Intelligent Design

Origin of Life: Professor James Tour points the way forward for Intelligent Design

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Professor James Tour’s recent video, The Origin of Life – An Inside Story, managed to accomplish three things at once: it shattered the credibility of abiogenesis as a theory; it provided American high school science teachers with an excellent classroom resource for countering evolutionary propaganda; and (perhaps unintentionally), it set a new research agenda for the Intelligent Design movement, which will transform it into a bona fide scientific discipline: the task of reverse-engineering life itself.

Readers who wish to view the talk may do so here:

Why Tour’s talk is the perfect resource for American high school science teachers who want to counteract evolutionary propaganda

At the beginning of his talk, Tour explicitly declared that he would make no reference to “scientifically unknown entities that have been proposed to have seeded life on Earth, such as a design agent (personal or impersonal)”, or the outlandish theory that the Earth was seeded by aliens (panspermia), which merely pushes back the question of life’s origin: where did the aliens come from? This is an important point, because as most readers will be aware, the Dover vs. Kitzmiller decision of 2005 ruled that the teaching of Intelligent Design in public school biology classes violates the Establishment Clause of the First Amendment to the U.S. Constitution, on the grounds that Intelligent Design is not science and “cannot uncouple itself from its creationist, and thus religious, antecedents.” No such objection could possibly be made against Professor Tour’s talk, which will (I believe) prove to be an invaluable teaching resource in American high school science classrooms. For the question of how life evolved cannot be divorced from the question of how life originated: the straitjacket of methodological naturalism, which currently reigns supreme in the scientific world, demands a naturalistic answer to both questions. If the origin of life cannot be explained in this way, then that should weaken scientists’ confidence that macroevolution can be explained without appealing to any intelligently guided processes.

It is important to note that Professor Tour never attempted to refute abiogenesis as a scientific theory, in his talk. Rather, his aim was more modest: to show that the Emperor has no clothes, and that current theories about how life might have evolved are mere speculation, unsupported by a shred of evidence. The take-home message of his talk was that currently, scientists know nothing about how the ingredients of life originated, let alone life itself. Nevertheless, I believe that precisely because Professor Tour’s talk was framed as an expose of the inadequacy of current theories of abiogenesis rather than as a scientific refutation, it did a much better job of undermining the credibility of the idea. For what it showed is that for sixty years, scientists have been “telling lies for Darwin” (to adapt a phrase coined by Ian Plimer) and presenting the problem of life’s origin as a work in progress, when in reality, the progress made to date by scientists in the field is precisely zero.

What is abiogenesis, anyway?

In his talk [2:10], Professor Tour defined abiogenesis as “the prebiotic process whereby life, such as a cell, arises from non-living simple organic compounds: carbohydrates, nucleic acids, lipids and proteins (polymers of amino acids).” Tour added: “On our planet, this is what it is; in our universe, this is what it is. As far as we can tell, we’re the only ones here so far. But certainly on our planet, it’s carbohydrates, nucleic acids, lipids and proteins.

This is an important point to grasp. Defenders of abiogenesis are prone to speculate on the existence of exotic life-forms elsewhere in the cosmos, or in other universes. Even if such exotic life-forms existed, the question which concerns us is: how did cellular life, which relies on the four kinds of chemicals listed by Tour, arise? This is a non-trivial scientific question, and it demands an answer. Moreover, since any process that gave rise to life must have had a computable probability of success, it qualifies as a target, in the special sense of the word, as used by information scientists. In a nutshell: life can be defined as an improbable outcome. Some targets are highly specific (e.g. build this molecule), but the target we call “life,” even if it is narrowed down to “cellular life which is based on carbohydrates, nucleic acids, lipids and proteins,” is a very broad one, which can only be given a general description, since it makes no reference to any particular species (such as Homo sapiens or E. coli). Describing life as a “target” (in this sense) in no way assumes that the process which generated life must have been a guided one: that would be begging the question. All it means is that it must have been an improbable process (to some degree).

So the scientific question we have to address is: how improbable is the emergence of life on an Earth-like planet, over a period of (say) four billion years? Is it moderately probable, astronomically improbable, or somewhere in between?

Professor Tour debunks abiogenesis

(a) The current state of scientific ignorance

In his talk, Professor Tour was refreshingly candid about how little scientists know, not only about the origin of life, but also about the origin of the basic building blocks of life:

We have no idea how the molecules that compose living systems could have been devised such that they would work in concert to fulfill biology’s functions. We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids and proteins, were made and how they could have coupled in proper sequences, and then transformed into the ordered assemblies until there was the construction of a complex system, and eventually to that first cell. Nobody has any idea on how this was done when using our commonly understood mechanisms of chemical science. Those who say that they understand are generally wholly uninformed regarding chemical synthesis.

From a synthetic chemical perspective, neither I nor any of my colleagues can fathom a prebiotic molecular route to construction of a complex system. We cannot even figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids and proteins. Chemists are collectively bewildered. Hence I say that no chemist understands prebiotic synthesis of the requisite building blocks, let alone assembly into a complex system.

That’s how clueless we are. I’ve asked all of my colleagues: National Academy members, Nobel Prize winners. I sit with them in offices. Nobody understands this. So if your professor says, “It’s all worked out,” [or] your teachers say, “It’s all worked out,” they don’t know what they’re talking about. It is not worked out.

(b) The difficulties involved in making structures, such as nanocars, which are far simpler than living organisms

Professor Tour then provided his audience with a highly entertaining presentation of his work in designing nano-sized cars (one of which is pictured above), constructed from individual atoms. The key points in his discussion were that a great deal of foresight was needed to complete the task, and even then, it wasn’t smooth sailing: there were a lot of setbacks. Making even minor changes in function to the nanocars often necessitated going back to square one and redesigning them from scratch: something which an unguided process is incapable of doing. Additionally, synthesizing the various products at the desired level of purity was excruciatingly difficult process. Finally, the reagents had to be mixed in a very specific sequence, in order to get the desired product. But the task of building life is far more complex than that of building nanocars, as Tour openly acknowledged:

Some may contend that [in making nanocars], I did not use Nature’s building blocks, such as carbohydrates, amino acids, nucleic acids and lipids. I concede, I took the easy route and used simple synthetic molecules, not Nature’s far more complex compounds where chirality and diastereoselectivity can be enormously problematic in synthesis. Thus here we will consider Nature’s building blocks, showing that many of the common parameters hold, yet they become far more difficult for prebiotic systems than for the synthetic chemist today.

(c) Eleven enormous obstacles confronting unguided processes, in generating even the basic building blocks of life

In his talk, Professor Tour decided to focus on the origin of just one of the four basic building blocks of life: carbohydrates. He then proceeded to list eleven enormous hurdles faced by any blind, unguided process, in generating these compounds:

Let us begin at ground zero with the construction of one basic building block of life: carbohydrates.… So we will just consider the basic building blocks, carbohydrates, prior to their polymerization which requires enzymes… DNA and RNA are like beads hanging on a string. You’ve got to have the string. You’ve got to have carbohydrates…

The 11-point details with Nature’s constructs

1. A choice of target was needed for the nanocars. How do we know what to target? Towards which structure do we optimize to have an adequately functional system for a task? Take for example the pentose sugars, one of the more common carbohydrate sizes, and that used for DNA and RNA.

Pentose sugars have three stereogenic centers, so eight possible isomers (substructures, some being the enantiomers which are mirror-image related and the others being diastereomers which involve subtle orientational differences), and all are chiral, meaning [that] they have a nonsuperimposable mirror image. But what if we do not know the target, then the complexity of the problem would certainly be compounded.

Specifically, we needed a five-carbon sugar, D-(-)-ribose in particular, selected from the set of eight possible pentoses. Further, for DNA, it has to be one hydroxyl group deficient, or deoxyribose. If it is not, then it will be suitable for RNA, but far less stable. But prebiotic systems never knew any of this; there was a blinded pathway to a host of products, somehow selecting the one desired long before any selection agent could have been biologically available. And what are the selection criteria? It is hard to know if we do not know the target. And even if the target were known, the selector would be another molecule at least as complex as the desired analyte [a chemical substance that is the subject of chemical analysis – VJT]. And what selected the selector?

2. Solubility problems were confronted in the nanocar. Same problem for abiogenesis.

3. Molecular flexibility (a less rigid chassis) was needed… This was part of the redesign needed. Prebiotic chemistry would have to do the same, redesigning structures when desired function (and what is desired function since no target was foreseen?) was not realized. Thus much of [the] work that was done to that point would likely have to be discarded, increasing the difficulty for a prebiotic system.

4. When we added a motor to the motorcars, the former chassis were not sufficient to accommodate the motors. Likewise, in prebiotic chemistry, this again sends the system back to the beginning.

5. When we desired to go from a slow motor to a fast motor, though the stator was reusable, the rotor was not. The rotor had to be redesigned, from step one, so as to become a faster unidirectional rotor. In prebiotic systems, for small changes, we cannot use a blackboard to delete atoms or to insert atoms. Often redesigns are needed which send the system back to the origin of the synthesis. This is further exacerbated by the fact that there is no specified target in abiogenesis. [As I explained above, the target in abiogenesis is a general one, rather than a predefined one – VJT.]

6. Just as our motor no longer functioned when the original wheels were present, and we did not realize it until the synthesis was complete, any prebiotic system is destined, at least some of the time, to experience such a disappointment, thereby sending the system back to the beginning. But it does not know how to stop it current course of progression, or why to stop. The prebiotic system will continue to make derivatives of nonfunctioning entities.

7. To get chemical reactions occurring in high yield is difficult. In our synthetic case, we design the reactions to minimize diastereomic mixtures that can be nearly impossible to separate. Hence, even with all of our developed separation protocols and equipment, we try our best to avoid the undesired diastereomers because the separations are too time-consuming and expensive. Plus they waste a huge amount of the starting materials generating unwanted products. And enantiomeric separations are all the more difficult. Nature has chosen a far harder route, using only one enantiomer (homochiral) in a system with multiple stereogenic centers.

8. In the synthesis of the nanocars, we had the convenience of the JIT [just-in-time] delivery of chemicals, and storage of intermediates in safe and stable conditions until needed for the next step… In the laboratory, as anywhere else, it is essential to stop a reaction before the desired product degrades… Time is your enemy, when you’re making kinetic products…. Thus after a few years, which is a brief moment in time by prebiotic terms, there would be little if any of the pentoses left, let alone the more rapid loss of the desired ribose 2,4-diphosphate… Prebiotic chemistry is extremely difficult to perform even for the world’s best synthetic chemists like Eschenmoser, so he chose a more convenient model study system.

9. Reagent addition order is critical as seen in the detailed experimental protocols. In other words, A needs to be added before B and then C, and each at its own specific temperature to effect a proper reaction and coupling yield.

10. The parameters of temperature, pressure, solvent, light or no light, pH, oxygen or no oxygen, moisture or no moisture, have to be carefully controlled to build complex molecular structures. Unless one can devise sophisticated promoters or catalysts that are stable in air and moisture and can work at common atmospheric conditions, precise control must be maintained.

11. The characterization at each step is essential, and even more so if we ever have to bring up more material for the synthesis.

Summary of the 11 criteria

Therefore, small changes in ultimate functioning require major rerouting in the synthetic approaches. All changes, when doing chemistry, are hard and cannot be done by the usual hand-waving arguments or simple erasures on a board. Laborious and intentional elements of forethought are required.

(d) Why chemists need to resort to reverse engineering, in order to resolve problems regarding life’s origin

Next, Professor Tour explained why chemists need to engage in reverse engineering, when trying to synthesize desired products:

Why do synthetic chemists use retrosynthetic approaches to build complex molecules? Because without the retrosynthetic approach, discerning one’s way to desired products is far too complex, leading to dead-ends that are overwhelmingly abundant, generating massive amounts of undesired products, and exhausting precious supplies that might have taken huge efforts to prepare. But Nature cannot perform retrosynthetic analyses, if we presuppose that the starting points progressed to a non-predefined endpoint. Again, this is utterly perplexing for the synthetic chemist.

How could this have happened in prebiotic chemistry? How do you go from a starting material to a product that’s a complex product? What we do is we work our way back slowly. But Nature doesn’t know what its product is going to be at the end! It doesn’t know! It’s just blindly going along.

(e) The ultimate problem: even if you had all the ingredients of life, they can’t assemble without enzymes

Professor Tour provided the final coup de grace in his expose of current scientific theories regarding abiogenesis. It turns out that even if you could get all the ingredients of life together, at a high level of purity, and store them over long periods, they can’t assemble without enzymes:

Let us assume that all the building blocks of life, not just their precursors, could be made in high degrees of purity, including homochirality where applicable, for all the carbohydrates, all the amino acids, all the nucleic acids and all the lipids. And let us further assume that they are comfortably stored in cool caves, away from sunlight, and away from oxygen, so as to be stable against environmental degradation. And let us further assume that they all existed in one corner of the earth, and not separated by thousands of kilometers or on different planets. And that they all existed not just in the same square kilometer, but in neighboring pools where they can conveniently and selectively mix with each other as needed.

Now what? How do they assemble? Without enzymes, the mechanisms do not exist for their assembly. It will not happen and there is no synthetic chemist that would claim differently because to do so would take enormous stretches of conjecturing beyond any that is realized in the field of chemical sciences…

I just saw a presentation by a Nobel prize winner modeling the action of enzymes, and I walked up to him afterward, and I said to him, “I’m writing an article entitled: ‘Abiogenesis: Nightmare.’ Where do these enzymes come from? Since these things are synthesized, … starting from the beginning, where did these things come from?” He says, “What did you write in your article?” I said, “I said, ‘It’s a mystery.'” He said, “That’s exactly what it is: it’s a mystery.”

(f) Even a Dream Team of chemists wouldn’t know how to assemble life, if they had all the ingredients, including enzymes

As Professor Tour pointed out, what makes the puzzle of life’s origin all the more baffling is that even if you had a “Dream Team” of brilliant chemists and gave them all the ingredients they wanted, they would still have no idea how to assemble a simple cell:

All right, now let’s assemble the Dream Team. We’ve got good professors here, so let’s assemble the Dream Team. Let’s further assume that the world’s top 100 synthetic chemists, top 100 biochemists and top 100 evolutionary biologists combined forces into a limitlessly funded Dream Team. The Dream Team has all the carbohydrates, lipids, amino acids and nucleic acids stored in freezers in their laboratories… All of them are in 100% enantiomer purity. [Let’s] even give the team all the reagents they wish, the most advanced laboratories, and the analytical facilities, and complete scientific literature, and synthetic and natural non-living coupling agents. Mobilize the Dream Team to assemble the building blocks into a living system – nothing complex, just a single cell. The members scratch their heads and walk away, frustrated…

So let’s help the Dream Team out by providing the polymerized forms: polypeptides, all the enzymes they desire, the polysaccharides, DNA and RNA in any sequence they desire, cleanly assembled. The level of sophistication in even the simplest of possible living cells is so chemically complex that we are even more clueless now than with anything discussed regarding prebiotic chemistry or macroevolution. The Dream Team will not know where to start. Moving all this off Earth does not solve the problem, because our physical laws are universal.

You see the problem for the chemists? Welcome to my world. This is what I’m confronted with, every day.

(g) A call for scientific modesty

Professor Tour concluded his talk on a somber note:

Those that think scientists understand the details of life’s origin are wholly uninformed. Nobody understands. Maybe one day we will. But that day is far from today. So to make ad hominem attacks upon those who are skeptical of the science to-date can be inhibitory to the process if science. Would it not be helpful to express to students the massive gaps in our understanding so that they, as the next generation of academic soldiers, could seek to propel the field upon a firmer, and possibly radically different scientific basis, rather than relying on increasingly ambitious extrapolations that are entirely unacceptable in the practice of chemistry? The basis upon which we as scientists are relying is so shaky that it would be best to openly state the situation for what it is: a mystery.

Unmasking a recent example of scientific triumphalism on the origin of life

In the last few days, there has been much talk about a new paper in Nature Communications (vol. 7, article number 11328) by Brian Cafferty, David M. Fialho, Jaheda Khanam, Ramanarayanan Krishnamurthy and Nicholas V. Hud, titled, Spontaneous formation and base pairing of plausible prebiotic nucleotides in water. The abstract sounds very promising:

The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant beta-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life.

However, when one looks more carefully at the paper itself, it becomes apparent that the authors are glossing over the challenges that their proposed synthesis would have faced in the real world:

The ability of C-BMP and MMP to form supramolecular assemblies might have also facilitated the emergence of early RNA-like polymers by selecting nucleotides with sugars (or earlier trifunctional linkers) that were structurally compatible with the assemblies and their subsequent coupling into covalent polymers. In the present study, we have, for practical reasons, used D-ribose and D-R5P for our nucleoside and nucleotide reactions with melamine and BA, but L-ribose or L-R5P would exhibit equivalent reactivity with these two heterocycles. Nevertheless, it has been often postulated that a racemic mixture of nucleotides would have inhibited the prebiotic synthesis of RNA polymers(41), and so the question of how the present system might address this challenge deserves some discussion. Although we have not shown chiral nucleotide selection, in the current study we have demonstrated that the beta-anomer of MMP is enriched in supramolecular assemblies over the alpha-anomer of MMP, and this selection leads to a detectable increase in the ratio of the beta-anomer over the alpha-anomer of MMP in the entire solution (presumably due to anomerization and selective stabilization by the assembly). As a recent example of the ability of supramolecular polymers to promote local chiral resolution, Aida and co-workers demonstrated that racemic solutions of chiral macrocycles self-sort into homochiral supramolecular polymers(42). It is therefore possible that supramolecular assemblies, formed by nucleotides with different sugars, including different anomers and enantiomers, could have been selectively enriched in individual supramolecular assemblies before polymerization. Current investigations of this possibility are actively being pursued in our laboratory.

The paper by Aida et al. which the authors cite is titled, “Homochiral supramolecular polymerization of bowl‐shaped chiral macrocycles in solution” (Chem. Sci. 2014, 5, 136‐140). However, it turns out that the abstract is very modest, and does not support the sweeping conclusions drawn by Cafferty et al. in their article for Nature Communications:

Chiral monomers 1 and 2, carrying C4‐ and C3‐symmetric bowl‐shaped peptide macrocycle  cores, respectively, undergo supramolecular polymerization in solution via van der Waals  and hydrogen bonding interactions. Size‐exclusion chromatographic studies, using UV and CD detectors, on the supramolecular copolymerization of their enantiomers demonstrated that these monomers are the first chiral macrocycles that polymerize enantioselectively with a strong preference for chiral self‐sorting.

In other words, Aida et al. were talking about just two monomers, which are the first – and to date, the only – chiral macrocycles that are known to polymerize with a strong preference for chiral self‐sorting. (Note: a macrocycle is defined by IUPAC as “a cyclic macromolecule or a macromolecular cyclic portion of a molecule.”) To generalize from this solitary instance to the grandiose claim that “supramolecular assemblies, formed by nucleotides with different sugars, including different anomers and enantiomers, could have been selectively enriched in individual supramolecular assemblies before polymerization,” is going far beyond the available evidence.

How Professor Tour’s talk has created a new scientific research agenda for the Intelligent Design movement

One of the criticisms most frequently hurled at the Intelligent Design movement is that it solves the problem of origins by positing a science-stopper: “God did it,” or “A Designer did it.” After listening to Professor Tour’s talk, I had a kind of epiphany. I suddenly realized that Tour had created a perfect research agenda for the Intelligent Design movement: that of reverse-engineering life itself. If life was intelligently designed, then there is no reason in principle why scientists cannot retrace the steps whereby the first living cell was assembled. Indeed, Professor Tour himself, in response to a question from a member of the audience, expressed optimism that scientists would one day solve the question of life’s origin.

But what if scientists’ attempt to reverse-engineer life turns up empty-handed?

What if the attempt to reverse-engineer life fails?

In his talk, Professor Tour highlighted the immense difficulty of intelligently designing a living cell, even if we assembled a “Dream Team” of chemists, and gave them all the ingredients they could possibly ask for. Let’s imagine that after 50 years of searching for a plausible pathway that a Designer might have used to get from the chemical ingredients of life to a functional living cell, Intelligent Design scientists come up empty-handed. “We’ve followed up every promising avenue we could think of,” they say. “We’ve even used super-computers, with their advanced ‘look-ahead’ capabilities, to help us in our search. Nothing has worked, and there appears to be nothing that’s even remotely promising on the horizon, either.” What should we then conclude?

Here, I believe, is where it gets really interesting. Failures in science can tell us just as much as successes. If the attempt to find a guided pathway leading to the first living cell turns up empty-handed after a diligent search of all promising options, then the only remaining conclusion for us to draw is that life wasn’t assembled. That, however, does not mean that life wasn’t designed. Rather, what it means is that the first living cell was created holus-bolus, in its entirety.

A Transcendent Designer?

What kind of agent could create a living cell, in its entirety, without any intermediate steps? Certainly not a natural agent, that’s for sure. That only leaves an Agent Who stands outside the cosmos and Who created the entities we find within it: in other words, a supernatural Being.

What I’m suggesting here is that the scientific attempt to reverse-engineer life is a winner as an Intelligent Design project, no matter which way it pans out. If it succeeds, then Intelligent Design scientists will gain some well-earned kudos, as well as “street cred,” in the scientific community at large: they will have accomplished a feat that puts Watson and Crick’s discovery of the structure of DNA in the shade.

But if it fails, then the Intelligent Design movement will have a ready response to a theological charge which is often leveled against the Intelligent Design movement: that the Designer it points to is not the God of classical theism, but a mere architect. The discovery that life was (in all likelihood) not assembled, step by step, but created in its entirety, would strongly indicate that the Designer of life is a Transcendent Being.

In other words, what we have is a win-win situation for the Intelligent Design movement. All that remains is to get moving with the scientific project of trying to reverse-engineer a simple living cell, as soon as possible.

What do readers think?

280 Replies to “Origin of Life: Professor James Tour points the way forward for Intelligent Design

  1. 1

    I’m sorry to post off-topic, but some of you may remember Hannah Maxson, former Cornell student and founder of the Cornell IDEA club (now inactive). When she was here at Cornell I invited her to make presentations in my evolution course and to co-moderate my grad seminar in “design vs evolution in nature” (see http://www.uncommondescent.com.....ign-class/).

    To make a long story short, she went back to Mongolia (where she grew up) as a missionary, got married, and started a family. Two weeks ago her son Zackary (still a babe in arms) was horribly burned. He and Hannah are in the national hospital in Ulan Baator waiting for an emergency medical flight to the Shriners’ Hospital in Cincinnati. You can find out more by searching “Hannah Maxson” on FaceBook. She is asking for thoughts and prayers, and could use financial help as well.

    Here’s a link (hope it works): https://www.facebook.com/hannah.maxson?fref=nf

    Hannah and I had our differences, but they did not prevent us from becoming lasting friends. I hope that those who frequent this site may be able to help her out in some way.

  2. 2

    Also, the chairman of the Cornell Department of Ecology and Evolutionary Biology – Rick Harrison – who opposed my “design and evolution seminar” in 2006, died suddenly and unexpectedly while on a field trip in Australia (he was 70). So Cornell has lost both Will Provine – who championed open debate between creationists, ID supporters, and evolutionary biologists (as do I) – and the department chairman who opposed it are now both gone. I am still here, however, and planning on teaching my evolution course this summer (for the 15th year).

  3. 3

    Finally, I’m deep in the middle of writing two books that might be of interest to those at this site:

    • On Purpose: The Evolution of Design by Means of Natural Selection, or the Proliferation of Intentional Agents in the Struggle for Life (sound familiar?)

    and

    • The Metaphysical Foundations of the Biological Sciences

    These have consumed my life, which partly explains why I haven’t posted here in a long while.

  4. 4

    As for abiogenesis, I agree that it is not “all worked out” – indeed, I think it will never be so in either direction (i.e. design vs evolution). To me, this has almost no bearing on the current state of the theory of evolution, since the current theory of biological evolution assumes that life already exists and makes no direct claims about how this happened. Darwin himself never claimed to know how life originated (certainly not in any of his published works), but that didn’t stop him from proposing a theory about how life has evolved,

  5. 5

    Thank you for the information about your former student Allen, and for the link.

  6. 6

    As for abiogenesis, I agree that it is not “all worked out” – indeed, I think it will never be so in either direction (i.e. design vs evolution) …

    This is a punt. Rhetoric, to freeze the conversation and negate evidence.

  7. 7

    All that remains is to get moving with the scientific project of trying to reverse-engineer a simple living cell, as soon as possible.

    This is likely of some interest on this topic: “Here we report a new cell”

  8. 8
    Mung says:

    No such objection could possibly be made against Professor Tour’s talk…

    I’m not so sure about that. Over at “The Skeptical Zone” they tried to employ the “it’s what he didn’t say” argument. I cant’ wait for that one to hit the courts.

  9. 9
    Mung says:

    So the scientific question we have to address is: how improbable is the emergence of life on an Earth-like planet, over a period of (say) four billion years?

    Why four billion years? The earth is estimated to be about 4.5 By old and life has existed on earth for the vast majority of that time.

  10. 10
    tjguy says:

    Allen MacNeill @4

    As for abiogenesis, I agree that it is not “all worked out” – indeed, I think it will never be so in either direction (i.e. design vs evolution).

    So Dr. MacNeill, are you saying that you are open to the possibility of intelligent design when it comes to abiogenesis?

    It won’t ever be solved? You are probably right.

    Design enthusiasts can never prove that it didn’t/couldn’t happen because you can’t prove a negative.

    The best they can do is to show that for all practical purposes, it looks impossible. And personally, I think they can give pretty good data to support the design thesis! All you have to do is to listen to Professor Tour’s talk.

    I think it is fair to say that as of now, the data fits so much better in a design paradigm than a Materialist paradigm, wouldn’t you agree?

    To me, this has almost no bearing on the current state of the theory of evolution, since the current theory of biological evolution assumes that life already exists and makes no direct claims about how this happened.

    I certainly understand that, however, I think you are overlooking one big thing here.

    IF life was designed, then how do you know the Designer was not involved in the evolution of that first cell into all the varied lifeforms we see today?

    How do you know?

    Why would you assume that this Designer, if they designed the first cell would be hands off from then on?

    I don’t think this is a valid assumption at all. It doesn’t make sense in my mind. In fact, it would make more sense to assume the Designer probably did have a role in the evolution of life from cell to humanity. Opinions may differ and that’s fine.

    But the point is that this calls into question the whole foundational assumption of Materialism and methodological naturalism that every effect has a totally natural cause.

    Therefore, I think the origin of life problem is very important because the answer to that question will influence how we look at the data and interpret the data when it comes to evolution.

  11. 11
    Mung says:

    All that remains is to get moving with the scientific project of trying to reverse-engineer a simple living cell, as soon as possible.

    I agree that this ought to be seen as ID research and that a research program like this would look good in the ID portfolio.

    I’ve long thought that we should stop arguing about common descent and concentrate on the simplest cells. Common descent is not a mechanism for generating novelties, so arguing about it is of no benefit to ID.

    But would researchers associated with ID be welcomed by the OoL community?

  12. 12
    Mung says:

    Thanks Allen.

  13. 13
    vjtorley says:

    Hi Allen MacNeill,

    Thank you very much for your posts. I’m not on Facebook, but did some searching on the Internet. Is this the Hannah Maxson you were referring to? It seems that her baby’s name is Zachary Anchin. I would urge any readers who are financially able to contribute to do so.

    https://www.facebook.com/humansofnewyork/posts/10154195344339319 (I can’t access the site.)

    I was sorry to hear that Rick Harrison had passed away. As you know, Will Provine got a highly respectful obituary over at ENV.

    I look forward to the release of your two books, On Purpose: The Evolution of Design by Means of Natural Selection, or the Proliferation of Intentional Agents in the Struggle for Life and The Metaphysical Foundations of the Biological Sciences.

  14. 14

    Here is Hannah Maxson’s contribution page for her son:

    https://www.gofundme.com/operationzachary

  15. 15
    ziggy lorenc says:

    Just so I know the ground rules here, if humans travelled to another planet and seeded it with an handful of selected bacteria (not modified), and the life deposited evolved into multicellular forms, would we consider life on that planet to have been designed?

  16. 16
    vjtorley says:

    Hi Upright Biped,

    Thanks very much for the link to Operation Baby Zachary in Ulanbator:

    https://www.gofundme.com/operationzachary

    The target is $20,000, of which $13,600 has been raised so far (at the time of writing).

    Thanks also for the link you provided to your recent post about Dr. Craig Venter’s research on building a cell:

    http://www.uncommondescent.com.....-new-cell/

    Very thought-provoking.

  17. 17
    vjtorley says:

    Hi ziggy lorenc,

    Thank you for your post. I would answer your question by saying that selection is not the same thing as design. I might add that Professor James Tour stated early on in his talk that he would not be considering panspermia as an explanation for the origin of life, because it pushes back the question.

  18. 18
    vjtorley says:

    Hi Mung,

    I’m sorry to hear that your post about Professor Tour’s talk was so poorly received over at the Skeptical Zone. I was particularly amused to read the remarks written by sophomoric commenters who claimed that Tour wasn’t qualified to talk about the problem. For the record, Tour was named among “The 50 most Influential Scientists in the World Today” by TheBestSchools.org in 2014, and he was also named “Scientist of the Year” by R&D Magazine in 2013. As if that were not enough, Tour was ranked one of the top 10 chemists in the world over the past decade by Thomson Reuters in 2009, the year in which he was also made a fellow of the American Association for the Advancement of Science.

    Re my four-billion-year time period, I was deliberately being generous. Actually, it seems that life may have begun on Earth as far back as 4.1 billion years ago, just 300 million years later than the date for the oldest known Earth rock:

    http://www.livescience.com/525.....s-ago.html

  19. 19
    gpuccio says:

    ziggy lorenc:

    “Just so I know the ground rules here, if humans travelled to another planet and seeded it with an handful of selected bacteria (not modified), and the life deposited evolved into multicellular forms, would we consider life on that planet to have been designed?”

    Well, there are different problems here:

    1) The origin of prokaryota would not be explained (humans did not design the bacteria)

    2) The arrival of prokaryota on that planer would be designed (by humans)

    3) The following evolution of bacteria on that planet, if observed to happen without any design intervention, would prove that evolution of life can happen without design. I don’t believe it would happen, however.

  20. 20
    john_a_designer says:

    I posted a link to Dr. Tour’s talk at Thinking Christian.

    https://www.thinkingchristian.net/posts/2016/04/falsification-and-theology-continuing-a-topic-raised-by-feser/#comment-121841

    Like Tour I see a distinction between ID as a philosophical position (Phil-ID) and a scientific one (Sci-ID). I have no problem with the former. I do with the latter. In my opinion ID at present is in pretty much in the same position as is SETI. To be considered a science it first must make a key discovery. Neither SETI nor ID has so far crossed that threshold.

    The Thinking Christian thread deals with the question whether basic philosophical assumptions are falsifiable. For example is the existence of God falsifiable? I would argue that it is not.

    I think Tour is making a similar claim when it comes to OoL.

    Watch his lecture and see if he claims that because we do not know how life originated that this necessarily falsifies the hypothesis that the origin of life can be explained naturalistically. His argument for this lecture is simply that nobody knows but also sadly there are a lot of influential scientists who are unwilling to be honest about that fact.

    However, if we compare explanations on the basis of one’s world view—theism vs. naturalism, for example—I would argue that theism AS A WORLD VIEW has more explanatory scope and power than naturalism. Indeed, theism as a world view has the best explanation for not only the origin of life but for the origin of the universe as well as mind and consciousness. While in the above lecture Tour was limiting himself to simply the science, as an out spoken Christian himself I think he would undoubtedly agree with me that theism is a better explanation than naturalism or any other world view.

    In other words, unlike certain kinds of hypotheses in science, the basic assumptions of any logically possible world view are unfalsifiable. One can only argue for a world views truth by abductive inference— inference to the best explanation.

  21. 21
    bill cole says:

    ciao gpuccio

    “Just so I know the ground rules here, if humans travelled to another planet and seeded it with an handful of selected bacteria (not modified), and the life deposited evolved into multicellular forms, would we consider life on that planet to have been designed?”

    Well, there are different problems here:

    1) The origin of prokaryota would not be explained (humans did not design the bacteria)

    2) The arrival of prokaryota on that planer would be designed (by humans)

    3) The following evolution of bacteria on that planet, if observed to happen without any design intervention, would prove that evolution of life can happen without design. I don’t believe it would happen, however.

    Regarding this thought experiment. If we seeded another planet that is similar to earth in make up with bacteria my prediction is that 2 billion years later we would have bacteria. If a that point we seeded fish and returned 2 billion years later we would have fish and bacteria. If then we seeded mice and returned in 300 million years we would have bacteria, fish and mice. The problem with a unified theory of life is we are not dealing with a single origin event but millions of them. What is the mechanism that can drive a theory?

  22. 22

    Hi JAD,

    Neither SETI nor ID has so far crossed that threshold.

    What would you consider a discovery?

  23. 23
    john_a_designer says:

    Upright BiPed.

    With SETI: a signal, an ET probe or artifact… or a visit.

    With ID: clear evidence of pre-programming. For example, genetic pre-programming that would lead more or less directly from prokaryote to eukaryote and then on to multi-cellular evolution. This would be hard, if not impossible, to explain by Darwinian evolution. There is some suggestion of this already but it has been directed out-of-hand by Darwinian group think. I’m surprised that ID researchers aren’t looking into this. Maybe they are and I haven’t heard about it.

  24. 24
    Zachriel says:

    vjtorley: If the attempt to find a guided pathway leading to the first living cell turns up empty-handed after a diligent search of all promising options, then the only remaining conclusion for us to draw is that life wasn’t assembled.

    That is incorrect. Only if we can show that we have exhausted the universe of possibilities, and not just the limits of human technical and scientific capabilities, would such a negative argument have merit.

  25. 25
    Origenes says:

    Allen_MacNeill: As for abiogenesis, I agree that it is not “all worked out” – indeed, I think it will never be so in either direction (i.e. design vs evolution).

    Alright then, let’s call it a draw.

    BTW I have this theory that Iphones self-assemble/’evolve’ from scrap metal. My wife doesn’t agree and holds that Iphones are designed. I have to admit that it is not “all worked out” – indeed, I think it will never be so in either direction (i.e. design vs evolution).
    Oh well, just another draw.

  26. 26
    gpuccio says:

    bill cole:

    I agree. I don’t believe that even a single new species can appear without a design intervention.

    Technically, ID theory implies that no new complex functional information can be generated without a conscious design intervention. Therefore, even one single new complex functional protein is evidence of design. This is what I call “strong ID theory”, and it is absolutely my personal and convinced position.

    However, it is equally true that there in natural history some special transitions which scream design with much greater strength than all the rest, because they imply such a jump in information that any alternative explanation is simply and obviously a folly.

    The main examples of such huge transitions are. IMO:

    1) OOL. For obvious reasons.

    2) Eukaryogenesis. This is often overlooked, but believe me, the quantity of new information necessary to explain the appearance of eukaryotes is so astonishing that whoever says that we understand how that happened is as much a liar as whoever says that we understand OOL.

    3) Origin of metazoa and of animal phyla. IOWs, the Ediacaran and Cambrian explosions.

    There are certainly many other important examples, but those three are really amazing.

  27. 27
    gpuccio says:

    Origenes:

    As in other occasions, I have to disagree with Allen MacNeill: it is perfectly worked out, and only design can explain it.

  28. 28
    JDH says:

    Allen McNeil – Let me start by offering condolences for your losses.

    BUT then you had to say something which, sorry for the direct language, I consider really foolish. I have messaged back and forth with you before sir and found you intelligent and competent. That’s why such an odd statement concerns me.

    To me, this has almost no bearing on the current state of the theory of evolution, since the current theory of biological evolution assumes that life already exists and makes no direct claims about how this happened

    Let me please point out clearly why I don’t think this is logical.

    1. It would be ok to use your language if both disciplines did not have the same unremovable assumptions. For example, a theory of how the wheel was invented would have no bearing on an argument about who invented the car. So one could say, “To me, this has almost no bearing on the current state on the theory of who was the first to invent a working automobile, since the current theory of the history of the car assumes that the wheel already existed and makes no direct claims about how this happened.

    This is in sharp contrast to Evolution and OOL which both presume no intervention by GOD or any other intelligent designer. As a matter of fact, both theories propose things which under current knowledge could not have happened without divine intervention. They are precisely related because both Evolution and OOL are modern man’s desperately foolish attempt to get around the impossibly long odds of life coming to be without a designer.

    Who invented the wheel has no bearing on a theory about the car.

    If it is shown that the odds of life coming about without a designer is hopelessly improbable, then the theory of evolution is moot. Both Evolution and OOL are suggested because they are the only alternative to creation. IF OOL is false, then there is no reason to stick with the impossibilities of the theory of evolution.

  29. 29

    JAD at #23.

    I would suggest that both SETI and ID in this instance are searching for different manifestations of the same phenomena. Only ID has found it.

    http://biosemiosis.org/index.p.....-of-design

  30. 30
    Daniel King says:

    gpuccio:

    As in other occasions, I have to disagree with Allen MacNeill: it is perfectly worked out, and only design can explain it.

    “Perfectly worked out,” indeed.

    In what way is “design” an explanation?

    Lay those who, what, when and how details on us, please.

  31. 31
    Seversky says:

    Professor James Tour’s recent video, The Origin of Life – An Inside Story, managed to accomplish three things at once: it shattered the credibility of abiogenesis as a theory;…

    There’s a Theory of Abiogenesis? Why does nobody tell met these things?

    … it provided American high school science teachers with an excellent classroom resource for countering evolutionary propaganda;…

    I don’t see how. The theory of evolution isn’t about the origins of life.

    and (perhaps unintentionally), it set a new research agenda for the Intelligent Design movement, which will transform it into a bona fide scientific discipline: the task of reverse-engineering life itself.

    So ID isn’t a bona fide scientific discipline as it stands?

    Okay, all joking aside, I’m all for ID devoting whatever scientific resources it can muster to the task of reverse-engineering life itself. That enterprise needs all the help it can get.

  32. 32
    Mung says:

    In what way is “design” an explanation?

    In what way is “troll” an explanation?

  33. 33
    gpuccio says:

    Daniel King:

    It’s very simple. Allen MacNeill’s statement was:

    “As for abiogenesis, I agree that it is not “all worked out” – indeed, I think it will never be so in either direction (i.e. design vs evolution).”

    So, the problem referenced here is the kind of process driving OOL, not the details of its natural history.

    IMO, that is perfectly worked out: we already have huge evidence of the amount of functional information implied in OOL and of the impossibility to get that result through unguided evolution. Science can already give a fact supported inferential judgment on that point: design did it.

    This is my position, and it is obviously very different from MacNeill’s position, which seems to be that science will never be able to decide on that point.

    Design is an explanation for the huge amount of functional information implied in OOL, because design is the only known process capable of generating huge amount of complex functional information. It’s as simple as that.

    You ask “who, what, when and how details”. But I never said that the details are worked out. They obviously are not, neither for an explanation based on unguided evolution nor for an explanation based on design. But U an sure that, once the correct process is accepted and recognized in scientific approach, details will be found.

    So again, for clarity, what IMO is “all worked out” is the problem of deciding between design and unguided evolution as a credible scientific explanation for OOL.

  34. 34
    Bob O'H says:

    Let’s imagine that after 50 years of searching for a plausible pathway that a Designer might have used to get from the chemical ingredients of life to a functional living cell, Intelligent Design scientists come up empty-handed. “We’ve followed up every promising avenue we could think of,” they say. “We’ve even used super-computers, with their advanced ‘look-ahead’ capabilities, to help us in our search. Nothing has worked, and there appears to be nothing that’s even remotely promising on the horizon, either.” What should we then conclude?

    That Bertrand Russell was wrong about the chicken:
    “The man who has fed the chicken every day throughout its life at last wrings its neck instead, showing that more refined views as to the uniformity of nature would have been useful to the chicken.”
    The more refined version of this argument is to ask when do you stop looking for abiogenetic explanations. How can you have a stopping rule that guards against you not having the imagination to find the actual explanation?

    Basically, your suggestion is similar to the approach taken by ID: try to show that X doesn’t happen, and so conclude that Y must have.

    There’s also a political (with a small p) problem. Proponents of ID start with the claim that abiogenesis didn’t happen on its own. So there may be some scepticism about IDists then claiming that they have shown that abiogenesis didn’t happen on its own. This relates to the stopping rule: you have to have one that will convince people that you have been thorough.

  35. 35
    Dionisio says:

    vjtorley

    Very interesting article. Thank you for posting it.

    In other words, what we have is a win-win situation for the Intelligent Design movement. All that remains is to get moving with the scientific project of trying to reverse-engineer a simple living cell, as soon as possible.

    What do readers think?

    reverse-engineer a simple living cell?

    How would that look like, from your own perspective?
    What would it take, in your own opinion?

    BTW, your interesting proposition reminded me of a related story:

    Back during the so called ‘cold war’ reverse-engineering was part of the ‘game’ -at least on the red corner of the boxing ring.

    The then powerful IBM 360/370 mainframe systems were literally reverse-engineered into the “Edinaya Systems” (EC-1020, EC-1030, EC-1040, etc). DEC PDP minicomputers were reverse-engineered into minicomputers produced behind the so called ‘iron curtain’. Those systems were technologically several years behind their sources, but still worked (kind of). The technical documentation, specially regarding the software, were literally copied and sometimes translated.

    That reverse-engineering was a very important high-priority project that received strong support from the highest hierarchies of the political structure.

    Apparently it took a number of dedicated engineers and scientists working tirelessly on trying to understand the information that was either provided by IBM and DEC or simply acquired somehow by other means.

    Since the source systems were designed in a top-down approach, the reverse-engineering process also followed a top-down path.

    Would the work done by Dr. Venter’s organization suitable for being considered as a source of information for the reverse-engineering project?

    Currently, the best information available on the intricacies of the biological cells and multicellular systems comes -in overwhelmingly increasing volumes- from scientific research done in both wet and dry labs around the world using mainly what seems like a bottom-up approach, kind of like looking for a black cat in a completely dark room, assuming the cat is in the room.

    One observable problem seen in some interesting research papers is that the researchers get easily ‘surprised’ by ‘unexpected’ discoveries they report. That could indicate that their research is not done completely open-minded, i.e. perhaps they don’t think completely out of the box. That ‘biased’ approach (with la priori’ expectations) could unnecessarily slow down the research process and delay some important discoveries.

    However, since that is the source of the bulk of reliable scientific data one can rely on -even taking into account the problems in the peer-review publications –so well (and humorously) documented here in UD by Ms. Denyse O’Leary– the ID reverse-engineers must review/study the available research papers in order to clearly understand the state of affairs in biology.

    Also, wouldn’t you consider the interesting information posted here in UD by GP, UB and other folks in the ID heterogeneous society as examples of what must be researched for the reverse-engineering task?

    Wouldn’t the reverse-engineers have to identify -in a top-down approach- all the components, their functions, their interconnections, how exactly they are assembled, how they work, what makes them robust with respect to different kinds of noisy stochastic environments, all that and more in order to do what you suggested?

  36. 36
    gpuccio says:

    Bob O’H:

    There can never be a stopping rule in science, because no scientific theory, however good and supported by known facts, will ever be final. That is an important epistemological point.

    So, the problem is not “when do you stop looking for abiogenetic explanations”. You never stop, if you think you can find one some day. That is really a false problem.

    The real problem is simply: what is the best scientific explanation according to what we know today?

    And the best explanation is design.

  37. 37
    Origenes says:

    Gpuccio: So again, for clarity, what IMO is “all worked out” is the problem of deciding between design and unguided evolution as a credible scientific explanation for OOL.
    (…)
    The real problem is simply: what is the best scientific explanation according to what we know today?

    And the best explanation is design.

    I fully agree and I hold that everyone does. Everyone — Allen_MacNeill, Zachriel, Dawkins, Coyne and so forth — agrees that design is the best scientific explanation according to what we know today.

    There is only one problem with this ….

    most of them have metaphysical reasons to reject intelligence as a cause.

  38. 38

    Thank you, Dr. Tour.

  39. 39
    john_a_designer says:

    Upright BiPed @ 29,

    Like I said earlier I wholeheartedly agree with Phil-ID. The problem of how a semiotic code got into early self-replicating life forms is a big problem for Darwinian materialists—no argument there. However, pointing out problems is not the same as providing a scientific explanation. The problem at the moment is not the ID argument, as far as it goes, but the ideological blindness and political bullying of the materialists. The best argument we can make for the time being is what Tour is doing. Essentially he is asking “HOW did this evolve naturalistically?” If the Darwinian “theory” is indeed a truly scientific explanation shouldn’t its proponents be able to answer that question?

    My short term prediction: the “scientific” materialists commenting here will try to switch the HOW in my question above to some version of “could”. But that turns the question into a philosophical one. I am interested in whether they have a truly scientific answer. The honest person can admit when they are bluffing. Honest people seek the truth where ever it leads them.

  40. 40
    PeterJ says:

    John @ 39

    Very well put.

    I look forward to the materialist response.

    Perhaps Nick Matzke could provide one?

    After all isn’t it this very problem he seems to think he can answer.

  41. 41
    Origenes says:

    john_a_designer: Like I said earlier I wholeheartedly agree with Phil-ID. The problem of how a semiotic code got into early self-replicating life forms is a big problem for Darwinian materialists—no argument there. However, pointing out problems is not the same as providing a scientific explanation.

    Indeed, however you labour under the assumption that pointing out problems is all that ID does. You are mistaken. ID offers a cause which, according to repeated experience, is capable of generating the kind of information necessary to produce life — e.g. semiotic codes — : intelligence.

  42. 42
    Mung says:

    Perhaps Nick Matzke could provide one?

    After all isn’t it this very problem he seems to think he can answer.

    No, Nick was going to provide the chemical basis of macroevolution.

    Over at TSZ someone remarked that is a fool’s errand. Doesn’t that make Nick the perfect person for the job though?

  43. 43
    Zachriel says:

    gpuccio: The real problem is simply: what is the best scientific explanation according to what we know today? And the best explanation is design.

    “Design” lacks the specificity and entailments to call it a scientific explanation. Rather, it’s a fallback position due to the limitations of abiogenetic knowledge, something which was made explicit in the original post.

    vjtorley: If the attempt to find a guided pathway leading to the first living cell turns up empty-handed after a diligent search of all promising options, then the only remaining conclusion for us to draw is that life wasn’t assembled.

  44. 44
    Zachriel says:

    Origenes: most of them have metaphysical reasons to reject intelligence as a cause.

    Our reasons for rejecting a scientific claim of “intelligence as a cause” of life are scientific, not metaphysical.

  45. 45
    Origenes says:

    Zachriel: Our reasons for rejecting a scientific claim of “intelligence as a cause” of life are scientific, not metaphysical.

    And what are those scientific reasons for this rejection?

  46. 46
    Zachriel says:

    Origenes: And what are those scientific reasons for this rejection?

    The primary problems with a scientific claim of “intelligence as a cause” of life are the lack of specified mechanisms, and the lack of testable entailments.

  47. 47
    Origenes says:

    Zachriel,
    What are the specified mechanisms and testable entailments of intelligent design as cause of the Antikythera mechanism, Stonehenge, an extraterrestrial artificial signal or the Mona Lisa?

  48. 48
    Zachriel says:

    Origenes: What are the specified mechanisms and testable entailments of intelligent design as cause of the Antikythera mechanism, Stonehenge, an extraterrestrial artificial signal or the Mona Lisa?

    The Antikythera mechanism was found in a Roman shipwreck, is made of bronze, had Greek inscriptions, and included a cycle for the Olympiads. Let’s venture a guess that it was manufactured by a peculiar form of ape that was prevalent at the time in that area of the planet Earth, who are known to have worked in brass, to have had a great interest in the movements of the planets, and held regular athletic competitions.

    Need we go on? Do you want a citation to a study of Greek bronze-working?

  49. 49
    Origenes says:

    Zachriel, you did not answer the question. Kindly provide a list of the specified mechanisms and testable entailments of intelligent design as the cause of the Antikythera mechanism.

  50. 50
    Zachriel says:

    Origenes: Kindly provide a list of the specified mechanisms and testable entailments of intelligent design as the cause of the Antikythera mechanism.

    What part of “Greeks bearing tools” did you not understand?

  51. 51
    Origenes says:

    Zachriel, I’m not sure I understand. Are you saying that Greek bearing tools designed the Antikythera mechanism?

  52. 52
    Mung says:

    In what way is “Greeks with tools” an explanation?

  53. 53
    Mung says:

    Rather, it’s [design is] a fallback position due to the limitations of abiogenetic knowledge, something which was made explicit in the original post.

    IOW, design is the current best explanation. So until someone comes up with a better explanation, design has it.

  54. 54
    Origenes says:

    Zachriel,
    I would like a list of the specified mechanisms that were involved during the design the Antikythera mechanism. So we are talking about the stage of design, don’t bother about the subsequent manufacturing process. And please provide a list of testable entailments.

  55. 55
    gpuccio says:

    Zachriel:

    ““Design” lacks the specificity and entailments to call it a scientific explanation. Rather, it’s a fallback position due to the limitations of abiogenetic knowledge, something which was made explicit in the original post.”

    Trivial propaganda. Completely untrue, as shown many times here.

    Design detection is a science. In the presence of true complex functional information, design can be safely inferred and is the best explanation.

    Of course the hypothesis of detectable design has entailments, and in biology the main entailment is that all cases of major evolution of species, including OOL, imply a huge amount of complex functional information.

    Your hope that evolutionary pathways will one day be found has really no entailments at all, because even if we go on not finding them for ceturies, which is all that we can expect if they don’t exist, you can go on hoping that they will one day be found. So, it’s your position which is not scientific, and nased only on personal faith and commitment.

    Therefore, the reasons why you reject design detection in biology are purely metaphysical. QED.

  56. 56
    Zachriel says:

    Origenes: I would like a list of the specified mechanisms that were involved during the design the Antikythera mechanism. So we are talking about the stage of design, don’t bother about the subsequent manufacturing process. And please provide a list of testable entailments.

    Manufacture is a necessary entailment of saying some thing is designed. That’s the whole point. The entailments are the who, what, when, where, why, and how.

    Origenes: Of course the hypothesis of detectable design has entailments, and in biology the main entailment is that all cases of major evolution of species, including OOL, imply a huge amount of complex functional information.

    Leaving aside the ambiguity of quantifying complex functional information, evolution results in complex functional structures, so it provides an alternative explanation, but one with specific and testable entailments.

  57. 57
    bill cole says:

    Zachriel

    Leaving aside the ambiguity of quantifying complex functional information, evolution results in complex functional structures, so it provides an alternative explanation, but one with specific and testable entailments.

    This is true but the problem is that the overall claim of known mechanisms causing diversity has not been successfully tested and is almost certainly wrong.

  58. 58
    es58 says:

    Allen MacNeill wrote:

    To me, this has almost no bearing on the current state of the theory of evolution, since the current theory of biological evolution assumes that life already exists and makes no direct claims about how this happened.

    The earliest life we know is extremely complex. Somehow we got from OOL to current life. Wherever the OOL leaves off, evolution had to fill in the rest. It’s a continuum. If OOL left off somewhere with, eg: less than 4 bases, then evolution had to get you to from less than 4 bases, to 4 bases, before it could start doing everything else that is claimed on its behalf.

    If OOL was designed, there’s no real reason to assume other things weren’t.

    If original OOL reached a point far less complex than the earliest forms we know (making it more plausible), evolution had to do much more than is currently claimed.

    Either way, the 2 seem inextricably linked.

  59. 59
    Bob O'H says:

    gpuccio @ 36 –

    There can never be a stopping rule in science, because no scientific theory, however good and supported by known facts, will ever be final. That is an important epistemological point.

    I agree with you on this, but VJ apparently does not. I think this is important to clear up: either he’s thought this through and has some clear idea of what such a stopping rule would look like, or he hasn’t, and theres a severe weakness in his proposal.

  60. 60
    Querius says:

    If you have a process comprising a series of steps, but the first step seems impossible, what do you focus on?

    Yep, everything except the first step.

    -Q

  61. 61
    bornagain77 says:

    Actually, there is a ‘stopping rule’ in science. It is called falsification/demarcation. The problem is that Abiogenesis and Darwinian Evolution both have no falsification or demarcation criteria that will tell us when to ‘stop’ using them as hypothesis in science and when to look for another hypothesis, whereas ID does have a falsification/demarcation criteria that tells us when to look for another hypothesis.

    “In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.”
    Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge

    “Darwinism is not a testable scientific theory, but a metaphysical research program.”
    Karl Popper – Unended Quest: An Intellectual Autobiography (1976)
    unsourced variant: “Evolution is not a fact. Evolution doesn’t even qualify as a theory or as a hypothesis. It is a metaphysical research program, and it is not really testable science.”
    Dubitable Darwin? Why Some Smart, Nonreligious People Doubt the Theory of Evolution By John Horgan on July 6, 2010
    Excerpt: Early in his career, the philosopher Karl Popper ,, called evolution via natural selection “almost a tautology” and “not a testable scientific theory but a metaphysical research program.” Attacked for these criticisms, Popper took them back (in approx 1978). But when I interviewed him in 1992, he blurted out that he still found Darwin’s theory dissatisfying. “One ought to look for alternatives!” Popper exclaimed, banging his kitchen table.
    http://blogs.scientificamerica.....evolution/

    Darwinian Evolution is a Unfalsifiable Pseudo-Science – Mathematics – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1132659110080354/?type=2&theater

    The Origin of Information: How to Solve It – Perry Marshall
    Where did the information in DNA come from? This is one of the most important and valuable questions in the history of science. Cosmic Fingerprints has issued a challenge to the scientific community:
    “Show an example of Information that doesn’t come from a mind. All you need is one.”
    “Information” is defined as digital communication between an encoder and a decoder, using agreed upon symbols. To date, no one has shown an example of a naturally occurring encoding / decoding system, i.e. one that has demonstrably come into existence without a designer.
    A private equity investment group is offering a technology prize for this discovery (up to 3 million dollars). We will financially reward and publicize the first person who can solve this;,,, To solve this problem is far more than an object of abstract religious or philosophical discussion. It would demonstrate a mechanism for producing coding systems, thus opening up new channels of scientific discovery. Such a find would have sweeping implications for Artificial Intelligence research.
    http://cosmicfingerprints.com/solve/

    It’s (Much) Easier to Falsify Intelligent Design than Darwinian Evolution – Michael Behe, PhD
    https://www.youtube.com/watch?v=_T1v_VLueGk

    “The National Academy of Sciences has objected that intelligent design is not falsifiable, and I think that’s just the opposite of the truth. Intelligent design is very open to falsification. I claim, for example, that the bacterial flagellum could not be produced by natural selection; it needed to be deliberately intelligently designed. Well, all a scientist has to do to prove me wrong is to take a bacterium without a flagellum, or knock out the genes for the flagellum in a bacterium, go into his lab and grow that bug for a long time and see if it produces anything resembling a flagellum. If that happened, intelligent design, as I understand it, would be knocked out of the water. I certainly don’t expect it to happen, but it’s easily falsified by a series of such experiments.
    Now let’s turn that around and ask, How do we falsify the contention that natural selection produced the bacterial flagellum? If that same scientist went into the lab and knocked out the bacterial flagellum genes, grew the bacterium for a long time, and nothing much happened, well, he’d say maybe we didn’t start with the right bacterium, maybe we didn’t wait long enough, maybe we need a bigger population, and it would be very much more difficult to falsify the Darwinian hypothesis.
    I think the very opposite is true. I think intelligent design is easily testable, easily falsifiable, although it has not been falsified, and Darwinism is very resistant to being falsified. They can always claim something was not right.”
    – Dr Michael Behe

    The Law of Physicodynamic Incompleteness – David L. Abel
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”
    If only one exception to this null hypothesis were published, the hypothesis would be falsified. Falsification would require an experiment devoid of behind-the-scenes steering. Any artificial selection hidden in the experimental design would disqualify the experimental falsification. After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided.
    The time has come to extend this null hypothesis into a formal scientific prediction:
    “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
    https://www.academia.edu/Documents/in/The_Law_of_Physicodynamic_Incompleteness

    Evolutionary Computing: The Invisible Hand of Intelligence – June 17, 2015
    Excerpt: William Dembski and Robert Marks have shown that no evolutionary algorithm is superior to blind search — unless information is added from an intelligent cause, which means it is not, in the Darwinian sense, an evolutionary algorithm after all. This mathematically proven law, based on the accepted No Free Lunch Theorems, seems to be lost on the champions of evolutionary computing. Researchers keep confusing an evolutionary algorithm (a form of artificial selection) with “natural evolution.” ,,,
    Marks and Dembski account for the invisible hand required in evolutionary computing. The Lab’s website states, “The principal theme of the lab’s research is teasing apart the respective roles of internally generated and externally applied information in the performance of evolutionary systems.” So yes, systems can evolve, but when they appear to solve a problem (such as generating complex specified information or reaching a sufficiently narrow predefined target), intelligence can be shown to be active. Any internally generated information is conserved or degraded by the law of Conservation of Information.,,,
    What Marks and Dembski prove is as scientifically valid and relevant as Gödel’s Incompleteness Theorem in mathematics. You can’t prove a system of mathematics from within the system, and you can’t derive an information-rich pattern from within the pattern.,,,
    http://www.evolutionnews.org/2.....96931.html

    Verse, Video, and Music:

    Luke 24:5
    In their fright the women bowed down with their faces to the ground, but the men said to them, “Why do you look for the living among the dead?

    The Resurrection of Jesus Christ from Death as the “Theory of Everything” – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1143437869002478/?type=2&theater

    Natalie Grant – Alive – video
    https://www.youtube.com/watch?v=Ap2vrLCU85w

  62. 62
    john_a_designer says:

    Origenes @ #41

    Indeed, however you labour under the assumption that pointing out problems is all that ID does. You are mistaken. ID offers a cause which, according to repeated experience, is capable of generating the kind of information necessary to produce life — e.g. semiotic codes — : intelligence.

    But, that doesn’t explain HOW life first originated. The point Tour made at the conclusion of his talk is that nobody, including creationist or ID’ists, understands how. When you argue that an intelligent cause is the best explanation based on what we presently know (a position with which I agree) you are answering the philosophical question not the scientific one.

    BTW I do not assume “that pointing out problems is all that ID does,” or can do. Even as a metaphysical paradigm ID can raise some interesting questions that can be explored scientifically.

  63. 63

    bornagain77@61 – Excellent post! Thank you.

  64. 64
    kairosfocus says:

    VJT:

    Judge NCSE/ACLU “copycat” Jones: Intelligent Design is not science and “cannot uncouple itself from its creationist, and thus religious, antecedents.”

    A strawman tactic with a built in smear.

    He could easily have known thatin our civilisation design thinking preceeded Biblical Creationism, and is quite materially distinct.

    But this is a handy rhetorical club.

    A revealing one.

    KF

    PS: besides the reading of the 1st Amdt US Const is demonstrably tendentious and false.

  65. 65
    Zachriel says:

    gpuccio: Of course the hypothesis of detectable design has entailments, and in biology the main entailment is that all cases of major evolution of species, including OOL, imply a huge amount of complex functional information.

    So does evolution. The difference is that evolutionary theory has many other specific and testable entailments, including direct observations of evolution, and a testable history.

    bill cole: This is true but the problem is that the overall claim of known mechanisms causing diversity has not been successfully tested and is almost certainly wrong.

    The origin of diversity seems a pretty obvious entailment of evolution, and something that can be directly observed. That’s why IDers typically want to talk about functional complexity complex specified information Functionally Specific, Complex Organisation and Associated Information (FSCO/I).

    Querius: If you have a process comprising a series of steps, but the first step seems impossible, what do you focus on?

    If you’re Newton, and don’t know the origin of the Solar System, you might instead attempt to explain how the planets move.

  66. 66
    bill cole says:

    Zachriel

    The origin of diversity seems a pretty obvious entailment of evolution, and something that can be directly observed

    Yes it can be observed but what is the cause. Without a cause you don’t have a theory. We can observe the result but have not observed the change process.

  67. 67
    vjtorley says:

    Hi Bob O’H, gpuccio and bornagain77,

    Thank you for your posts. I’d like to respond to your remarks on the stopping rule.

    In the case we are discussing, the stopping rule relates to the search for a plausible pathway that a Designer might have used to get from the chemical ingredients of life to a functional living cell. Let’s say that there are N molecules that had to be combined together (in some ordered sequence) to create a living cell, and let’s assume (for the sake of argument) that scientists know exactly what those molecules are. [If my memory serves me rightly, I believe the estimate that someone came up with for N, on an Uncommon Descent thread back in 2009, was somewhere in the ballpark of 10^6.] Since the number of ordered permutations of N items is 2^N, that gives us 2^1,000,000 or about 1 with 300,000 zeroes after it – an astronomically large number. There’s simply no way to search through all possible sequences within the lifetime of the universe. Hence falsification of the statement that there was some pathway from the chemical ingredients of life to a functional living cell is physically impossible. We don’t have enough time for that.

    Given that we don’t have enough time to falsify the statement, how should we proceed? I addressed this question in my OP. The answer I proposed was: “a diligent search of all promising options.” In other words, we need scientists to rank the search options in terms of how promising they look, and pursue the best ones. When I say, “rank the search options,” I don’t mean: rank 10^300,000 pathways. What I had in mind was: focus on a few steps at a time – for example, the last 100 steps leading up to a living cell, using a reverse-engineering approach. Even with just 100 steps, the number of possible pathways is very large. Let’s suppose that chemists, with the aid of computers, were able to pick out 1,000,000 of these pathways as more promising than the rest, on purely chemical grounds, and let’s suppose that (after many years of testing), they found that each of these pathways hit a snag, leading to a dead end. I think it would be sensible at that point to call it quits.

    Regarding the stopping rule, Bob O’H writes that “you have to have one that will convince people that you have been thorough.” I agree. I think the procedure I described above is thorough.

    Bob O’H also writes: “Basically, your suggestion is similar to the approach taken by ID: try to show that X doesn’t happen, and so conclude that Y must have” and he adds that “there may be some scepticism about IDists then claiming that they have shown that abiogenesis didn’t happen on its own.”

    First, the search I’m talking about here is not a search for a plausible pathway whereby blind processes might have generated a functional living cell from its chemical ingredients (as in abiogenesis), but rather, the search for a plausible pathway that a Designer might have used to get from the chemical ingredients of life to a functional living cell. ID theory has no position on whether such a pathway exists. The Designer may well have created the first cell via a series of steps, or alternatively, the Designer may have made it holus-bolus. If ID scientists found a viable pathway for an intelligent agent to synthesize life from scratch, I imagine they’d be very pleased. Hence the skepticism you refer to is misplaced.

    Second, I’m not trying to show that X doesn’t happen, and then concluding that Y must have. Rather, I’m provisionally concluding (after a diligent search of the most promising options) that X probably didn’t happen, and I’m then arguing that not-X probably did – where X is the hypothesis that a simple living cell is capable of being assembled in a series of steps, and not-X is the hypothesis that a simple cell is incapable of being assembled, which entails that the first cell to appear on the primordial Earth must have been created in its entirety (assuming that panspermia is ruled out). If you can think of any other possibilities, please let me know.

  68. 68
    vjtorley says:

    Daniel King asks: “In what way is ‘design’ an explanation?” and Zachriel asserts: “‘Design’ lacks the specificity and entailments to call it a scientific explanation.”

    Surely you jest. If you found a monolith on the Moon, the lengths of whose sides had the ratio of 1:4:9, you would consider the hypothesis that the monolith was designed to explain absolutely nothing about its shape?

    In any case, even if you don’t think that mere design qualifies as an explanation, you cannot deny that “design,” coupled with a list of the steps whereby the designer generated the product, counts as a legitimate scientific explanation. The research project which I have proposed for the Intelligent Design movement over the next 50 years in my OP is to find one possible sequence of steps leading to a simple living cell. If that’s not science, then I’m a Dutchman.

  69. 69
    vjtorley says:

    Dionisio asks an interesting question regarding the attempt to reverse-engineer life:

    Wouldn’t the reverse-engineers have to identify -in a top-down approach- all the components, their functions, their interconnections, how exactly they are assembled, how they work, what makes them robust with respect to different kinds of noisy stochastic environments, all that and more in order to do what you suggested?

    First, I agree that a top-down approach is necessary, and that a bottom-up approach can’t work, as it generates too many dead ends.

    Second, I would also agree that a top-down approach requires a knowledge of all the components of the cell, as well as their functions and their interconnections. However, I don’t think that it’s necessary to know in advance exactly how these components were assembled. That would be a bottom-up approach. The aim of a top-down approach, as I see it, is to identify the sequence of steps whereby the macro-components of the cell were put together, before attempting to identify the the sequence of steps whereby their sub-components were assembled.

  70. 70
    bill cole says:

    VJ Thanks for the interesting post.

    he research project which I have proposed for the Intelligent Design movement over the next 50 years in my OP is to find one possible sequence of steps leading to a simple living cell. If that’s not science, then I’m a Dutchman.

    I think two things to consider:
    If design is ultimately the right hypothesis then it appears that first life is just a small piece of the puzzle since different aspects of life seem to be interdependent i.e. our dependence on plants and bacteria and plants dependence on bacteria etc.

    Life and matter are dependent on the structure of atoms. Part of reverse engineering life is understanding the structure of its key components (atoms). If i am reverse engineering a PC I must be able to understand the function of its semiconductors. String theory and supersymmetry are areas to keep an eye on.

  71. 71
    Zachriel says:

    vjtorley: Hence falsification of the statement that there was some pathway from the chemical ingredients of life to a functional living cell is physically impossible. We don’t have enough time for that.

    General statements of that sort are not scientifically falsifiable. Only specific hypotheses are falsifiable. Consider a statement made by an ancient that the planets move by natural laws; and the equivalent statement that the motions are due to supernatural (telic) causes. If we found direct evidence of angels, that would falsify the former. Absent that, though, a natural explanation may just be beyond the human imaginings of the pre-Newtonian era.

    That’s the whole point of the scientific method. It allows us to peer into the darkness and discover bits of knowledge, even while most of the universe remains shrouded in mystery.

    You propose an exhaustive search, but the search is limited by human ingenuity and technical ability. While modern humans look on universal gravitation as obvious; for millennia, it was beyond human understanding. While a search for your keys on the dresser top may be considered exhaustive (even then they are sometimes overlooked!), you can’t possibly exhaust the universe of possibilities beyond your imagination.

  72. 72
    Zachriel says:

    bill cole: Yes it can be observed but what is the cause. Without a cause you don’t have a theory. We can observe the result but have not observed the change process.

    Biological diversity is observed to be due to mutations of various sorts, along with recombination.

    vjtorley: If you found a monolith on the Moon, the lengths of whose sides had the ratio of 1:4:9, you would consider the hypothesis that the monolith was designed to explain absolutely nothing about its shape?

    Humans often imagine things that are designed, and imagine things that are supposedly natural which are not. So? Crystals exhibit symmetry.

    vjtorley: In any case, even if you don’t think that mere design qualifies as an explanation, you cannot deny that “design,” coupled with a list of the steps whereby the designer generated the product, counts as a legitimate scientific explanation. The research project which I have proposed for the Intelligent Design movement over the next 50 years in my OP is to find one possible sequence of steps leading to a simple living cell.

    Let us know how it goes. If it just means that you find two more gaps every time a gap is filled, then it won’t mean much. But if you had actual evidence of manufacture, then that would be significant.

  73. 73
    Daniel King says:

    VJT @ 68:

    Daniel King asks: “In what way is ‘design’ an explanation?” and Zachriel asserts: “‘Design’ lacks the specificity and entailments to call it a scientific explanation.”

    Surely you jest. If you found a monolith on the Moon, the lengths of whose sides had the ratio of 1:4:9, you would consider the hypothesis that the monolith was designed to explain absolutely nothing about its shape?

    No jest. Wouldn’t “design” be one of several possible hypotheses? Without further investigation wouldn’t it be premature to decide?

    In any case, even if you don’t think that mere design qualifies as an explanation, you cannot deny that “design,” coupled with a list of the steps whereby the designer generated the product, counts as a legitimate scientific explanation.

    No denial. Wouldn’t the designer’s steps have to involve the kinds of chemical processes that have been and are currently being explored? If not, what new approaches does the design hypothesis suggest?

    The research project which I have proposed for the Intelligent Design movement over the next 50 years in my OP is to find one possible sequence of steps leading to a simple living cell.

    Isn’t that what Szostak and others have been doing? (See http://molbio.mgh.harvard.edu/szostakweb/)

    What improvement does your research project offer?

    If that’s not science, then I’m a Dutchman.

    It would be science.

  74. 74
    MatSpirit says:

    john_a_designer @39: “The problem at the moment is not the ID argument, as far as it goes, but the ideological blindness and political bullying of the materialists. The best argument we can make for the time being is what Tour is doing. Essentially he is asking “HOW did this evolve naturalistically?” If the Darwinian “theory” is indeed a truly scientific explanation shouldn’t its proponents be able to answer that question?”

    Tour isn’t asking how anything evolved. He’s claiming that a modern cell, complete with RNA, DNA and all the other internal organelles found in a modern cell, was the FIRST living thing and demanding to know how such an extraordinarily complex cell could could poof into existence through natural, non-intelligent means.

    Evolution proponents say that claim is ridiculous, people who actually work in the OOL field believe the first living thing was small and simple enough to form via stochastic processes and its only ability was to self-reproduce. All the gew-gaws in modern cells got there through the slow step by step process of evolution.

    They also wonder why an accomplished scientist like Dr. Tour doesn’t know this and, more importantly, how anybody with an ounce of responsibility could set out to “teach” OOL to others without getting such basic facts straight. I’ll betcha a bright shiney nickel that his religious beliefs were responsible.

    I also wonder why he didn’t “defeat science” by “proving” that mice are too complex to be produced by dirty rags, therefore Jesus. Perhaps that was too much even for him.

    Here’s a challenge for Professor Tour: Give your speech to an audience of actual OOL researchers. When they stop laughing, they will set you straight.

  75. 75
    gpuccio says:

    Zachriel, BA, VJ:

    Just a brief clarification about what I think of stopping rules and falsifications:

    I maintain that there are no generic stopping rules in science, as I have said in my post #36:

    “No scientific theory, however good and supported by known facts, will ever be final. That is an important epistemological point.”

    What I mean is that we can never have a rule that tells us to stop because a final theory about something has been verified and therefore should be considered as true. That is impossible, for the nature itself of science.

    BA, however, makes a good point: any scientific theory can be falsified, and if it is falsified, then we have a stopping rule that tells us not to investigate further that specific theory.

    That is true, but it is a completely different concept: we discard that specific theory, but there is no stopping rule to looking for some other one, even if of the same kind.

    IOWs, the falsification of a specific theory can be achieved only if the theory is explicit and specific, and it is always possible to propose some other theory which is not really falsified by our falsification process. So, we can either try some completely different theory, or just adjust our theory so that it is not falsified by the previous falsification process. In doing that, we may be right or still wrong, but the process is correct from a scientific point of view.

    The point remains that the best scientific explanation should be tentatively chosen among the available scientific explanations which have not been falsified, and it should be the one which is best supported by facts and explains best what is observed.

    Now, generic statements, like Zachriel’s:

    “We can always find some evolutionary pathway in the future”

    or, even more generically:

    “We could always find some naturalistic (in the sense of non design) explanation for biological complexity”

    are not explicit and specific scientific theories. Indeed, they are not scientific theories at all, and that’s why they cannot be falsified. For the same reason, they have no scientific value.

    ID theory is completely falsifiable, as I have said many times here. The main core of ID theory is that design is often detectable, when it is complex enough, and that for any object exhibiting true complex functional information a design origin can be safely inferred, with practically no risk of being wrong.

    That statement is very strong, and can easily be falsified exhibiting any object which shows true complex functional information, and for which a non design origin can be safely and independently proven.

    So, the core of ID theory is completely scientific, is completely falsifiable, and has never been falsified. That’s why ID theory offers the best explanation for all objects exhibiting complex functional information, including biological objects.

    Is neo darwinism falsifiable? My position is very simple.

    The generic faith in neo darwinism is not falsifiable, because it is not science. As said, Zachriel, or any other neo darwinist, can always hope that new facts will make of his/their theory the best explanation for biological data. That is a question of personal hope, faith, and conviction. But not science.

    Instead, any specific explanation of observed biological data in terms of the neo darwinist theory can be falsified. Therefore, specific explanations basaed on RV + NS can be considered as scientific, and can be falsified. Indeed, they often are (see for example the argument made many times here against Ohno’s explanation of nylonase; Ohno’s theory was specific and scientifically detailed, and that’s why it was possible to falsify it).

    As you can see, there is a difference between ID theory and neo darwinism. ID theory is about the scientific validity of a design inference based on functional complexity. It is falsifiable, it has never been falsified, and it does not imply the specifics of the inferred design origin (the famous who, what, how, and so on).

    As I have said many times, those specifics are scientific problems, must be addressed scientifically, but are not part of the original design inference, as many of our interlocutors from the other side badly want to be true.

    The conscious origin of all objects exhibiting complex functional information is an empirical observation which can be repeatedly tested: it can be falsified, and it has never been falsified. Therefore, design remains the best scientific explanation for that kind of objects, unless and until a better explanation is provided, or the design explanation is independently falsified in specific cases.

    Neo darwinism remains the worst explanation for biological objects exhibiting complex functional information for the simple reason that it has never explained any of them. If and when it can do that, we can seriously consider it. Until then, there is no stopping rule, and all those who believe, for personal faith or simply for personal intuition, that some day neo darwinism will give the desired results, are welcome to dedicate their time, efforts and patience to research under that paradigm.

    Until then, it is perfectly worked out that design is for now the best explanation. And we should certainly dedicate a lot of time, efforts and patience to the investigation of specifics under that paradigm.

  76. 76
    bill cole says:

    Zachriel

    Biological diversity is observed to be due to mutations of various sorts, along with recombination.

    IMHO this is not a coherent statement.

  77. 77
    Zachriel says:

    gpuccio: “We can always find some evolutionary pathway in the future”

    Of course, many evolutionary pathways have already been found.

    gpuccio: they are not scientific theories at all, and that’s why they cannot be falsified. For the same reason, they have no scientific value.

    They may have scientific value if they lead to testable hypotheses. Even ID could have scientific value, but it’s very unlikely for several reasons: ID is in all probability false; those inspired by ID rarely do any scientific research of note; and ID is fraught with fallacious reasoning.

    gpuccio: The main core of ID theory is that design is often detectable, when it is complex enough, and that for any object exhibiting true complex functional information a design origin can be safely inferred, with practically no risk of being wrong.

    Leaving aside the problem of quantifying complex functional information, evolution can also create complex functions, so your “safe inference” is anything but.

    gpuccio: That statement is very strong, and can easily be falsified exhibiting any object which shows true complex functional information, and for which a non design origin can be safely and independently proven.

    That’s just another negative proof as discussed above. Planets move like a complex clocklike mechanism. The only complex clocklike mechanism whose origin is independently known are human designs. Hence, planetary movement is designed.

  78. 78
    Zachriel says:

    Zachriel: Biological diversity is observed to be due to mutations of various sorts, along with recombination.

    bill cole: IMHO this is not a coherent statement.

    Hmm. It seems coherent. We directly observe mutations, hence we directly observe the creation of biological diversity. We directly observe recombination, hence we directly observe the creation of biological diversity.

  79. 79
    Daniel King says:

    gpuccio @ 33:

    It’s very simple. Allen MacNeill’s statement was:

    “As for abiogenesis, I agree that it is not “all worked out” – indeed, I think it will never be so in either direction (i.e. design vs evolution).”

    So, the problem referenced here is the kind of process driving OOL, not the details of its natural history.

    The devil is in those pesky details, as any designer knows.

    Design is an explanation for the huge amount of functional information implied in OOL, because design is the only known process capable of generating huge amount of complex functional information. It’s as simple as that.

    “Only known process.” On the contrary,”design” is not known to be a process that generated life at the outset. That has to be demonstrated.

    Finding out how the natural world works is not at all simple, viz. “complex functional information.”

    You ask “who, what, when and how details”. But I never said that the details are worked out. They obviously are not, neither for an explanation based on unguided evolution nor for an explanation based on design. But U an sure that, once the correct process is accepted and recognized in scientific approach, details will be found.

    How does one get from “design” to hypotheses that guide research into uncovering those devilish details?

    So again, for clarity, what IMO is “all worked out” is the problem of deciding between design and unguided evolution as a credible scientific explanation for OOL.

    You haven’t worked out anything. You’ve made a decision that has no apparent consequences. You need to show that making that decision at this time actually has consequences for advancing knowledge..

  80. 80
    Zachriel says:

    bill cole: Yes it can be observed but what is the cause. Without a cause you don’t have a theory.

    What is the cause of gravity in Newton’s Theory of Universal Gravitation? What is the cause of variation in Darwin’s original Theory of Evolution?

    bill cole: We can observe the result …

    And we can show that many mutations are random with respect to fitness.

    bill cole: but have not observed the change process.

    Actually, mutations are a well-researched topic. Here’s an overview of a few known causes of mutation:
    https://en.wikipedia.org/wiki/Mutation#Causes

  81. 81
    Querius says:

    Newton and Kepler didn’t claim that orbital mechanics evolved to account for planetary motions. They found mathematical relationships that were verifiably predictive of future motion (which was reasonably close for that time) and these were later able to be questioned and then falsified.

    In contrast, Darwinism has been able to predict nothing that hasn’t already happened, and there’s nothing that can be questioned or observed that could ever possibly falsify Darwinism.

    With Darwinism, we must accept miracles that are given names such as Cambrian Explosion, Living Fossils, Polystrate Fossils, Convergent Evolution, RNA World, Billions and Billions, Spontaneous Generation of DNA, Spontaneous Generation of Cell Walls, Spontaneous Generation of Chemical Cycles, Spontaneous Generation of Life, Deep Time and Warm Ponds, Index Fossils, Inverted Strata, Massively Improbable Combinations of Mutations, The Fossil Record, Fossil Beds, Out of Place Fossils, The Tree of Life, 65 Million Year Blood Cells, The Strong Anthropic Principle, Uniformitarianism, The Multiverse, and on and on.

    The reality is as if Einstein were never permitted to question Newton.

    You observe a mutation that breaks a function without killing the organism and then extrapolate that to evolving all life on earth, all genetic and epigenetic codes, new organs with new functions, structures, and chemical cycles regardless of complexity by slathering everything over with a thick layer of time and chance. Oh and Darwinism is the only scientific game in town.

    Wouldn’t it be great if we could pry Darwin’s cold, dead hands off the throat of science?

    -Q

  82. 82
    vjtorley says:

    Hi everyone,

    Good news: Baby Zachary from Ulanbator and his mother are now on their way to America:

    https://www.gofundme.com/operationzachary

    Thanks to everyone for their support.

  83. 83
    Origenes says:

    Daniel King,

    Gpuccio: Design is an explanation for the huge amount of functional information implied in OOL, because design is the only known process capable of generating huge amount of complex functional information. It’s as simple as that.

    Daniel King: “Only known process.” On the contrary,”design” is not known to be a process that generated life at the outset. That has to be demonstrated.

    You twist Gpuccio’s words. This is what he said: “design is the only known process capable of generating huge amount of complex functional information”. He argues that, contrary to chance and necessity, intelligent design is an adequate cause. A cause capable of generating the kind of information necessary to produce life — e.g. semiotic codes.

    And therefore:

    Gpuccio: The real problem is simply: what is the best scientific explanation [for life] according to what we know today?

    And the best explanation is design.

  84. 84
    Zachriel says:

    Querius: Newton and Kepler didn’t claim that orbital mechanics evolved to account for planetary motions.

    That’s right. They didn’t propose a scientific theory of the origin of the Solar System.

    Querius: They found mathematical relationships that were verifiably predictive of future motion (which was reasonably close for that time) and these were later able to be questioned and then falsified.

    Newton proposed a theory of gravity, yet didn’t know the cause of gravity, contrary to bill cole’s statement.

    Querius: In contrast, Darwinism has been able to predict nothing that hasn’t already happened, and there’s nothing that can be questioned

    That’s not correct. Evolution predicts many facets of biology, such as the evolution of influenza, important in the fight against disease.

    Querius: … or observed that could ever possibly falsify Darwinism.

    If you mean evolution hasn’t been falsified, then you are correct. It is, however, falsifiable.

    Querius: The reality is as if Einstein were never permitted to question Newton.

    Question away!

    Querius: You observe a mutation that breaks a function without killing the organism and then extrapolate that to evolving all life on earth, all genetic and epigenetic codes, new organs with new functions, structures, and chemical cycles regardless of complexity by slathering everything over with a thick layer of time and chance.

    You might want to start with common descent and the phylogenetic tree.

  85. 85
    vjtorley says:

    Hi MatSpirit,

    Thank you for your post. You write:

    Tour isn’t asking how anything evolved. He’s claiming that a modern cell, complete with RNA, DNA and all the other internal organelles found in a modern cell, was the FIRST living thing and demanding to know how such an extraordinarily complex cell could could poof into existence through natural, non-intelligent means.

    Evolution proponents say that claim is ridiculous, people who actually work in the OOL field believe the first living thing was small and simple enough to form via stochastic processes and its only ability was to self-reproduce. All the gew-gaws in modern cells got there through the slow step by step process of evolution.

    Let me remind readers that when Professor Tour gave his speech, he specifically asked if there was a chemist in the audience, and he asked that chemist to call him out if he told any lies. He never got called out.

    Professor Tour also disclosed that he had personally discussed the origin of life with Nobel Laureates and members of the National Academy of Science:

    I’ve asked all of my colleagues: National Academy members, Nobel Prize winners. I sit with them in offices. Nobody understands this. So if your professor says, “It’s all worked out,” [or] your teachers say, “It’s all worked out,” they don’t know what they’re talking about. It is not worked out.

    Nowhere in his talk did Professor Tour claim that the first living cell “poofed into existence.” Indeed, he specifically alluded to the RNA world hypothesis.

    You claim that the first living thing was non-cellular. That’s a legitimate hypothesis, but it’s unsupported by a shred of evidence. It also runs afoul of the fact that although there are many simple bacteria living on earth today (despite the fact that more complex eukaryotes also exist), there is no niche anywhere on the planet where non-cellular life-forms can be found. Why is that?

    You contend that the first living thing was “small and simple enough to form via stochastic processes and its only ability was to self-reproduce.” Question: did this proto-organism contain enzymes? If so, then you have to account for the origin of these proteins. If not, then you confront the difficulty I alluded to in part (e) of my OP above: even if you could get all the ingredients of life together, at a high level of purity, and store them over long periods, they can’t assemble without enzymes.

  86. 86
    Querius says:

    You might want to start with common descent and the phylogenetic tree.

    A reasonable effort with some significant issues.

    – A thought experiment: If you eliminated all dogs except great danes and chihuahuas, would they be different species, and wouldn’t their genomes be as confusing as the great apes?

    – A real experiment: Repeat the E.coli citrate experiment with raised levels of mutagens, including radiation levels to simulate the passage of long periods of time and many generations. The LD 50/30 of bacteria is very high, so we would be able to observe just how much evolution takes place if the bacteria were humans instead.

    -Q

  87. 87
    gpuccio says:

    Zachriel:

    My post #75 was intentionally provocative. I must say that the reactions are rather lame. 🙂

    “Of course, many evolutionary pathways have already been found.”

    Molecular evolutionary pathways to new complex functional proteins? Really?

    “ID is in all probability false;”

    Thank for “in all probability”! That’s certainly more than I usually get from your field. 🙂

    “ID is fraught with fallacious reasoning.”

    Is that an example of non fallacious reasoning?

    “Leaving aside the problem of quantifying complex functional information,”

    Why leave it aside? Because, believe me, there is really no problem at all.

    “evolution can also create complex functions”

    Examples, please? With molecular pathways, if possible. Thank you.

    “Planets move like a complex clocklike mechanism. The only complex clocklike mechanism whose origin is independently known are human designs. Hence, planetary movement is designed.”

    Not your best performance, Zachriel. When even you have nothing better to do than recurring to meaningless word plays, that must certainly mean something.

  88. 88
    gpuccio says:

    Daniel King:

    “The devil is in those pesky details, as any designer knows.”

    Details are searched under general paradigms. Those paradigms are very important. If your paradigm is wrong, you will never understand details correctly.

    I maintain that “design is the only known process capable of generating huge amount of complex functional information. It’s as simple as that.” Because it is absolutely true.

    You say:

    “On the contrary,”design” is not known to be a process that generated life at the outset. That has to be demonstrated.”

    My point is not about life, but about the huge amount of complex functional information which is necessary for life to exist. And only design can generate that.

    You say:

    “Finding out how the natural world works is not at all simple, viz. “complex functional information.”

    Is that an argument? I am probably not intelligent enough to understand it.

    You say:

    “How does one get from “design” to hypotheses that guide research into uncovering those devilish details?”

    By scientific reasoning. Correct scientific reasoning. Design means that new functional information has been outputted to biological matter throughout natural history. It is perfectly natural then to try to understand when, by what modalities, with what purposes, by whom, and so on. Those are all legitimate scientific questions, and only facts and scientific reasoning can give the answers.

    But if you go on looking for evolutionary pathways which don’t exist to explain functional information which was designed, you are hopeless.

    “You haven’t worked out anything. You’ve made a decision that has no apparent consequences. You need to show that making that decision at this time actually has consequences for advancing knowledge..”

    Strange argument. What can I say? I believe that making the right decision about the right paradigm which can explain what we observe has certainly important, and good, consequences. Maybe you think differently.

    The only guiding criterion I can accept in science and, more generally, in cognition, is adherence to truth. Consequences will come accordingly.

  89. 89
    Zachriel says:

    Querius: – A thought experiment: If you eliminated all dogs except great danes and chihuahuas, would they be different species,

    They may become different species due to the lack of gene exchange. They haven’t been separated for long enough, and can presumably still exchange genes through intermediate breeds.

    Querius: and wouldn’t their genomes be as confusing as the great apes?

    Confusing in what way? The dog genome is complex, if that is what you mean, but clearly part of the tree of life.

    Querius: – A real experiment: Repeat the E.coli citrate experiment with raised levels of mutagens, including radiation levels to simulate the passage of long periods of time and many generations.

    While raising the mutation rate can simulate some aspects of time, it doesn’t represent a complete history. That’s because it takes time for population genetics to sort through the variants. Be happy to see your results, though.

  90. 90
    Zachriel says:

    gpuccio: Molecular evolutionary pathways to new complex functional proteins?

    The claim was about evolutionary pathways generally, and there are complex morphological structures that have left fossils so we can see how they evolved.

    With molecular biology, we have to infer the history, and most of the metabolic structures evolved very early in the history of life, so the evidence is necessarily tentative. However, we have evidence of the evolution of complex molecular systems, such as the vertebrate blood clotting system which occurred due to a series of gene duplications. See Jiang & Doolittle, The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes, PNAS 2003.

    gpuccio: When even you have nothing better to do than recurring to meaningless word plays, that must certainly mean something.

    It’s a parallel situation which shows the fallacy of your position.

  91. 91
    gpuccio says:

    Zachriel:

    You must be kidding. I asked:

    “Examples, please? With molecular pathways, if possible. Thank you.”

    And you give me a paper about some homologues? You must be kidding.

    “It’s a parallel situation which shows the fallacy of your position.”

    If that kind of argument shows the fallacy of my position, I am really very proud.

  92. 92
    Zachriel says:

    gpuccio: And you give me a paper about some homologues?

    The paper claims that gene duplication was a major factor that led to the complex structure of vertebrate blood clotting. What about the paper did you find in error?

    gpuccio: If that kind of argument shows the fallacy of my position

    If you want to dispute that it does, you need to address the purported parallel.

  93. 93
    MatSpirit says:

    Hi vjtorley,

    Thanks for your response. You write, “Let me remind readers that when Professor Tour gave his speech, he specifically asked if there was a chemist in the audience, and he asked that chemist to call him out if he told any lies. He never got called out.”

    Yes, that was at 13:42 where he asks, “How many people in here are synthetic organic chemists?” Somebody raises their hand and Tour says, “If I tell a lie, just say, ‘Liar, liar, pants on fire!'”

    The problem is that Tour’s thesis is that the first living thing was a highly complex cell like the modern cell he uses as an illustration. He then goes on to list the many extremely difficult / unknown steps required to synthesis that modern, complex cell. As far as I (and the unseen chemist) knows, he’s right. It would be extremely difficult to build a complex modern type cell from scratch.

    THE PROBLEM IS THAT NOBODY IN THE WORLD EXCEPT CREATIONISTS AND ID ENTHUSIASTS BELIEVES THAT THE FIRST LIVING THING WAS COMPLEX!

    Everybody I’ve ever heard of that is actually associated with OOL research thinks the first living thing was an extremely simple entity of a few hundred atoms or less, probably enveloped in a simple lipid membrane, and that its only life-like ability was to reproduce itself from available materials.

    Tour’s whole speech is based on the strawman belief that the first living thing was enormously complex. It wasnt, so all his arguments about how hard that would be are in vain.

    Tour says he’s personally discussed the origin of life with various experts. Given his delusions, who knows what he actually talked about and I’m not surprised that they expressed befuddlement. One thing I’m sure of, he didn’t discus it with anybody in the OOL field or they would have knocked down his straw man and set him straight on a few of the basics of OOL research.

    You said, “Nowhere in his talk did Professor Tour claim that the first living cell “poofed into existence.” Indeed, he specifically alluded to the RNA world hypothesis.”

    Tour’s basic thesis is that A: The first living thing was astoundingly complex, complete with DNA, RNA and all the other accoutrements of a modern cell and B: There is no possible way such a highly complex cell could form naturally. He then leaves it to the reader to deduce that it must have been produced by an intelligent designer, which non IDers normally refer to as poofing. His reference to the RNA world was to shoot it down as something that could build his dream cell.

    In other matters, I didn’t say anything about first life being non cellular and the smallest enzyme I’ve ever heard of is made from about 60 amino acids, which would make it substantially bigger than the first organism, so no, I don’t think any enzymes were used to make the first living thing.

    I know this is not the first time you’ve been embarrassed by this kind of claim about OOL. You were going on about some other scientist who didn’t know jack about the OOL field a few months ago. I think he claimed the first living thing was so complex it would somehow require a multiverse to poof it into existence. I don’t think there’s much doubt that it will happen again if you don’t learn something about the OOL field. So why don’t you do everybody, especially yourself, a favor and watch Tour’s speech again. See for your self that he’s claiming that the first living thing was an ultra complex cell with DNA and RNA. Then get Google working for you and read up on the origin of life FROM OOL SOURCES. Not just scientists, but scientists who are actually working in that field. Don’t read creationist / ID sources because they are uniformly full of crap. Read them afterwards if you want.

    Then tell us what you’ve found. I know you’ve turned around on junk DNA and global warming. OOL is no harder. Good luck.

  94. 94
    MatSpirit says:

    A few words on reverse engineering: Reverse engineering means to figure out how something works by examining and experimenting with the object. You can use any knowledge you may have about physics, electronics, chemistry and so on. You can disassemble the object and operate it if you want. You can use any knowledge you may have about similar objects, but you can’t use any plans, schematics, repair manuals or other designer generated knowledge to figure out how it works.

    Is everybody ok on this definition? I could probably phrase it better, but does everybody understand what it means to reverse engineer something?

    Ok, now imagine a scientist peering into a microscope looking at a cell. What do you thing he’s doing? Looking at pretty pictures? Admiring the shape or colors of the cell? Gathering possible designs for wall paper?

    Of course not! He’s trying to figure out how the cell is constructed and how it works by examining and experimenting with it. He doesn’t have any plans or repair manuals to consult or written explanations from the cell’s designer or manufacturer.

    He’s reverse engineering the cell! Reverse engineering is how science works! Science means figuring out how the universe works by examining and experimenting with it. Physics, biology, geology, astronomy – ALL science is reverse engineering.

    The idea that ID is going to add to science by introducing it to the art of reverse engineering is silly, insulting to science and mainly shows how little ID understands what it criticizes.

  95. 95
    MatSpirit says:

    Now that I’ve said a few words about Professor Tour’s lecture, does anybody still think it would be an excellent resource for teachers? Would anybody like to speculate on the outcome of a parent’s lawsuit?

  96. 96

    Hello Mat,

    Just a quick question. Do you think whatever simple life form that is proposed as the precursor to the modern cell — as just a matter of general logic — had to be able to organize the modern cell?

    I’m sure you would agree that if the modern cell is the outgrowth of a precursor, then that precursor had to in some way be capable of organizing the modern cell (or it wouldn’t exist).

    Here is my question: In leading to organization of the modern cell, did that precursor require the capacity to somehow specify any of the constituent parts of the modern cell?

  97. 97
    Querius says:

    While raising the mutation rate can simulate some aspects of time, it doesn’t represent a complete history. That’s because it takes time for population genetics to sort through the variants. Be happy to see your results, though.

    Thoughtless gibberish. You can’t hide behind time when you have massive numbers of generations “to sort through the variants” in a relative short amount of time. That’s the whole point of using bacteria. Duh.

  98. 98
    EugeneS says:

    Zachriel

    “Our reasons for rejecting a scientific claim of “intelligence as a cause” of life are scientific, not metaphysical.”

    You have neither scientific nor metaphysical reasons. Your case is void (unless you are tacitly playing in favour of ID by constantly providing void arguments against it).

  99. 99
    EugeneS says:

    MatSpirit,

    You seem to be suggesting that life reduces to chemistry. Is that right? If so, here are two largish quotes for you.

    The concept of Biosemiotics requires making a distinction between two categories, the material or physical world and the symbolic or semantic world. The problem is that there is no obvious way to connect the two categories. This is a classical philosophical problem on which there is no consensus even today. Biosemiotics recognizes that the philosophical matter-mind problem extends downward to the pattern recognition and control processes of the simplest living organisms where it can more easily be addressed as a scientific problem. In fact, how material structures serve as signals, instructions, and controls is inseparable from the problem of the origin and evolution of life. Biosemiotics was established as a necessary complement to the physical-chemical reductionist approach to life that cannot make this crucial categorical distinction necessary for describing semantic information. Matter as described by physics and chemistry has no intrinsic function or semantics. By contrast, biosemiotics recognizes that life begins with function and semantics.

    Biosemiotics recognizes this matter-symbol problem at all levels of life from natural languages down to the DNA.

    The problem also poses an apparent paradox: All signs, symbols, and codes, all languages including formal mathematics are embodied as material physical structures and therefore must obey all the inexorable laws of physics. At the same time, the symbol vehicles like the bases in DNA, voltages representing bits in a computer, the text on this page, and the neuron firings in the brain do not appear to be limited by, or clearly related to, the very laws they must obey. Even the mathematical symbols that express these inexorable physical laws seem to be entirely free of these same laws.

    The legacy of classical reductionism is the support of a common illusion. It is the illusion that because everything must obey detailed microscopic physical laws, it follows that such a description of this detail forms the most fundamental or most “real” explanation for all higher-level behaviors. For at least a century physicists have recognized, sometimes only tacitly, that this is not the case. The first failure of reductionism was thermodynamics with its irreversible laws that can never be formally derived from or reduced to the reversible microscopic laws. The conceptual problem is that in the microscopic laws the observables are about individual particles,while the observables in statistical laws are about populations. These descriptions illustrate the concept of complementarity used in the special sense that neither of two descriptions can be derived from, nor reduced to the other. Max Planck (1960) made the point: “For it is clear to everybody that there must be an unfathomable gulf between a probability, however small, and an absolute impossibility . . . Thus dynamics and statistics cannot be regarded as interrelated.”

    The laws of physics are assumed to be inexorable. That is, the laws do not allow alternatives and therefore the concept of information that is defined by the number of alternatives does not apply to the laws themselves. A measurement, in contrast, is an act of acquiring information about the state of a specific system that has many alternative states.

    Biosemiotics also recognizes that to objectify the concept of the epistemic cut between matter and symbol we must make explicit what we mean by the acts of observation and interpretation at the most primitive level. This requirement for an irreducible triad of sign, interpreter, and referent was a central point of C. S. Peirce’s semiotics.

    Howard Patee. “The physics and metaphysics of biosemiotics”. Emphasis mine.

    Life cannot exist without programming, and the processing of that programming.

    Neither the programming, nor the processing of that programming, can exist without purposeful choices at bona fide decision nodes.

    “Bifurcation points” (mere forks in the road) don’t hack it! Programming of any kind requires true decision nodes. Coin flips won’t do!

    Two kinds of determinism exist, not one: Physicodynamic Determinism and Choice Determinism. Choice Determinism always arises from the far side, the formal side, of The Cybernetic Cut.

    The only way formal choice contingency can enter the physical world across the great ravine of The Cybernetic Cut is via the one-way CS (Configurable Switch) Bridge.

    Configurable switches are physical devices. But they are designed and engineered to record formal purposeful choices into the physical world. Only Choice Determinism can set configurable switches, not the laws of physics and chemistry; Chance cannot set them, either, not if one expects sophisticated function or successful computation.

    Chance is not a cause of anything. Chance is nothing more than a probabilistic description of stochastic events. Chance doesn’t prescribe anything.

    The choice of symbols from an alphabet of symbols to create a linear digital symbol system is another way to cross the CS Bridge from the formal to the physical world, at least when physical symbol vehicles (tokens) are used (e.g., the Scrabble game).

    DNA is a material symbol system (MSS), where nucleotides are tokens. The sequencing of those tokens is not physicodynamically determined. The sequencing is determined by formal rules, not laws, as is the translation of that symbol system into a different material symbol system of tRNA tokens.

    The philosophic naturalist makes the mistake of thinking that because the tokens are physical, the material symbol system is physical. Representation of any kind is always formal, not physical. Symbol systems, language, code, and translation are every bit as formal as mathematics!

    The metaphysical naturalist has no explanation for any formalism, including the mathematical laws of physics themselves.

    Biosemiosis is impossible without choice contingency. Nature is not sufficient to explain nature.

    David Abel. “The First Gene”, “Primordial Prescription: The most plaguing problem in life origin science”. Emphasis mine.

  100. 100
    gpuccio says:

    Zachriel:

    I hoped I could spare the time to answer those two “arguments” of yours, given their obvious weakness. However, here are my answers:

    1) Let’s start with the clock example, which is clearly the simplest. You should really have avoided insisting, but you did insist. Strange.

    Your statement:

    “Planets move like a complex clocklike mechanism. The only complex clocklike mechanism whose origin is independently known are human designs. Hence, planetary movement is designed.”

    This is really silly, from one like you who should be familiar with ID theory, at least judging from the many long discussions we had in the last few years.

    The movement of planets is not an example of obvious and detectable complex functional information. It can be explained by known physical laws, and the configuration of the solar system can (probably) be explained in terms of the same laws, given certain assumptions about physics and astrophysics.

    I really don’t understand why you say that planets move “like a complex clocklike mechanism”. What do you mean?

    If you mean that we can measure time observing the sun, you are certainly right. But we can measure time using any natural event which is cyclical and /or has a definite and reliable duration. Atomic events can be used as clocks. So, it is obviously wrong to state that any kind of object which can be used as a clock is functionally complex. Any natural object which is approximately one meter long, fro example, can be used to measure lengths in meters, but that does not mean that such an object is designed, least of all that it exhibits functional complexity.

    As you should know, simple functions are not enough to infer design. Measuring time or length by some object or event is not a complex function.

    What about men made clocks? Indeed, they usually are functionally complex, but not simply because we can measure time with them.

    Let’s consider a traditional clock, or even a digital clock. Those objects have a complex configuration, which can never be explained in terms of some known law. IOWs, a clock has a physical configuration which is a likely as any other from a huge number of possible physical configurations, and that configuration makes it possible to use it to objectively measure time with great precision and in terms of natural events (like the duration of a day), and to read the measure on a display in symbolic numerical form. That is much more than simply looking at the sun to know what time it is.

    How is that achieved? By a special configuration of analogical parts (the gears, and so on), which use energy to generate specific movements, and a reading system driven by those parts. Or, in the case of digital watches, by a special configuration of circuits.

    Well, that is certainly functional complexity. As you should know, the functional complexity of an object measure the complexity of the information linked to the specific configuration which is necessary top achieve some defined functional achievement, which corresponds to the probability of that kind of configuration among all those available to the object.

    Therefore, there is no “parallel situation which shows the fallacy of my position”. Simply a completely wrong and superficial attempt on your part, which you could well have avoided.

    I will comment about the paper in next post (do you remember? distributed posts).

  101. 101
    gpuccio says:

    Zachriel:

    2) Now, the paper.

    First of all, let’s recall how that discussion started:

    Zachriel: ““Of course, many evolutionary pathways have already been found.”

    gpuccio: “Molecular evolutionary pathways to new complex functional proteins? Really?”

    So, for those who do not understand English quite well, I am obviously asking: “Are you referring to “evolutionary pathways” in the sense of “Molecular evolutionary pathways to new complex functional proteins?” Because in that case, I really don’t understand what you are referring to, and I invite you to give explicit examples”.

    Is that OK?

    Now, in your post #90, as usual, you first retreat to morphology, which obviously is not a “molecular pathway”.

    Then you say:

    “However, we have evidence of the evolution of complex molecular systems, such as the vertebrate blood clotting system which occurred due to a series of gene duplications.”

    And you give the reference to that paper. As an answer, I suppose, to my request for “”Molecular evolutionary pathways to new complex functional proteins”.

    Well, here is the abstract of the paper:

    The blood coagulation scheme for the puffer fish, Fugu rubripes, has been reconstructed on the basis of orthologs of genes for mammalian blood clotting factors being present in its genome. As expected, clotting follows the same fundamental pattern as has been observed in other vertebrates, even though genes for some clotting factors found in mammals are absent and some others are present in more than one gene copy. All told, 26 different proteins involved in clotting or fibrinolysis were searched against the puffer fish genome. Of these, orthologs were found for 21. Genes for the “contact system” factors (factor XI, factor XII, and prekallikrein) could not be identified. On the other hand, two genes were found for factor IX and four for factor VII. It was evident that not all four factor VII genes are functional, essential active-site residues having been replaced in two of them. A search of the genome of a urochordate, the sea squirt, Ciona intestinalis, did not turn up any genuine orthologs for these 26 factors, although paralogs and/or constituent domains were evident for virtually all of them.

    From the paper:

    “The recent publication (5) of the genome sequence for the puffer fish, Fugu rubripes, makes it possible to test that prediction. Additionally, the availability (6) of the complete genome sequence for a urochordate, the sea squirt, Ciona intestinalis, allows a direct comparison of two early diverging chordates. The results confirm that the main lines of the vertebrate clotting pathway were evolved in the interval between the last common ancestor of these two creatures, a period thought to be significantly less than a hundred million years..”

    Emphasis mine.

    Is that good news for your theory? I suppose not. Is that any example of a molecular pathway to some new functional protein? Absolutely not.

    Again from the paper:

    “In the present study, 26 proteins involved in mammalian blood clotting (Table 1) were examined to see whether they have counterparts in the puffer fish and/or the sea squirt. The processes of fibrin formation and destruction are inextricably linked, and the proteins selected include both lytic factors and inhibitors. Because many paralogs could be involved (the result of recent gene duplications), stringent criteria were set for deciding whether or not a gene for a given coagulation factor was present. In the end, 21 orthologs of the coagulation factor genes were found in the puffer fish genome, but not one authentic ortholog was identified in the sea squirt genome.”

    Emphasis mine.

    The other notion in the paper is that, however, some domains which already existed in the sea squirt are found in some of the blood clotting system proteases. And so?

    Let’s try to understand better with an example from the paper.

    Protein S is a vitamin K-dependent protein implied in coagulation. In Puffer fish, it is 675 AAs long. It includes a GLA domain, which is about 40 AAs long, and 4 EGF domains, each of about 35 AAs.

    The human and Puffer fish form are homologs, and share 703 bits homology (342 identities, 469 positives).

    Protein S is not present in Ciona intestinalis, but the GLA and EGF domains can be found.

    From the paper:

    “Only four GLA domains were found to be encoded in the sea squirt genome. None of these were associated with kringles, making it unlikely that there is a prothrombin-like gene. On the other hand, all of the GLAs are associated with multiple EGF domains, but none of these is near a serine protease domain.”

    The highest homology between vertebrate Protein S and Ciona intestinalis is with gamma-carboxyglutamic acid protein 4 (136 bits, 104 identities, 163 homologies), and is due mainly to those domains.

    IOWs, to sum it up:

    Blood coagulation is a novel biological system which appears in vertebrates (like many other complex protein systems typical of vertebrates).

    All those systems seem to “evolve” in a period which is thought to be “significantly less than a hundred million years”.

    Of course, a few domains which can be found in some of the components of the coagulation cascade were already present in earlier animals, like other chordates. That is absolutely common in all protein systems.

    So, is that in any way an answer to my question?

    No. I was asking for molecular pathways which can generate new functional information. That new functions may in part reuse existing modules is well known. However, the new proteins have huge new molecular information which has nothing to do with those old domains, and even the reuse of those domains is original and new.

    So the question is, again: can your theory show a pathway to all that huge amount of new functional information?

  102. 102
    john_a_designer says:

    MatSpirit @ 93-95,

    Tour’s point is that no one knows HOW life originated. To claim otherwise is to be either ignorant or dishonest.

    Simply saying that it COULD have started with biochemical replicators that were capable of some kind of Darwinian evolution is not scientifically explaining how. It is a metaphysically based speculation. Speculation alone doesn’t eliminate other logically possible alternatives.

  103. 103
    Zachriel says:

    Upright BiPed: I’m sure you would agree that if the modern cell is the outgrowth of a precursor, then that precursor had to in some way be capable of organizing the modern cell (or it wouldn’t exist).

    Primordial life is posited to have evolved into the modern cell. It didn’t have the capability of organizing the modern cell.

    Querius: You can’t hide behind time when you have massive numbers of generations “to sort through the variants” in a relative short amount of time.

    While radiation may increase the rate of mutations, it doesn’t speed up generation times. (Indeed, organisms evolve to reproduce more slowly in order to more carefully replicate.) That means the rates of fixation will remain the same, while the ratio of mutation to time of fixation will no longer match the natural ratio.

    Querius: Duh.

    How long does it take, on average, for a beneficial mutation to fix in a population? A neutral mutation?

    gpuccio: The movement of planets is not an example of obvious and detectable complex functional information.

    You didn’t address the argument.

    1. The only objects whose origin is known which have property X are designed.
    2. This object has property X.
    3. Therefore this object is designed.

    Now substitute your preferred notion for X.

    gpuccio: It can be explained by known physical laws, and the configuration of the solar system can (probably) be explained in terms of the same laws, given certain assumptions about physics and astrophysics.

    After Newton explained it. Before then, the motions were unexplained. For something you feel is so easy to refute, you didn’t even grasp the basic notion. The whole point of the parallel is that we do know why planets move — now, and can compare to a state of ignorance.

    gpuccio: Let’s consider a traditional clock, or even a digital clock.

    The more appropriate example is the astrolabe, one of the most complex devices ever made in ancient times. Astrolabes are clearly designed. Astrolabes clearly mimic the movements of the planets. The conclusion is obvious: The planetary motions are designed!

    gpuccio: but not one authentic ortholog was identified in the sea squirt genome.”

    Much of the vertebrate clotting system postdates the split with the common ancestor with sea squirts. Reading further, “Nine of the proteases under discussion can be accounted for by six domain-swapping events. Indeed, the presence of a multiple-kringle protease in the sea squirt genome provides a reasonable model for a step-by-step parallel evolution of the clotting and lysis systems.”

    Of course, it doesn’t include every mutation. Molecules don’t usually leave fossils, so we wouldn’t expect to determine a complete history. Rather, we would expect a phylogeny, in this case, based on duplication and divergence.

  104. 104
    gpuccio says:

    Zachriel:

    I didn’t address the argument?

    You say:

    “1. The only objects whose origin is known which have property X are designed.
    2. This object has property X.
    3. Therefore this object is designed.”

    The correct form should be:

    “1. The only objects whose origin is known which have property X are designed.
    2. This object has property X.
    3. Therefore I reasonably and empirically infer that this object is designed, and all the inferences made this way have been correct.”

    It is an empirical inference, not a logical deduction. But for some strange reason, you neo darwinists continue to try to make it a logical deduction. You are simply wrong.

    That said, the only property which empirically satisfies the requisites for a sound inference, as far as I know, is complex functional information. And probably UB’s semiosis.

    So, what is your problem with that? Do you want to suggest other properties which would make the inference empirically false? Because, you know, you have not done that.

    Regarding the “argument” that once we did not know the scientific explanation of many things, and now we know, therefore we will one day explain everything with the same kind of reasoning we have used in the past, it is so clearly false that I don’t know why you make it.

    The relationship between complex functional information and design is deeply understandable, and is related to the special properties of conscious cognition. It is not something that we have to explain, it is something that we can observe daily.

    The special and unlikely configurations which generate function in human design are not amenable to laws of necessity and regularity, nor to chance. They are connected to design because only design gives the understanding and purpose which can structure possible configurations for a specific result.

    Your “arguments” are not arguments at all, only dogmatic denial of what is obvious and observable.

    Finally, as I have always said, reuse of existing modules is a reality, but it is not the generation of new huge complex functional information, exactly as the Cit+ phenotype in Lenski’s experiment is not the generation of new complex functional information (by the way, have you seem the last news about that?).

    Nobody has ever denied the reuse of modules, more or less modified and adapted, in biological engineering. It is common practice also in human programming, especially OOP.

    What remains to be explained is how new complex functional information is generated.

  105. 105
    gpuccio says:

    Zachriel:

    “The more appropriate example is the astrolabe, one of the most complex devices ever made in ancient times. Astrolabes are clearly designed. Astrolabes clearly mimic the movements of the planets. The conclusion is obvious: The planetary motions are designed!”

    Is this just a joke, or do you really believe in what you are saying? Just to know, given the cognitive level of your last interventions…

  106. 106
    Zachriel says:

    gpuccio: It is an empirical inference, not a logical deduction.

    Perfect. Now have our ancient scholar plug in the astrolabe-like motions of the planets:

    1. The only objects whose origin is known which have astrolabe-like motions are designed.
    2. This object has the property of astrolabe-like motions.
    3. Therefore I reasonably and empirically infer that planetary motions are designed,
    4. and all the inferences made this way have been correct!

    gpuccio: Regarding the “argument” that once we did not know the scientific explanation of many things, and now we know, therefore we will one day explain everything with the same kind of reasoning we have used in the past, it is so clearly false that I don’t know why you make it.

    The scientific explanation for things we don’t have a scientific explanation for is “We don’t have a scientific explanation. Perhaps we could come up with a testable hypothesis.”

  107. 107
    gpuccio says:

    Zachriel:

    Astrolabe-like motions? Please, define. Your reasoning is really pure and intentional confusion of thought. If and when you decide to become again a reasonable person, please let me know.

    Are you against using Hb A2 level to screen for thalassemia carriers? Or using the presence of three 21 chromosomes in the chromosome map to diagnose Down syndrome? Are those examples of false reasoning, and wrong inferences? Should we renounce all inferential science because of your rantings about astrolabes?

    We do have a scientific explanation of complex functional information when we observe it: it’s design. Design detection is scientific. For biologic complex functional information, it is the best available explanation and, certainly, a testable hypothesis, like all scientific theories.

  108. 108
    bill cole says:

    Zachriel

    What is the cause of gravity in Newton’s Theory of Universal Gravitation? What is the cause of variation in Darwin’s original Theory of Evolution?

    The cause is mass of both objects and distance which includes a mathematical predictable model. This did not work for planetary motion a gap that GR filled.

    What has not been observed is the mechanism causing novel origin events such as the origin of eukaryotic cells, multicellular life, birds, mammals, primates and man. The magnitude of the biochemical changes here put any mechanism that has been suggested in extreme doubt.

  109. 109
    Mung says:

    Would anybody like to speculate on the outcome of a parent’s lawsuit?

    Sure. It would get laughed out of court.

  110. 110
    Mung says:

    MatSpirit: The problem is that Tour’s thesis is that the first living thing was a highly complex cell like the modern cell he uses as an illustration.

    This is patently false.

  111. 111
    MatSpirit says:

    john_a_designer @ 102 “Tour’s point is that no one knows HOW life originated. To claim otherwise is to be either ignorant or dishonest.

    Simply saying that it COULD have started with biochemical replicators that were capable of some kind of Darwinian evolution is not scientifically explaining how. It is a metaphysically based speculation. Speculation alone doesn’t eliminate other logically possible alternatives.”

    Tour’s point is not that no one knows how life originated. That’s generally agreed on. Instead, Tour claims:

    (A) The first living thing was as complex as the modern cell he uses as an illustration.

    (B) Such a cell is impossibly unlikely to have been produced by nature.

    Therefore (C) An intelligence had to design it.

    (A) is wrong so (C) is invalid.

  112. 112
    Mung says:

    Zachriel: Primordial life is posited to have evolved into the modern cell. It didn’t have the capability of organizing the modern cell.

    Since no precursor to the modern cell had the capability to organize the modern cell, the modern cell never came to exist. You don’t exist. That’s where your logic gets you.

    Did you not understand the question?

  113. 113
    Zachriel says:

    gpuccio: Astrolabe-like motions? Please, define.

    An astrolabe is a precision device with a number of interlocking circles or gears which mimic the movements of the planets. Here’s an exploded model of the Antikythera mechanism:
    https://upload.wikimedia.org/wikipedia/commons/7/76/Antikythera_model_front_panel_Mogi_Vicentini_2007.JPG

    The thinking was that if is took such complex craftsmanship to mimic the movement of the planets, then it must have taken a master craftsman to put those planets on their paths.

    gpuccio: We do have a scientific explanation of complex functional information when we observe it: it’s design.

    Or evolution with regards to complex functional information in biology.

    bill cole: The cause is mass of both objects and distance which includes a mathematical predictable model.

    No. Newton actually addressed this issue: “Hypotheses non fingo.”

    bill cole: What has not been observed is the mechanism causing novel origin events such as the origin of eukaryotic cells, multicellular life, birds, mammals, primates and man.

    Of course not! They happened before there were people to observe them. That doesn’t mean we reach reasonable conclusions based on evidence.

  114. 114
    Mung says:

    MatSpirit:

    Tour claims:

    (A) The first living thing was as complex as the modern cell he uses as an illustration.

    This is false. Please stop making false statements.

  115. 115
    Zachriel says:

    Mung: Since no precursor to the modern cell had the capability to organize the modern cell, the modern cell never came to exist.

    Perhaps you are using the word “organize” in some special fashion, but if you look at the precursor cell, it is capable only of organizing the precursor cell. The precursor evolved into the modern cell. In other words, the precursor cell changed and became the modern cell.

  116. 116
    Mung says:

    Because we can make a model of ‘x’, ‘x’ must be designed.

    That’s the Zachriels argument. Yes, it’s silly, but apparently Zachriels have nothing better to do with their times.

  117. 117
    Mung says:

    Zachriel: The precursor evolved into the modern cell. In other words, the precursor cell changed and became the modern cell.

    So you do agree with Upright BiPed after all.

    Upright BiPed: I’m sure you would agree that if the modern cell is the outgrowth of a precursor, then that precursor had to in some way be capable of organizing the modern cell (or it wouldn’t exist).

  118. 118
    Zachriel says:

    Mung: So you do agree with Upright BiPed after all.

    You seem to be using the word “organize” in some special manner. Is there is translation dictionary into English?

    Mung: Because we can make a model of ‘x’, ‘x’ must be designed.

    1. The only objects whose origin is known which have property X are designed.
    2. This object has property X.
    3. Therefore I reasonably and empirically infer that this object is designed,
    4. and all the inferences made this way have been correct.

    Property X is clocklike movements. And yes, the ancients did consider the complex movements of the planets as evidenced in the astrolabe to be clear evidence of design.

  119. 119
    EugeneS says:

    MatSpirit,

    I actually listened to the entire lecture. He is very clear and very accurate in what he says.

    What he says is that nature cannot fine-tune or control the synthesis, it cannot purify components to fractions of percent, which is critical to produce complex nano-machinery. For trial-and-error, nature needs to have the capability of analysis and learning, which it does not.
    Nature cannot make decisions.

    So your critique misses the point. I understand that it is a very convenient position to keep referring to the purported simplicity of the first cell. But this argument does not stand. Natural forces are insufficient to explain life, because life is not reducible to chemistry.

    The first cell whatever it looked like absolutely must have included the irreducible semiotic triad of symbol, interpreter and referent, inexplicable in terms of mere chemistry. That is already common place knowledge.

  120. 120
    EugeneS says:

    Zachriel

    The Belousov-Zhabotinsky reaction is clock-like and yet it is natural.

    Your ‘argument’ is a caricature.

  121. 121
    Zachriel says:

    EugeneS: The first cell whatever it looked like absolutely must have included the irreducible semiotic triad of symbol, interpreter and referent, inexplicable in terms of mere chemistry.

    The first life is posited to be some sort of self-replicating molecule or network of molecules, such that the symbol, interpreter and referent are all the same structure. We have evidence that molecules can self-replicate.

    EugeneS: The Belousov-Zhabotinsky reaction is clock-like and yet it is natural.

    There are all sorts of clock-like phenomena with known natural causes. This information wasn’t available to our ancient scholar, though. That’s rather the reason to use planetary orbits — because we know something the ancient scholar doesn’t know.

  122. 122
    Querius says:

    Z,

    How long does it take, on average, for a beneficial mutation to fix in a population? A neutral mutation?

    LOL. You still don’t understand that genetic processes depend on the NUMBER OF GENERATIONS, not elapsed time. Duh.

    It’s such a waste of time reading your posts. Yet you fill this forum with blather and unsupported assertions.

    Goodbye.

    -Q

  123. 123
    MatSpirit says:

    EugeneS @ 99: (Quoting Howard Pattee) “Life cannot exist without programming, and the processing of that programming.”

    Pattee is wrong. Supposed you have five molecules, A, B, C, D and E strongly bonded together as a polymer like this:

    A
    B
    C
    D
    E

    Now suppose there are large quantities of five other molecules floating around the polymer: a, b, c, d and e.

    Suppose A is weakly attracted to a, B is weakly attracted to b, C to c, D to d and E to e.

    Brownian motion will shuffle the a-e molecules past every atom in the A-E polymer and a will stick to A, b will stick to B etc and we will get this:

    A-a
    B-b
    C-c
    D-d
    E-e

    Where the dashes represent weak bonds while the atoms in the abcde polymer are bound together with stronger bonds like the ones in the ABCDE polymer.

    Eventually the two polymers will cleave apart and you’ll have two separate polymers like this where you only had the one before:

    A a
    B b
    C c (The two Polymers should be widely
    D d separated, but the auto-formatting
    E e is messing things up)

    The abcde polymer will be able to line up separate A, B, C, D and E molecules and split them off as a brand new ABCDE polymer like this and we will have reproduced the original ABCDE polymer:

    A a A
    B b B
    C c C
    D d D
    E e E

    This can go on and on until we have scads of ABCDE polymers (plus scads of waste abcde polymers).

    So, we have achieved reproduction. Where’s the program? It’s not the existence of the A, B, C, D, E, a, b, c, d and e molecules or the bonds they can make. Those are just the raw materials and their properties. It’s not the Brownian motion that moves them around, that’s purely random. There is no program.

    You don’t need a program to reproduce.

  124. 124
    MatSpirit says:

    Zachriel said it much more simply.

  125. 125
    MatSpirit says:

    EugeneS @ 119:

    “What he says is that nature cannot fine-tune or control the synthesis, it cannot purify components to fractions of percent, which is critical to produce complex nano-machinery.”

    Then how does Professor Tour stay alive? His body is manufacturing, operating and repairing trillions of cells as I write these words. That requires tons of fine-tuning, controlling, synthesising, purifying and producing of complex nano-machinery!

    How do you think this is done? Do you believe your cellular machinery is run by natural processes or magic?

    Has it occured to anybody here that Tour and Nature are building molecules from opposite directions? Cells move individual atoms, molecules and electrons. Tour shovels atoms into test tubes and then complains about how hard it is to maintain purity and yield. He’s doing it wrong!

  126. 126
    EugeneS says:

    As I say, Zachriel, you have no case. Try again.

    MatSpirit,

    You did not get to the bottom of Pattee’s argument. Something tells me that it is you who is wrong, not Pattee. Your code-denialist position is already outdated and has been debunked many times starting from von Neumann. You are arguing with a whole school of thought (Pattee is far not alone there).

    Life is about symbolic replication and control. To kick-start life you absolutely need symbolic memory and IO to/from it of a symbolic description of the entire system for sustainable replication. Life is code based. The {symbol,interpreter,referent} triple is irreducible to chemistry.

    Something tells me you do not appreciate how hard it is just to maintain error-free replication alone. Imagine you need to build a house. You hire an eager builder, and with him as a package deal you get ten demolishers who are far more enthusiastic than the builder.

    The basic epistemological distinction is between the laws of particle motion and specific boundary conditions governing the motion of particles of matter. Biosemiotics views life as specific non-integrable symbolic boundary conditions irreducible to the laws of dynamics.

    It appears that you have a gap in understanding what the issue is.

  127. 127
    MatSpirit says:

    I just spotted this: “Natural forces are insufficient to explain life, because life is not reducible to chemistry.”

    You DO believe in magic!

  128. 128
    Origenes says:

    MatSpirit: You DO believe in magic!

    We both believe in magic. The only difference is that my position believes in one magical event — one Uncaused Cause — that explains all, while your position believes in numerous unrelated magical events all over the place.

  129. 129
    EugeneS says:

    “Do you believe your cellular machinery is run by natural processes or magic?”

    Have you heard of control theory?

    “You do believe in magic”.

    I believe in God and I am an Orthodox Christian priest.

    Am I right in thinking that all your scientific arguments have been exhausted?

  130. 130
    Mung says:

    Tour shovels atoms into test tubes and then complains about how hard it is to maintain purity and yield. He’s doing it wrong!

    Right. He should use enzymes.

  131. 131
    Mung says:

    Zachriel: Property X is clocklike movements.

    What object is ‘Property X’ a property of?

    Also, my clocks are stationary.

  132. 132
    Zachriel says:

    Querius: You still don’t understand that genetic processes depend on the NUMBER OF GENERATIONS, not elapsed time.

    There are many factors which influence evolution, including the size of the genomes. In any case, the mutation rate in bacteria increases due to radiation, not the rate of reproduction. That means mutations will accumulate before selection or drift have time to act.

    MatSpirit: You don’t need a program to reproduce.

    What you described is called template replication, which forms the basis of DNA replication.

    EugeneS: Zachriel, you have no case.

    RNA World is a valid hypothesis with some empirical support. It has the interest of some of the best scientists in abiogenetics. That doesn’t make it true, but it certainly deserves more than handwaving.
    http://molbio.mgh.harvard.edu/szostakweb/

  133. 133

    UB: I’m sure you would agree that if the modern cell is the outgrowth of a precursor, then that precursor had to in some way be capable of organizing the modern cell (or it wouldn’t exist).

    Here is my question: In leading to organization of the modern cell, did that precursor require the capacity to somehow specify any of the constituent parts of the modern cell?

    Zach: Primordial life is posited to have evolved into the modern cell. It didn’t have the capability of organizing the modern cell.

    That’s an interesting proposition Zach. Let us say that the extant heterogeneous cell is the end product of a chemical evolution of some unspecified sort. Are you suggesting that at no time in this process was there any need to retain any structure or structures as being those which would be part of the final heterogeneous result?

    So if one had the opportunity to watch the entire process on time-lapse photography, it would perhaps appear as a formless mass that — at some unspecified point in time — suddenly crystalized into the modern heterogeneous cell?

    Gone is the gradual piece by piece imagery of evolution. Instead, all the parts of the extant cell fortuitously appeared together somehow at the same time and place, and apparently began functioning. And among those constituent parts to appear (or otherwise be available) was a genome and translation machinery — such that the extant cell finally had the capacity to specify objects (as we observe it in nature today) and retain those objects within its organization.

    Seems rather unlikely.

  134. 134
    bill cole says:

    Zachrael

    Of course not! They happened before there were people to observe them. That doesn’t mean we reach reasonable conclusions based on evidence

    We agree here that there is no direct evidence for major origin events.

    What are the reasonable conclusion based on evidence? This is the inference argument which allows for design. Are you ready to honestly compare current evolutionary explanations like RMNS or neutral theory against design given the genome is a sequence? A start might be the novel eukaryotic molecular macro machines the spliceosome and the structure of chromosomes including histones and nuclear proteins that cause transcriptional events.

  135. 135

    EugeneS: (Quoting Howard Pattee) “Life cannot exist without programming, and the processing of that programming.”

    Matt: Pattee is wrong. Supposed you have five molecules, A, B, C, D and E strongly bonded together as a polymer like this:

    A
    B
    C
    D
    E

    I’m not sure if you ever grasped your mistake, but your example is not “Life” and has no resemblance to the replication of “Life”. I suspect this little fact may not be of much importance to you, but I’m fairly sure it matters to Pattee. He even writes about physics-free models such as yours. Perhaps you should read some of his 50 years of OoL research before you discount him with irrelevant examples.

  136. 136

    Matt, quoting ES

    I just spotted this: “Natural forces are insufficient to explain life, because life is not reducible to chemistry.”

    You DO believe in magic!

    You are apparently unaware of this, but the issue is not magic. To organize the heterogeneous cell you have to organize a system containing a local discontinuity in the control of its output. This is simply to say that the input to the system cannot use inexorable law to physically determine the output of the system. Why? Because no object in the universe specifies any other object in the universe. So a temporal output that equals “present leucine for binding” is not a phenomena that can be derived from the surface properties of its nucleic input. It requires the discontinuity mentioned above, and thus, is not reducible to local chemistry. Physicist (like Pattee, and others) have known this for about half a century.

  137. 137
    Zachriel says:

    Upright BiPed: Are you suggesting that at no time in this process was there any need to retain any structure or structures as being those which would be part of the final heterogeneous result?

    Of course some structures were retained. That’s how evolution works, modifying structures opportunistically. Have no idea what you are on about.

    bill cole: What are the reasonable conclusion based on evidence?

    Among the most important evidence is the evidence for common descent, with all that implies about the history of life.

  138. 138
    bill cole says:

    Zachraiel

    Among the most important evidence is the evidence for common descent, with all that implies about the history of life.

    How does the evidence for common decent differentiate the nature vs design argument. Common biochemistry can exist in both cases.

  139. 139
    Zachriel says:

    bill cole: How does the evidence for common decent differentiate the nature vs design argument.

    It provides the historical context for evaluating the mechanisms involved in the diversification of species from their common ancestors. Knowing that humans descended from a common ancestor with chimpanzees is important to understanding how that happened. It’s a fundamental and profoundly important fact of biology.

  140. 140
    bill cole says:

    Zachriel

    Knowing that humans descended from a common ancestor with chimpanzees is important to understanding how that happened. It’s a fundamental and profoundly important fact of biology.

    How do you know this is true? This is a fact? Who is the common ancestor? What is the mechanism that caused DNA, Splicing codes and gene expression timing to change?

  141. 141
    Zachriel says:

    bill cole: How do you know this is true?

    Which is why we said you have to start with common descent. You would agree that if humans descended from a primitive fish that this would be a profoundly important fact in understanding the origin of humans?

    bill cole: This is a fact?

    The most important evidence is the nested hierarchy and fossil succession.
    http://www.uncommondescent.com.....-graphics/

  142. 142
    bill cole says:

    Zachrael

    Which is why we said you have to start with common descent. You would agree that if humans descended from a primitive fish that this would be a profoundly important fact in understanding the origin of humans

    When you say decent do you mean closest specie in terms of physical and biochemical structure. Where is there evidence of the common ancestor or is this assumed to be true a priori? In the case of design would a common ancestor be necessary?

  143. 143
    john_a_designer says:

    Mung to MatSpirit @ 114,

    MatSpirit:

    Tour claims:
    (A) The first living thing was as complex as the modern cell he uses as an illustration.

    Mung: This is false. Please stop making false statements.

    As an analogy Tour cites his own pioneering work in the field of Nano-technology. The example he uses in his discussion is the nanocar. But the nanocars that he and his team were able to artificially synthesize are not all that complex. They are certainly far less complex than simple cells or even some types of organelles within a simple cell. However, he can tell you step-by-step how his nanocars were synthesized. Would a hypothetical biochemical replicator be simpler or more complex than Tour’s nanocar? How could you even answer such a question without knowing what they were, how they were made or even if they existed? You are certainly not in a position to describe step-by-step how they originated. That is what Tour means when he says that nobody knows how.

  144. 144
    Dionisio says:

    vjtorley @69

    I don’t think that it’s necessary to know in advance exactly how these components were assembled. That would be a bottom-up approach.
    The aim of a top-down approach, as I see it, is to identify the sequence of steps whereby the macro-components of the cell were put together, before attempting to identify the sequence of steps whereby their sub-components were assembled.

    I completely agree. My last statement @35 was not written clearly. My use of the word ‘assembled’ was incorrect. It was about how (in what sequence) different components were placed where they are seen now. Thank you for clarifying this important concept.

    The pituitary gland may signal the thyroid gland to signal the kidneys to retain more or less sodium or other electrolytes. Each of those organs have their separate morphogenesis but functionally they are interrelated.
    As we move down into tissues, cellular, molecular mechanisms, that higher interrelationship must be kept in the picture.

  145. 145
    EugeneS says:

    Zachriel,

    (In response to UB) “Have no idea what you are on about.”

    That is why I say you have no case.

  146. 146
    EugeneS says:

    Zachriel

    “That’s how evolution works, modifying structures opportunistically. ”

    You have no idea of how it works on the biochemical level. Neither do I, nor even Professor Tour, nor anybody else.

    Opportunity of what?! For what purpose?! What is the biochemical mechanism for detecting and actively using a detected opportunity?!

    Opportunities can only be detected given a defined optimization function and foresight. No foresight – no opportunity detection. For a hundredth time, evolution selects only from among existing functions, not for a future function. For a future function evolution is helpless, one needs decision making with foresight. That is exactly what humans do in programming: a program is nothing but rule-based formal decision making specified for future execution. And that is exactly what the cell is doing (formal rule-based organization and programmed behaviour). A program is meaningless without a compiler. Likewise, biological codes are useless without interpreters. Evolution is not a prerequisite of a functioning cell, it is the other way around.

  147. 147
    Zachriel says:

    bill cole: When you say decent do you mean closest specie in terms of physical and biochemical structure.

    We mean mother and child, bill cole. It means your distant ancestor cradling her child was a monkey(-like organism).

    bill cole: Where is there evidence of the common ancestor or is this assumed to be true a priori?

    Again. The most important evidence is the nested hierarchy and the fossil succession.
    http://www.uncommondescent.com.....-graphics/

    Again. Would you agree that if humans descended from a primitive fish that this would be a profoundly important fact in understanding the origin of humans?

    EugeneS: That is why I say you have no case.

    The question was “Do you think whatever simple life form that is proposed as the precursor to the modern cell — as just a matter of general logic — had to be able to organize the modern cell?”

    The answer is no. The primordial cell did not have the ability to organize the modern cell, anymore than a Homo erectus genome has the ability to organize a Homo sapiens.

    EugeneS: You have no idea of how it works on the biochemical level.

    There are entire scientific journals, such as Molecular Biology and Evolution, filled with research into molecular evolution.

  148. 148

    Upright BiPed: I’m sure you would agree that if the modern cell is the outgrowth of a precursor, then that precursor had to in some way be capable of organizing the modern cell (or it wouldn’t exist).

    Zach: Primordial life is posited to have evolved into the modern cell. It didn’t have the capability of organizing the modern cell.

    Upright BiPed: Gone is the gradual piece by piece imagery of evolution. Instead, all the parts of the extant cell fortuitously appeared together somehow at the same time and place, and apparently began functioning.

    Zach: Of course some structures were retained. That’s how evolution works

    Context. Don’t leave home without it.

  149. 149
    gpuccio says:

    Zachriel:

    “An astrolabe is a precision device with a number of interlocking circles or gears which mimic the movements of the planets.”

    As you can easily see, your definition of an astrolabe includes an explicit reference to the movements of the planets. That’s why your whole “argument” is junk.

    “The thinking was that if is took such complex craftsmanship to mimic the movement of the planets, then it must have taken a master craftsman to put those planets on their paths.”

    That’s ridiculous thinking. Complex craftmanship is necessary to mimic the movement if the planets, while the movement itself, with real planets, is governed by simple gravitational laws. Your whole discussion about this point makes no sense at all, and has no implications to my discussion about complex functional information.

    “Or evolution with regards to complex functional information in biology.”

    You are right. Evolution by RV + NS is a scientific explanation, which does not work and does not really explain anything. That’s why we have to choose the best explanation between the two, which is design.

    I am happy that you have finally understood the idea. 🙂

  150. 150
    EugeneS says:

    “There are entire scientific journals, such as Molecular Biology and Evolution, filled with research into molecular evolution.”

    Really? You must be kidding. Has anyone presented such a ground breaking discovery yet? Again, by a discovery I mean the actual details, not the usual evo hand-waving.

    I suspect it is prof Tour, who is right, not evos. Professor Tour’s characterization is supported by my own personal professional experience, however limited, in my field. Almost always, difficulties emerge in the detail, not in the big picture. As soon as the difficulties are recognized as insurmountable, a drastic change in modelling is required. The big picture is always philosophy, the detailed account is real science. Those who actually do real science all in one accord testify to the huge challenges in the field. The further down the line, the larger the challenges become.

  151. 151
    Mung says:

    Zachriel: “An astrolabe is a precision device with a number of interlocking circles or gears which mimic the movements of the planets.”

    Mung: Because we can make a model of ‘x’, ‘x’ must be designed.

    That’s the Zachriels argument. Yes, it’s silly, but apparently Zachriels have nothing better to do with their times.

  152. 152
    Zachriel says:

    Origenes: Context. Don’t leave home without it.

    That’s right. We even asked if you were using a special definition of “organization”. To repeat: the primordial cell did not have the ability to organize the modern cell, anymore than a Homo erectus genome has the ability to organize a Homo sapiens.

    gpuccio: As you can easily see, your definition of an astrolabe includes an explicit reference to the movements of the planets.

    And yet, the wisest of the ancients thought it was convincing evidence that the celestial movements were designed.

    gpuccio: Complex craftmanship is necessary to mimic the movement if the planets, while the movement itself, with real planets, is governed by simple gravitational laws.

    We know now. Remember, this is from the point of view of an ancient scholar.

    EugeneS: Has anyone presented such a ground breaking discovery yet?

    Did you bother to crack a journal on the subject? Or a textbook perhaps? There are a number of good texts on the subject, such as Nei & Kumar, Molecular Evolution and Phylogenetics, Oxford University Press 2000.

    Mung: Because we can make a model of ‘x’, ‘x’ must be designed.

    The model is of complex design, therefore the celestial motions are of complex design. It’s only because we know a simple underlying principle that we no longer consider planetary motions to be so complex. For instance, the retrograde of Mars is just a happenstance of the relative orbits of Earth and Mars, rather than part of some complicated apparatus.
    http://www.zachriel.com/blog/Angels.jpg

    PS. Technically, an astrolabe doesn’t model the planets, but predicts their position. It’s a type of celestial clock.

  153. 153
    EugeneS says:

    Zachriel,

    A lot of this ‘research’ is just question begging. If we discount it, the actual solid research, whose validity I am not questioning, is necessarily to do with details. As it happens, the actual research very weakly depends (if at all) on the evolutionary assumptions. According to some people working in the field, evolution does not provide a useful heuristic. On the contrary, non-trivial findings are sooner obtained if one’s research is based on more meaningful assumptions. Randomness is never an explanation for anything.

  154. 154
    gpuccio says:

    Zachriel:

    “And yet, the wisest of the ancients thought it was convincing evidence that the celestial movements were designed.”

    Maybe they were right. The laws of nature could well be designed, and you certainly know that the cosmological aspect of ID theory deals with that. But it is another kind of problem.

    What we are dealing with here, instead, is the biological aspect of ID theory, the one based on detectable design in biological digital sequences which bear function, IOWs, on digital complex functional information, dFSCI.

    It is a fact, a fact that you try stubbornly to deny, that dFSCI is always associated to designed objects in all cases where the origin of the object can be independently assessed. That is the sound epistemological foundation to consider it a reliable marker of the design process.

    It is a fact that dFSCI can be well defined so that its meaning is universally understood, and so that it can be objectively measured in real cases, like proteins.

    It is a fact that complex language and complex machines (including software) are the only examples of dFSCI that we can observe in nature, except for biological objects, whose origin cannot be independently assessed (at least for now).

    It is a fact that both complex language and complex machines are human artifacts.

    It is a fact that biological objects have all the properties of complex biological machines, and almost universally exhibit dFSCI.

    Those are the foundation for design inference in biology. All your discussions about astrolabes and wise ancients have no epistemological bearing to all that.

    The fact remains that in your (corrected) “reasoning”:

    “1. The only objects whose origin is known which have property X are designed.
    2. This object has property X.
    3. Therefore I reasonably and empirically infer that this object is designed, and all the inferences made this way have been correct.”

    the only property X which really satisfies the reasoning is complex functional information (and maybe semiosis).

  155. 155
    gpuccio says:

    Zachriel:

    “It’s only because we know a simple underlying principle that we no longer consider planetary motions to be so complex. ”

    Are you suggesting that some “simple underlying principle” will some day explain language and machines, so that we can safely avoid to infer design in front of Hamlet or of Windows 10?

  156. 156
    EugeneS says:

    Zachriel,

    “It’s only because we know a simple underlying principle that we no longer consider planetary motions to be so complex.”

    Is that your argument? I admit that it may seem ‘simple’ to a person who is unaware of the underlying theory. But it is nowhere near as simple as you imagine it is.

    ‘Simple’ and ‘complex’ need to be properly defined. By complexity semiotics means a special organization of a multi-component system such that one component acts as a symbol of another component (i.e. specifies it) while there is no direct physical relationship between the two. The specification is interpreted by a third component, which acts as a protocol. Every constituent of the triple is a key contributor to the joint effect of information translation. Not a single one can be removed without destroying the function of the information translation system. This formal non-physical organization of the system is irreducible to the motion of the particles of matter. The different roles of the constituents are a specific form of non-integrable constraints on the dynamics of the system.

  157. 157
    Querius says:

    All,

    Isn’t it obvious by now that all Z wants to do is waste your time? Z neither understands nor answers your carefully prepared arguments with anything but new assertions.

    -Q

  158. 158
    bill cole says:

    Z

    bill cole: When you say decent do you mean closest specie in terms of physical and biochemical structure.

    We mean mother and child, bill cole. It means your distant ancestor cradling her child was a monkey(-like organism).

    bill cole: Where is there evidence of the common ancestor or is this assumed to be true a priori?

    Again. The most important evidence is the nested hierarchy and the fossil succession.

    I do not think a nested hierachy is evidence. It is humans making assumptions based on fossil evidence and biochemical evidence. Based on your definition of common ancestor I don’t think this is a fact or a theory or even a viable hypothesis based on the biochemical differences. I think the real explanation may be over 1 million individual trees in the ground:-)

  159. 159
    Mung says:

    Zachriel: The model is of complex design, therefore the celestial motions are of complex design.

    Where’s your evidence of interlocking gears in space connecting the planets?

  160. 160
    MatSpirit says:

    Sorry for being AWOL. The first clear night in a week, a new camera and a friend who wanted to shoot star trails.

    Catching up, Origines @ 128, what magical events are you talking about? Hopefully not in the mere operation of living cells because vitalism is pretty much dead, killed by the microscope. In the evolution that created the cell? No magic there either.

    EugeneS @ 129: What control theory is found in my example? I don’t think simple attractive forces between atoms rises to that level.

    Mung @ 130: Every enzyme I know of is much larger and more complex than one of Tour’s cars.

    UprightBiped @ 135: First Life has little in common with highly evolved contemporary life. If it reproduces itself and can undergo evolution, like my self reproducing polymeric example, it qualifies.

    I googled Pattee and read some of his stuff before writing. The last time I saw anything like it, it was from a retired nutcase running an impressively titled foundation offering a million dollar prize for refuting its views whose address googled to his garage. I’m hoping Pattee does better than this, but if he doesn’t know the difference between First Life and modern life I have my doubts.

  161. 161
    MatSpirit says:

    UprightBiped @ 136: “You are apparently unaware of this, but the issue is not magic. To organize the heterogeneous cell you have to organize a system containing a local discontinuity in the control of its output.”

    Are you aware of oscillators? They provide an output without any input at all. You have several of them in your computer. That’s all my example is, but its a powerhouse that can drive evolution.

    “This is simply to say that the input to the system cannot use inexorable law to physically determine the output of the system.”

    No inputs, no problems.

    “Why? Because no object in the universe specifies any other object in the universe.”

    Except for the dozens of varieties of tRNA which map to specific DNA triplets on one end and one SPECIFIC amino acid on the other. This allows DNA to SPECIFY the sequence of amino acids in a protein.

    “So a temporal output that equals “present leucine for binding” is not a phenomena that can be derived from the surface properties of its nucleic input.”

    So tRNA doesn’t work and we’re all dead.

    “It requires the discontinuity mentioned above, and thus, is not reducible to local chemistry. Physicist (like Pattee, and others) have known this for about half a century.”

    I think you may misunderestimate Dr. Pattee, but maybe not the Important Sounding International Scientific Foundation Which is Located in a Garage.

  162. 162

    Matt, newsflash: tRNA do not establish the genetic code.

  163. 163
    Origenes says:

    MatSpirit: Catching up, Origines @ 128, what magical events are you talking about?

    The numerous magical events that naturalists like you believe in. Allow me to provide some examples:
    A (fine-tuned) universe from nothing. Consciousness and rationality from blind non-rational chemistry. Organization from chaos. Life from dead matter. Irreducible complexity from a step-by-step selection process. Finding functional proteins in vast spaces of non-functionality. Homeostasis in trillions of organisms without any bottom-up explanation whatsoever.
    Need I go on?

    MatSpirit: Hopefully not in the mere operation of living cells because vitalism is pretty much dead, killed by the microscope.

    Only to those who hold the naïve belief that a microscope allows us to see all there is.

    MatSpirit: In the evolution that created the cell? No magic there either.

    A cell is a prerequisite to evolution, so you have just provided a demonstration of your magical thinking.

  164. 164

    I feel bad for mentioning Dr Pattee. He’s one of the world’s most-noted authorities on the physics of symbol systems. He has my respect because regardless of his atheist/materialist worldview, he doesn’t write it into his research. The science is the science, and he keeps his metaphysics out of it. Yet, here we have an obviously dull juvenile (regardless of his age) who doesn’t know shit about what he’s talking about, and hasn’t even a second thought about publically spitting in Dr Pattee’s face for not being a proper ideologue.

    Matt, your post at 160 and 161 betray the simple fact that the actual physics of the translation system has never even occurred to you. What do you do after you spit in a man’s face, only to find out that you can be proven wrong by sources from one end of biology to the other? Do you man-up and apologize, or do you double-down and attempt to justify yourself?

    If you need to cheese out, then blame your comments on me, and retract your slur against Pattee.

  165. 165
    MatSpirit says:

    I’ll skip a few back-messages to answer UprightBiped @ 164 first.

    I feel bad for Dr. Pattee too. To think of a man spending his entire adult life researching a subject and then finding people like UprightBiped and The Foundation in Some Nut’s Garage using his name to advance ignorant claptrap must cast a pall on his entire life.

    “Matt, your post at 160 and 161 betray the simple fact that the actual physics of the translation system has never even occurred to you.”

    What ARE you talking about? The physics of tRNA is well understood. Do you believe there’s something mysterious about putting atoms together into molecules and atomic bonding going on in tRNA that we don’t understand?

    Of course, you’re arguing ad insultam (juvenile who doesn’t know what he’s talking about spitting in Pattee’s eye), which has been characteristic of creationism / ID / religion as long as they have existed, but now you’re using the most modern, up to the minute apologetic tactic, swearing.

    And all this coming from a man who is presumably proud of message 133. You did write that voluntarily, right? No gun to your head, no threats of hell fire if you didn’t? You really thought you were being smart and delivering the latest up to the minute science when you wrote that? Maybe you should stick to four letter words.

  166. 166
    Mung says:

    MatSpirit: I googled Pattee and read some of his stuff before writing.

    Well then, you must be all caught up.

    I pointed out where you made at least two false statements about Tour. Any reason we should expect anything different from you when you talk about Pattee?

  167. 167
    Dionisio says:

    Querius @457

    I thought like you, but now I kind of realize that some interlocutors are used to motivate our friend GP and others to write their interesting comments here.

    🙂

  168. 168

    Matt, tRNA doesn’t establish the genetic code. Your argument falls apart because your conception of translation is technically flawed. This can be verified in every biology textbook on the surface of the planet. So you chose to double down.

  169. 169
    Zachriel says:

    EugeneS: A lot of this ‘research’ is just question begging.

    Do you have a specific example?

    gpuccio: The laws of nature could well be designed, and you certainly know that the cosmological aspect of ID theory deals with that.

    The difference is that gravity is a simple principle, and it doesn’t require a complex interlocking mechanism to explain planetary motions, just simple integration (continuous movement under the inverse square law).

    gpuccio: that dFSCI is always associated to designed objects in all cases where the origin of the object can be independently assessed.

    Except for biological objects, which are due to evolution.

    gpuccio: the only property X which really satisfies the reasoning is complex functional information (and maybe semiosis).

    For an ancient, the only objects whose origin is known which have clock-like workings are designed.

    gpuccio: Are you suggesting that some “simple underlying principle” will some day explain language and machines

    Evolution is the underlying principle that explains the overall patterns in biology.

    EugeneS: I admit that it may seem ‘simple’ to a person who is unaware of the underlying theory.

    The three-body problem doesn’t change the fact that there is a simple underlying mechanism, and repetition of this pattern predicts the resulting pattern over finite times.

    EugeneS: Simple’ and ‘complex’ need to be properly defined. By complexity semiotics means a special organization of a multi-component system such that one component acts as a symbol of another component (i.e. specifies it) while there is no direct physical relationship between the two.

    The standard definition of complex, a whole made up of complicated or interrelated parts, includes timepieces. Indeed, Paley’s argument is based on the discovery of a timepiece.

    bill cole: I do not think a nested hierachy is evidence. It is humans making assumptions based on fossil evidence and biochemical evidence.

    Branching descent implies the nested hierarchy; hence the observation of the nested hierarchy supports the hypothesis of branching descent. Now, combine this with the fossil succession.

    Mung: Where’s your evidence of interlocking gears in space connecting the planets?

    That’s why an astrolabe is not an actual model, but a timepiece.

  170. 170
    Phinehas says:

    Z:

    It’s only because we know a simple underlying principle that we no longer consider planetary motions to be so complex.

    You mean besides all the fine-tuned constants and such that make it possible for one of those planets to function as the incubator of life? No doubt assembling an astrolabe is kid’s play comparatively speaking.

  171. 171

    gpuccio: that dFSCI is always associated to designed objects in all cases where the origin of the object can be independently assessed.

    Zach: Except for biological objects, which are due to evolution.

    You haven’t independently assessed that the origin of biological information is evolution. You are assuming your conclusion against universal evidence to the contrary.

  172. 172

    gpuccio: Are you suggesting that some “simple underlying principle” will some day explain language and machines

    Zach: Evolution is the underlying principle that explains the overall patterns in biology.

    Darwinian evolution requires the very informational medium and translation apparatus it is attempting to explain. If A requires B for A to exist, then A cannot be the source of B.

  173. 173
    Dionisio says:

    MatSpirit @161

    Are you aware of oscillators? They provide an output without any input at all. You have several of them in your computer. That’s all my example is, but its a powerhouse that can drive evolution.

    Do you know how people have built the oscillators seen in biological systems so far?
    Or can you point to serious literature where a hypothetical process to build them is fully explained in details?

  174. 174
    Dionisio says:

    MatSpirit @161

    Except for the dozens of varieties of tRNA which map to specific DNA triplets on one end and one SPECIFIC amino acid on the other.

    and one SPECIFIC amino acid on the other.“?

    Are you sure of that? Can you either describe that or point to the literature where it is explained in details?

    This allows DNA to SPECIFY the sequence of amino acids in a protein.

    Can concepts like “pleiotropic” and “splicing mechanisms” be somehow related to the above-quoted statement?

    What’s the difference between proto-mRNAs and mRNAs?

    Can concepts like “post-translational modifications” be somehow related to the above-quoted statement?

    [emphasis mine]

  175. 175
    bill cole says:

    Z

    bill cole: I do not think a nested hierachy is evidence. It is humans making assumptions based on fossil evidence and biochemical evidence.

    Branching descent implies the nested hierarchy; hence the observation of the nested hierarchy supports the hypothesis of branching descent. Now, combine this with the fossil succession.

    Fossil succession is not biochemical evidence. The biochemical evidence is contradictory to the fossil evidence. The biochemistry tells the story and the fossil evidence can only support. Common decent theory as you have defined it is almost certainly false. When you say you are observing nested hierarchy you are observing a man made diagram based on incomplete observation which does not include contradictory biochemical evidence.

  176. 176
    Dionisio says:

    Upright BiPed @168

    Matt, tRNA doesn’t establish the genetic code. Your argument falls apart because your conception of translation is technically flawed. This can be verified in every biology textbook on the surface of the planet. So you chose to double down.

    Maybe we should give him an opportunity to explain what he wrote?
    🙂

  177. 177
    Querius says:

    Dionisio @ 167,

    I thought like you, but now I kind of realize that some interlocutors are used to motivate our friend GP and others to write their interesting comments here.

    Yeah, I see what you mean.

    So the idea is to create articulate responses to emergent narrative points, ignoring Z’s vacuous, unsupported assertions unless you can use it to create additional explanations for everyone else.

    Well, I admit that your approach is practical.

    Thanks,

    -Q

  178. 178
    Zachriel says:

    Phinehas: You mean besides all the fine-tuned constants and such that make it possible for one of those planets to function as the incubator of life?

    No one has a scientific explanation for the so-called fine-tuning of the cosmos, any more than they had an explanation for the equivalence of the gravitational and inertial masses before Einstein.

    Upright BiPed: You are assuming your conclusion against universal evidence to the contrary.

    If the evidence is universal, then why do scientists in so many different fields of study, in many different cultures and political systems, not agree with your position?

    Upright BiPed: Darwinian evolution requires the very informational medium and translation apparatus it is attempting to explain. If A requires B for A to exist, then A cannot be the source of B.

    That is incorrect. Self-replicating molecules and molecular networks. are capable of darwinian evolution.

    bill cole: Fossil succession is not biochemical evidence.

    No. It’s paleontological evidence. Or what is known in science as “evidence”.

    bill cole: The biochemical evidence is contradictory to the fossil evidence.

    The biochemical evidence supports the same overall phylogeny as the fossil evidence.

    bill cole: When you say you are observing nested hierarchy you are observing a man made diagram based on incomplete observation which does not include contradictory biochemical evidence.

    The molecular and morphological phylogenies are largely congruent.

  179. 179

    gpuccio: that dFSCI is always associated to designed objects in all cases where the origin of the object can be independently assessed.

    Zach: Except for biological objects, which are due to evolution.

    UB: You haven’t independently assessed that the origin of biological information is evolution. You are assuming your conclusion against universal evidence to the contrary.

    Zach: If the evidence is universal, then why do scientists in so many different fields of study, in many different cultures and political systems, not agree with your position?

    Why scientist do what they do is irrelevant to the fact. You haven’t independently assessed that the origin of biological information is evolution. Thus, you are assuming your conclusion.

  180. 180

    Darwinian evolution requires the very informational medium and translation apparatus it is attempting to explain. If A requires B for A to exist, then A cannot be the source of B.

    That is incorrect. Self-replicating molecules and molecular networks. are capable of darwinian evolution.

    a) there is no documentation that any autonomous self replicators exist.

    b) there are no non-autonomous “self replicators” that are not also the product of intelligent design.

    c) all homogeneous self-replicators are template replicators

    d) a template replicator is not capable of translation, and cannot organize a heterogeneous cell.

    e) all life forms are heterogeneous, and reproduce by the translation of a genome.

  181. 181
    Mung says:

    Dionisio: Maybe we should give him an opportunity to explain what he wrote?

    Is “I’m ignorant” an acceptable explanation? Either ignorant or lying.

  182. 182
    gpuccio says:

    Zachriel:

    “That is incorrect. Self-replicating molecules and molecular networks are capable of darwinian evolution.”

    And the examples are? And that darwinian evolution has generated how much functional information? Details, please.

    Moreover, I would like to mention here that life is more than self-replication. While there is probably no clear definition of what life is, it is rather obvious that all autonomous life we know has at least the following important properties:

    1) A huge informational content which can be self-replicated and expressed

    2) Metabolism, which can get energy from the environment and use it to maintain a highly ordered state

    3) A dynamic condition of all its components which is typically “far from equilibrium”

    4) A strong separation between the inner environment of the living being and the outer environment, generated by active and highly specific membrane systems

    5) As UB always reminds us, a highly symbolic semiotic system, with inherent translation systems

    We know that the simplest autonomous life we have ever observed has all those components, even in its artificallly reduced forms à-la-Venter.

    We know that LUCA, certainly an extremely ancient common precursor of all life, had all those components.

    We know really nothing, and have never observed anything, about any living or non living form which could possibly have existed before LUCA. Or not. All we have about that is mere speculation, and very unsatisfying speculation indeed.

    And someone here is still arguing that Tour is not right?

  183. 183
    gpuccio says:

    Mung:

    “Is “I’m ignorant” an acceptable explanation? Either ignorant or lying.”

    In this case, I would say “ignorant” is more probably correct.

  184. 184
    EugeneS says:

    Zachriel

    “The difference is that gravity is a simple principle, and it doesn’t require a complex interlocking mechanism to explain planetary motions, just simple integration (continuous movement under the inverse square law).”

    Just simple integration indeed.

  185. 185
    EugeneS says:

    Zachriel

    An example of question begging for you. It is when somebody assumes common descent and then concludes that common descent is a fact.

    Measure homology of the chimp and human genome and conclude that they have a common ancestor (conveniently forgetting that the measurements assume the existence of common ancestors for every pair of compared genomes).

    Logically, to demonstrate (not assume!) whether a pair of organisms have a common ancestor, there must be something scientifically verifiable which is absolutely independent of common descent. Otherwise, the argument is circular.

  186. 186
    Zachriel says:

    Upright BiPed: Why scientist do what they do is irrelevant to the fact.

    If the evidence were subtle, or novel, or otherwise hard to discern, then sure, we might not expect immediate notice by the scientific community. But you claimed the evidence was universal. As such, it probably should have been noticed by the vast majority of biologists who accept evolutionary science. It’s a reasonable question.

    Upright BiPed: a) there is no documentation that any autonomous self replicators exist.

    gpuccio: And the examples are?

    The claim was that “Darwinian evolution requires the very informational medium and translation apparatus it is attempting to explain.” As it is an appeal to necessity, pointing out a plausible counterexample is sufficient to contradict the claim.

    Upright BiPed: b) there are no non-autonomous “self replicators” that are not also the product of intelligent design.

    Assuming your conclusion.

    EugeneS: Just simple integration indeed.

    That’s correct. It’s a matter of simply applying the same basic laws of motion over and over and over again in order to model a gravitational system.

    EugeneS: It is when somebody assumes common descent and then concludes that common descent is a fact.

    Of course, that’s not how science works. Rather it considers a hypothesis (a tentative assumption) in order to determine its empirical entailments. Then those entailments are tested against observation. That’s why scientists mount expeditions to find fossils.

    EugeneS: Measure homology of the chimp and human genome and conclude that they have a common ancestor

    It takes more than two data-points to form a nested hierarchy. Are you saying there is no objective nested hierarchy?

  187. 187
    Dionisio says:

    Querius @177

    So the idea is to create articulate responses to emergent narrative points, ignoring Z’s vacuous, unsupported assertions unless you can use it to create additional explanations for everyone else.

    Exactly, you said it better than I did.
    Sometime ago a few nice folks in this site persuaded me to think of the many anonymous visitors who read these discussion threads. Imagine how many people can read UB’s and GP’s interesting comments written in response to nonsense posted by some of their interlocutors.

  188. 188

    But you claimed the evidence was universal. As such, it probably should have been noticed by the vast majority of biologists who accept evolutionary science. It’s a reasonable question.

    The evidence is universal because no single person has ever independently assessed that the origin of biological information is evolution. If a single person had ever done so, then the evidence would not be universal. There would be an exception to universal experience. But there isn’t. Thus, you are assuming your conclusion against universal evidence to the contrary.

    The claim was that “Darwinian evolution requires the very informational medium and translation apparatus it is attempting to explain.” As it is an appeal to necessity, pointing out a plausible counterexample is sufficient to contradict the claim.

    Template replication is not a counter-example to translation. One process is an entirely different physical phenomenon than the other, with an entirely dissimilar physical structure, and is fundamentally incapable of producing the same effects. Thus it is not a plausible counterexample, it is a category error.

    Assuming your conclusion.

    It is a provisional conclusion, not an assumption, which is supported universally by the entire body of findings from the entire scientific and OoL establishments. It has no counter-examples, despite sustained efforts to falsify it.

  189. 189
    EugeneS says:

    Zachriel

    You are a champion of this blog. You write nearly on everything and yet your ability to write so much without any actual concrete meaning cannot be outperformed.

  190. 190
    MatSpirit says:

    Gpuccio:

    “1. The only objects whose origin is known which have property X are designed.
    2. This object has property X.
    3. Therefore this object is designed.”

    The correct form should be:

    “1. The only objects whose origin is known which have property X are designed.
    2. This object has property X.
    3. Therefore I reasonably and empirically infer that this object is designed, and all the inferences made this way have been correct.”

    No, the correct form should be:

    1. The only objects whose origin is known which have property X are designed by a human being.
    2. This object has property X.
    3. Therefore this object is designed by a human being.

    But that doesn’t make a very convincing case for ID, does it?

  191. 191
    MatSpirit says:

    Mung, what two lies did I tell about Dr. Tour?

    john_a_designer @ 102: Everybody agrees that we don’t know how life started. Tour claims, citing absolutely no evidence, that the first living thing was as complex as a modern cell. He realizes such cells are much too complex to have formed naturally, and wants his audience to conclude that Jesus did it.

    People outside of creationism agree that a modern cell is too complex to form naturally and see no reason to imagine Jesus mucking around in the hot rocks four billion years ago. They theorize that something much much simpler formed naturally and then evolved into a complex cell.

    They don’t claim to have explained how life formed, they just like to restrict themselves to hypothesis that are physically possible.

    Mung @ 109: “Would anybody like to speculate on the outcome of a parent’s lawsuit?

    Sure. It would get laughed out of court.”

    I haven’t heard such confidence since about a day before the Dover trial begin.

    I think it’s going to be a little harder than you think to get a court to agree that teaching falsehoods to school children to make it look like supernatural assistance was needed to create life is gonna fly.

    Mung again: “MatSpirit: The problem is that Tour’s thesis is that the first living thing was a highly complex cell like the modern cell he uses as an illustration.

    This is patently false.”

    Watch the video again.

    Mung yet again: “MatSpirit:

    Tour claims:

    (A) The first living thing was as complex as the modern cell he uses as an illustration.

    This is false. Please stop making false statements.”

    Ah, this must be my second “lie”. Well, actually my first one again. ID truth, ID math. I think I’m going to go back to ignoring you.

  192. 192

    Matt, the remainder of the scientific community is not following your flawed logic:

    No, the correct form should be:

    1. The only objects whose origin is known which have property X are designed by a human being.
    2. This object has property X.
    3. Therefore this object is designed by a human being.

    SETI searches for unknown intelligence by the following general logic:

    1) Narrow-band radio signals are only produced by intelligence.

    2) This interstellar radio signal has a narrow band.

    3) Therefore this radio signal is the product of intelligence.

    This methodology is explicitly endorsed by NASA, the National Academy of Sciences, the National Science Foundation, the British Royal Society, and university science departments around the world.

    Yet you say they are all wrong.

    In actuality, serious thinkers came to the conclusion several years ago that all of these artificial attempts to disallow ID inferences from science kept having the unintended consequence of cutting off their own science projects and funding. You might want to keep that in mind when presenting flawed logic.

  193. 193
    Origenes says:

    MatSpirit: No, the correct form should be:

    1. The only objects whose origin is known which have property X are designed by a human being.
    2. This object has property X.
    3. Therefore this object is designed by a human being.

    I think we can and must do better and provide a clear definition. “Designed by a human being” is such a vague generic statement. Which ability of the human being is specifically involved with design? Not the ability to grow nose hair I’m sure. The correct answer is: intelligence.
    Now, since it would be a presumptuous to hold that only human beings can be equipped for intelligence, the correct form should be:

    1. The only objects whose origin is known which have property X are designed by intelligence.
    2. This object has property X.
    3. Therefore this object is designed by intelligence.

  194. 194
    Mung says:

    MatSpirit: Mung, what two lies did I tell about Dr. Tour?

    See my posts @ 110 and 114.

  195. 195
    Mung says:

    Thus it is not a plausible counterexample, it is a category error.

    Bingo!

  196. 196
    Mung says:

    MatSpirit: I think I’m going to go back to ignoring you.

    Your defense is that you made only one false statement but you made it two times therefore it was only one lie?

    Better yet, cease making false statements.

  197. 197
    vjtorley says:

    MatSpirit,

    You write:

    The problem is that Tour’s thesis is that [he thinks] the first living thing was a highly complex cell like the modern cell he uses as an illustration. He then goes on to list the many extremely difficult / unknown steps required to synthesis that modern, complex cell. As far as I (and the unseen chemist) knows, he’s right. It would be extremely difficult to build a complex modern type cell from scratch.

    THE PROBLEM IS THAT NOBODY IN THE WORLD EXCEPT CREATIONISTS AND ID ENTHUSIASTS BELIEVES THAT THE FIRST LIVING THING WAS COMPLEX!

    Everybody I’ve ever heard of that is actually associated with OOL research thinks the first living thing was an extremely simple entity of a few hundred atoms or less, probably enveloped in a simple lipid membrane, and that its only life-like ability was to reproduce itself from available materials.

    Tour’s whole speech is based on the strawman belief that the first living thing was enormously complex. It wasn’t, so all his arguments about how hard that would be are in vain.

    Tour says he’s personally discussed the origin of life with various experts. Given his delusions, who knows what he actually talked about and I’m not surprised that they expressed befuddlement. One thing I’m sure of, he didn’t discus it with anybody in the OOL field or they would have knocked down his straw man and set him straight on a few of the basics of OOL research.
    (Bolding & square brackets mine – VJT.)

    You claim that the first living thing contained only a few hundred atoms. That’s preposterous. Even a simple nucleotide such as deoxyadenosine monophosphate (which was synthesized in the lab back in 2009 under highly artificial laboratory conditions by Matthew Powner, Beatrice Gerland and John Sutherland) typically has a few dozen atoms. You’re saying that the first living thing was just 10 times bigger than a molecule of deoxyadenosine monophosphate? Fine. Let’s see you make a living thing like that. It should be easy to make, if it’s that small.

    The reason why Tour claims the first living thing was a cell is quite simple: there are no living things anywhere on Earth which are not cells. (Viruses don’t count, as they’re inert on their own, and can only reproduce inside a cell.)

    The smallest known parasitic bacterium, M. genitalium, has a molecular weight of 360,110 kilodaltons (kDa), or 360,110,000 daltons, while the smallest known free-living bacterium, Pelagibacter ubique, is more than twice as massive. (One dalton can roughly be defined as the mass of a typical hydrogen atom.) If we assume that a typical atom in a bacterium has the same mass as a carbon-12 atom, then we can deduce that the smallest parasitic bacterium has about 30,000,000 atoms, while the smallest known free-living bacterium contains 60,000,000 atoms. The number of atoms in an E. coli bacterium is around 7,000,000,000.

    I think we can safely dismiss your claim that the first organism had only a few hundred atoms as an absurd fantasy.

    By the way, MatSpirit, what are your qualifications in chemistry, exactly? Are you a scientist?

    I might point out in passing that Professor Tour has talked to no less an authority than Francis Collins on the origin of life. He knows Nobel Prize winners who have worked in the field. You know none.

    Professor James Tour was named “Scientist of the Year” by R&D Magazine in 2013. He also won the ACS Nano Lectureship Award from the American Chemical Society in 2012. Professor Tour was ranked one of the top ten chemists in the world over the past decade by Thomson Reuters in 2009, and he is a fellow of the American Association for the Advancement of Science. I think you owe him some respect.

  198. 198
    Mung says:

    VJT to MatSpirit: I think we can safely dismiss your claim that the first organism had only a few hundred atoms as an absurd fantasy.

  199. 199
    MatSpirit says:

    EugeneS @ 119: “What he [Tour] says is that nature cannot fine-tune or control the synthesis, it cannot purify components to fractions of percent, which is critical to produce complex nano-machinery.”

    Now think about that for a moment. Nature is fine tuning the synthesis of complex chemicals and purifying them to fractions of a percent in every cell in Tour’s body. It’s how life works and its all natural. This is not speculation, it’s observed fact. We have understand how all the main functions of a cell work since the 20th century and it’s all chemistry and information processing.

    “Natural forces are insufficient to explain life, because life is not reducible to chemistry.”

    I know some people still believe life is somehow magic, that there’s something non-material and supernatural about life, but that position is no longer tenable. We understand way to much about life. We’re been at the stage where were we can actually engineer life for decades.

    For instance,we know how to make proteins. We know the general outline (DNA copied to mRNA, mRNA fed into ribosomes, ribosomes exposing three mRNA base pairs at a time to tRNA, tRNA handing the correct amino acid to the ribosome, ribosome joining the amino acid to the growing protein) and we also know a lot of the important details.

    We know exactly how a ribosome works. We know where every atom in the two pieces of RNA and fifty proteins that make it go. We know how molecules of ATP power the ratchet action of the two RNA pieces that pulls the ribosome along the mRNA, joining amino acids to the growing protein in accordance with the genetic code.

    We know where every atom in every variety of tRNA goes and how they implement the genetic code. We know exactly how they translate three codon groups in the mRNA into the the amino acid it specifies.

    Everybody’s heard about how we’re editing bits and pieces of DNA, and Craig Venter has reached the point where he can remove ALL of a cells DNA and substitute a new genome. He writes the DNA sequence into a text file and uploads it to a literal DNA factory. The factory ships the DNA he ordered to him in little vials and also as plasmids embedded in living bacteria.

    Tour and other chemists have to sweat bullets to manufacture a molecule from the top down. You read about all the trouble and steps he has to go through to make a tiny change in one of his cars. Nature changes a few base pairs in some DNA and runs it through the normal everyday protein manufacturing machinery that comes with every modern cell and a protein gets a new amino acid. If it doesn’t work, they throw the cell away and try it again.

    Notice too that nature doesn’t design four wheeled vehicles like Tour does. Most of nature’s work is done with proteins, long chains of amino acids that fold into three dimensional shapes. You don’t find four wheeled molecules in nature. Unlike Tour, Nature can’t make them. It has no foresight and can’t plan ahead. When it wants to move materials, it makes a creeper that moves along a trail by contracting and expanding a section of the protein so it inches along a track.

    We know how to turn genes on and off, we understand the various feedback loops that keep salinity and other levels constant, we know how cell walls work, how chlorophyll uses sunlight to turn carbon dioxide to sugar – we’re not at the point where we can build a cell from scratch yet, but we’re getting there.

    We know enough now so we can state with confidence that life is 100% material. Magic is not only unnecessary for life, there’s no need for it. It would get in the way.

    I’ll write more on this when (and if) I get caught up with the thread if you wish.

  200. 200

    We know where every atom in every variety of tRNA goes and how they implement the genetic code. We know exactly how they translate three codon groups in the mRNA into the amino acid it specifies.

    Matt, the structure of tRNA does not establish and does not specify the genetic code.

  201. 201
    Origenes says:

    MatSpirit: I know some people still believe life is somehow magic, that there’s something non-material and supernatural about life, but that position is no longer tenable. We understand way to much about life. We’re been at the stage where were we can actually engineer life for decades.

    It is as if you haven’t read or understood the OP.

    Even a Dream Team of chemists wouldn’t know how to assemble life, if they had all the ingredients, including enzymes. “The Dream Team will not know where to start.”

    MatSpirit: We know the general outline (DNA copied to mRNA, mRNA fed into ribosomes, ribosomes exposing three mRNA base pairs at a time to tRNA, tRNA handing the correct amino acid to the ribosome, ribosome joining the amino acid to the growing protein) and we also know a lot of the important details.

    The linear “central dogma” of the 1960s (DNA makes RNA makes protein makes us) is long gone; it has become clear that multiple players — DNA, RNA, proteins, splicers, epigenetic factors, post-transcriptional modifiers — interact in complex networks we can barely fathom.
    For one thing, there is no conceivable bottom-up explanation for the coordination of the numerous processes into a dynamic coherent homeostatic whole. From whence cometh the coordination when we e.g. recover from surgery?

    Surgery is war. It is impossible to envisage the sheer complexity of what happens within a surgical wound. It is a microscopical scene of devastation. Muscle cells have been crudely crushed, nerves ripped asunder; the scalpel blade has slashed and separated close communities of tissues, rupturing long-established networks of blood vessels. After the operation, broken and cut tissues are crushed together by the surgeon’s crude clamps. There is no circulation of blood or lymph across the suture.
    Yet within seconds of the assault, the single cells are stirred into action. They use unimaginable senses to detect what has happened and start to respond. Stem cells specialize to become the spiky-looking cells of the stratum spinosum; the shattered capillaries are meticulously repaired, new cells form layers of smooth muscle in the blood-vessel walls and neat endothelium; nerve fibres extend towards the site of the suture to restore the tactile senses . . . These phenomena require individual cells to work out what they need to do. And the ingenious restoration of the blood-vessel network reveals that there is an over-arching sense of the structure of the whole area in which this remarkable repair takes place. So too does the restoration of the skin. Cells that carry out the repair are subtly coordinated so that the skin surface, the contour of which they cannot surely detect, is restored in a form that is close to perfect. (Brian Ford 2009)

    MatSpirit: Everybody’s heard about how we’re editing bits and pieces of DNA, and Craig Venter has reached the point where he can remove ALL of a cells DNA and substitute a new genome. He writes the DNA sequence into a text file and uploads it to a literal DNA factory. The factory ships the DNA he ordered to him in little vials and also as plasmids embedded in living bacteria.

    I’m not sure that you have grasped the true mystery behind Venter’s Syn 3.0. Have you asked yourself the question: “Is it not utterly mysterious that an existing epigenome can cope with genomes modified by Ventor?”
    Gpuccio’s answer to this question: “Yes. it is. I am amazed each time I think of it.”
    Think about it. Venter completely reshuffled the genes. There can be no evolutionary explanation for the compatibility whatsoever. Also, what does this tell us about the central dogma?

    MatSpirit: We know enough now so we can state with confidence that life is 100% material. Magic is not only unnecessary for life, there’s no need for it.

    Looking at life is somewhat akin to watching a pianola without a pneumatic mechanism to explain it actions.

  202. 202
    gpuccio says:

    Zachriel:

    Zachriel: “Self-replicating molecules and molecular networks are capable of darwinian evolution.”

    gpuccio: “And the examples are? And that darwinian evolution has generated how much functional information? Details, please.”

    Zachriel: “The claim was that “Darwinian evolution requires the very informational medium and translation apparatus it is attempting to explain.” As it is an appeal to necessity, pointing out a plausible counterexample is sufficient to contradict the claim.”

    I don’t understand. What is the “plausible counterexample”? I asked for it, but I can see no answer in what you say.

  203. 203
    gpuccio says:

    EugeneS:

    “Zachriel

    You are a champion of this blog. You write nearly on everything and yet your ability to write so much without any actual concrete meaning cannot be outperformed.”

    Yes, he is very clever. I must confess that I admire him for that. But, however clever, he cannot perform magic. Unfortunately, he is on the wrong side of truth.

  204. 204
    gpuccio says:

    MatSpirit at #190:

    That is an old objection, may times answered. Origenes has already answered at #193. However, I will repeat the concept.

    Obviously, our examples of designed objects are human artifacts. Why? Because they are the only observable objects that exhibit dFSCI in huge amounts. Except for biological objects.

    So, should we infer that biological objects are designed by humans?

    Not at all. As Origenes correctly states:

    “Which ability of the human being is specifically involved with design?”

    Let’s start with my definition of design, which you can find here:

    http://www.uncommondescent.com.....ng-design/

    “Design is a process where a conscious agent subjectively represents in his own consciousness some form and then purposefully outputs that form, more or less efficiently, to some material object.

    We call the process “design”. We call the conscious agent who subjectively represents the initial form “designer”. We call the material object, after the process has taken place, “designed object”.”

    So, as you can see, the idea of design is based on the concept that some form starts as a conscious representation, and is then purposefully outputted to some material object.

    That also explains why designed objects can exhibit dFSCI: the cognitive faculty of understanding, and the faculty of desiring a purpose, both of them properties of consciousness, can easily overcome the probabilistic barriers inherent in unguided search.

    Therefore, what is needed for design to happen, and for dFSCI to exist, is some conscious, intelligent, purposeful being.

    Now, the simple question is: are human the only conscious, intelligent and purposeful beings which exist in reality?

    That is a big question. Now, you may believe so, but we are not obliged to believe as you believe.

    1) It is perfectly credible that other physical beings in the universe may be conscious, intelligent and purposeful. I think most people believe it.

    2) It is also perfectly possible that non physical beings exist which are conscious, intelligent and purposeful. I would say that probably most people believe that too, even today. I certainly believe it.

    So, as you can see, your “argument” about humans as the only possible source of design is strictly connected to your personal worldview, and there is no need to consider it sound, least of all to share it.

  205. 205
    Zachriel says:

    Upright BiPed: The evidence is universal because no single person has ever independently assessed that the origin of biological information is evolution.

    That’s a very strange use of the term “universal”. And yes, many individual scientists have independently assessed the origin of biological information as evolution in origin.

    universal, including or covering all or a whole collectively or distributively without limit or exception; especially : available equitably to all

    Upright BiPed: Template replication is not a counter-example to translation.

    DNA replicates by template. In any case, RNA template production is posited to have preceded DNA.

    Upright BiPed: It is a provisional conclusion, not an assumption

    It’s circular reasoning because you ignore by fiat the very hypothesis that you are attempting to refute.

    Upright BiPed: 1) Narrow-band radio signals are only produced by intelligence.

    The only known source.

    Upright BiPed: 2) This interstellar radio signal has a narrow band.

    Unlike ID, SETI has never claimed to have discovered extraterrestrial intelligence.

    Upright BiPed: 3) Therefore this radio signal is the product of intelligence.

    And that’s exactly why ID is not science. Number three should be “perhaps this radio signal is the product of intelligence”. Let’s investigate it further and if we can determine the who, what, when, where, why, and how of the signal’s origin.

    gpuccio: What is the “plausible counterexample”?

    Posited self-replicating molecules. Self-replicating molecules in contrived conditions have been observed.

    The claim was a logical one, so it is only necessary to show a logical counterexample. You can’t simply wave your hands and say that self-replicating molecules are *impossible*, even if you don’t think they are a likely precursor to extant life.

  206. 206
    gpuccio says:

    Zachriel:

    You disappoint me!

    Your statement was:

    “Self-replicating molecules and molecular networks are capable of darwinian evolution.”

    Emphasis mine.

    When pressed by me, you say:

    “Posited self-replicating molecules. Self-replicating molecules in contrived conditions have been observed.

    The claim was a logical one, so it is only necessary to show a logical counterexample. You can’t simply wave your hands and say that self-replicating molecules are *impossible*, even if you don’t think they are a likely precursor to extant life.”

    Excuse me, I was not saying that it was impossible. You had stated that self-replicating molecules are capable of darwinian evolution. I asked for examples.

    So, we learn that:

    1) You are referring to posited self replicating molecules

    2) You have no examples, or empirical arguments, about their being capable of darwinian evolution.

    If I understand well, darwinian evolution is much more than simple self-replication, be it posited or real.

    So, maybe you could have said, more reasonably:

    Self-replicating molecules can reasonably exist, and if they exist they could in principle be capable of darwinian evolution.

    That would have been better, wouldn’t it?

  207. 207
    gpuccio says:

    Zachriel:

    Let me paraphrase you:

    “Number three should be “perhaps this functional molecules we observe in all biological beings are the product of intelligence”. Let’s investigate it further and if we can determine the who, what, when, where, why, and how of the signal’s origin.”

    I can happily accept that as the reasonable leading paradigm for biological research. 🙂

  208. 208
    Mung says:

    A posited designer could design a posited self-replicating molecule.

  209. 209
    Mung says:

    Zachriel: DNA replicates by template.

    Does not.

    Zachriel: In any case, RNA template production is posited to have preceded DNA.

    So instead of one miracle we have two miracles. Such faith you have, Zachriel.

  210. 210
    Mung says:

    MatSpirit: Nature is fine tuning the synthesis of complex chemicals and purifying them to fractions of a percent in every cell in Tour’s body. It’s how life works and its all natural.

    Yes, that’s how life works. And it works with enzymes, which were not available in a pre-biotic world. And Tour is talking about a pre-biotic world and he specifically mentions the absence of enzymes.

    So why do you insist on continuing to misrepresent Tour?

  211. 211
    Mung says:

    If the critics really had anything they would not need to resort to lies and distortions.

  212. 212
    Zachriel says:

    Zachriel: Self-replicating molecules and molecular networks are capable of darwinian evolution.

    See Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014. Or for something antique, see Spiegelman et al., The Synthesis of a Self-propagating and Infectious Nucleic Acid with a Purified Enzyme, Proceedings of the National Academy of Sciences 1965. There is also evidence of ribozymes that can partially replicate their own template.

    gpuccio: Excuse me, I was not saying that it was impossible.

    That was Upright BiPed, whom we had quoted in the comment to which you replied.

    gpuccio: If I understand well, darwinian evolution is much more than simple self-replication, be it posited or real.

    Self-replication based on a competition for resources is thought to be sufficient for darwinian evolution.

    gpuccio: I can happily accept that as the reasonable leading paradigm for biological research.

    Good luck with that.

    Mung: Does not.

    See Crick & Watson, A structure for deoxyribose nucleic acids, Nature 1953: “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”

  213. 213

    That’s a very strange use of the term “universal”. And yes, many individual scientists have independently assessed the origin of biological information as evolution in origin.

    Its not a strange use, Zach, it’s what the word means. Also, go back and read the GPs original statement in 154. NO PERSON has “independently assessed” that the origin of biological information is evolution. You are now just throwing stuff up that you know to be absolutely false.

    DNA replicates by template. In any case, RNA template production is posited to have preceded DNA.

    This comment means absolutely nothing to the issue on the table. DNA replication is not a counter-example to translation. And the fact that something is “posited” doesn’t change the entirely dissimilar physics of the two processes.

    It’s circular reasoning because you ignore by fiat the very hypothesis that you are attempting to refute.

    A provisional conclusion based on universal evidence is not called “circular reasoning” Zach. It’s the logical discipline of an activity called “science”. Further, its is not a matter of ignoring a hypothesis. The proposed counter-example is physically incapable of producing the effects in question.

    The only known source.

    Yes. Intelligence is the only known source of a narrow-band radio signal. That fact forms the inferential basis of the SETI project, and is accepted throughout the scientific community.

    Unlike ID, SETI has never claimed to have discovered extraterrestrial intelligence.

    The statement is intellectually vacuous. Two projects use the same conceptual methodology to search for signs of intelligent action in different domains. One has a positive result while the other continues. You object to the positive result because the other has not succeeded. Your reasoning is empty. To follow it to its logical end, ID will be validated when SETI succeeds. (facepalm)

    And that’s exactly why ID is not science. Number three should be “perhaps this radio signal is the product of intelligence”. Let’s investigate it further and if we can determine the who, what, when, where, why, and how of the signal’s origin.

    If SETI receives a narrow band-radio signal they will conclude “an act of intelligence”, and immediately announce their findings to the public. They will also look for additional validation. They will seek that validation in the same semiotic phenomenon that has already been found in the cell. Given that this is deemed acceptable methodology, conduct, and reasoning, the same chain of events should be availed to ID based on the physical evidence.

  214. 214

    That was Upright BiPed, whom we had quoted in the comment to which you replied.

    I did not say self-replicating molecules are impossible. I said that template replication is an entirely different physical process than translation, and is incapable of achieving the same effects. Which is a fact.

  215. 215
    gpuccio says:

    Zachriel:

    “Self-replication based on a competition for resources is thought to be sufficient for darwinian evolution.”

    I think you are forgetting that RV and NS must be thrown in. Am I wrong?

    IOWs, there must be not only self-replication and competition, but also variation which generates some novelty which can give reproductive advantage and be positively selected.

    That’s much more than simple self-replication, either with competition or not.

    Now, a simple question. Have those processes been observed for self-replicating molecules, or are they simply posited? Or just hoped for?

  216. 216
    Zachriel says:

    Upright Biped: I did not say self-replicating molecules are impossible.

    What you said was “Darwinian evolution requires the very informational medium and translation apparatus it is attempting to explain.” Darwinian evolution doesn’t not require translation. It requires replication with limited resources.

    Upright Biped: I said that template replication is an entirely different physical process than translation

    That’s nice, but DNA replication is template replication.

    Upright Biped: Its not a strange use, Zach, it’s what the word means.

    We provided a definition. Try to reword your claim without the term “universal evidence”.

    Upright Biped: NO PERSON has “independently assessed” that the origin of biological information is evolution.

    Of course they have — starting with Darwin.

    Upright Biped: A provisional conclusion based on universal evidence is not called “circular reasoning”

    There’s no way to evaluate your claim when you keep using the term “universal evidence”. Do you have a reference for this use of terminology?
    https://www.google.com/search?site=&source=hp&q=%22universal+evidence%22

    Upright Biped: If SETI receives a narrow band-radio signal they will conclude “an act of intelligence”

    The scientific community will be very skeptical of any such claim. Additional evidence will be sought before it is considered a firm conclusion; the who, what, when, where, why, and how. For instance, if the signal is associated with a planetary system, that will lend strength to the hypothesis, because that helps answer the “who”. If the signal comes from a pulsar, other hypotheses may be forthcoming.

  217. 217
    Zachriel says:

    gpuccio: I think you are forgetting that RV and NS must be thrown in. Am I wrong?

    Yes, the replication requires some source of variation. And the competition for resources has to be related somehow to the structure of the replicator.

    gpuccio: Have those processes been observed for self-replicating molecules, or are they simply posited?

    Molecules can self-replicate and undergo darwinian evolution in highly contrived environments. We provided citations above.

  218. 218
    Origenes says:

    Zachriel: It [Darwinian evolution] requires replication with limited resources.

    What is the import of limited resources? How do limited resources help evolution?

  219. 219
    Mung says:

    What is the import of limited resources?

    It’s all part of the Zachriel dance.

    If A leaves more offspring than B then you have “evolution,” limited resources or not.

  220. 220
    Mung says:

    To follow it to its logical end, ID will be validated when SETI succeeds. (facepalm)

    LoL!

  221. 221
    Mung says:

    Zachriel: That’s nice, but DNA replication is template replication.

    Is not.

  222. 222
    Zachriel says:

    Origenes: What is the import of limited resources?

    If there are unlimited resources, then there is no competition, meaning no darwinian evolution — by definition.

    Mung: If A leaves more offspring than B then you have “evolution,” limited resources or not.

    But it’s not darwinian unless it is due to competition for resources, i.e. natural selection.

    Mung: Is not.

    That question was settled by the Meselson-Stahl Experiment, one of the most beautiful experiments in all of biology. See Meselson & Stahl, The replication of DNA in Escherichia coli, Proceedings of the National Academy of Sciences 1958:

    Meselson & Stahl: This suggested to Watson and Crick a definite and structurally plausible hypothesis for the duplication of the DNA molecule. According to this idea, the two chains separate, exposing the hydrogen-bonding sites of the bases. Then, in accord with the base-pairing restrictions, each chain serves as a template for the synthesis of its complement. Accordingly, each daughter molecule contains one of the parental chains paired with a newly synthesized chain.

    The results of the present experiment are in exact accord with the expectations of the Watson-Crick model for DNA duplication.

  223. 223
    Origenes says:

    Zachriel: It [Darwinian evolution] requires replication with limited resources.

    Origenes: What is the import of limited resources? How do limited resources help evolution?

    Zachriel: If there are unlimited resources, then there is no competition, meaning no darwinian evolution — by definition.

    What is the import of competition? How does competition help evolution?

  224. 224
    Zachriel says:

    Origenes: What is the import of competition?

    The question was what is required of darwinian evolution. Darwinian evolution is generally defined as evolution by natural selection.

    Origenes: How does competition help evolution?

    Natural selection leads to adaptation.

  225. 225
    Mung says:

    What is the import of competition?

    It’s all part of the Zachriel dance.

    If A leaves more offspring than B then you have “evolution,” competition or no competition.

  226. 226
    Origenes says:

    Origenes: How does competition help evolution?

    Zachriel: Natural selection leads to adaptation.

    Do you mean that limited resources and competition lead to less variety? If so, what is the import of less variety? How does less variety help evolution?

  227. 227
    Zachriel says:

    Mung: If A leaves more offspring than B then you have “evolution,” competition or no competition.

    Yes, but it wouldn’t be darwinian evolution without competition.

    Origenes: Do you mean that limited resources and competition lead to less variety?

    There are sources of novelty in biological reproduction. So you have novelty being sorted through the sieve of natural selection.

  228. 228
    Origenes says:

    Zachriel: There are sources of novelty in biological reproduction. So you have novelty being sorted through the sieve of natural selection.

    What we have here are these fragile self-replicating molecules performing the sheer impossible against the backdrop of the 2nd law and all. Now why would it help evolution to have, on top of that, limited resources which results in less variety due to some sort of death sieve?

    I mean … who came up with that clever idea?

  229. 229
    Zachriel says:

    Origenes: What we have here are these fragile self-replicating molecules performing the sheer impossible against the backdrop of the 2nd law and all.

    Life “beats on, boats against the current”. So what?

    Origenes: Now why would it help evolution to have, on top of that, limited resources which results in less variety due to some sort of death sieve?

    Resources are necessarily limited, so competition for resources is inevitable.

  230. 230
    Origenes says:

    Zachriel: Resources are necessarily limited, so competition for resources is inevitable.

    Maybe so, but who came up with the muddled idea that evolution (or any project for that matter) benefits (!) from little resources? I’m pretty sure that this warped 19th-century teaching doesn’t make any sense whatsoever to those poor fragile self-replicating molecules.

  231. 231
    EugeneS says:

    MatSpirit

    “Nature is fine tuning”

    Nature does not do anything like that. If that is the basis of your views, I can understand why you and the likes of you cannot see the wood for the trees. Intelligence is necessary to extract pragmatic (non-physical) utility from physical systems simply because nature does not care about pragmatic (non-physical) gain. How can it select from among physically equivalent states of minimum total potential energy? Based on what?

    The properly articulated evo argument (disregarding misunderstandings, misrepresentations, etc) is different from the properly articulated ID argument (again disregarding all possible distortions) in only one thing. The evos, being dedicated followers of ancient pantheists, attribute intelligence (i.e. the capability of creating organized complexity, making decisions, learning) to nature itself, whereas a systematic ID supporter basically claims that nature is void of any such capability. ID recognizes that nature is insufficient to describe itself scientifically (here, by the way, come in handy all the interesting developments in physics and mathematics in the 20-th century). There is simply no empirical support for the claim that nature is intelligent in this sense. None whatsoever. People who work in science and understand that problem are very rare indeed.

    I understand that this can be inconvenient and that the party line must be maintained at all costs including the denial of the obvious.

    Regarding Pattee and other evolutionists, I respect their work and dedication to science. However the impression I get reading the work of Pattee, for that matter, is very much like the impression one gets reading Soviet papers.

    In USSR, you could not publish unless you cited Lenin’s work or praised the decisions of the most recent Communist party congress (better both). It painfully rings a bell with me reading Howard. Where he speaks about the scientific problems of information, replication, instructions, symbol-matter relation, etc. his insights are really profound. But as soon as he delves into the metaphysics of it, he reveals himself as a hard core evolutionary Platonic. I think that evolution has become an ideology to such an extreme that it blinds very clever people’s minds…

    Again, the actual dissent is entirely philosophical and is buried deep inside under the piles of words. As far as actual research is concerned, I feel that the real worth of each argument must be judged based on what impact each has on the scientific research agenda. I believe that the ID research agenda is more fruitful, at least at this moment in the history of science. A manifestation of this is the frequency of words like “surprise” in evolutionary scientific papers. Of course, one is bound to be surprised that the actual world is not behaving in line with their silly simplistic expectations. The evo thought has grown stale and, dialectically, hinders the development of science. I am not under the illusion that the dissent can be resolved once and for all. It will continue, not necessarily in its current form, for as long as this world exists.

  232. 232
    Zachriel says:

    Origenes: Maybe so, but who came up with the muddled idea that evolution (or any project for that matter) benefits (!) from little resources?

    Not sure why you find this so difficult. Resources are necessarily limited, so those organisms with traits the are best at acquiring those resources are more likely to leave descendants. We can directly observe natural selection, so it’s not a secret.

  233. 233
    Origenes says:

    Zachriel:

    Origenes: (…) who came up with the muddled idea that evolution (or any project for that matter) benefits (!) from little resources?

    Not sure why you find this so difficult. Resources are necessarily limited, so those organisms with traits the are best at acquiring those resources are more likely to leave descendants.

    I have no difficulty whatsoever understanding natural selection elimination. It is as simple as dirt. Obviously limited resources is bad news for fragile self-replicating molecules. Surely, only few will survive, if any.
    My problem is with ppl who hold the warped belief that lack of resources helps evolution. It obviously does not. It never does help matters, only does harm.

    Zachriel: Resources are necessarily limited.

    No, resources could be in abundance for self-replicating molecules, which would be helpful (obviously).

  234. 234
    Zachriel says:

    Origenes: I have no difficulty whatsoever understanding natural selection elimination. It is as simple as dirt. Obviously limited resources is bad news for fragile self-replicating molecules.

    Quite the contrary. The less fragile, more successful replicators will acquire the most resources and leave the most descendants. Indeed, that’s how self-replicating molecules behave in experimental evolution. See Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014: “The enzyme also can cross-replicate with a partner enzyme, resulting in their mutual exponential growth and enabling self-sustained Darwinian evolution.”

    Origenes: No, resources could be in abundance for self-replicating molecules

    Resources are always limited, whether local supplies of nucleic acids, access to energy, or even just space.

  235. 235
    Origenes says:

    Zachriel: The less fragile, more successful replicators will acquire the most resources and leave the most descendants.

    Quite a contrived way of saying that limited resources lead to death and less variety at best, if I may say so. But, even so, you are quite right. Less variety implies less chance of finding improvements. So, no matter how we spin it, limited resources is a bad thing for evolution — and everything else for that matter.

    Zachriel: Resources are always limited

    Resources can be in abundance.

  236. 236
    Mung says:

    Zachriel: Resources are necessarily limited.

    Resources are always limited…

    Is this supposed to be a universal observable? Because I don’t see it.

  237. 237
    MatSpirit says:

    Hi vjtorley,

    As far as my credentials are concerned, nothing special. I did spend four years teaching electronics at the technician level about thirty years ago and found that I really enjoy explaining things. I’m retired from a much better paying job now and I’m getting back to explaining things again.

    Professor Tour

  238. 238
    MatSpirit says:

    Hi vjtorley,

    As far as my credentials are concerned, nothing special. I did spend four years teaching electronics at the technician level about thirty years ago and found that I really enjoy explaining things. I’m retired from a much better paying job now and I’m getting back to explaining things again.

    Professor Tour doesn’t just claim the first living thing was A cell, he holds up a slide of a modern eukaryotic cell complete with a nucleus, nucleoli, mitochondria, ribosomes, golgi apparatus and a few dozen other major components and then demonstrates at length why this is much too hard for nature to have produced out of zip. And I agree with him 100%! And I know enough about OOL research to say that the whole OOL community agrees with him!

    Why do they agree with him? Well, ultimately because the odds against forming anything useful in one step by randomly assembling atoms increases exponentially as you put together more and more atoms. By the time you get to even a few hundred atoms, the odds against getting anything useful go beyond astronomical.

    That’s one reason why science agrees 100% with Dr. Tour that the first living thing was not a eukaryotic cell like the only cell he shows us.

    Another reason is that eukaryotic cells didn’t exist back then! They’ve only been around for about two billion years and life is a lot older than that! But before the first eukaryotic cell appeared, there were simpler organisms alive, such as bacteria. In fact, current theory is that bacteria created eukaryotes when one bacteria ingested, but did not kill a smaller bacteria and the two began a symbiotic relationship that eventually became eukaroytics.

    So Dr. Tour’s logic has a big hole here: Yes, a modern eukaryotic cell could not have been the first living thing, but there’s no need to bother Jesus yet because there were in fact simpler cells, namely bacteria, that lived before eukaryotics and gave rise to them.

    Were there simpler cells that gave rise to bacteria? The general assumption is yes because of the size and complexity of even the simplest bacteria. What were they like? We don’t know because it’s hard to even find a rock four billion years old that hasn’t been melted at least once, let alone anything resembling a fossil embedded in it.

    If we repeat the “eukaryotes from simpler bacteria” transition over and over, we get simpler and simpler cells with fewer and fewer capabilities until finally we have the simplest possible life, something that does nothing but copy itself. And such a life form would be so simple it could be synthesized from random chemical activity.

    Yes, it would have no DNA or RNA or copying machinery or anything else Tour’s modern cell has, but there are simpler, slower ways of copying. As long as the chemical makes copies of itself in less time than it takes nature to destroy it, it’s living and its numbers will increase exponentially. And if one of those copies is slightly different from the original, and makes copies faster, we have evolution and we’re off!

    On Professor Tour’s qualifications, he may be the world’s best structural chemist and he is surely the man to go to if you need a molecular car, but when it comes to OOL, as he says on his website at goo.gl/K8Xs56

    “Assuming that I have something significant to contribute to the evolution vs. creation debate, many ask me to speak and write concerning my thoughts on the topic. However, I do not have anything substantive to say about it. I am a layman on the subject. Although I have read about a half dozen books on the debate, maybe a dozen, and though I can speak authoritatively on complex chemical synthesis, I am not qualified to enter the public discussion on evolution vs. creation.”

    That makes you wonder why he gave that lecture then. He certainly based it on a Newby error. Frankly, I think he owes us all an apology for making it. A big hint why he did it can be found in his personal statement here at goo.gl/dJljJ4

  239. 239
    Origenes says:

    MatSpirit: So Dr. Tour’s logic has a big hole here: Yes, a modern eukaryotic cell could not have been the first living thing, but there’s no need to bother Jesus yet because there were in fact simpler cells, namely bacteria, that lived before eukaryotics and gave rise to them.

    It is as if you did not read or did not understand the OP. For instance, when Tour says …

    “We cannot even figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids and proteins. Chemists are collectively bewildered. Hence I say that no chemist understands prebiotic synthesis of the requisite building blocks, let alone assembly into a complex system.”

    … he is not just talking about the assembly of the modern eukaryotic cell, as you seem to think. Obviously our inability to conceive of prebiotic routes to the basic building blocks of life, also pertains to bacteria and any posited precursor of bacteria that uses any of these basic building blocks.

  240. 240
    gpuccio says:

    MatSpirit:

    “So Dr. Tour’s logic has a big hole here: Yes, a modern eukaryotic cell could not have been the first living thing, but there’s no need to bother Jesus yet because there were in fact simpler cells, namely bacteria, that lived before eukaryotics and gave rise to them.”

    LUCA was already incredibly complex. And it’s the oldest living being about which we can really discuss empirically. There is absolutely no evidence that any simpler living being ever existed.

    You know, science should be based on observed facts.

  241. 241
    EugeneS says:

    GP,

    Their usual tactic is to mess around with definitions. In this particular case, of complexity and organization. They will stubbornly maintain that ice is organized water and tell you this without winking. Butter wouldn’t melt…

  242. 242
    Zachriel says:

    Origenes: Quite a contrived way of saying that limited resources lead to death and less variety at best, if I may say so.

    Depending on the environment, evolution can result in a great deal of variation, both within a population, and between populations.

    Origenes: Resources can be in abundance.

    Due to exponential population growth of biological organisms, resources are inevitably limited.

    Mung: Is this supposed to be a universal observable?

    Due to exponential population growth of biological organisms, resources are inevitably limited.

  243. 243

    Upright Biped: I did not say self-replicating molecules are impossible.

    Zach: What you said was “Darwinian evolution requires the very informational medium and translation apparatus it is attempting to explain.”

    If you’ll notice, the text you posted does not say that self-replicating molecules are impossible, so your statement is indeed false. No big deal, but it’s false.

    Zach: Darwinian evolution doesn’t require translation.

    Every biological organism (prokaryote or eukaryote, single-celled or multicellular, animal, plant, fungus, bacteria) requires translation, Zach, and every virus requires the translation apparatus within its host in order to evolve. It is the physical process that enables the organization of the cell, and is the very thing that has to be explained. Yet, your counter-example is not even physically capable of it. It’s an entirely different physical process altogether, and is fundamentally incapable of producing the effects of translation. You want to argue for a definition that is irrelevant; Darwinian evolution – the evolution of living organisms — requires translation.

    Upright Biped: I said that template replication is an entirely different physical process than translation

    Zach: That’s nice, but DNA replication is template replication.

    And again, that’s irrelevant.

    Upright Biped: It’s not a strange use, Zach, it’s what the word means.

    Zach: We provided a definition. Try to reword your claim without the term “universal evidence”.

    Sorry, I have no interest in playing pitter-pat about what the word “universal” means.

    The remainder of your comments do not really warrant a response.

  244. 244
    Origenes says:

    Zachriel: Depending on the environment, evolution can result in a great deal of variation, both within a population, and between populations.

    Indeed, if the environment offers resources in abundance, then there is a maximum chance of variety. If, on the other hand, the environment offers few resources, then death and less variety follows as sure as night follows day.

    Zach:

    Origenes: Resources can be in abundance.

    Due to exponential population growth of biological organisms, resources are inevitably limited.

    As in, ‘there is inevitably a shortage of water in the sea due to population growth’? As in, ‘there is inevitably a shortage of atoms for molecular replicators’?
    Stop with the nonsense please.

  245. 245
    Zachriel says:

    Origenes: If you’ll notice, the text you posted does not say that self-replicating molecules are impossible, so your statement is indeed false.

    What you said was “Darwinian evolution requires the very informational medium and translation apparatus it is attempting to explain.” However, self-replicating molecules are capable of darwinian evolution, and they don’t use translation.

    Origenes: You want to argue for a definition that is irrelevant; Darwinian evolution – the evolution of living organisms — requires translation.

    Darwinian evolution is generally defined as evolution by natural selection. Self-replicating molecules are capable of darwinian evolution.

    Origenes: As in, ‘there is inevitably a shortage of water in the sea due to population growth’?

    If humans continue their current rate of reproduction, they will outweigh the sun in about five thousand years. Humans have relatively low rates of fecundity. Bacteria reproduce somewhat faster.

  246. 246
    Zachriel says:

    Origenes: As in, ‘there is inevitably a shortage of water in the sea due to population growth’?

    Just for fun, we might assume humans expand rapidly into space. Maybe humans could swallow the sun in five thousand years.

    At their present rate of population growth, humans would outweigh the galaxy in about seven thousand years. However, even at the speed of light, humans could not cross the galaxy in that amount of time in order to convert the mass of the galaxy into human biomass (much less whatever infrastructure might be required to sustain them).

  247. 247
    MatSpirit says:

    Gpuccio @ 239: “LUCA was already incredibly complex. And it’s the oldest living being about which we can really discuss empirically. There is absolutely no evidence that any simpler living being ever existed.

    You know, science should be based on observed facts.”

    http://star.psy.ohio-state.edu/coglab/Miracle.html

    Sometimes the facts are not available for observation – molecular fossils in four billion year old rock, for instance.

    In those cases, science draws what clues it can from what is observable, an orderly succession of ever simpler species receding into the past for instance.

    ID just declares a miracle. As Mr, Harris implies, that does not wash in science.

  248. 248
    MatSpirit says:

    Upright Biped @ 243: “Every biological organism (prokaryote or eukaryote, single-celled or multicellular, animal, plant, fungus, bacteria) requires translation, Zach, and every virus requires the translation apparatus within its host in order to evolve.”

    Why is it so difficult for ID theorists to realize that prokaryotes, eukaryotes, animals, plants, fungi and bacteria DID NOT EXIST back when Life first appeared? They are modern, much improved species thar reproduce much faster and do many more things than the simpler, cruder first living things.

    “Darwinian evolution – the evolution of living organisms — requires translation.”

    Nonsense! Who even says that? Casey Luskin? Darwinian evolution requires reproduction with occasional variation and an environment that cannot support every new organism produced.

    Translation lets us use DNA to increase the speed and accuracy of reproduction to levels that translation can never acheive, but translation can still get the job done, though it’s a lot slower.

  249. 249
    MatSpirit says:

    Origenes es @239 again (It looks like a half message I posted was deleted [thanks, moderator] and subsequent messages were renumbered)

    Nice job of moving the goal post! I point out that Tour says the modern cell he shows us and talks about couldn’t have been the first living thing (because it didn’t exist, among other reasons) and you “counter” by saying,

    “We cannot even figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids and proteins. Chemists are collectively bewildered.

    Well yeah, we can’t figure out the prebiotic routes to first life because there are a gazillion potential ways to do it and we have no samples to figure out which path was actually used.

    “Hence I say that no chemist understands prebiotic synthesis of the requisite building blocks, let alone assembly into a complex system.”

    Do you know anything at all about OOL? Have you even read the “abiogenesis” article in Wikipedia? Surely you’ve heard of the Miller-Urey experiment where sparks in an atmosphere of methane hydrogen and ammonia produced five different amino acids? I’m sure you’ve at least read ID writers crow that the earth’s atmosphere was different or that the aminos were racemic? But did you hear that reanalyzing vials saved from the original experiment with more sensitive modern apparatus showed that the Miller-Urey experiment actually produced 21 amino acids?

    How about this sentence from the article?

    “Bernal shows that based upon this and subsequent work there is no difficulty in principle in forming most of the molecules we recognise as the basic molecules of life from their inorganic precursors.”

    Have you heard of orgics being synthesised in space? “Organic compounds are relatively common in space, formed by “factories of complex molecular synthesis” which occur inmolecular clouds and circumstellar envelopes, and chemically evolve after reactions are initiated mostly by ionizing radiation.”

    I used to have a list of organic molecules that have been discovered in space. It was over a page long, single spaced.

    We know quite a bit about how organic molecules are formed, both on earth and in space. Professor Tour is right that we don’t know so much about how they are put together, but we learn more about it every day. And by “we”, I mean science because ID isn’t doing squat.

  250. 250
    MatSpirit says:

    EugeneS @231:

    “MatSpirit

    “Nature is fine tuning”

    Nature does not do anything like that. If that is the basis of your views, I can understand why you and the likes of you cannot see the wood for the trees. Intelligence is necessary to extract pragmatic (non-physical) utility from physical systems simply because nature does not care about pragmatic (non-physical) gain. How can it select from among physically equivalent states of minimum total potential energy? Based on what?”

    And I can see you’ve must have gotten your “facts” about evolution from ID / creationist sources. Nature “cares” a whole lot about whether a newly mutated organism lives or dies and it reacts in a very pragmatic way: The organisms that live can reproduce and pass their “design” on, those that die can’t and their “design” dies with them. Life or death. You can’t get much more pragmatic than that.

    “The properly articulated evo argument (disregarding misunderstandings, misrepresentations, etc) is different from the properly articulated ID argument (again disregarding all possible distortions) in only one thing. The evos, being dedicated followers of ancient pantheists, attribute intelligence (i.e. the capability of creating organized complexity, making decisions, learning) to nature itself, whereas a systematic ID supporter basically claims that nature is void of any such capability. ID recognizes that nature is insufficient to describe itself scientifically (here, by the way, come in handy all the interesting developments in physics and mathematics in the 20-th century). There is simply no empirical support for the claim that nature is intelligent in this sense. None whatsoever. People who work in science and understand that problem are very rare indeed.”

    Yeah, you definantly got your “understanding” of evolution from creationists. Evolution is not intelligent and we don’t claim it is. Ditto for the world. Evolution uses a very simple algorythm:

    1) Make lots and lots of identical copies of an organism.

    2) Occasionally make a small change to ONE of the copies.

    3) Let it try to make a living with its new genome.

    4) If it can’t, throw it away and the accurately copied offspring will continue the line.

    5) If it does survive and does better than the original line, it’s proportion of the population will increase and it will either become a second variety of the organism or it may replace the original completely and become an improved organism.

    Please show us where the intelligence is in this algorythm, if you can.

  251. 251
    MatSpirit says:

    Mung @221:

    “Zachriel: That’s nice, but DNA replication is template replication.

    Is not.”

    Ok, then what is it called when you split a DNA molecule into two complementary pairs and use each pair as a template to synthesize the other half of the molecule?

  252. 252
    MatSpirit says:

    Gpuccio @ 204: “MatSpirit at #190:

    That is an old objection, may times answered. Origenes has already answered at #193. However, I will repeat the concept.

    Obviously, our examples of designed objects are human artifacts. Why? Because they are the only observable objects that exhibit dFSCI in huge amounts. Except for biological objects.”

    And biological objects don’t look anything like the products of humanity. We’re asking the Big Question: Is life designed by an Intelligent Designer or was it produced naturally?

    Except, I’ve read every message you’ve posted in this thread and many others in other threads and as far as I can see, you don’t even consider evolution. You seem to have dismissed it so thoroughly you don’t even bring it up as a possibility in your arguments.

    That’s mighty convenient, but since the question is “ID or evolution” and one of your unspoken premises is that evolution can’t do it, it makes your argument completely circular.

  253. 253
    Mung says:

    MatSpirit: Ok, then what is it called when you split a DNA molecule into two complementary pairs and use each pair as a template to synthesize the other half of the molecule?

    I’ve never split a DNA molecule into two complementary pairs and used each pair as a template to synthesize the other half of the molecule. Have you? Has Zachriel?

    Do you think protein synthesis is a matter of template replication? If not, what do you call protein synthesis?

  254. 254
    Mung says:

    MatSpirit: Why is it so difficult for ID theorists to realize that prokaryotes, eukaryotes, animals, plants, fungi and bacteria DID NOT EXIST back when Life first appeared?

    Why is it so difficult for you to realize that Dr. Tour specifically denied that enzymes existed to help the process of abiogenesis along?

  255. 255
    Mung says:

    MatSpirit: Professor Tour doesn’t just claim the first living thing was A cell, he holds up a slide of a modern eukaryotic cell complete with a nucleus, nucleoli, mitochondria, ribosomes, golgi apparatus and a few dozen other major components and then demonstrates at length why this is much too hard for nature to have produced out of zip.

    This is false. Please stop lying.

  256. 256
    MatSpirit says:

    Origenes @ 201:

    “MatSpirit: We know the general outline (DNA copied to mRNA, mRNA fed into ribosomes, ribosomes exposing three mRNA base pairs at a time to tRNA, tRNA handing the correct amino acid to the ribosome, ribosome joining the amino acid to the growing protein) and we also know a lot of the important details.”

    OrigeneS: “The linear “central dogma” of the 1960s (DNA makes RNA makes protein makes us) is long gone; it has become clear that multiple players — DNA, RNA, proteins, splicers, epigenetic factors, post-transcriptional modifiers — interact in complex networks we can barely fathom.”

    Hey, watch those goalposts! You almost hit me when you moved that one! What are you trying to claim, that we’ll never understand all of the details of how a cell functions, like they used to say we’d never understand the Krebs cycle? That’s a God of the Gaps argument and historically it’s been a disaster for creationism because we keep filling the gaps in our knowledge in and you have to hide God somewhere else.

    OrigeneS: “For one thing, there is no conceivable bottom-up explanation for the coordination of the numerous processes into a dynamic coherent homeostatic whole.”

    I think you’ve got that backwards. There is no conceivable top-down explanation for the co-ordination of the numerous processes into a dynamic coherent homeostatic whole except an intelligence that can plan everything in advance. But we can’t seem to find such an intelligence and evolution can build a cell from the bottom up without using it.

    For example, suppose you’ve got a simple cell that works, but sodium levels are too high for maximum efficiency. The cell reproduces and you have a lot of identical cells that work, but they all have sodium levels that are too high and it slows reproduction.

    One cell gets a mutation that enlarges a pore just enough so an occasional sodium atom can escape. Sodium levels go down a bit in that cell, it works a little better and reproduces a little faster and it soon replaces the original cells. Now all of the cells have better regulated sodium levels.

    Now one of those cells developes a slightly mutated pore that allows lots of sodium atoms to escape when there are lots of them slamming into it, but which shrinks and won’t let any out when sodium levels are too low. Now this new atom has found a way to REGULATE sodium levels, it’s more efficient and reproduces faster and it eventually replaces the other cells and becomes the new “normal” cell.

    Note that through all of the steps, the cell remains a dynamic whole and that its homeostasis actually increases! Back in 1975 a man named John Gall said this:

    “A complex system that works is invariably found to have evolved from a simple system that worked. A complex system designed from scratch never works and cannot be patched up to make it work. You have to start over with a working simple system.” He was talking specifically about computer systems, but it applies to nearly everything.

    OrigeneS: “From whence cometh the coordination when we e.g. recover from surgery?”

    I’ll bet you don’t know much about evo-devo. It’s the story of how a single egg can develop into a complete organism, ready to enter the world, using only commands like “All you brain cells in the temporal lobe, grow your axons up this chemical gradient for 73 hours and then connect to the nearest nuron.”

    I imagine repairs are done similarly.

  257. 257
    MatSpirit says:

    Upright Biped @200:

    MatSpirit: “We know where every atom in every variety of tRNA goes and how they implement the genetic code. We know exactly how they translate three codon groups in the mRNA into the amino acid it specifies.”

    UB: “Matt, the structure of tRNA does not establish and does not specify the genetic code.”

    I’ve seen you write that two or three times now and I’m not sure what you mean. If you’re saying, “No tRNA molecule or group of tRNA molecules ever sat down and thought up the genetic code,” I agree with you.

    But if you’re trying to tell us that the structure of the tRNA molecule doesn’t define and instantiate the Genetic code, I wonder if you even know what transfer RNA is.

    What exactly are you claiming here?

  258. 258
    MatSpirit says:

    Upright Biped @ 188:

    Zack: “But you claimed the evidence was universal. As such, it probably should have been noticed by the vast majority of biologists who accept evolutionary science. It’s a reasonable question.

    UB: “The evidence is universal because no single person has ever independently assessed that the origin of biological information is evolution. If a single person had ever done so, then the evidence would not be universal. There would be an exception to universal experience. But there isn’t. Thus, you are assuming your conclusion against universal evidence to the contrary.”

    What in the world are you talking about? What does it matter if zero, one, ten or fifty million people look at the evidence and give their opinion on something? Their OPINIONS don’t affect the EVIDENCE one whit!

    If the evidence is available to everybody, it’s universal. If its not, it isn’t. Opinions based on that evidence don’t even matter here!

  259. 259
    Origenes says:

    MatSpirit: Hey, watch those goalposts! (…) What are you trying to claim, that we’ll never understand all of the details of how a cell functions, (…)? That’s a God of the Gaps argument (…)

    You misunderstand. What I’m saying is that your ‘general outline’, which posits DNA as the ‘master-controller’ of life, has failed and is incoherent.

    MatSpirit:

    OrigeneS: “For one thing, there is no conceivable bottom-up explanation for the coordination of the numerous processes into a dynamic coherent homeostatic whole.”

    I think you’ve got that backwards. There is no conceivable top-down explanation for the co-ordination of the numerous processes into a dynamic coherent homeostatic whole (…)

    Nope, when things work in concert without a bottom-up explanation, then top-down explanations are all we got.

    MatSpirit: (…) But we can’t seem to find such an intelligence (…)

    You seem to expect to find intelligence under the microscope. Earlier you wrote: “Hopefully not in the mere operation of living cells because vitalism is pretty much dead, killed by the microscope.”, which I answered thusly: “Only to those who hold the naïve belief that a microscope allows us to see all there is.”
    Instead of finding it under the microscope, intelligence can be inferred when we witness coordination at higher levels without a conceivable bottom-up explanation.
    You wrote that the one and only top-down explanation is “intelligence that can plan everything in advance.”, yet Shapiro offers an alternative top-down explanation for the coordination at the level of the cell as a whole, by proposing that a cell is intelligent. Cells, according to Shapiro, are intelligent in that they do their own natural genetic engineering, taking existing structures through horizontal DNA transfer or symbiogenesis, say, and reworking them in new contexts for new uses. Moreover I put it to you that there are other concepts accommodating top-down explanations.

    MatSpirit: (…) and evolution can build a cell from the bottom up without using it.

    Unsubstantiated claim contrary to the evidence; see OP.

    MatSpirit: For example, suppose you’ve got a simple cell that works, (…)

    Assuming what you need to explain.

    MatSpirit: I’ll bet you don’t know much about evo-devo.

    What I do know is that there is no conceivable bottom-up explanation for the mind bottling coordination of this process — for one thing we can safely rule out DNA as a candidate for the role of ‘master-controller’.

  260. 260
    EugeneS says:

    MatSpirit,

    You definitely got your understanding of evolution from pantheists. Evolution is only a system’s dynamics. Dynamics cannot be responsible for the emergence of sign in semiotic systems. Sign is quiescent and independent of a system’s dynamics. Sign is choice contingent.

    In order to explain evolution in biology you absolutely must explain the sign-matter relation. Apparently, you don’t even understand what the problem is and how difficult it is.

    “Evolution uses a very simple algorithm”

    I work with algorithms for bread and butter. Again, MatSpirit, an algorithm is choice contingent. There is no choice contingency in nature alone. It cannot choose. An algorithm is goal oriented. Nature is not goal oriented (the only ‘goal’ is minimal total potential energy but that is trivial). Nor is evolution, in the Darwinian model at least. There is no IF-THEN-ELSE in inanimate nature.

    What I don’t like about the evolutionists’ approach is their slack use of terminology. “A simple algorithm, just integration of equations”. Just a couple of stokes by the magic wand.

    In your explanations, guys, you tacitly assume what cannot be assumed because it must be explained.

    Naturalism is fine until such time as it is used in attempts to shed light on the origin of nature. It assumes the existence of matter, space, time, life. But it is no good at explaining how they came about.

    You need to dig deeper.

  261. 261
    EugeneS says:

    MatSpirit,

    How do you explain for yourself that we cannot see abiogenesis happening today? How is it that today’s environment cannot naturally produce life, for all we know, and yet it is perfectly life-friendly?

    Do you agree that all life is instruction based? If you don’t, there is nothing more to discuss. If you do, how do you then explain for yourself the appearance of the first set of instructions for the first instruction processor in the first generation of organisms?

  262. 262
    Origenes says:

    MatSpirit: Nice job of moving the goal post! I point out that Tour says the modern cell he shows us and talks about couldn’t have been the first living thing (because it didn’t exist, among other reasons) and you “counter” by saying:

    “We cannot even figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids and proteins. Chemists are collectively bewildered.” [Origenes quoting Tour]

    Well yeah, we can’t figure out the prebiotic routes to first life because there are a gazillion potential ways to do it and we have no samples to figure out which path was actually used.

    It should be perfectly obvious that from any posited first life, although it may have used alternative basic building blocks, there must be a route to the basic building blocks of life as we know it.
    So when Tour says: “We cannot even figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids and proteins. Chemists are collectively bewildered.”, this does include routes from any posited first life to the basic building blocks of life as we know it.

    // This is the second time that I have to explain it. Why is this so hard to understand? //

  263. 263
    Zachriel says:

    Mung: I’ve never split a DNA molecule into two complementary pairs and used each pair as a template to synthesize the other half of the molecule.

    The technique is called polymerase chain reaction.

    Mung: Do you think protein synthesis is a matter of template replication?

    Your claim was that DNA replication is not template replication. That claim was false. See Meselson & Stahl, The replication of DNA in Escherichia coli, Proceedings of the National Academy of Sciences 1958

    Mung: Why is it so difficult for you to realize that Dr. Tour specifically denied that enzymes existed to help the process of abiogenesis along?

    RNA can act as both genetic memory and as a catalyst.

    Origenes: So when Tour says: “We cannot even figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids and proteins.

    That is not correct. There are plausible prebiotic pathways for the synthesis of many of those substances. For instance, see Powner et al., Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions, Nature 2009.

  264. 264
    Origenes says:

    James Tour: We cannot even figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids and proteins. Chemists are collectively bewildered. Hence I say that no chemist understands prebiotic synthesis of the requisite building blocks, let alone assembly into a complex system.

    ENTERS Zachriel:

    That is not correct. There are plausible prebiotic pathways for the synthesis of many of those substances.

    State your case clearly. Which plausible prebiotic pathways for the synthesis of which of the requisite building blocks (carbohydrates, nucleic acids, lipids and proteins) are there?

  265. 265
    Zachriel says:

    Origenes: Which plausible prebiotic pathways for the synthesis of which of the requisite building blocks (carbohydrates, nucleic acids, lipids and proteins) are there?

    Kim et al., Synthesis of Carbohydrates in Mineral-Guided Prebiotic Cycles, Journal of the American Chemical Society 2011;

    Hargreaves et al., Synthesis of phospholipids and membranes in prebiotic conditions, Nature 1977;

    Jiang et al., Altmetric: Abiotic synthesis of amino acids and self-crystallization under prebiotic conditions, Nature 2014;

    Pascal et al., From the Prebiotic Synthesis of alpha-Amino Acids Towards a Primitive Translation Apparatus for the Synthesis of Peptides, Topics in Current Chemistry: Prebiotic Chemistry 2005;

    Powner et al., Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions, Nature 2009.

  266. 266
    gpuccio says:

    MatSpirit:

    “And biological objects don’t look anything like the products of humanity.”

    They do. But they are much smarter.

    “We’re asking the Big Question: Is life designed by an Intelligent Designer or was it produced naturally?”

    I agree. That’s the Big Question, indeed.

    “Except, I’ve read every message you’ve posted in this thread and many others in other threads and as far as I can see, you don’t even consider evolution. You seem to have dismissed it so thoroughly you don’t even bring it up as a possibility in your arguments.”

    I am afraid your have read very badly. My main activity here is to analyze in detail, at the molecular level, why “evolution” (or, to be more precise, unguided evolution based on RV + NS) cannot explain what we observe in biological objects. Just as an example, look at this OPs of mine:

    http://www.uncommondescent.com.....ion-jumps/

    http://www.uncommondescent.com.....ted-genes/

    and at the long discussions in the corresponding threads.

    Again, that’s just an example. I have been debating the neo darwinian model in great detail for years, both here and in some blogs “from the other side”. You may certainly disagree with what I say, but to state that I “don’t even consider evolution” is one of the strangest statements about my activity here that I have ever seen.

    “That’s mighty convenient, but since the question is “ID or evolution” and one of your unspoken premises is that evolution can’t do it, it makes your argument completely circular.”

    The question is, indeed, “ID or evolution”. I agree. That’s why in my posts I do present positive arguments for ID and, most of the time, I do analyze the reasons why the neo darwinian evolutionary paradigm is obviously wrong from a scientific point of view. I am absolutely available to take any points you like about that aspect and discuss them with you.

    And please, don’t take the “argument” of circularity. I have dedicated maybe hundreds of posts to show that ID theory and the argument from dFSCI is not circular. We can do that again, if you like, but first you should offer some detailed discussion about the circularity you seem to catch.

  267. 267
    Origenes says:

    Zachriel #265,

    VJTorley writes that “In his talk, Professor Tour decided to focus on the origin of just one of the four basic building blocks of life: carbohydrates. He then proceeded to list eleven enormous hurdles faced by any blind, unguided process, in generating these compounds.”

    You don’t show how Kim et al. overcome the eleven hurdles listed by Tour.

    Moreover, it’s long-standing tradition for scientists who are sympathetic to evolution, to choose misleading titles, and even abstracts.

    A typical case is described in the OP:

    In the last few days, there has been much talk about a new paper in Nature Communications (vol. 7, article number 11328) by Brian Cafferty, David M. Fialho, Jaheda Khanam, Ramanarayanan Krishnamurthy and Nicholas V. Hud, titled, Spontaneous formation and base pairing of plausible prebiotic nucleotides in water. The abstract sounds very promising: (…)
    However, when one looks more carefully at the paper itself, it becomes apparent that the authors are glossing over the challenges that their proposed synthesis would have faced in the real world: (…)

  268. 268
    Zachriel says:

    Origenes: You don’t show how Kim et al. overcome the eleven hurdles listed by Tour.

    The claim is that “We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids and proteins, were made”. We actually have some tentative knowledge of plausible mechanisms of abiogenetic synthesis. Pointing out that we don’t everything doesn’t support the claim that “we have no idea” at all.

  269. 269
    Origenes says:

    Zachriel: The claim is that “We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids and proteins, were made”.

    To be clear, the claim is: “We cannot even figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids and proteins.”

    Zachriel: We actually have some tentative knowledge of plausible mechanisms of abiogenetic synthesis.

    If by “plausible mechanisms” you mean “plausible prebiotic routes”, then you should make your point. Show Tour and us how it works.

    Zachriel: Pointing out that we don’t everything doesn’t support the claim that “we have no idea” at all.

    If we cannot come up with plausible prebiotic routes, then it’s correct to say that “we have no idea at all”, or as Tour puts it: “Chemists are collectively bewildered.”

  270. 270
    Zachriel says:

    Origenes: To be clear, the claim is: …

    Quote: “We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids and proteins, were made”.

    Origenes: If by “plausible mechanisms” you mean “plausible prebiotic routes”, then you should make your point.

    We have cited plausible routes to prebiotic compounds, including nucleic acids.

  271. 271
    Origenes says:

    Zachriel, show how Kim et al. overcome the eleven hurdles listed by Tour.

  272. 272
    Mung says:

    If by “plausible mechanisms” you mean “plausible prebiotic routes”, then you should make your point.

    I think he means chemistry.

  273. 273
    Eric Anderson says:

    Allen Mac_Neill:

    I’m sorry to hear about Hannah, and appreciate you posting about the situation.

    I am grateful for your general willingness to discuss the issues in the debate and look forward to your new books.

    Regarding this:

    As for abiogenesis, I agree that it is not “all worked out” – indeed, I think it will never be so in either direction (i.e. design vs evolution).

    If by “all worked out” you simply mean that we will know exactly how it occurred, with precision, in every detail, then I can agree. That is the case with essentially every historical inquiry. But that doesn’t prevent us from drawing reasonable inferences and conclusions from the data that are before us. We must be careful not to avoid addressing the issues by pretending they are unadressable or unknowable.

    If by “all worked out” you mean that we will never know how life could have arisen by purely natural and material means, then I absolutely agree. There will never be a good naturalistic narrative for something that defies naturalistic principles.

    If by “all worked out” you mean that we will never be able to determine whether there was any design involved in the origin of life, then I have to respectfully disagree. The inference regarding design in the origin of life is already exceedingly strong and growing moreso with each passing year. We can draw a reasonable inference in this case with more certainty than we can with many other historical claims regularly made in the name of science. Again, we might wish to avoid drawing an inference for political or philosophical reasons, but a reasonable inference can and should be drawn, based on the best evidence we have before us.

  274. 274
    Zachriel says:

    Origenes: show how Kim et al. overcome the eleven hurdles listed by Tour.

    Those are problems Tour faced when constructing an artificial machine. The question we addressed is the claim “We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids and proteins, were made”. In fact, we do have some idea of how this may have happened.

    Origenes: I think he means chemistry.

    Which is why the references are to prebiotic chemistry.

  275. 275
    Origenes says:

    Zachriel: Those are problems Tour faced when constructing an artificial machine.

    That is correct. But, since their relevancy to prebiotic routes have been explained, I do not see the point of you mentioning it.

    Zachriel: The question we addressed is the claim “We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids and proteins, were made”.

    Well the “We have no idea how” is obviously supported by the eleven hurdles, as in ‘we have no idea how prebiotic routes could have overcome those hurdles’.

    Zachriel: In fact, we do have some idea of how this may have happened.

    Unsubstantiated claim.

  276. 276
    Zachriel says:

    Origenes: But, since their relevancy to prebiotic routes have been explained, I do not see the point of you mentioning it.

    The hurdles primarily concern his artifice.

    1. A choice of target was needed for the nanocars.

    This is obviously not the case for natural evolutionary processes.

    Origenes: Unsubstantiated claim.

    Citations were provided. Powner et al., Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions, Nature 2009.

  277. 277
    Steve says:

    Plausibility means jack all in scientific research especially when all the known plausible routes have been known for decades.

    What Zachriel are saying is: ‘we haven’t the faintest ideas whats going on but we are loath to change direction’, especially if it means looking in the direction of information as an independent entity that is imprinted on matter.

    Waaaayyyy too much teleology to stomach. Waaay too much!

    So it woulbe be a bad move for any lab to consider Zachriel as members of a research team.

    Maybe run a horserace. But be effective members of a research lab?

    Forgedaboutit.

    The claim is that “We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids and proteins, were made”. We actually have some tentative knowledge of plausible mechanisms of abiogenetic synthesis. Pointing out that we don’t everything doesn’t support the claim that “we have no idea” at all.

  278. 278
    Zachriel says:

    Steve: Plausibility means jack all in scientific research especially when all the known plausible routes have been known for decades.

    That’s not the case, as is clear from Powner 2009.

    Consequently, pointing to current limitations in human technical ability and ingenuity are not very good arguments.

  279. 279

    Zach at 245,

    When you reply to my posts, but title your comments to someone else, you make it very easy for me to not see your reply. I don’t know if that’s the effect you’re going after, but this is the second or third time you’ve done it.

    “self-replicating molecules are capable of darwinian evolution, and they don’t use translation.

    Life requires translation Zach. All life.

    A self-replicating RNA precursor to the existing translation system requires the physical capacity to specify the existing system, which it doesn’t have. Nature clearly and unambiguously demonstrates how that capacity manifests itself in a material system, and we as methodical observers have an entirely coherent understanding of it. Your precursor is physically incapable of the very thing it is proposed to explain. Among other things, one process is wholly dynamic, and the other is the expression of a medium to control dynamics. These are physical implementations that can be identified. Your RNA doesn’t have (the set of) discontinuous associations required to establish a medium, and therefore it doesn’t have the capacity or independence required to specify the translation system. You’ve assumed the existence of an autonomous RNA self-replicator, and then with a certain sense of bluster, you exclaim that your RNA precursor doesn’t do translation. You are correct. And therefore it doesn’t have the physical capacity to specify the system it’s proposed to be the precursor of. That’s why it’s irrelevant as an answer.

  280. 280

    Matt. I’ll be brief.

    Why is it so difficult for ID theorists to realize that prokaryotes, eukaryotes, animals, plants, fungi and bacteria DID NOT EXIST back when Life first appeared?

    Your reading comprehension is off. The point is not that all forms of life existed at the beginning; it’s that all forms of life require translation to specify objects and organize the cell. That’s what genes do.

    “Darwinian evolution – the evolution of living organisms — requires translation.”

    Nonsense!

    If the thing that is evolving is alive, then it will require translation.

    “Matt, the structure of tRNA does not establish and does not specify the genetic code.”

    I’ve seen you write that two or three times now and I’m not sure what you mean.

    That is evident. The set of aaRS establishes the code.

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