: Simplicio and Profundo..

    CbyD: “1st — the theory requires predictions. The theory is supported when the predictions come true. It is weakened when we are surprised (mind-boggled) with the results.”

    Unlike, say, the Bible, a scientific theory is not a static, unchanging entity–it can be extended and modified with new data. (By definition, a theory exceeds the data.) Theory says that humans and chimpanzees are descended from a common ancestor. There is all kinds of evidence for this, including seemingly contrary evidence.

    For example, humans and chimps have different numbers of chromosomes, an unexpected finding which weakens the hypothesis of common descent. Is this the ultima thule? No. We look deeper. And we find that human chromosome 2 has three telomeres and two separate centromeres–that is, that it is the result of a fusion between two separate chromosomes.[1] There was no other reason to suspect this. In this case, an unexpected result actually strengthened the evolutionary theory.

    Ardi provides another type of example. The Ardipithecus ramidus fossil was surprising. At more than 4My, paleontologists had expected a knuckle-walking ancestor, more like an ape Although Ardi presented a prehensile toe still adapted for climbing, she had a fully upright stance. This was unexpected—it modifies the details, yet it does not weaken the hypothesis of common descent. Perhaps there was no knuckle-walking stage at all in the human line–perhaps it was the ape line that evolved this gait, and the human line did not participate. So we have an unexpected finding that does not affect the basic theory—AND which provokes further research and understanding.

    (Forget about the Bible stuff. the point was that awe arises from understanding, not mystery, even in religious matters.)[2]

    As to understanding and appreciation, that was not the antithesis. I can appreciate things that I will probably never understand. But awe is reserved for the epiphany that comes with digging into ever deeper levels of understanding. Bacteria infect our cells. Appreciation. Some do it by building a hypodermic needle and squirting up to 80 different toxins into their victim. Awe. Some of the toxins not only destroy the victims, they confuse the body’s defenses. Deeper understanding; more awe. Many bacteria don’t infect at all until their number is great enough to overwhelm the victim in one coordinated attack. More understanding, more awe. How do they do this? By “quorum sensing”; they actually signal each other and sound the charge.[2.5] Even deeper understanding, and even more awe. And so it goes on, saecula saeculorum.

    CbyD: “It’s a mystery how it performs these functions. There are no detailed evolutionary paths given for its origin and developmentIt’s a mystery how it performs these functions. There are no detailed evolutionary paths given for its origin and development…”

    This is pure God-of-the-gaps argument. What happens as the gaps are filled? Two of Michael Behe’s poster children at the Kitzmiller trial were the blood-clotting mechanism and the adaptive immune system. They prove intelligent design, he averred, because there are no detailed evolutionary paths. But he was shown to be wrong. He’s still barely breathing on the bacterial flagellum, because we only have some of the paths, but research continues.[3] He said (The Edge of Evolution) that malaria couldn’t have evolved because of the low probabilities of multiple coordinated mutations. But these were later shown to be unecessary for evolution to occur.

    Another major issue in the last point. Creationists insist upon ever more detailed “evolutionary paths”—that scientists show how something evolved before accepting its evolution. And yet, they provide absolutely no “creation paths” to show how anything at all might have been created—or even what was created. Was it by breathing raw “essence of information” into inorganic chamicals? Was it by hands on microassembly of atoms into DNA? Was all genetic ingformation front-loaded into the first organisms, or were there infusions of creation along the way? How can you tell? The Bible never mentions bacteria—were they created, or did they evolve?[4]

    A theory has no use if it does not allow us to see how a phenomenon occurred–it doesn’t explain anything. It doesn’t make any predictions as to how to control the phenomenon. Scientists are interested in creating new life forms iin the laboratory, for a number of purposes. So, tell me how creation theory informs us how to go about this? Yet evolutionary theory tells us how to fight drug resistance, how to breed better salmon, how to fix certain infant heart defects–because the theory tellls us how their evolution occurred. Special creation, on th other hand, is stillborn as science; it offers no understanding whatsoever, no “how” that can predict future results or form the basis for beneficial applicaions.

    This is actually my main cavil with creationism. Not that it’s wrong, but that it is vacuous, empty, barren, feckless.

    Enough ramble. I am about 2/3 of the way through “Signature.” It takes a long time, because there is something either wrong or misleading on almost every page. Meyer introduces “biological information,” never defines it, then says that an intelligence is necessary to create it–without ever even speculating upon the nature of the intelligence, its attributes, characteristics, or limitations. Here’s another form of the same argument: Certain fundamental particles have “charm.” Personality is necessary to create charm. Therefore, people created fundamental particles.

    One of his basic claims is that DNA represents an arbitrary code for specifiying amino acids. He asserts many times that there is absolutely no physico-chemical basis for the DNA code. Yet, last October, a paper demonstrated chemical affinities, based upon confiurations and charge distributions, for tying 15 of the 20 amino acids with their respective DNA codes.[5]

    This is the problem with this and all other God-of-the-gaps argumernts. The gaps get filled in. Then you have to say, as Behe does, well that’s not enough details, or the evidence is not undisputed–or, I just don’t ‘believe’ it.. At the same time, creationists offer no explanations at all, and no evidence. If evolutionary scientists must propose ever more detailed explanations, why do creationists not have to demonstrate anything?

    As the Kitzmiller trial demonstrated 4 years ago, creationism is entirely faith-based, and is not science.

    ==========

    [1] And the genes in the fused human chromosome correspond almost letter for letter with the genes in two corresponding chimp chromosomes.

    [2] The “rain” example was meant to illustrate different historical perspectives. We today assume that the rain falling on the just and the unjust means that bad things can happen to good people—that is, that rain is a bad thing. In the biblical conterxt, however, it means that good things can happen to bad people—when you live in a desert, rain is a good thing.

    [2.5] Quorum sensing was discovered by evolutionary research into the origins of multicellularity. As to applications, it offers a way to fight infections in a way that the bugs can’t avoid by evolving drug resistance—because the treatment does not kill them, and thus offers no selection opportunities.

    [3] Actually of the 40 proteins that Behe claims form the irreducible core of the flagellum, only two (2) are both unique to that structure and necessary to its function. So maybe you might even say we are 38/40ths of the way to the goal.

    [4] Ironically, the Bible requires more evolution thatn Darwin does. If dinosaurs, say, were created at the same time as everything else in a couple of days, and if they were herbivorous until the Fall, then they had to evolve (remember, they had already been “created”) carnivorous dentition, stronger jaws, great running speed, hunting behaviors, and hundreds of other biological features in a few days, weeks, or years. Evolutionists find this humorous.

    [5] The others are still under investigation, and it is within acceptable probability that a couple of them could in fact be randomly associated.

  17. Olorin — thanks for your detailed reply. Personally, I think you’re building your worldview more on the speculative than on the certainty that you seem to project (about evolutionary conclusions). Regarding Michael Behe, he offered a view of a few of the irreducibly complex features in nature — not by any means, all of them. This story posted by Michael merely offers another one (which Dr. Behe has not addressed, to my knowledge).
    We have a gap – this I think we agree on.
    For you, it’s “evolution of the gap” (or a better term for that). This is speculative and not based on the evidence. It assumes that science can solve every mystery of the universe. But as I see it, the gaps are getting bigger not smaller.
    Darwin thought the gaps would be filled by the finding of more fossils.
    We found more fossils and the gaps (lack of knoweldge, contradictory information, unsolved mysteries) got bigger.

  18. CbyD: “But as I see it, the gaps are getting bigger not smaller.”

    Faith can be based upon unseen certitude, but science bows to the evidence.

    So it is legitimate to ask what actual evidence condemns evolution, or which particular gaps may be getting bigger. J.B.S. Haldane once said that finding a rabbit in a precambrian fossil bed might do the trick. Also remember that ignorance is not evidence, unexpected results are not evidence, finding other mechanisms besides natural selection is not evidence against evolution.

    Then, since disproving Theory A does not confirm Theory B, we need to know what positive evidence supports special creation, biblical or otherwise. Scientists observe evolution taking place every day—small increments,but that’s how evolution works. Who has ever observed new organisms being created—even small ones? Bacteria, for example. Who has ever observed any mechanism that could possiby power creation of new species? As, say, we observe new species develop by allopatry over a few decades? Who has written a simuation for any possible pathway by which any lifeform was or could have been created? As we model evolution of proteins from their living descendants. (Using, by the way, exactly the same technique that courts employ to prove paternity.)

    Creationists daily accuse scientists of telling just-so stories to explain evolution, rather than providing hard evidence. Yet, creationists can’t even manage that, much less provide positive evidence.

    By avoiding the primary literature, you may easily convince yourself that the science of evolution grows weaker. Some people say that ignorance is bliss. But ask yourself in the recesses of your reasoning mind whether 484,000 biological researchers are deluded—including the ones you trust to develop new drugs for you. Ask yourself how 1,850 reviewed papers per year could misinterpret their experimental results so grossly. How computer-based simulations could lead to unexpected predictions that are later confirmed.

    Best of all, study up on what evolution actually is, rather than what creationists say it is. Read Neil Shubin’s “Your Inner Fish” and Sean B. Carroll’s “The Making of the Fittest,” and, yes, even arch-atheist Richard Dawkins’ “The Ancestor’s Tale” and “The Greatest Show on Earth. Then ask yourself why God could not have unfolded the grandeur of life over three billion years, rather than having to break all His own laws in order to accomplish His purposes.

    You are certainly welcome to your religious beliefs. But the subject here iis science. You need not take my word for it. A number of court cases have decided that creationism—including the teratoma called intelligent design—is not science. A number of large Christian denominations find no theological problem with evolution.

    Are there two realities, God and science? Or just one, God working through science?

    evidence/facts

  19. Sorry. An evil twin from another thread hijacked my good name. Read “Olorin” for “Upson Downes” above.

    Mahalo,

    ==Beckan Forth

  20. CbyD: “This story posted by Michael merely offers another one (which Dr. Behe has not addressed, to my knowledge). We have a gap – this I think we agree on.”

    Sorry, we still do not agree. Michael has presented a couple of interesting cellular functions which are just now being winkled out. Would you no agree that finding out where something came from must await knowledge of exactly what it is? So, now that we know what is going on, we can look for similar structures, and plug in the evolutionary paradigm to find out where they came from.

    When you use Behe’s irreducible complexity as a guidon for design, please remember that this concept actually dates back almost a century. In 1918, Hermann Mueller wrote a paper on what he called “interlocking complexity,” which has the same definition as irreducible complexity. His paper argued that this concept is actually evidence for evolution, not against it. That living systems would tend to evolve toward this state.

    A simple example. A biological function uses molecules A, B, C, and D—any three of which can perform function F. This system is obviously not irreducible. The D mutates so that it can no longer participate. This leaves A, B, and C, which, by definition, now do form an irreducible system. Lest you think this is a contrived example, it parallels the story of the 12-factor blood-clotting cascade. Dolphins manage on 7 factors. Some primitive worms have none at all. The early evolution of this system occurred when organisms had much lower blood pressures, and only a few factors were sufficient to stop fatal hemorrhages. As pressures rose with increased metabolism, more factors appeared. Where did they come from? The factors are very much alike. They formed mostly from mutated duplications of other factors.

    Even today, the human clotting cascade, one of Behe’s favorites, is not quite irreducible. There are several grades of hemophilia. One of the 12 factors may be missing. Mild hemophilia. A fatal form does not ensue until 3 or 4 have become nonfunctional. These are experimental results; you can check them out—as Behe was forced to do in Dover.

    Michael: “Major discoveries are being made about how these cellular factories work while evolutionary explanations are used as a passing reference or not mentioned at all which is quite refreshing!”

    Michael failed to mention, of course, that creation was not referenced or mentioned at all. But why should it be? It has never contributed anything to scientific progress. Once again, Michael spins hope from gossamer wishes.

  21. A couple of quick points before I have to run …

    So it is legitimate to ask what actual evidence condemns evolution, or which particular gaps may be getting bigger.

    The easiest evidence to provide is the revision of evolutionary theory that occurs continually. Clearly, if the gaps were getting smaller, the theory would not need radical change, which it does, in fact. If you’re suggesting that the move from fossil evidence alone to the complexity of microbiological development did not increase knowledge gaps, then it would be good to consult the “source material” on this.

    Then, since disproving Theory A does not confirm Theory B, we need to know what positive evidence supports special creation, biblical or otherwise.

    I think you’re on the right path here. Disproving Theory A confirms that Theory A has been disproven. If we want to start the conversation with an agreement there, then we can move forward to other considerations. But the fact that we can’t and won’t reach that agreement prevents us from considering alternatives (since Theory A is believed to answer any and all questions already). So yes — let’s disprove Theory A. Otherwise, why bother with an alternative?

    Creationists daily accuse scientists of telling just-so stories to explain evolution, rather than providing hard evidence. Yet, creationists can’t even manage that, much less provide positive evidence.

    As above — I think this is a mistake in your strategy to defend neo-Darwinian evolution (and your cite of Dawkins as an authority leads me to conclude that you support NDE). Here, you’re saying that hard-science has been accused of storytelling. But look — people who propose Bible based solutions do also. Therefore … ??? It’s not really hard-science? Scientists need some story-telling also? Scientific claims are best validated by observing what Creationists do? Ok, lots of problems here. Again, I wouldn’t advise turning your sights away from evolution to start demanding things of Creationism, unless you want the two measured on the same scale somehow.

    By avoiding the primary literature, you may easily convince yourself that the science of evolution grows weaker.

    Well, like you with your reading of Stephen Meyer’s book — I consult the primary literature also. The cutting-edge of evolutionary thought today is away from the Neo-Darwinian synthesis of the Dawkins variety. It simply doesn’t work. Self-organization, convergence, HGT, “latent evolutionary potential” … this is all of the radical break with Darwin and natural selection. Why? Because the theory cannot explain what really happens. The gaps are insurmountable for the theory as it stands. The source literature supports that.

    In any case — sorry I skipped over many of your points. I agree with some and not with others. I’ve learned some new things from your insights also, and I appreciate that.

  22. Let’s clear up one matter before we start. The choice is not between creationism and neo-Darwinism. Evidence that natural selection is not sufficient to have powered the evolution from goo to you has been known by scientists for a long time. Neutral drift is not a Darwinian mechanism—but is accepted universally. Epigenetic phenomena (such as DNA methylation) is Lamarckian, the main early competitor to Darwinism. So disproving NDE does not disprove evolution.

    Gaps. Creationists measure gas differently from scientists.

    30 years ago, a 40MY old fossil land precursor of a whale was found.[1] How did it become aquatic? A huge gap. Since then, a dozen fossils have documented phases of the transition—including a transition from head-first birth (land animals) to breech first (aquatic mammals). Scientists say that the gap has been narrowed. Creationists say, no, now we have ELEVEN gaps! A counting difference.

    60 years ago, the basis of heredity was unknown. A huge gap. Watson & Crick showed how DNA specifies and regulates proteins. Scientists say that the gap has been narrowed. Creationists say, no, now you have to explain all the complex interactions of the genes (the proteome)–that the number of unknowns has increased, not decreased. A levels difference.

    100 years ago, evolution was based entirely upon natural and sexual selection. Then neutral drift was introduced, as a non-Darwinian mechanism. Scientists say that the added model reduces the knowledge gap. But creationists say, no, a completion gap has yawned open. Another difference.

    There are probably other types of gap as well. Scientists tend to measure gaps by the total amount of knowledge amassed; since that is (mostly) cumulative, the gaps decrease. Creationists measure gaps by the total number of unexplained facts between the explained ones. Since an explanatory model that explains all facts in the universe would necessarily be as large as the universe itself, the gaps increase. I’ll take my measure, I guess you;ll take yours.[2]

    CbyD: “The easiest evidence to provide is the revision of evolutionary theory that occurs continually. Clearly, if the gaps were getting smaller, the theory would not need radical change, which it does, in fact.”

    First, we are talking about evolution, not evolutionary theory. Evolution is the fact (vel non) that all living organisms descend from one or a few ancestors.[3] This is a broad statement. The argument is of a type known in rhetoric as “convergent.”[4] This is the type of argument employed in legal proceedings, where we speak of “the weight of the evidence.” The more evidence there is, the better the case–in court, motive, opportunity, etc are types of evidence; they cumulate to prove the case.[5] In evolution, we have genetic evidence, fossil evidence, biogeographic evidence, cladistic evidence, radiometric evidence—all of these are independent of each other, therefore more reliable.

    We have predictive evidence. The location and timing of the whale fossils was predicted; we didn’t just dig randomly in the dirt. The (surprising!) fusion of human chromosome 2 was predicted, not merely observed. This is an example where a supposed refutation of ancestry actually confirmed evolution.

    There is also the question of level confusion. Finding that Ardi had unexpectedly bypassed the knuckle-walking gait of apes refutes human/ape common ancestry as much as the refusal of your car start one morning refutes the theory of internal-combustion engines. To the extent you do not understand that, you do not understand the nature of science.

    There is no single “theory of evolution.” In two respects. A theory is a model or mechanism that explains a number of facts.

    First, a single theory need not explain all the facts. Darwinian selection does not explain neutral drift. Epigenetics does not explain the DNA code. Disproving group selection,[6] entirely, for example, does not disprove evolution.

    Second, theories operate at different levels. Creationists trumpeted that the discovery of horizontal gene transfer is evidence against evolution in toto because it overthrew a current theory of bacterial heredity. HGT is a theory on a more detailed level from the overall theory of, say, natural selection.

    Therefore, falsifying one theory of evolution does not falsify evolution.as such.[7]

    CbyD: “But the fact that we can’t and won’t reach that agreement prevents us from considering alternatives (since Theory A is believed to answer any and all questions already):

    Sorry, that’s a cop-out. If it were true, heliocentrism could never have got off the ground (so to speak), because Ptolemaic theory did explain the motions of the heavenly bodies—well enough to predict eclipses hundreds of years in advance. Copernicus won because his theory is more parsimonious–it did not explain more facts until much later.[8] As noted above, theories are like a legal proceeding—weight of the evidence. Both sides come up with a “theory of the case”—wht actually happened, and what legal principles are relevant? Then each side simultaneously gaters evidence for its theory; the trial court then decides who has the bettr evidence.

    CbyD: “Well, like you with your reading of Stephen Meyer’s book — I consult the primary literature also.”

    I consult what “primary” creationist literature there is—and find it totally unconvincing. First because it does not follow the scientific process, and second because its contentions are unsupported by evidence. If you doubt this, look up my recent detailed critique of Andrew Snelling’s ARJ paper on this blog.[9] I think I understand the creationist literature.

    In addition, I have worked daily with research scientists for almost a half century. As a patent attorney, my job is to drink in a number of new technologies to the limits of current knowledge, and understand it sufficiently well to persuade an examiner that it is functional, novel, and unobvious over all previous wok. The technologies covered have ranged from astronomy to zoology. For the past few years, I have chaired a committee on bioinformatics, and have given lectures to university faculties in computer science and biotechnology. This is by way of forestalling an argument that I don’t understand the operation, theories, or literature of science.[10]

    A whole other subject waits in the wings: why creationism is pernicious to science. But the hour is late, even here in the Islands.

    Once again—your beliefs are perfectly valid as religion. I only argue that creationism is not good science.

    ===========

    [1] How do we know what the fossil precurese? Whales have a unique ear structure, not found in any other lineage.

    [2] Meanwhile, how many “gaps” does creationism have? Creationists say none, because “God did it” explains every fact in the entire universe. Scientists would say an infinite number, because it increases useful understanding of nothng at all.

    [3] As we type, at least one group of evolutionary scientists are in the field searching for living organism that might not be descended from the ones we know about. Fact.

    [4] A opposed to “serial” or “parallel.

    [5] Remember that even eye-witness testimony is not always conclusive—eye-witnesses are notoriously unreliable.

    [6] A current bone of contention—see David Sloan Wilson’s recent blog posts.

    [7] I’ve just finished a very interesting book, “The Foundations of Complex-System Theories in Economics, Evolutionary Biology, and Statistical Physics.” Because the entire subject was then (1998) new, Sunny Auyang (a theoretical physicist) spends a great deal of time explaining the nature of scientific theories in general.

    [8] In fact, a huge gap remained for two and a half centuries. If heliocentrism is correct, we must observe parallax of the stars at different points in the earth’s orbit. Yet the parallax was measured at 0.000000 seconds of arc until 1859! Did this cause anyone to doubt heliocentrism? Only biblical creationists, who clung to belief in a flat earth through the 1920s and even beyond. (You can check it out; see “Flat Earth: The History of an Infamous Idea,” Garwood, 2008 )

    [9] “2009 Represented An Outstanding Year For Creationism,” 12/31/09, Olorin comments at 1/11/10 and 1/13/10.

    [10] Ironic but true. Very few research scientists understand the nature of a scientific theory. Their noses are to close to the subject matter. Ms. Auyang (above) is a notable exception. (If you’d like to read up on complex systems per se, try the more recent book “Complex Systems: A Guided Tour.”

  23. Let’s clear up one matter before we start. The choice is not between creationism and neo-Darwinism.

    Some might call this “moving the goalposts”. If neo-Darwinism is insufficient as an explanation (for what it claimed — “all of the variation found in nature”), then it has been refuted – falsified. Period. It’s not what it claimed it was. All of the rhetoric notwithstanding, we’ve reached a milestone. Critics of NDE, Creationist or not, have been proven correct. “That” particular theory (which was claimed as the explanation for the development of all of nature) is not sufficient.

    Sure, this is the scientific process, but my interest is in watching the reactions and attempts to cover-up this problem. NDE as a theory was claimed to have the highest degree of certainty. We learn later that it could be almost entirely discarded. The claims of “certainty” do not decrease with the introduction of new concepts which replace a flawed idea. As a result of what I observe from the scientific community, I can now regard various claims from evolutionists with a greater degree of distrust and suspicion.

    Evidence that natural selection is not sufficient to have powered the evolution from goo to you has been known by scientists for a long time. Neutral drift is not a Darwinian mechanism—but is accepted universally. Epigenetic phenomena (such as DNA methylation) is Lamarckian, the main early competitor to Darwinism. So disproving NDE does not disprove evolution.

    Gaps. Creationists measure gas differently from scientists.

    I thought that was a good explanation. I thought your conclusion was good also — you have your view of the gaps and I have mine. We agree that there are gaps. Whether they are growing smaller or larger is difficult to measure precisely and it depends on what we’re measuring them against (e.g. “any increase in knowledge necessarily decreases the overall knoweldge gap”).

    First, we are talking about evolution, not evolutionary theory. Evolution is the fact (vel non) that all living organisms descend from one or a few ancestors.[3] This is a broad statement.

    Ok, again with the goalposts — or perhaps, just a subtle shift of the topic? Ok, if the discussion is merely and strictly about “evolution” then that is difficult without some kind of theory. But even still … the fact that you provide is, as you say, a “broad statement”. We moved in recent years from “a common ancestor” to”a few ancestors”. From my perspective, I don’t think this particular “fact” has stopped evolving even to this point. But if we accept it as given, as many ID-supporters do (and are therefore accused of moving the goalposts themselves), then the problem is how it happened — the mechanisms and processes. Common descent cannot be differentiated from “Common Design”.

    There is also the question of level confusion. Finding that Ardi had unexpectedly bypassed the knuckle-walking gait of apes refutes human/ape common ancestry as much as the refusal of your car start one morning refutes the theory of internal-combustion engines.

    Aside from the fact that some prominent evolutionary-biologists believe that supposed (long-standing, “irrefutable”) fact that humans descended from an chimp-like ancestor has already been refuted — what this evidence does is open up more questions (e.g. more gaps) insteat of closing them. One thing was predicted. A theory should explain all of the evidence that will appear in the future. Instead, the evidence conflicted with the claim. Thus — the theory has not been refuted?

    I have an “addition theory”. I predict that 5 cars +8 cars equals 15 cars. We seek to validate that with empirical evidence and actually add 5 cars to 8. We count the cars. Oops! We have only 13 cars. Do we now say that my theory has not yet been refuted?

    That’s one major problem, as I see it (and we’re back to discussing the theory and not just “evolution”). There is a severe lack of precision and major errors are covered-up. Whether humans evolved from chimp-like ancestors or exactly the opposite happened (as Mr. Lovejoy claims) — this is relatively meaningless.

    There is no single “theory of evolution.” In two respects. A theory is a model or mechanism that explains a number of facts.

    First, a single theory need not explain all the facts. Darwinian selection does not explain neutral drift. Epigenetics does not explain the DNA code. Disproving group selection,[6] entirely, for example, does not disprove evolution.

    Yes, but is this revisionism? It seems like it’s adjusting the theory to fit the facts — and therefore, it’s not a theory but just a “description of what we find in nature”. Plus, I think a theory must explain all of the facts that it claims to explain. With “evolutionary theories” we have an amazingly inelegant collection of ideas. In every case, there are layers of exceptions, mysteries and anomalies.

    Personally, I could live with that if it was explained in the way you’ve explained it above (and through your past few postings). You have not taken the ordinary knee-jerk defense of evolutionary theory, and I would say that if your approach was used more widely in education, there would be less hostility towards science and actually more productive ideas coming forward. Instead, the fierce defense of evolution tends to seal-off honest inquiry.

    Therefore, falsifying one theory of evolution does not falsify evolution.as such.[7]

    Yes, true. But we can get confused here again. Evolution is claimed as a fact. Therefore, it shouldn’t be able to be falsified. I think it’s enough to say that falsifying one theory of evolution means that that particular theory does not explain the evidence. Do we have an alternative one which explains it all? If not, the most honest answer is that “we don’t know”.

    Sorry, that’s a cop-out. If it were true, heliocentrism could never have got off the ground (so to speak), because Ptolemaic theory did explain the motions of the heavenly bodies—well enough to predict eclipses hundreds of years in advance.

    I think we’re saying the same thing here. Ptolemaic theory was falsified, thus giving Copernicus’ ideas support. But P’s theory could have been falsified on its own, without a competing idea to take its place. There’s nothing wrong about saying that we do not know how it works. No current theory explains it, etc. But as long as we can’t say that about evolution, the discussion centers on the current (claimed to be non-refuted) theory.

    Then each side simultaneously gaters evidence for its theory; the trial court then decides who has the bettr evidence.

    Sure, if there is a competing theory. But falsification does not require a new theory. That’s why we have peer-review. An idea is advanced. If it is falsified, then it doesn’t fly.

    Got to run — sorry. Many thanks again for a truly excellent reply. I appreciate your time with this (and I acknowledge your expertise).

  24. Naturalistic chemical-bonding theory grows weaker by the month.

    Just last year, scientists discovered a new entirely unexpected phase of water. Water! What’s not to know about the most pedestrian form of matter that one can imagine? The entire theory of water is in turmoil. A huge, unexpected gap has opened.

    Femtosecond laser pulses probe the genesis of chemical compounds. And stumble upon phenomena that controvert what scientists have “always known” about bond formation. Some of the most basic theories must be revised, and a few have been overturned entirely.

    Materials have been made that have a negative index of refraction. Impossible, say hidebound theoreticians. Not allowed; physicochemical laws forbid it.

    Organic compounds form in space from elementary gases and carbon. Yet long-standing chemical laws prohibit such reactions at the concentrations found in the interplanetary environment. Scientists are at an utter loss for any naturalistic explanation.

    Yes, indeed. Conventional chemistry is in crisis. Widening gaps. Revised theories. Lack of explanations. But the Hand of God appears out of the wreckage of smug naturalism. The inference to the best explanation is inescapable. Creationistic Chemistry offers all the answers—in fact, offers one simple, all-encompassing theory that never needs revision and is 100% certified gap-free. One single answer explains all facts from the simplest to the most complex: God did it.

  25. Stephen Jay Gould, “Evolution as Fact and Theory,”
    Discover 2 (May 1981): 34-37

    ———————————————-

    Here is the first bit of a classic essay. I can send you the rest if you like, or it might till be available on-line at http://www.stephenjaygould.org/library/gould_fact-and-theory.html Some of the material is becoming dated, but Gould still represents core scientific thinking. (Altho creationists love to misquote him, a he notes near the end.)

    ———————————————–
    ……..

    According to idealized principles of scientific discourse, the arousal of dormant issues should reflect fresh data that give renewed life to abandoned notions. Those outside the current debate may therefore be excused for suspecting that creationists have come up with something new, or that evolutionists have generated some serious internal trouble. But nothing has changed; the creationists have presented not a single new fact or argument. Darrow and Bryan were at least more entertaining than we lesser antagonists today. The rise of creationism is politics, pure and simple; it represents one issue (and by no means the major concern) of the resurgent evangelical right. Arguments that seemed kooky just a decade ago have reentered the mainstream.

    The basic attack of modern creationists falls apart on two general counts before we even reach the supposed factual details of their assault against evolution. First, they play upon a vernacular misunderstanding of the word “theory” to convey the false impression that we evolutionists are covering up the rotten core of our edifice. Second, they misuse a popular philosophy of science to argue that they are behaving scientifically in attacking evolution. Yet the same philosophy demonstrates that their own belief is not science, and that “scientific creationism” is a meaningless and self-contradictory phrase, an example of what Orwell called “newspeak.”

    In the American vernacular, “theory” often means “imperfect fact”—part of a hierarchy of confidence running downhill from fact to theory to hypothesis to guess. Thus creationists can (and do) argue: evolution is “only” a theory, and intense debate now rages about many aspects of the theory. If evolution is less than a fact, and scientists can’t even make up their minds about the theory, then what confidence can we have in it? Indeed, President Reagan echoed this argument before an evangelical group in Dallas when he said (in what I devoutly hope was campaign rhetoric): “Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science—that is, not believed in the scientific community to be as infallible as it once was.”

    Well, evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world’s data. Theories are structures of ideas that explain and interpret facts. Facts do not go away when scientists debate rival theories to explain them. Einstein’s theory of gravitation replaced Newton’s, but apples did not suspend themselves in mid-air, pending the outcome. And humans evolved from apelike ancestors whether they did so by Darwin’s proposed mechanism or by some other, yet to be discovered.

    Moreover, “fact” does not mean “absolute certainty.” The final proofs of logic and mathematics flow deductively from stated premises and achieve certainty only because they are not about the empirical world. Evolutionists make no claim for perpetual truth, though creationists often do (and then attack us for a style of argument that they themselves favor). In science, “fact” can only mean “confirmed to such a degree that it would be perverse to withhold provisional assent.” I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.

    ………

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