Taking “ID is science” out of the ID/Creation argument

I have committed the unpardonable sin of promoting ID as theology and arguing ID is not science. ID is the lineal descendant of Paley’s natural theology (as in contrast to “revealed theology”). I’ve publicly disputed the use of the 2nd Law of Thermodynamics as a general argument in favor of ID/Creation, and I’ve been mildly critical of the concept of specified complexity and its successors. I’ve suggested ID is most appropriately taught in college/seminary theology and philosophy departments. When I published a 2005 exchange between myself and Eugenie Scott of the NCSE regarding the appropriateness of ID being taught in college religion and philosophy departments, Eugenie was much kinder to me than some in the ID community who insist “ID is science.” See: Correspondence between Salvador Cordova and Dr. Eugenie Scott

To that end, in conjunction with university professors, deans of Christian and secular colleges (who are favorable to both Intelligent Design and belief in Special Creation), I’m helping build out the electronic component of courses that teach ID and concepts of Creationism for such venues.

The first order of business in such a course is studying Paley’s watch argument and modern incarnations of Paley’s watch. But I’ve found compartmentalizing the pure science and math from the theological issues is helpful. Thus, at least for my own understanding and peace of mind, I’ve considered writing a paper to help define terms that will avoid the use of theologically loaded phrases like “materialism”, “naturalism”, “theism”, and even “Intelligent Design”, etc. I want to use terms that are as theologically neutral as possible to form the mathematical and physical foundation of the ID argument. The purpose of this is to circumvent circular arguments as best as possible. If found what I believe are some unfortunate equivocations and circularity in Bill Dembki’s definition of Design using the explanatory filter, and I’m trying to avoid that.

VJ Torley was very kind to help me phrase the opening of my paper, and I have such high respect for him that I’ve invited him to be a co-author of the paper he so chooses. He of course is free to write his own take on the matters I specify in the opening of my paper. In any case, I’m deeply indebted to him for being a fellow traveler on the net as well as the example he has set as a meticulous scholar.

Here is a draft opening of the papers which I present here at TSZ to solicit comments in the process of revising and expanding my paper.

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Multiverse or Miracles of God?
Circumventing metaphysical baggage when describing massive statistical or physical violations of normative expectations

Intro/Abstract
When attempting to set up a framework for expressing the improbability of phenomena that may turn out to have metaphysical implications, it may be helpful to isolate the metaphysical aspects of these phenomena from the actual math used to describe them. Additionally, the probabilities (which are really statements of uncertainty) can be either observer- or perspective-dependent. For example, in a raffle or a professional sporting league, there is a guaranteed winner. Using more formal terminology, we can say that it is normative that there is a winner, from the perspective of the entire system or ensemble of possibilities; however, from the perspective of any given participant (e.g. an individual raffle ticket holder), it is by no means normative for that individual to be a winner.

With respect to the question of the origin of life and the fine-tuning of the universe, one can postulate a scenario where it is normative for life to emerge in at least one universe, when we are considering the ensemble of all universes (i.e. the multiverse). However, from the perspective of the universe in which an observer happens to be situated, the fine-tuning of that particular universe and the origin of life in that universe are not at all normative: one can reasonably ask, “Why did this universe turn out to be so friendly to life, when it could have been otherwise?” Thus, when someone asserts that it is extremely improbable that a cell should arise from inanimate matter, this statement can be regarded as normative from the perspective of human experience and experimental observations, even though it is not necessarily normative in the ultimate sense of the word. Putting it more informally, one might say that abiogenesis and fine-tuning are miraculous from the human point of view, but whether they are miraculous in the theological or ultimate sense is a question that may well be practically (if not formally) undecidable.

The objective of this article is to circumvent, or at least minimize, the metaphysical baggage of phrases like “natural”, “material”, “supernatural”, “intelligent,” when formulating probabilistic descriptions of phenomena such as the fine-tuning of the universe and the origin of life. One can maintain that these remarkable phenomena are not explicable in terms of any accepted normative mechanisms which are known to us from everyday experience and scientific observation, and remain well within the realm of empirical science. However, whether fine-tuning and the origin of life are normative in the ultimate sense, and whether they are best explained by God or the multiverse, are entirely separate issues, which fall outside the domain of empirical science.

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662 thoughts on “Taking “ID is science” out of the ID/Creation argument

  1. keiths: Not according to Dembski. The non-physicality of intelligence is a built-in assumption of the explanatory filter. That’s why intelligence is the default conclusion after “Darwinian and other material mechanisms” have been excluded.

    Only if you equate physical with stochastic process. The explanatory filter just filters out stochastic processes. But, if we’re free to call anything physical, then might as well call intelligence physical.

    Anyways, there are a number of materialistic atheists who are supporters of ID, so it’s not obvious that ID has anything to do with gods. Or, call god physical, and you have materialism that is consistent with theism.

    These definition games are mostly silliness. Best to stick with the hard math where definitions are unambiguous.

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  2. stcordova: I’ve been at odds with the idea of Specified Complexity as part of the modern incarnation of the design argument. Partly for simple reasons such as, the example pictured below which one could reasonably assume a human intelligence was responsible for making the dominos stand up that way.

    How does this show specified complexity is incorrect or that there is a problem with the concept?

    It’s hard to apply quantum physics to cooking a pizza, but that doesn’t mean quantum physics is incorrect nor useless. In fact, most of science, and academic knowledge for that matter, is pretty useless in everyday life. Yet, it still seems valuable for specialized applications.

    Say we have an example where it is difficult or impossible to apply specified complexity in a rigorous mathematical manner, and yet we easily seem to make a design inference. Why does this show there is a problem with specified complexity?

    In everyday life I easily recognize other intelligent agents all around me and infer their causation from their effects. I never am explicitly calculating specified complexity when I do this. Yet, I don’t feel the need to call into question the logic and math of the explanatory filter.

    Or, take my own field, computer science. I have rarely, if ever, needed to use what I learned throughout all my degrees in my everyday job as a software engineer. Especially the concepts that seem most interesting to me, such as algorithmic information theory, are actually inherently useless since they are uncomputable. Yet, that does not make any of it false nor imply there cannot be specialized ways to apply the concepts. For example, this practical application derived from AIT is pretty cool:
    https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=1412045

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  3. Hi BruceS,

    What has to be fine-tuned in eternal inflation theory?

    Even an eternal universe would still require an explanation, if it possessed features pointing to an intelligence behind it. Robin Collins has an excellent discussion of the fine-tuning required for inflation to work, as well as the beauty of the laws of nature, in his paper, Universe or Multiverse? A Theistic Perspective (see sections V and VI).

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  4. Eric,

    I’m continually surprised by how unfamiliar you are with Dembski’s writings and views. What you wrote above would not fly with him.

    He explicitly states, regarding P(T|H):

    Moreover, H, here, is the relevant chance hypothesis that takes into account Darwinian and other material mechanisms.

    He is thereby excluding intelligence from the category of “other material mechanisms”.

    He is also on record saying this:

    One of the consequences of methodological naturalism is to exclude intelligent design from science.

    Dembski is firmly in the supernaturalist camp with respect both to human and divine intelligence.

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  5. Hi everyone,

    The following discussion may be of interest to some readers:

    Fine tuning and the multiverse (Physics Forums, March 8, 2019). It features an interview with David Deutsch (13 minutes).

    Deutsch rejects the design hypothesis because he thinks it kicks the design problem up one level, but I don’t see why it would. It’s not at all clear to me that the designer of a universe would itself need to be fine-tuned. Why should it be?

    Interestingly, Deutsch also rejects the multiverse hypothesis, on the grounds that in the vast majority of universes, the universe is only just good enough for observers to frame the question, “Why are we here?” In most cases, the universe should collapse almost immediately after the observers frame the question, because short-lived universes are vastly more likely than long-lived ones.

    Deutsch himself prefers the hypothesis that unknown laws of physics, relating to emergent phenomena, can explain the appearance of fine-tuning.

    One reader on the Physics Forum thread comes up with an analogy that’s highly pertinent to the foregoing discussion about puddles, on this thread:

    There are many ponds on earth where fish might just barely live. So a fish in a perfect pond might not be justified in saying the reason it is so fortunate to be in that pond is that it can’t be found in any other environment – the only potentially existing environments where it even might be able to live is the perfect pond it finds itself in. Such a fish would not be making a valid anthropic argument – there are lots and lots of barely survivable brackish nasty ponds the fish would be more likely to find itself in. Unless it can find a reason it ended up in a perfect pond, it must conclude it is a lucky fish after all. There are many ponds on earth that dry up. A fish in a long lasting pond would (imo) be correct in saying the long lasting pond is the only type of pond it can exist in long enough to ponder the question of its own existence. IMO this fish is making a valid anthropic argument – so if I did understand Mr Deutsch correctly, then I am missing something about his reasoning.

    Questions to ponder:

    (i) does the unexpected beauty of the laws of physics in our universe constitute a strong argument for inferring design?

    (ii) does the unexpected longevity (and size) of our universe constitute a strong argument for inferring design?

    Thoughts?

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  6. keiths: He is thereby excluding intelligence from the category of “other material mechanisms”.

    If it has a probability, it is a stochastic process.

    If you have a material entity that is not a stochastic process, it is not excluded.

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  7. vjtorley: Deutsch rejects the design hypothesis because he thinks it kicks the design problem up one level, but I don’t see why it would. It’s not at all clear to me that the designer of a universe would itself need to be fine-tuned. Why should it be?

    Not the designer(s), but their realm of existence. Intelligence has requirements Vince. Have you ever thought about that? Our own requires something to be intelligent about, and attributes that need a nature that can sustain such attributes. So, if an intelligence is needed to “fine-tune” our universe so that our intelligence can develop, function, exist, and have something to be intelligent about, the same goes for an “upper-level” intelligence. There’s no way around this. How could an intelligence exist without some natura that makes it possible? Without anything to be intelligent about? Otherwise what would “intelligence” even mean? How could anybody claim, honestly, that their “model” for ID is scientific, and based on our own intelligence as exemplar, without considering that intelligence has requirements?

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  8. EricMH:
    It’s hard for me to see why ID is not science.

    ID as presented now isn’t science because it has no testable hypotheses and isn’t falsifiable.

    So, I would go the other direction and remove the religion from ID.

    So what’s stopping you?

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  9. Eric,

    If it has a probability, it is a stochastic process.

    If you have a material entity that is not a stochastic process, it is not excluded.

    By that odd reasoning, design has no probability. Oops.

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  10. vjtorley: Even an eternal universe would still require an explanation, if it possessed features pointing to an intelligence behind it.

    That seems more like PSR which I think is a separate issue from fine tuning.

    Thanks for the link to the paper.

    It is true that the the mechanisms which generate universes must be capable of generating universes like ours. I don’t know if we know enough about those mechanisms to claim that is an existence of a type of fine tuning. Instead, perhaps something analogous to Deutsch’s unknown laws explanation will apply at this level instead of fine tuning. Of course, that would lead us back to PSR.

    The beauty issue is something different. Is the beauty in the laws? Or is it in us, as a result of how we do science in a universe that made our evolution possible? That is another important issue, but it is not fine tuning. Or at least it is not a separate problem of fine tuning from the one that makes universes supporting beings like us possible.

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  11. EricMH: It just seems like ID is science.

    I think you would find an undergrad text on philosophy of science helpful for understanding the issue of what constitutes science (the so-called demarcation problem).

    Entropy has already pointed out the nature of scientific outputs and how they differ from those of math or ID.

    In addition, successful science is practice of human communities. To be a successful scientific community, scientific norms of behaviour are followed. These include among others the Merton norms.
    https://scienceblogs.com/ethicsandscience/2008/01/29/basic-concepts-the-norms-of-sc
    https://en.wikipedia.org/wiki/Mertonian_norms

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  12. stcordova:

    In my experience saying “ID is science” does more harm to promoting ID than help because it becomes a read herring when in fact what should be the focus is the failure to explain life in terms of accepted normative mechanism like the ordinary behavior of chemistry and physics. Ordinary chemistry and physics explains a lot of the the reasons life can perpetuate, but it doesn’t explain it’s origins, in fact suggests life is improbable (as in far from normative expectation).

    Do you really not see that this is just the old God-of-the-gaps- argument again? A couple of hundred of years ago you could have used this argument to ‘demonstrate’ that lightning is improbable (because the physics and chemistry of the day couldn’t explain it) and therefore it must be designed. You would have been wrong then, so why would you not be wrong now?

    Why do you assume that we have now finally reached the limits of our understanding of nature? Don’t you think that people a few hundreds of years into the future may have a much better and different understanding than we have now? That, after all, is the clear historical trend in the development of human knowledge. What makes you think we are now at the end of that trend?

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  13. colewd:
    stcordova,

    It is right on the edge of science and philosophy.Its biggest problem is that it is limited.A mind is a mechanism and it can be tested as for its ability to arrange parts or sequences.

    The people that insist it is not science are generally opposing the ideological/political implications for categorizing ID as science.

    You are making a classical logical error here:

    If A, then B (if a mind, it can create arrangements and sequences)
    B, therefore A (arrangements and sequences, therefore a mind was involved)

    Nope.

    Put your proposed mind on the test bed and we will see if it can create the arrangements and sequences of life. Then we would be doing some science.

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  14. vjtorley:

    Deutsch rejects the design hypothesis because he thinks it kicks the design problem up one level, but I don’t see why it would. It’s not at all clear to me that the designer of a universe would itself need to be fine-tuned. Why should it be?

    Is that designer alive? If so, wouldn’t he have to live in a meta-universe? Would that meta-universe not have to be fine-tuned to allow the designer to be alive?

    It is universes all the way up.

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  15. faded_Glory: Is that designer alive?

    Good question. Let’s just start here. What was the problem addressed by the fine tuning argument again?

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  16. faded_Glory: Do you really not see that this is just the old God-of-the-gaps- argument again?

    Absolutely!

    But what if the Gap is real?

    I asked this question on an atheist call-inTV show last December to Tracie Harris. I was as humble and meek as possible because it was not my intent to be my usual combative self. Tracie Harris is an ex-evangelical Christian turned atheist, so I especially wanted to talk to her when I called in.

    I related this account by Astronaut Charles Duke who was one of the few men to ever walk on the moon:

    from his book Moon Walker pages 271-273:

    I have seen miracles of healing, miracles of deliverance as demons fled in the name of Jesus, and wonderful manifestations of the love and power of God, just like in the Bible.

    One such instance was at a military prayer breakfast in San Antonio, Over the years I have spoken for a number of prayer breakfasts–conventions, states, cities, and military. During this particular meeting held at Fort Sam Houston, there was opportunity for ministry following the program. A number of people came up for prayer; one was a young girl and her father.

    The father explained, “My daughter’s eyesight is failing. She has this disease and is declared legally blind. All she can make out are shadows and shades of light. The doctors say that within a month she will be totally blind.”

    General Ralph Haines, who had organized the breakfast, and I laid hands on this young girld and asked God to heal her eyes and restore her sight. After the prayer, they thanked us and left. Nothing seemed to have happened–no-miracles-so we continued to pray for other who were waiting in line.

    A few minutes later, this same girl came running throught the back door of the NCO Club, joyously happy! She was screaming at the top of her lungs, “I can See…I can see… I can see!” Everyone stopped what they were doing while she came running over to us to explain what had happened.

    …..

    several years later I saw her father, and he confirmed that her sight was still perfect.

    Now one could be skeptical for many reasons, but Duke isn’t professional preacher trying to get TV air time, he’s a national hero, a retired Air Force general, a successful business man, an MIT graduate, a Naval Academy graduate, etc. etc. He now ministers to the outcasts of society by visiting prisons. By investing time reaching out to the outcasts of society, he’s living his life as if he really was visited by the Lord.

    So I asked Tracie Harris, “If I were that blind girl who was healed, I would serve the Lord the rest of my life.” I also related the story of the Bling Beggar in John 9, which is a more severe account. I said I would serve the Lord the rest of my life if that happened to me. In a sense, that is a God-of-the-Gaps issue.

    So I asked Tracie, if hypothetically she were in the position of the blind girl who got healed (and by way of extension the Blind Beggar), what she would do.
    She was gracious enough to answer the question. She said, “no.” She said she would try to figure out the mechanism of how the blind were healed so that all blind people could be healed. I thanked her for her candor and cordial response. But her answer is not for me and it’s not adequate for a lot of people who don’t believe science plus “the right” political system can be the ultimate remedy to the human condition by ushering a Utopia (or dystopia depending on how on looks at it). I didn’t openly ridicule her answer, and she didn’t openly ridicule mine, and that was the end of the conversation. Lot’s of athiests tuning in sneered and ridiculed me on the internet for that exchange. That’s fine, but their ridicule didn’t describe a better alternative for me than the Christian God…

    That said, atheists have said they would believe if there were testable predictions of God. There is a certain logic to that. I believe in the principles of a light switch because I can get it to operate on demand. I flip the switch up and it turns on a light, I flip the switch down and it turns off a light. We tend to believe what we can describe, predict, and control. Victor Stenger and others said they would believe in God if they could subject Him to experiments — that is to say they (in so many words) would believe in God if God would do what they demand in the lab when they want and how they want. In fact, why restrict it to the lab, how about the field? They would believe in God if they could tell God to show up and do their bidding when they want, and how they want, and how many times they want. Yes, there is a logic to that, but on some level that is in effect say they would believe in God if they themselves were greater than God. But if God is greater than they are, as a matter of principle, somewhat as Godel showed, it cannot be resolved to human comprehension, nor would it seem appropriate God would bow down to every demand by mere mortals for experimental proof. So if such a God exists, as a matter of principle, to accept that truth, one must be as a little child relative to an infinite God, because finite mortals cannot comprehend the infinite. Cantor did a rather good job showing that mathematically.

    But with respect to the origin of life. At first we believe in spontaneous generation of insects, then after Redi’s experiment, it was reduced to belief in microbes, but after Pasteur’s experiment, it was reduced to one-or-a-few abiogenesis events on the Earth, but after more knowledge, it’s now reduced to hoping desperately for even a few bio-polymers on Earth in a vast Universe, and then of late, even more remote odds in multiverses. It seems the gaps are getting bigger. Besides what does the multiverse profit me? It might only serve as passing entertaining fiction/fact, but the amusement seems rather fleeting and ultimately meaningless at a personal level. But if the Christian God is real…

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  17. EricMH: there are a number of materialistic atheists who are supporters of ID, so it’s not obvious that ID has anything to do with gods.

    They are not pro-ID. They are pro-IDM & Discovery Institute. Big difference.

    Berlinski isn’t pro-ID; he’s anti-Darwinism. Denton is pro-id, not pro-ID. James Tour isn’t pro-ID, he’s anti-Darwinian evolution & anti-Darwinism.

    Were you aware of this EricMH, or was this hidden & unknown from you until now? Or do you disagree with my assessment & insist that any or all of those 3 is actually pro-ID?

    Do you know about IDism’s univocal predication & the DI’s implied theology of imago Dei?

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  18. EricMH:
    It just seems like ID is science. … It’s hard for me to see why ID is not science.

    I do not think ID is a particularly good apologetic. It is perfectly consistent with atheism (intelligent agency is just another physical cause like Tom English has argued), and any argument that would move from ID to theism applies equally well to most other scientific phenomena, i.e. where do matter and energy come from?

    So, I would go the other direction and remove the religion from ID.

    This is where EricMH goes off the rails & just doesn’t understand what he’s dripping in with ideological IDism. He’s one of the few IDists who thinks atheists (& even anti-theists, Eric?) can actually (not just DI-fake) be pro-ID.

    No, accepting ID ‘theory’ isn’t possible for an atheist. This is understandable, Eric, once you realize & openly admit that ‘theism’ & ‘supernaturalism’ are the only suggested alternatives to ‘naturalism,’ as the founding father of the IDM Phillip Johnson explained.

    You likewise can’t “remove the religion from ID,” as if Charles Thaxton didn’t have the imago Dei fully 100% in mind & heart when he came up with/coined the term ‘Intelligent Design’. Did you meet Thaxton, as I did EricMH, at the DI’s Summer Program?

    This is a point at which every IDist seems to arrive when they’re getting pummeled on all sides, by theists & atheists. They then tend to start individualizing IDT, making it into their own ‘thing’ as if they are a ‘theorist’ in their own right & on par with Dembski, Behe, Meyer & Axe, adapting it for the moment’s argument that they are losing, trying to bend it away from what multiple leading IDists have mistakenly said, in order to try to save it from what it has become by this highly political Seattle ‘think tank’. I feel sad when I witness this happen because the unaccounted for shame of the DI is exposed in such moments, by sincerely seeking ‘students’ who they have trained to be ‘Revolutionaries!’ and yet who have come to actually disagree with the philosophical & moral basis upon which the DI is making its ideological arguments.

    There’s really quite little a thinking person can do when ignorant individuals on ideological missions-to-convert use devious natural theology arguments and make statements like “It just seems like ID is science.” That person must grow out of IDism on their own. If a reminder about this along the way is good for them, so be it.

    You don’t need to give up theism to properly reject IDism, EricMH. Be welcome to check-in again when you realize that.

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  19. Thank you for displaying how praying works:
    A particular prayer in a particular church
    Thank you Sal for the chance to acknowledge this
    Omnipotent ophthalmologist

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  20. faded_Glory: Is that designer alive? If so, wouldn’t he have to live in a meta-universe? Would that meta-universe not have to be fine-tuned to allow the designer to be alive?

    It is universes all the way up.

    I don’t see how anyone can expect to discuss aspects of realms outside of our universe and experience, and try to define those parameters and meaning, using only our experiences of this world, and expect to say anything logical or meaningful at all.

    Its like saying, well, if there is a God, where does their food come from.

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  21. EricMH: How does this show specified complexity is incorrect or that there is a problem with the concept?

    Paul Nelson had good advice for me (though when he said it, it wasn’t directed as me specifically): “tearing someone else’s house down, isn’t the way to build your own house up.”

    I think Specified Complexity, if it is good will be eventually vindicated in ID circles. I really don’t know many ID proponents who can even state succinctly what it is, whereas, at least qualitatively, and in some cases quantitatively we can say when something violates expected chemical and/or physical behavior. A lot of ID proponents now are coming from the quarters of Biochemistry and Cellular Biology — “violation of chemical/physical expectation” is a more simple framing of the improbability argument. It resonates with the new breed of ID proponents, whereas SC does not.

    Given that many of the ID arguments deal with biological systems and the origin of life, I’m deferring to the language practitioners in the field understand. There are whispers in the ID community that they can’t get SC to improve their ID arguments. Same for the general application (or lack thereof) in the use of the 2nd Law of Thermodynamics.

    I think succinct and simple arguments as to why the following is designed, work best. If a Design argument can’t be readily applied to a system of simple dominoes or fair coins, why should we expect it to be of practical value in evaluating far more complex systems?

    Hence, for a college-level course, at least in my version, I’m avoiding 2nd Law and Specified Complexity altogether. FWIW, I managed to get tentative approval to deliver my course at a small Bible College already.

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  22. DNA_Jock:
    Thank you for displaying how praying works:
    A particular prayer in a particular church
    Thank you Sal for the chance to acknowledge this
    Omnipotent ophthalmologist

    You’re welcome DNA_jock. 🙂

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  23. The college-level course will be someone like a buffet because when I’ve given ID/Creation talks sometimes in the audience I’ll have simultaneously a freshman drama major in one seat and a PhD molecular biologist in another. It’s might be more helpful to provide materials that are appropriate for their background. And the computer will present to them a list of learning modules from which they can learn appropriate to their back ground.

    Thankfully, I don’t have to author much of the material, as some of it is being provided for me by my colleagues.

    This is one of the “DOMINOS problem” in abiogenesis stated by a physical organic chemist:

    let us consider assembling a genomic DNA of only two base pairs (adenine and cytosine on one strand paired with thymine and guanine on the opposite strand), using the components of natural DNAs: nitrogenous bases, deoxyribose, and phosphate acids. Assuming, the top strand (also known as the sense strand or the Watson strand) of our imaginary genome is a dinucleotide with the sequence of 5’-AC-3’ , a dinucleotide made of dAMP (deoxyadenosine-5’-monophsphate) and dCMP (deoxycytidine-5’-monophsphate). Since the bottom strand (also known as the anti-sense strand or the Crick strand) is the reverse and complementary of the top strand, its sequence has to be 5’-GT-3’ , a dinucleotide made of dGMP (deoxyguanosine-5’-monophsphate) and dTMP (deoxythymidine-5’-monophsphate).
    A deoxyribose nucleotide is composed of a deoxyribose sugar ring, a nitrogenous base, and a phosphate group (Figure 3). The nitrogenous base is attached to the deoxyribose sugar ring via a carbon-nitrogen (C-N) bond (Figure 3, boxed with dotted red lines), which is formed from a hydroxyl group (OH) in the sugar ring and an amine group (NH) in the nitrogenous base (Figure 3, bottom). The phosphate group is attached to the sugar ring via a phosphoester (P-O) bond (Figure 3, boxed with dashed red lines), which is formed from a hydroxyl group (OH) in the sugar ring and a hydroxyl group (OH) in the phosphate group (Figure 3, top).

    The numbers of possible isomers of our two-base-pair genome can be calculated in three steps: calculating the isomers of the first strand of the genomic DNA (5’-AC-3’), calculating the isomers of the second strand of DNA (5’-GT-3’), and calculating the total isomers of both strands, as detailed below.

    1.2.1. Calculating the number of isomers of the first strand of the genomic DNA
    To calculate the number of possible isomers for the first strand of DNA of our imaginary genome, 5’-AC-3’, we need to determine the number of isomers of dAMP, the number of isomers of dCMP, and possible ways of linking them together.
    The number of isomers of one dAMP molecule can be calculated by multiplying the number of OH groups in a deoxyribose by the number of amine (NH) groups in an adenine that can be used to form C-N bonds and by the number of linking the molecules to a phosphate group.
    Note that deoxyribose exists in five forms in water solutions, each of the forms has three OH groups (red in Figure 4) that can be used to link with an adenine via a C-N bond. The six-membered ring forms are the most stable, while the linear form is the least stable. The two five-membered ring forms are energetically identical, thus, each five-membered ring form will make up 12.5% of the mixture. The two six-membered ring forms are also
    energetically equal to each other, thus, each making up 37.5% of the mixture. It is interesting that the isomer used in DNA is not the most stable isomer of deoxyribose.
    Adenine exists in two forms in water solutions, thus there are three NH groups in an adenine molecule (N7H, N9H and NH of the NH2 of C6) that can be used to link with the sugar ring via a C-N bond (Figure 5 A). The number of NH groups that can be used to link to the sugar ring via a C-N bond in a cytosine is also three (N1H, N3H and NH of the NH2 of C4) (Figure 5 B). That number is five for guanine (N1H, N3H, N7H, N9H, and NH of the NH2 of C2), and two for thymine or uracil (N1H and N3H) (Figure 5 C-E). The two NH groups of the NH2 of C6 of adenine are indistinguishable and are counted as one, same is true for the NH groups of the NH2 of C4 of cytosine and the NH groups of the NH2 of C2 of guanine.
    Therefore, there are 3 (OH groups for each deoxyribose form) x 3 (NH groups in an adenine) x 5 (forms of deoxyribose) = 45 ways of linking an adenine with a deoxyribose via a C-N bond. The same is true for a cytosine. For a guanine molecule, there are 75 ways to link it with a deoxyribose via a C-N bond. Thymine has 30 such ways. Uracil also has 30 such ways, but it is not a component of DNA, but of RNA.
    Now that for each particular deoxyribose form, when one of its three OH groups has been used to link adenine (or any other bases), there will be two OH groups left to be used to link to a phosphate group. Therefore, there are a total of 2 x 45 = 90 ways of linking an adenine, a deoxyribose, and a phosphate group together (Figure 6). That number is 90, 150, and 60 for cytosine, guanine, and thymine, respectively. These are the numbers of isomers of dNMP in which N is an adenine (A), a cytosine (C), a guanine (G), or a thymine (T), excluding all the isomers of deoxyribose that are not a deoxyribose, all the isomers of A/C/G/T that are not A/C/G/T and all the isomers of linking the phospho-group through non-phosphoester bond.
    The last step of calculating the isomers of 5’-AC-3’ is to determine the possible ways of linking the isomers of dAMP and the isomers of dCMP together. Note that in each of the isomers of dAMP or dCMP, one of the three OH groups of its deoxyribose is occupied by a nitrogenous base, another by a phosphate group. Therefore, there is only one OH left in each isomer of dAMP that can be used to link to the phosphate group of an isomer of dCMP, and vice-versa. Consequently, there are two possible ways to link an isomer of dAMP and an isomer of dCMP. For example, a dAMP and a dCMP can be linked via a phosphodiester bond to form 5’-AC-3’, or 5’-CA-3’.
    Taken together, there are 90 x 90 x 2 = 16,200 ways of linking an adenine, a cytosine, two deoxyribose, and two phosphate groups together via C-N bonds and phosphoester bonds (Figure 7), only one of these is our desired DNA sequence 5’-AC-3’.

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  24. phoodoo: I don’t see how anyone can expect to discuss aspects of realms outside of our universe and experience, and try to define those parameters and meaning, using only our experiences of this world, and expect to say anything logical or meaningful at all.

    If the supernatural interacts with this Universe, it is part of this Universe.

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  25. phoodoo: Its like saying, well, if there is a God, where does their food come from.

    Or asking where is the body of Jesus?

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  26. stcordova: FWIW, I managed to get tentative approval to deliver my course at a small Bible College already.

    From who? God?

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  27. FWIW, if one rejects the considerations in my previous comment from the physical organic chemist, one could of course, go to the chemistry considerations that led Koonin to start invoking multiverses.

    I personally think it’s nice, for completeness sake, to see how the estimates were derived. And afterall, theory agrees with observation. Put nucleobases, sugars, and phosphorous, and water and see what happens. Normative chemical expectation doesn’t result in anything resembling a linearly-readable genome as we know it.

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  28. newton: If the supernatural interacts with this Universe, it is part of this Universe.

    So if other universes interact with this universe, they are part of this universe?

    Thus, it is not possible to discover evidence of other universes.

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  29. Just for completeness, the problem of creating a somewhat linear genome from a soup of nucleobases and sugars was solved by the intelligently designed Blue Herron technology. They solved “the Dominos” problem for short strands of DNA (DNA oligos) which have to be intelligently stitched together.

    The above problem described by the physical organic chemist was solved by an intelligently designed chemical process that involved a recipe of steps.

    https://www.blueheronbio.com/

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  30. faded_Glory: Do you really not see that this is just the old God-of-the-gaps- argument again?

    stcordova:

    Absolutely!

    But what if the Gap is real?

    Doesn’t matter if the gap exists, the argument is fallacious anyway, that’s the point.

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  31. dazz,

    Doesn’t matter if the gap exists, the argument is fallacious anyway, that’s the point.

    How would you support this claim?

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  32. dazz:
    Doesn’t matter if the gap exists, the argument is fallacious anyway, that’s the point.

    Not trying to be polemic here, but how will one know God (like a personal Christian God vs. a Deist God) exists except He works a miracle?

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  33. stcordova: Not trying to be polemic here, but how will one know God (like a personal Christian God vs. a Deist God) exists except He works a miracle?

    That seems like a completely unrelated question. God might prove himself to exist by showing up, like he purportedly did in the form of Jesus, and perform miracles, but turning water into wine wouldn’t show that life was designed or automatically fill the gaps in our knowledge of biology.

    At any rate, the fact that you require miracles to vindicate your position is your problem, not ours. I know you think there are reasons to believe some aspects of nature were miraculous events, but I don’t think you ever showed that to be the case. It’s arguments from ignorance and complexity all the way down. Sorry, but gets old pretty quick.

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  34. stcordova:..
    But what if the Gap is real?

    We know the gaps are real. It’s the god that we never seem to find in any of them.

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  35. stcordova: The six-membered ring forms are the most stable, while the linear form is the least stable. The two five-membered ring forms are energetically identical, thus, each five-membered ring form will make up 12.5% of the mixture. The two six-membered ring forms are also
    energetically equal to each other, thus, each making up 37.5% of the mixture.

    An interesting concept. I wonder if it might be applicable to the rest of the analysis.

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  36. vjtorley: Deutsch rejects the design hypothesis because he thinks it kicks the design problem up one level, but I don’t see why it would.

    If designers are physical, then there is a regress of designers. That’s probably obvious to you, once it’s pointed out. (In fact, Dembski has made much of it, insisting that, when design is the result of a physical process, the process itself must have been designed.) I suspect that you didn’t see the regress for yourself because you believe in a supernatural Creator of the Universe. And I suspect that Deutch did not see a supernatural Creator as a way out of the regress because he believes in Physics.

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  37. Fair Witness,

    We know the gaps are real. It’s the god that we never seem to find in any of them.

    It’s the totality of the evidence from which the inference is made.

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  38. Tom English: Any putatively scientific account of a physical process including scientists-doing-science is paradoxical. I do not believe that there can be a logically consistent model of physicists doing the physics that led to the model.

    keiths: Could you elaborate?

    Sorry. Don’t have it in me.

    keiths: I can see why a mind would be incapable of holding a complete model of itself, but what about coarser models?

    Self-reference always gives rise to paradox (logical inconsistency). I don’t believe that David Wolpert provides exactly what I need here, but you might want to have a look at his “Constraints on physical reality arising from a formalization of knowledge” (2018), an update of his “Physical limits of inference” (2008).

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  39. EricMH: intelligent agency is just another physical cause like Tom English has argued

    Never, ever have I made an argument about intelligent agency. What I have pointed out, quite a number of times over the past 20 years, is that psychologists and ethologists regard intelligence as a hypothetical construct — not something that is physically real.

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  40. dazz: know you think there are reasons to believe some aspects of nature were miraculous events, but I don’t think you ever showed that to be the case.

    I felt Koonin (not a Creationist, an anti-ID proponent as far as I can tell) argued that life is not well explained by expected behaviors of chemistry and physics, but rather a massive violation of expected behaviors of atoms.

    Thus, abiogenesis qualifies as a miracle, imho, in at least the statistical sense. Whether it qualifies as a miracle in the theological sense, is a separate question.

    I provided one example of such an analyses at the molecular level. There are others such analyses available, and some that are implicit in the mainstream literature.

    But, if such analyses won’t suffice, what will suffice to show origin of life is a miracle? If the answer is, “nothing will suffice short of me hopping in a time machine and seeing it with my own eyes”, I respect that, and I’d say on some level it’s commendable to have such a high standard of proof.

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  41. Fair Witness: We know the gaps are real.It’s the god that we never seem to find in any of them.

    Is it far to say won’t believe God created life unless He shows up to say, “I did it?” I commend your skepticism. But I’m just trying to clarify what standard of evidence would make the God-explanation an acceptable one to you.

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  42. DNA_Jock: An interesting concept. I wonder if it might be applicable to the rest of the analysis.

    Better yet, if you don’t like the analysis, and since you’re a DNA_Jock, I’d welcome an alternative analysis describing the odds of forming a circular or linear chromosome or genome from a primordial soup. If that’s too general a question, you can describe the minimal requirements in terms of concentrations, chemicals, and forbidden contaminants in the requisite mix.

    The first question is what is the role of water!

    There is something to be said for the “Water Paradox”
    https://phys.org/news/2018-01-water-based-life.html

    When trying to understand the origins of life on Earth, researchers run into a paradox: while water is an indispensable solvent for all known life forms that exist today, water also inhibits the formation of string-like chains of nucleic acid polymers such as RNA that were likely precursors of life. This raises the question: how could the nucleic acids have formed in the first place? One solution to this “water paradox” is that life may have originated in something other than water, and only later adapted to the presence of water.

    Ah, yes, a fortuitous events needed to make life that utilizes water.

    But there is a glaring problem with this proposal: formamide does not occur naturally in any significant quantity anywhere on Earth. Although formamide is widely used in industry as a solvent for making pharmaceuticals and pesticides, all of this formamide is synthetically produced.

    Synthetically produced? As in, intelligently designed. But even then, that’s not quite enough by miles, maybe light years.

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  43. DNA_Jock: An interesting concept. I wonder if it might be applicable to the rest of the analysis.

    for completeness, here is the diagram :

    Figure 4: Chemical equilibrium of deoxyribose in water solutions. Note that deoxyribose exists in five forms. All five forms exist in an equilibrium; none of them can exist alone. Percentages of different forms of deoxyribose are according to Akane700 for ja:Wikipedia .

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  44. From the abiogenesis hall of fame:

    https://www.facebook.com/138681233223461/photos/a.138683993223185/619160918508821/?type=3

    A Structure for Deoxyribose Nucleic Acid
    J. D. Watson and F. H. C. Crick (1)

    April 25, 1953 (2), Nature (3), 171, 737-738

    We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest.

    We wish to put forward a radically different structure for the salt of deoxyribose nucleic acid. This structure has two helical chains each coiled round the same axis (see diagram). We have made the usual chemical assumptions, namely, that each chain consists of phosphate diester groups joining beta-D-deoxyribofuranose residues with 3′,5′ linkages.

    So if we have the other 4 kinds in solution:

    alpha-D-deoxyribofuranose
    alpha-D-deoxyribopyranose
    beta-D-deoxyribopyroanose
    linear-D2-deoxyribose

    wouldn’t it be unlikely to form a “genome” the way we know it spontaneously where there is uniformity with beta-D-deoxyribofuranose? We could a apply a simple binomial distribution on the generous assumption we have some sort of linearly-readable genome right? How about 1000 bases?

    Oh, that would be something like (12.5%)^1000 which is some outrageously remote number that would dwarf Doug Axe’s statistics.

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  45. stcordova: But, if such analyses won’t suffice, what will suffice to show origin of life is a miracle? If the answer is, “nothing will suffice short of me hopping in a time machine and seeing it with my own eyes”, I respect that, and I’d say on some level it’s commendable to have such a high standard of proof.

    The answer is, if you want to do it scientifically, you need a scientific theory for miracles. No need for a time machine, or stuff like that, that’s a classic creationist misrepresentation of science. You need a model that explains the data and makes testable predictions. All you have right now is lots of wishful thinking and a bunch of recurrent fallacies.

    But you know all this already.

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  46. dazz: ly, you need a scientific theory for miracles.

    How can you have a scientific theory for miracles as a matter of principle? To have a scientific theory you need mechanisms that are repeatable when you want and how you want and how many times you want. If that is the only mechanism you’ll accept, then even if a miracle really happened which is outside of science, you’d never accept it.

    I’m just pointing out the that the approach to what you believe is true will fail as a matter of principle if miracles are outside of scientific description. I believe (as in can’t prove) a miracle outside of scientific description is the cause of life.

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  47. dazz: The answer is, if you want to do it scientifically, you need a scientific theory for miracles. No need for a time machine, or stuff like that, that’s a classic creationist misrepresentation of science. You need a model that explains the data and makes testable predictions. All you have right now is lots of wishful thinking and a bunch of recurrent fallacies.

    You’d also need a rigorous definition of “miracle” and an objective way to test if particular observed phenomenon qualified.

    Ain’t gonna happen.

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  48. stcordova: How can you have a scientific theory for miracles as a matter of principle?To have a scientific theory you need mechanisms that are repeatable when you want and how you want and how many times you want.If that is the only mechanism you’ll accept, then even if a miracle really happened which is outside of science, you’d never accept it.

    I’m just pointing out the that the approach to what you believe is true will fail as a matter of principle if miracles are outside of scientific description.I believe (as in can’t prove) a miracle outside of scientific description is the cause of life.

    That’s why I said that the fact that your position requires miracles is your problem, not ours. There are many other gaps in our scientific knowledge, but for some not unknown reason, you guys are only fixated on origins related issues. If you think the origin of life and the universe, for some reason, are better explained by some epistemic doctrine other than science, make your case, but what you do, in my opinion, is to muddy the waters, pretending that you have reasons to believe that miracles are proper scientific explanations. In short, you’re lying to your students. And once again, you know that, since you admit it’s impossible in principle to devise a scientific theory of miracles.

    I will keep on believing that those are mysteries for science to unravel, for good reasons, I think. Call it scientism if you will, but your guys have had thousands of years to explain nature and they have failed miserably. If you want to replace science, come up with something better, but rehashing the same old crap (tornado-in-junkyard, for instance) over and over again, simply won’t cut it. Sorry

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  49. stcordova: Oh, that would be something like (12.5%)^1000 which is some outrageously remote number that would dwarf Doug Axe’s statistics.

    But Sal, you need to take into account the different ways the base could be attached to the sugar (9, 9, 15 and 6 for A, C G, & T respectively). That’s
    12.5% / 9 x 12.5% / 6 = 0.029% for an A:T base pair and
    12.5% / 9 x 12.5% / 15 = 0.012% for a C:G base pair.
    You cannot even make a 42-mer of dsDNA without surpassing the UPB!
    If you’re right, this is a true show-stopper for abiogenesis. You should publish this.

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  50. dazz: , pretending that you have reasons to believe that miracles are proper scientific explanations. In short, you’re lying to your students. And once again, you know that, since you admit it’s impossible in principle to devise a scientific theory of miracles.

    But what I’m teaching is for a religion/philosophy class, like I said in the OP!

    Like from the very title:

    Taking “ID is science” out of the ID/Creation argument

    and first paragraph

    I have committed the unpardonable sin of promoting ID as theology and arguing ID is not science. ID is the lineal descendant of Paley’s natural theology

    Now, you may dislike religion, but at least what you dislike can’t be based on me saying that my ultimate belief in God is necessarily a scientific one. What is scientific is that “a cell comes from a pre-existing cell [except by some unexplained exceptional mechanism]”.

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