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. Rumraket notes: “This has nothing to do with polymers of DNA forming in water. So first of all, RNA, not DNA. ”
    So Sal puts him in his place::

    Sure it does, because thus saith the abiogenesis RNA world community, “from RNA came DNA. ” But in any case, if one want’s a pre-biotic soup to make DNA genomes first, try this:

    https://www.nature.com/articles/s42004-019-0130-7

    In a 7-ml glass reaction vessel the below reagents were added: 1000 µl of 0.1 M glycine, 1000 µl of 0.1 M 5′-phosphate D-ribose and 1000 µl of 0.1 M adenine.

    Huh?
    Sal thinks they are making DNA from ribose? The authors of the paper he cites didn’t.
    Sal doesn’t know the difference between DNA and RNA.
    I’ll get me coat.

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  2. I like the idea of a creationist and an atheist walking into a room and finding a table full of 100 coins, all sitting exactly on their edges, and parallel to each other, neither on heads or tails.

    The creationist says, “Well, I wonder who did that?

    The atheist says, “Well, it just goes to show you, there really are multiple universes, and this just happens to be the one where all those coins fell on their edges. In other universes they are in different patterns.”

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  3. phoodoo:
    I like the idea of a creationist and an atheist walking into a room and finding a table full of 100 coins, all sitting exactly on their edges, and parallel to each other, neither on heads or tails.

    The creationist says, “Well, I wonder who did that?

    The atheist says, “Well, it just goes to show you, there really are multiple universes, and this just happens to be the one where all those coins fell on their edges. In other universes they are in different patterns.”

    This implies that rather than make the slightest effort to understand how anyone else thinks, you simply project nonsense on them, and then mock them for thoughts none of them would ever entertain. Is this fun for you?

    I don’t know a single person, of any religious affiliation, who would not first think someone set even a single coin on edge. This hypothesis would probably never prove wrong.

    Now, it might be amusing to try to dream up a universe where coins can ONLY fall on their edges and stay there. I admit I’d have problems doing so — maybe if I put a strong magnet in the table, and used coins with iron in one edge… Someone would still probably have to set them up that way, but at least they’d stay put long enough for an observer to see them.

    But let’s turn this around. Imagine a creationist and an atheist walking into a room and finding that all the furniture is resting on the floor, none on the ceiling. The atheist might suspect gravity is responsible, but the creationist would assume his god had miracled them all that way, and was using a miracle to keep them down. How’s that work for you? Isn’t that how creationists think?

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  4. DNA_Jock: Sal doesn’t know the difference between DNA and RNA.

    That’s false. But if you can’t actually attack the substance of the argument you’ll attack something I didn’t say, nor intended to say, nor actually said.

    I’ll get me coat.

    Well, thanks anyway for your participation.

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  5. Rumraket: This has nothing to do with polymers of DNA forming in water.

    Well, without the appropriate monomer, it’s kind of hard to form a polymer. Comprende? 🙂 The issue is the quibble about “soup”. Do you prefer “pot of soup” or “pool”? The RNA world is a hypothetical path to life with DNA, so yes it is hypothesized to begin in a pool, or in Darwin’s “pond” or whatever you want to call it — how about an uncertain mixture in solution with uncertain ingredients and uncertain trajectory and uncertain products at each step. Anything but “soup”.

    Well anyway, thanks for your responses and taking time to read.

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  6. stcordova: Sure it does, because thus saith the abiogenesis RNA world community

    No they don’t say that DNA monomers magically polymerized in water without any catalysts.

    “from RNA came DNA. ”

    By evolution, but then that’d be chemistry catalyzed by RNA and peptides.

    But in any case, if one want’s a pre-biotic soup to make DNA genomes first, try this:

    https://www.nature.com/articles/s42004-019-0130-7

    That’s a paper on the chemical synthesis of RNA monomers under DEHYDRATION conditions(not DNA). It is also not about their polymerization into strands of RNA. But even then, the constituents are dissolved in water, which is then allowed to evaporate.

    “Here, we study the co-reactivity of amino acids and nucleotide building blocks under simple dehydration conditions (90 °C for 5 h) (Supplementary Figs. 1, 2). Through simple one-pot dehydration reaction of an aqueous mixture (pH 2.5) containing nucleotide building blocks (ribose, phosphate and nucleobase) without additional activated or catalytic agents, simultaneous formation of nucleotide and nucleoside isomer structures from both purines and pyrimidines are obtained.”

    Oh look, it’s a wet-dry cycle again. Do you even read the papers you link?

    In a 7-ml glass reaction vessel the below reagents were added: 1000 µl of 0.1 M glycine, 1000 µl of 0.1 M 5′-phosphate D-ribose and 1000 µl of 0.1 M adenine. The pH was adjusted to the desired value using acid (HCl) or base (NaOH) and finally the total volume was taken to 4 ml using the corresponding amount of HPLC water….

    The very next part you left out reads:

    “…Then, the hot plate (equipped with Drysyn hotplate inserts) was pre-heated at 90 °C. Glass reaction vessels were placed in the corresponding Drysyn hotplate inserts. Lids with three integrated holes were placed on each vial which facilitated the evaporation during the drying step (see Supplementary Fig. 1). The vials were kept at 90 °C for a given time, in order to evaporate the solution to complete dryness.”

    No wonder you cut it out. HAHAHAHA you can’t make this shit up!

    They even use the phrase ” the simultaneous one-pot formation”. As in a pot of soup.

    Which evaporates. The point about one pot is it’s contrasted to multiple-pot reactions, which means this particular reaction doesn’t require multiple mutually incompatible reaction conditions to synthesize both the purine and pyrimidine ribonucleotides. This makes it more prebiotically plausible, as they could form in the same place, the “one pot”.

    And it spontaneously creates nucleoside isomers, which is part of the problem that must be overcome regarding the Law of Large numbers.

    Read it and weep:

    https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs42004-019-0130-7/MediaObjects/42004_2019_130_Fig1_HTML.png?as=webp

    I’m looking at the nice graphic you think should make me weep and by now it’s clear that your initial claim was so completely idiotic, and your reading comprehension so abysmal I think my job here is done.

    Weeping indeed, from laughter.

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  7. Rumraket: Weeping indeed, from laughter.

    You should dry those tears, Sal has had provisional approval to give his presentation in a Church basement.

    Now, tremble in fear as the land is swept clean and the truth of a Young Cosmos is known to all.

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  8. Rumraket,

    Thank you for motivating me to click through to Sal’s “Read it and weep” .png image.
    After seeing his “making DNA from ribose” howler, I had moved on. I had assumed that the image was entirely irrelevant to his “Law of Large Numbers” argument.
    How could I have known that the image explains how the presence of glycine [I mean glycine, FFS!] completely changes the distribution of isomers, making the correct AMP isomer nearly 100 times more prevalent. So it pretty much destroys Sal’s LLN argument.
    I am somewhat entertained to learn that his reading comprehension is that bad. Hopefully he will go back to touting his homochirality argument. That’s always good for a laugh.

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  9. Rumraket:

    No they don’t say that DNA monomers magically polymerized in water without any catalysts.

    I didn’t say that they said that. But if you want to focus the conversations on what I didn’t say, or intended to say, then we avoid actually addressing the problem of why :

    “Cell only come from pre-existing cells” except in exceptional circumstances. Unless of course you dispute that.

    That’s the central issue for the abiogenesis problem. But if you want to continue redirect the conversation to something I didn’t say, nor intended to say, then we really have no basis for discussion. So this is the issue:

    “Cell only come from pre-existing cells” except in exceptional circumstances.

    Agree or disagree?

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  10. DNA_Jock:
    Rumraket,

    Thank you for motivating me to click through to Sal’s “Read it and weep” .png image.
    After seeing his “making DNA from ribose” howler, I had moved on. I had assumed that the image was entirely irrelevant to his “Law of Large Numbers” argument.
    How could I have known that the image explains how the presence of glycine [I mean glycine, FFS!] completely changes the distribution of isomers, making the correct AMP isomer nearly 100 times more prevalent. So it pretty much destroys Sal’s LLN argument.
    I am somewhat entertained to learn that his reading comprehension is that bad. Hopefully he will go back to touting his homochirality argument. That’s always good for a laugh.

    First off, what I actually did was quote a paper:

    In a 7-ml glass reaction vessel the below reagents were added: 1000 µl of 0.1 M glycine, 1000 µl of 0.1 M 5′-phosphate D-ribose and 1000 µl of 0.1 M adenine. The pH was adjusted to the desired value using acid (HCl) or base (NaOH) and finally the total volume was taken to 4 ml using the corresponding amount of HPLC water….

    Now DNA_jock is saying that was a howler of something I said, but I merely quoted a paper specifically.

    Besides, I specifically said (by quotation) earlier here:

    http://theskepticalzone.com/wp/taking-id-is-science-out-of-the-id-creation-argument/comment-page-2/#comment-259032

    nitrogenous bases, deoxyribose, and phosphate acids.

    and I even specified 4 species:

    http://theskepticalzone.com/wp/taking-id-is-science-out-of-the-id-creation-argument/comment-page-2/#comment-259054

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

    If DNA _jock wants to then give the most uncharitable reading by saying:

    “making DNA from ribose”

    When I’m referring to the ribose in the context of DEOXYribose being it’s derivative, that’s rather an uncharitable reading in light of the fact I quoted:

    nitrogenous bases, deoxyribose, and phosphate acids.

    and then said explicitly:

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

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  11. I mean, I provided a paper here:

    https://www.nature.com/articles/s42004-019-0130-7

    that said:

    they have not been synthesised directly from the base and ribose.

    And then one of course could take out of context what is say:

    they have not been synthesised directly from …ribose.

    and then declare they said a howler.

    But I clearly pointed out earlier

    nitrogenous bases, deoxyribose, and phosphate acids

    Where regarding deoxyribose and ribose from the dictionary:

    a sugar derived from ribose by replacing a hydroxyl group with hydrogen

    But if one doesn’t really have a substantive rebuttal, the recourse is to focus on criticizing claims I wasn’t actually making. This can be done in any number of ways as I’m trying to point out by dissecting the rhetoric of my detractors.

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  12. Rumraket,

    Since you don’t like “soup” do you think “pool” is a better word. How about a “warm little pond”. Or would you prefer we actually described the experimental apparatus, a systems of beakers and test tubes, and other insulating glassware using purified substances in solvent that were carefully selected that don’t resemble the unpurified mess of uncertain chemical in an uncertain unknown unknowable pre-biotic context.

    Btw, do you want to suggest the products of one pool then become the reactants of another pool?

    Ok so you don’t like the word “soup”, is “pool” more to your liking? What word would you choose.

    But since Rurmaket insists NO-one he knows of uses the term “soup”, maybe this will be helpful:

    https://en.wikipedia.org/wiki/Primordial_soup

    Primordial soup, or prebiotic soup (also sometimes referred as prebiotic broth), is the hypothetical set of conditions present on the Earth around 4.2 to 4.0 billions of years ago. It is a fundamental aspect to the heterotrophic theory of the origin of life, first proposed by Alexander Oparin in 1924, and John Burdon Sanderson Haldane in 1929.[1][2]

    So how is this worse than what we have today where we throw in man-made and God-made chemicals, carefully purifed, into a mix where chemicals are INTELLIGENTLY selected to drive the desired reactions.

    If any thing, “soup” was probably more representative of reality than the “garbage” (to quote James Tour) that we have today.

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  13. Yes Sal, you have achieved the extremely challenging double GSW to both feet:
    You were wittering on at length [brevity is the soul of wit, btw] about how unlikely it is that a decent length of DNA could ever form in solution, based off the idea that only 12.5% of deoxyribose is in the correct isomeric form.
    You went along with the idea that only 12.5% / 9 AMP isomers will be correct — that was something of a trap — we can come back to that if need be.
    Rumraket points out multiple ways in which you are wrong, including the fact that you should be talking about RNA, not DNA:

    This has nothing to do with polymers of DNA forming in water. So first of all, RNA, not DNA.

    Stung, you retort with references to Suárez-Marina 2019, stating

    Sure it does, because thus saith the abiogenesis RNA world community, “from RNA came DNA. ” But in any case, if one want’s a pre-biotic soup to make DNA genomes first, try this:

    First gunshot wound: Suárez-Marina 2019 are synthesizing RNA monomers, not DNA or DNA monomers.
    Second gunshot wound: the Figure that you link to demonstrates how your 12.5% number is utterly meaningless. The presence of glycine alters these ratios dramatically.
    It’s a two-fer.

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  14. First gunshot wound: Suárez-Marina 2019 are synthesizing RNA monomers, not DNA or DNA monomers.

    I was referring to the pool from which the RNA world comes and from which the DNA world must come if one presumes RNA came first. The issue is whether “soup” was ever used.

    You misread, mischaracterized, what I said, and again you and Rumraket are criticizing arguments I’m not making. But if you can’t actually rebut, what I’m trying to say, you’ll rebut what I didn’t say.

    I provided and example of a DNA first soup.

    But regarding the 100 times increase of a particular AMP isomer, that you said:

    the correct AMP isomer nearly 100 times more prevalent.

    were you referring to the supplementary discussion here?

    https://static-content.springer.com/esm/art%3A10.1038%2Fs42004-019-0130-7/MediaObjects/42004_2019_130_MOESM1_ESM.pdf

    I’m not familiar with how to read EIC chromatograms. So how is the 100x figure derived. I was looking at figure 146. Is that the right one.

    C’mon, try to be useful in educating me today in something.

    All you’ve shown so far is educating me in how you criticize arguments and claims I really am not making. At least teach me something useful rather than spewing out criticism of what I’m not claiming.

    Really, I may have to just start ignoring you if all I’ll be doing is dissecting your illegitimate strawman arguments. That just creates noise to make the discussion unreadable and gives the false impression I said things I really didn’t. Such techniques are employed if one doesn’t wish to engage that actual argument being made.

    So, where is the 100x isomeric amplification again in the paper again.

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  15. It’s even worse, because the part that stood out to me which initially made me respond to Sal was his point concertin condensation reations taking place uncatalyzed in water.
    He wrote:

    So we have water and DNA in a pre-biotic soup which has water.

    Will it spontaneosly connect like a genome (I’m not even requiring it be able to code for anything). It would seem a little difficulty given that the formation for the PhosphoDiester bond is a condensation reaction described here:

    https://teaching.ncl.ac.uk/bms/wiki/index.php/Phosphodiester_bond

    To get this to happen with water in the vicinity, well, one needs some sort of machinery, but without that machinery (such as in a living cell) this is kind of hard.

    So his point is clearly that there’s a huge problem in origin of life research with these “prebiotic soup” models because to get DNA (and RNA) to polymerize is a condensation reaction, and those are thermodynamically unfavorable in water.

    So I ask Sal to give me references to show a model of abiogenesis where the researchers actually propose that the first DNA strands just spontaneously polymerized themselves from a solution of monomers. He completely fails to supply this. First of all, all his references concern RNA, and none of them deal with the polymerization problem. His first reference concerns the artificial selection of a ligase-capable ribozyme, not what I asked for(and again about RNA), his second reference concerns the synthesis of RNA monomers from bases and ribose-phosphates(so still not DNA, and still not about polymerization).

    To make matters worse, I even give Sal references that explain how scientists have proposed polymerization could happen: Evaporation. Evaporate away the water, and the condensation reaction becomes thermodynamically favorable because the water has left the system.

    Even more hilariously, the article Sal linked which Sal asserted showed that researchers are actually suggesting that DNA monomers would be spontaneously polymerizing in watery solution, turns out to be a synthesis of monomers from their smaller constituents-paper, by EVAPORATION again.

    He failed at EVERY level. The wrong molecules(all of them RNA instead of DNA), the wrong reaction conditions(dry state reactions after evaporation, so not in solution), the wrong reactions(monomer synthesis, not polymerization).

    I have nothing more to say.

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  16. Rumraket:

    So I ask Sal to give me references to show a model of abiogenesis where the researchers actually propose that the first DNA strands just spontaneously polymerized themselves from a solution of monomers.

    The fictional RNA world which makes the DNA world (or whatever world with DNA). The alternative is a factory of soups where products of one reaction go to another pool of other reactions. Do I have to point out the RNA world model precedes the DNA (or whatever world with DNA) model.

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  17. Rumraket:

    So I ask Sal to give me references to show a model of abiogenesis where the researchers actually propose that the first DNA strands just spontaneously polymerized themselves from a solution of monomers.

    Ok, so we have the RNA world. It all stars out as an RNA soup (well that’s what experiments model anyway), and as Koonin points out, at some stage in the RNA world we need such improbable events that Multiverses are in order!

    Ok, so now we miraculously go from basic ingredients to a pool or mixtrure of RNA rybozymes and other stuff. What next? Whatever is next, it has to lead to DNA. This still boils down to DNA originating in from an ancestral soup. That’s what I meant.

    The scenarios are:

    basic ingredient soup ->???? -> DNA

    basic ingredient soup -> ????-> RNA -> ???? -> DNA

    basic ingredient soup ->????-> metabolism?? -> DNA

    basic ingredient soup -> ???? -> amino acids -> proteins -> ????->DNA

    They are all ingredient soup scenarios (or variants thereof) whether explicitly stated or not. The alternative is to invoke a cybernetic like factory process where products of one soup get nicely filtered and properly concentrated as reactants for the next soup — but that adds improbability.

    So now the proposed solutions is MULTIVERSE to fill in the problematic steps. The issues with this is then every path become feasible through MULTIVERSE, even scenarios that are pretty much indistinguishable from miraculous special creation!

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  18. DNA_Jock: , based off the idea that only 12.5% of deoxyribose is in the correct isomeric form.

    That again is a strawman misrepresentation of what is being said. You could actually try to characterize what I actually said for a change. There issue is that each of the nucleobases in a DNA genome are attached to one of 5 deoxyribose isomers found when in solution with a water solvent. They are:

    beta-D-deoxyribofuranose (the one found in life)
    alpha-D-deoxyribofuranose
    alpha-D-deoxyribopyranose
    beta-D-deoxyribopyroanose
    linear-D2-deoxyribose

    “correct” really isn’t the sense that heads for a fair coin is “correct”.

    That problem of emplacing only beta-D-deoxyribofuranose in the genome the is circumvented by the machinery in the cell.

    What I stated can be found in places like wiki (below) where the 75% (approx) is both the alpha and beta isoforms of D-deoxyribopyranose, and similarly for both the alpha and beta isoforms of D-deoxyribofuranose totaling to 25%(approx).

    I could of course talk to someone I know who won’t be straw-manning my words and who is a chemist, but I figured I’d try to waste 100 hours of your time first before imposing 1 hour of time from my friends. 🙂

    But if you don’t feel like having a real conversation but rather throw poop on things I didn’t say, then I’ll just have to ignore what you have to say since I won’t be learning much from you.

    Now, how about explaining how I can derive the 100x amplification of a particular AMP isomer by the presence of glycine. Maybe Rumraket can splain if for me if you are unwilling to.

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  19. stcordova,

    beta-D-deoxyribofuranose (the one found in life)
    alpha-D-deoxyribofuranose
    alpha-D-deoxyribopyranose
    beta-D-deoxyribopyroanose
    linear-D2-deoxyribose

    I could be mean an suggest the L-forms be included too. 🙂

    Maybe I’ll be mean since DNA_jock isn’t playing nice.

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  20. stcordova: I could be mean an suggest the L-forms be included too. 🙂

    Maybe I’ll be mean since DNA_jock isn’t playing nice.

    Don’t be so shy! Go for it, Sal.
    Although I should warn you that both threonine and phenyalalanine were even more impressive than glycine and, unlike glycine, they can distinguish between enantiomers.
    You know why that is, right?

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  21. DNA_Jock:

    completely changes the distribution of isomers, making the correct AMP isomer nearly 100 times more prevalent.

    So the if the “correct” AMP isomer was 100 times more prevalent with glycine than without in the pot. So what was the proportion of the AMP isomer in the absence of glycine? If it was 2% in the absence of glycine, and then 100 times more in the presence fo glycine, now its 100 times 2% = 200%. Well, that won’t work, so what was the proportion of the correct AMP isomer in the absence of glycine.

    Btw, what is the name of the “correct” AMP isomer by the way? What are the names of Adenosine monophosphate (AMP) isomers. C’mon, provide a little education for us.

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  22. “Correct” isomer is N9-ribosyl.
    My bad: I thought it was obvious (from the figure that you linked to) that I was referring to the relative prevalence between the N9-ribosyl isomer and the N(6)-ribosyl isomer, which is the ‘majority’ isomer formed in the absence of amino acids. Sorry if I confused you there — I assumed you could read the chemical structures.
    Have you figured out yet why threonine can distinguish enantiomers, but glycine cannot?

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  23. DNA_Jock:

    I assumed you could read the chemical structures.

    First nice thing you said about me all day.

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  24. DNA_Jock: DNA_Jock:

    I assumed you could read the chemical structures.

    Actually not really, I was allowed to study biochem without studying organic. I had to pick the organic pieces as needed. So thanks a million for the tip.

    The caption in the paper had the order wrong (adenenine, guanine, cytosine) it should be (cytosine, guanine, adenine). Any way, I see the N9 from the diagram below, except I have to rotate the Adenine. I also see the N6, but have to flip the adenine upside down.

    Thanks again.

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  25. phoodoo: Yet, in many of those gaps science has filed them with bad science.Should we also say since they were wrong then why should we believe they are right now?

    Bad science happens, but eventually gets replaced with good science.

    You can’t say that about theology. It stays stuck on stupid.

    You never responded to my earlier question. You said things that are orderly and non-chaotic must require a designer.

    I asked ” Don’t you think that such a designer would himself be ordered and non-chaotic?

    So, who designed him?”

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  26. phoodoo:
    Flint,

    Do you really think the many worlds interpretation is some farce from The Onion that no one has ever really proposed?

    I could understand why you think it is a joke.Its hard to parody materialist atheists though, it turns out.

    I somehow suspect that various hypotheses put forward to address puzzling quantum phenomena aren’t quite illustrations of “materialist atheist” thought patterns. I don’t think all such suggestions are necessarily jokes, but I know no “materialist atheists” who concern themselves with those topics.

    I sorta recall that there was at one time a very serious debate in religions circles about how many angels could dance on a pinhead. But these arguments were pretty much limited to the more abstract theological theorists, and of no great concern to the ordinary believer who found comfort in his faith. And to an atheist, such a debate begs too many questions to be taken seriously.

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  27. phoodoo:
    Flint,

    BTW, saying God made gravity, much much much less ridiculous than what atheists claim.

    Which is? For an unbeliever like me, what you find so much less ridiculous is unhelpful, because it explains nothing. Yes, I could equally claim that unicorns made gravity. But “you can’t prove me wrong” isn’t an explanation.

    Now, if you could explain exactly HOW your god makes gravity, in a way that could be tested, you’d get my attention immediately. Otherwise, it’s turtles all the way down. I would love to know the mechanism for such things as gravity, inertia, time, etc. But saying “it just is” (semantically equivalent to goddidit) falls short of satisfying any genuine curiosity.

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  28. 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.

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

    Fair witness, this response was also for you, it answers your question.

    All of this, ‘well who designed God, what does he have for breakfast, if he is all knowing how does he know, what size shoes does God where… ‘ nonsense I find rather pedantic and boring from materialists. They always want to demand, well if there is a God, how does he do it? Where is he? Why can’t I see him… Well guess what, there is a reason it is called a God and not a puppeteer. You can’t see the strings. You can’t go have a beer with God. You can’t have a sleepover with him.

    Maybe instead you can go ask Neil Degrasse Tyson for all the answers about what is happening in all those other universes he knows all about.

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  29. Flint: I know no “materialist atheists” who concern themselves with those topics.

    Really? Well.. That’s not my fault

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  30. phoodoo:
    They always want to demand,well if there is a God, how does he do it?Where is he?Why can’t I see him… Well guess what,there is a reason it is called a God and not a puppeteer.You can’t see the strings.You can’t go have a beer with God.You can’t have a sleepover with him.

    The reason that you can’t do those things with God is that he is an abstraction, a thought in people’s head – as we discussed elsewhere. God is the same type of phenomenon as Charlie’s ‘ideal triangle’. A proces in the brain.

    On the sixth day, man created God.

    It is all in your head, Phoodoo.

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  31. DNA_Jock:
    Have you figured out yet why threonine can distinguish enantiomers, but glycine cannot?

    Ooh! Ooh! I know! I know!

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  32. Allan Miller: Ooh! Ooh! I know! I know!

    I presume becuase Glycine in non-chiral. BUT, in solution if the chiral amino acids are racemic, such as 50% L-threonine and 50% D-threonine, I’m not so sure the net result would be all that helpful. 🙂 Remember the Gibbs free energy profile favors racemization over time, and for some amino acids the half-life isn’t that long.

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  33. stcordova: I presume becuase Glycine in non-chiral. BUT, in solution if the chiral amino acids are racemic, such as 50% L-threonine and 50% D-threonine, I’m not so sure the net result would be all that helpful. 🙂

    And if, for whatever reason, the mix is not 50:50, then that will affect the enantiomer prevalence of other chiral molecules in the ‘pot’.

    Remember the Gibbs free energy profile favors racemization over time, and for some amino acids the half-life isn’t that long.

    And for other amino acids (and sugars) it is long. So, anyone who assumed that the chirality of individual molecules in a ‘pot’ were mathematically independent events would be WRONG.
    There’s a poster hereabouts that you should tell about that.
    🙂

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  34. DNA_Jock: And if, for whatever reason, the mix is not 50:50, then that will affect the enantiomer prevalence of other chiral molecules in the ‘pot’.

    Not easy to achieve in a soup because it requires special conditions, eh, like the conditions a living cell. That’s one reason Virchow is right, cells come from pre-existing cells. Obviously it’s possible, otherwise we’d be dead.

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  35. DNA_Jock:

    the correct AMP isomer nearly 100 times more prevalent.

    First off the “correct” AMP isomer appears not to be called N9-ribosyl in the paper, because well, AMP is the shorthand for the “real” AMP isomer in living systems. I think actual longhand IUPAC name of “correct” AMP isomer is (gasp):

    [(2R,3S,4R,5R)-5-(6-Amino-9H-purin-9-yl)-3,4-dihydroxytetrahydro-2-furanyl]methyl dihydrogen phosphate

    from:
    http://www.chemspider.com/Chemical-Structure.5858.html

    That’s said, I’m still having a hard time figuring out the approximate proporitions of N6 vs. N9 AMP with or without Glycine. I don’t see the 100x increase in prevalence of N9 AMP because of glycine, in fact, I’m having a hard time seeing exact numbers from the experiment in the paper.

    Anyway, I learned about an instrument I never heard of before from the paper while trying figure out what the numbers were for %N6 vs. %N9.

    https://en.wikipedia.org/wiki/Mass_chromatogram#Extracted-ion_chromatogram_(XIC)

    In an extracted-ion chromatogram (XIC or EIC), also called a reconstructed-ion chromatogram (RIC), one or more m/z values representing one or more analytes of interest are recovered (‘extracted’) from the entire data set for a chromatographic run.[3] The total intensity or base peak intensity within a mass tolerance window around a particular analyte’s mass-to-charge ratio is plotted at every point in the analysis. The size of the mass tolerance window typically depends on the mass accuracy and mass resolution of the instrument collecting the data. This is useful for re-examining data to detect previously-unsuspected analytes, to highlight potential isomers, resolve suspected co-eluting substances, or to provide clean chromatograms of compounds of interest. An extracted-ion chromatogram is generated by separating the ions of interest from a data file with of the full mass spectrum over time after the fact; this is different from selected-ion chromatograms, discussed below, in which data is collected only for specific m/z values.

    Has anyone worked with this gizmo?

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  36. phoodoo: to stcordova,

    How can talk of multi universes be science and ID not be?That’s not logical.Ultimately science is about discovering to the best of our limited senses. You are not going to see a multiverse anymore than you will see the designer.

    In his introduction to, “The Case for Anthroposophy”, Owen Barfield gives his account of the limits of modern science.

    He begins by giving us a quick summary of the beginnings of modern science at which point the precise, measurable, material/physical sense world was set apart from the occult, non-measurable, non-material, psychic world. And each went their own separate way.

    It quickly became apparent that qualities fell under the psychic world and so could not be studied using the tools fashioned to study the material world. Materialistic science has self-imposed limits which it must not cross without becoming something different from what it has been set up to be. But many who practice and follow the science which deals with the material world have moved from the position that this science need not concern itself with anything out side its limits to the declaration that there is nothing beyond its purview.

    Barfield writes there is:

    a frustrating, if suppressed, conflict between the scientific impulse, which is a will to know and a refusal to acknowledge boundaries except for the purpose of overthrowing them — and the scientific tradition, followed for the last three hundred years, which has ended in itself erecting boundaries that claim to be no less absolute than the old theological ones it did overthrow.

    Modern science becomes problematic when hypotheses are taken as facts.

    Modern natural science is a justified endeavour when it confines itself to its area of inquiry. Steiner’s spiritual science concerns itself with the occult, non-measurable side of the split and I would say that Goethean science is a bridge between the two. Research in these domains need not come into conflict if their different forms of research are understood.

    IMO the multi-verse hypothesis deals with hidden/occult entities and is thus outwith the realms of natural science.

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  37. phoodoo:
    All of this,‘well who designed God,what does he have for breakfast,if he is all knowing how does he know,what size shoes does God where… ‘ nonsense I find rather pedantic and boring from materialists….

    Deflect all you want, but the question “who created God?” is neither pedantic nor boring, because it points out the logic flaw in the idea that complex, ordered things must always have a conscious creator.

    Said creator would also have to be complex and ordered, implying the need for an infinite series of creators, which is a logical contradiction, or paradox.

    Many theists respond with “God is eternal, he didn’t need to be created.” until you point out that an infinitely old creator is just as much of a paradox as an infinite series of them.

    Either way, you shot yourself in the foot, Phoodoo, and then limped away.

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  38. faded_Glory: The reason that you can’t do those things with God is that he is an abstraction, a thought in people’s head – as we discussed elsewhere. God is the same type of phenomenon as Charlie’s ‘ideal triangle’. A proces in the brain.

    You are objectifying the concept. See here for a link to Brady’s agrument about this. He wrote:

    It is the muddled habit that leads us to take mind, or its conceptual structures, as objects among objects, that provides the foundation for Cartesianism in our day and sends almost all modern thought into objectification, despite the trouble with recursive functions that this creates…

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  39. Fair Witness to phoodoo: Deflect all you want, but the question “who created God?” is neither pedantic nor boring, because it points out the logic flaw in the idea that complex, ordered things must always have a conscious creator.

    Said creator would also have to be complex and ordered, implying the need for an infinite series of creators, which is a logical contradiction, or paradox.

    Many theists respond with “God is eternal, he didn’t need to be created.”until you point out that an infinitely old creator is just as much of a paradox as an infinite series of them.

    Either way, you shot yourself in the foot,Phoodoo, and then limped away.

    You’re doing it again!

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  40. CharlieM: You’re doing it again!

    What am I doing again, Charlie?
    Actually calling Phoodoo on his BS?
    Yes, I am doing that again.

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  41. Fair Witness,

    Then what created gravity? What created the big bang? Where did all the matter for the big bang come from? What created atoms?

    Don’t know, couldn’t really say, just is, who knows, doesn’t matter….

    Deflect is a pretty good game for materialists.

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  42. phoodoo:
    Fair Witness,

    Then what created gravity?What created the big bang?Where did all the matter for the big bang come from?What created atoms?

    Don’t know, couldn’t really say, just is, who knows, doesn’t matter….

    Deflect is a pretty good game for materialists.

    I can’t answer those questions. Phoodoo.
    And I don’t rely on logical paradoxes in order to pretend to answer them.

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