Thanks @art.
@rope, for reference, I really do agree with his scientific assessment. He is an excellent scientists that can explain the details to you too.
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Please understand that Axeâs paper does not in any way determine the proportion of functional proteins. Itâs design is only capable of indirectly and very inaccurately estimating the proportion of proteins of a particular length that allows growth of visible colonies on agar plates containing the MIC of a particular type of beta-lactam antibiotic.
This is emphatically NOT an estimate of the proportion of protein sequence space that carries out biologically meaningful functions. It logically canât support any conclusions in that vein.
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Why is it less surprising? Can you unpack this idea of more or less surprising.
I also have to note youâre not really answering the question I posed to you. You wrote:
Rather, the point is that the affirming all of evolutionary biology is wholly compatible with arguing that the evolution of complex biological functions is better explained on the supposition that God has created the process, than on the supposition that cosmos just happens to have the capacity for this kind of evolution.
The evolution of complex biological function is better explained, you say, on the assumption that God created the evolutionary process, rather than if God did not create the evolutionary process. But you actually offer no such explanation. Instead you go on to talk about what explains that the universe is such that complex biological function can evolve. It really just seems like youâre offering a sort of fine-tuning argument. Youâre attempting to offer an account of why the universe is the way it is, but I see no improvement in the explanation for the evolution of complex biological function.
Sure, as I generally do. I think evolution is strictly compatible with the concept of design in some ways(heck, I have even stated on this website that I think if one is going to say there was any design, it must be at the level where it made evolution inevitable. At least on this view one does not need to deny the evidence for evolution, which is a massive upgrade over ID and creationism). What I am questioning here though is your proposal that you have offered a better explanation for the evolution of complex biological functions on theism over atheism.
I think what youâre actually trying to account for is why the world is the way it is. A very different thing than the evolution of complex biological function.
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Unless Iâm missing something, I have to agree with Rum. Fine tuning ( which I regard as real, and a serious discussion concerning teleology in the universe ), posits that a limited palette of parameters is precisely set sufficient for life to emerge. Beyond these parameters, there is no âordered natureâ distinct or necessary. We do not have to rehash fine tuning here, but I am not clear as to what superposed order in nature is supposed to exist over and above, or if fine tuning is regarded as insufficient and a further force is at play, designated as order.
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No, I never mentioned citing. I am challenging your claim of familiarity with the primary literature and asking if you had read it. Iâll take your straw man as a no.
No, I wrote that you conflated stability with activity, swallowing and regurgitating Axeâs misrepresentation.
Please try harder to accurately represent what others write, OK?
Itâs not about citations. Itâs about your claim:
I would not say that.
So, making the unlikely assumption that you are more interested in learning than in arguing your position, it would seem that any academic in any field, who chooses to write about Axeâs claims, would do two things at a minimum:
- Look for Axeâs other papers as a rough metric for his expertise and impact.
a) This would necessarily take you to the 1996 one, as there are very few. If you read it and understood it at the most basic level, you would question Axeâs later claims. If you didnât, just the title and abstract should alarm you:
Active barnase variants with completely random hydrophobic cores
Using a sensitive biological screen [Axe did not in 2004, why?], we find that a strikingly high proportion of these mutants (23%) retain enzymatic activity in vivo. Further substitution at the 13th core position shows that a similar proportion of completely random hydrophobic cores supports enzyme function. Of the active mutants produced, several have no wild-type core residues. These results imply that hydrophobicity is nearly a sufficient criterion for the construction of a functional core and, in conjunction with previous studies, that refinement of a crudely functional core entails more stringent sequence constraints than does the initial attainment of crude core function.
b) You would see a massive WARNING signâthat Axe hasnât published anything on it after 2004. Thatâs a huge tell that it is wrong and/or that Axe doesnât really believe it. No one does!
- You could look for later papers that cite Axe, but #1 should stop you in your tracks.
All these things would take less than an hour and are highly informative even if you donât understand the underlying science, which no one in the ID movement, including Axe, does.
You missed the fact that it is an insane outlier and not supported by anything published between 2004 and your writing about it. It is so wrong, simply based on the shoddy experiments Axe did, that it never should have been published. The lack of any followup by Axe himself screams this to you, if you listen.
Which is just as ludicrous, because function in virtually all but strictly structural cases requires some instability. Most protein functions, other than the strictly structural, consist of transitions between one or more metastable structures.
Axe is misleading you; whether he is doing so from ignorance or malice is irrelevant. This is the problem with starting with ID critiques as your ground state and misrepresenting those who respond to them as critics.
Please stop. That is a high-school debate approach, not an academic one.
Arguments simply donât matter here, Rope. We know that Axe is simply, spectacularly wrong based on massive amounts of evidence that you ignored and no amount of handwaving argument can erase.
I am addressing it in detail as an example of the intellectual defect of your dreadful overall approach. You repeat this approach again and again.
And you chose this as an example. It is instead a vivid demonstration of ID misrepresentation of the evidence that your approach missed.
Maybe yours would, but mine wouldnât. But then, I have far more, and far more relevant, expertise than Axe, while you havenât looked for the evidence.
But you are not engaging with any of the relevant science or evidence. In science, we donât simply argue. We test hypotheses that produce evidence. ID doesnât do that, which is why it is pseudoscience.
The simplest would be this very direct refutation:
https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.14012
Axe extrapolates to 10^-77. He went backwards, starting from a crippled mutant, and never measured activity (itâs cheap and easy).
These authors found (not argued, Rope!) better than 10^-8. They went forward, were constrained by the context of the Ig fold, and did measure activity.
Whom should you believe?
If you want more detail, Iâm happy to answer your questions on our papers, but they are much more complex. This is the best place to start:
https://www.jbc.org/article/S0021-9258(19)51632-5/fulltext
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Irrelevant. He is explicitly claiming:
Which I have done, but I see no evidence yet that it behooves us to do so.
Because @Rope is extremely contentious, of course. He only cites arguments, while he rarely, if ever, cites evidence.
I am sure and am an expert, you are not.
Your description does not capture the spectacular inanity of Axeâs extrapolation and his lousy experimental work. Josh, I would have rejected this paper in 15 minutes simply for the absence of enzyme assays that only cost $7 each, regardless of conclusions. It truly is that pathetic.
It does nothing of the sort. It treats Axe as the ground state. Rope should be credited for mentioning that others disagree, but thatâs literally the only good thing I can say about it. Other than that, itâs unadulterated IDcreationism.
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One would expect more rigor from a philosopher. Here you conflate belief in a creator god with theism. Not quite the same. Choirs of angels and arranged particles would certainly be evidence of some powerful entity (or entities), but they wouldnât be evidence that that entity created anything other than the observed miracles. And of course we have nothing of that sort. Is that how you deal with the objection in your book?
Sure, but do any of these ways actually work? They donât appear to. Godâs moral goodness is an unevidenced assumption, and the problem of evil is a big roadblock for that interpretation. Nor is it obvious that Godâs morality leads logically to âlife capable of interactionâ, whatever that means.
Whether thatâs an advantage depends on whether the data actually support such an account. And we arenât arguing about theism vs. ID but about theism/ID vs. science.
This is the complete absence of intellectual rigor. Your argument here boils down to âgolly, stuff kinda looks designed to meâ.
Two problems: first, ânaturalismâ isnât an explanation, itâs a working principle in science, and the reason for it is that one doesnât appeal to explanations for which there is no evidence and that donât actually explain anything. âGod did itâ is not an explanation. There is no expectation of what anything would look like if God did it as opposed to some natural process doing it. If we currently canât explain how something happens, itâs better just to say âwe donât knowâ. Further, in any sort of contingent situation, any realized data have an inherently low probability. I work with DNA sequences, and under any model of evolution, the sequences we observe have extremely low probability just because there are so many possible sequences, just as any particular set of bridge hands is extremely improbable. The question is whether adding God to a hypothesis increases the probability of the data. And again we have no way to estimate the comparative probability of data with or without God, since we have no model of Godâs action. Useless hypothesis.
I have asked several times for you to say what âcompatible with evolutionâ actually means to you. But depending on what youâre talking about, this is either trivially true or just false. Until you define your terms, itâs impossible to choose.
Is that whatâs at issue? If so, you seem to be talking about fine-tuning of physics. Is that it? With regard to Behe and Denton, you have said that your claim is not the same as either of theirs, but you havenât actually said what it is. What is it?
If one can interpret this, you are claiming that the laws of physics were fine-tuned so as to produce eyes. Is this true? Are you familiar with Nilsson D., Pelger S. A pessimistic estimate of the time required for an eye to evolve. Proceedings of the Royal Society of London, Series B 1994; 256:53-58? What design argument are you talking about here? What do you think is designed, and how?
Not, Iâm afraid, enough things. But the picture that seems to be emerging is fine-tuning of physics. Behe at one time actually proposed this, which he called the âcosmic billiard shotâ: the creator sets up physical law and initial conditions of the big bang such as to inevitably result in exactly what we see today. Is that what youâre talking about? (I would say that, given quantum uncertainty, such precision is impossible, but YMMV.) But there are hints that you go beyond this into some kind of subsequent intervention in biology. Or is that not the case?
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Except that @Artâs article was written in 2007. As he notes, we have learned much more since then, so more recent references would be more scholarly. Unlike philosophy, science progresses.
I donât see any such evidence. You only seem to be capable of seeing arguments, anyway, based on ID misrepresentations of the evidence.
I think that you misrepresent arguments as evidence when they are extraordinarily weak.
You cannot have an informed opinion on the evidence when you go to such great lengths to remain ignorant of it, particularly by grounding your position in the writings of people who go to great lengths to misrepresent said evidence.
Since you seem to admire Meyer, I suggest that we explore what is, IMO, his greatest and most shameless misrepresentation. Since you donât regurgitate it in your books, you just might more easily accept the truth!
Thatâs not evidence.
But you obviously have zero familiarity with the evidence for that. To elide that, youâre misrepresenting evidence as mere âstuff.â Youâre a hoot.
Intuition is not, and has never been, evidence. The scientific method that you obviously reject is based on the empirical fact that human intuition is often grossly misleading.
The juggle of sophistry consists, for the most part, in using a word in one sense in all the premises, and in another sense in the conclusion.
âSamuel Taylor Coleridge
Your juggling is much sloppier, as you are relentlessly equivocating between -isms, evidence, arguments, explanations, and intuitions. None of these five things are synonymous with any of the others. As inâŚ
Then there is zero reason for you to regurgitate the misrepresentations by the armchair critics of the ID movement. You could start from the actual science. Why donât you?
There is no such evidence. There are only vague intuitions and lame arguments.
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I wanted to summarize a little âŚ
I do not understand, based on limited information here (and linked), how this is an argument for divine design that both engages with science and yet distinguishes itself ID as proposed by the Discovery Institute and itâs associates. The philosophical argument for ID is nothing new, and this is the position of Old Earth Creationists and (some) Theological Evolutionists (guided evolution). This distinction is the belief that God has created using evolution, but refraining from scientific claims to Godâs actions. I do not see how science and religion can be âadditiveâ in the sense that @Rope is proposing. I touched on this in an early comment âŚ
Not useful scientifically, but honestly religious. This is along the lines of belief for the other Creationists - Old Earth, Theological Evolution, etc⌠A lot of these folks are generally science friendly, so if they want to see things that way I donât think there is any harm in it.
That is, I want to leave room for the proposition to be âhonestâ in a religious or philosophical sense.
Then we get into the arguments. I mentioned Bayesian reasoning, and we seem to have a prior assumption for Design that will never allow any posterior updates - the conclusion will forever be the assumption. That is acceptable in religion, but not in science.
We also have criticism of particular arguments, as amply (perhaps overwhelmingly) demonstrated by @mercer. I can make equally harsh criticism for the mathematical/statistical claim of Dembski and others. No need to repeat those criticisms here, I only mean to note that âID scienceâ is flawed to the core.
Instead Iâd like to pose a different criticism - that Ropeâs proposition is self defeating. If Rope is correct, and we can gain confidence in divine Creation through science, then it must also be the case that science can weaken that confidence - that Science could be evidence against the existence of God. I may be happily agnostic, but I think that claim fails on several levels, and so must the entire proposition.
I am no sort of theologian, but Iâve had this discussion before with knowledgeable theologians. The explanation given was, to paraphrase, this puts belief (perhaps the Bible itself) on a âpedestal of scienceâ, something it was never intended to be, and âdefeats the purpose of faith.â
@Rope, I would try to offer you more if I could, some way to salvage your thesis, but Iâm not seeing any good options. I also believe that faith can (and should) stand alone from science. This is not meant as any sort of criticism of your faith, only of your attempt to apply science in this context.
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I would suggest something more banal than Bayesian: @Rope took an academic shortcut by using hearsay, pseudoscientific ID critiques, as the ground state, blinding him to their misrepresentations of the evidence.
Thatâs a superior theological position to that of ID, which diminishes God to the status of a hoarder/tinkerer who repurposes virtually everything and rarely invents anything truly new.
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From everything he has written here, he does not. He hasnât even used the term âevolutionary theoryâ in this entire thread. Instead, he crosses the line into what appears to be overt dishonesty by denying that thereâs any science, using terms like âevolutionary explanationsâ instead. Youâre calling him a philosopher, but he doesnât admit that explanations are just an initial requirement for hypotheses and theories?
Thatâs flat-out denialism in my book.
No. If @Rope canât bring himself to verbalize that evolutionary biology is built on empiricism and well-tested theories, he is obviously choosing to avoid engaging with science.
Which ones, precisely? He has yet to articulate a single one clearly here. John Harshman asked this is you days agoâŚ
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Thanks for the comments Dan!
I agree, and state in the PS article that the philosophical argument for design is not new, but has a long history.
For some differences from the positions you mention: OECâs do not argue that design emerged through evolution, and most TEâs who argue for guided mutations state this as a consequence of belief in creation, a kind of theology of nature, rather than as part of a design argument. I think that is valid, but I want to argue that the revelatory potential of biology is also compatible with evolutionary biology - this position is a bit less often defended. Also, the design argument as Iâve stated it does not depend on guided mutations - although it does not rule these out either.
I do not claim to be the originator or only person defending the claim that evolution is compatible with design perceptions or design argumens in biology - I cite plenty of precedents in the book. Nor do I claim that there is no overlap between different versions of design arguments or theologies of evolution.
I do not see how science and religion can be âadditiveâ in the sense that @Rope is proposing.
I am not sure what you mean by this additiveness. I do not think I used this terminology. My argument would also fit with the general schema of arguing that âGod used evolution, but refraining from scientific claims to Godâs actionsâ.
Can you clarify which part of the articles or arguments gave you this impression? Just so I can be clearer on this in the future.
I do think design arguments can be part of a theology of nature, in which the existence of God (even the God as portrayed in the Bible and Christian doctrine, or the doctrines of another religion) is the starting point (at least provisionally). That would not mean that design arguments are religiously irrelevant or that there is no revising conclusions though - the success of design arguments could show that the evidence of nature does support the correctness of the starting point, and that it supports the idea that God does give signs of his existence in nature. Whereas the failure of design arguments could show that these features of nature do not provide such support.
However, I think design arguments can also be part of a natural theology not starting from the assumption of Godâs existence. In that case design arguments would provide one line of evidence supportive of Godâs existence, which is then the revisable conclusion of the argument. Bayesian proponents of this approach would give a certain epistemic probability to Godâs existence, always to be revised in light of ongoing evaluation of the evidence and the arguments. Belief in God could still be based on more than the arguments, even for the defender of this approach, though.
This explanation is simplifying things a lot: for example, there is then also a distinction between weak and strong evidentialism, as well as differences of opinion about what counts as âevidenceâ, and what sort of grounds religious beliefs and commitments have in addition to (or in contrast to) arguments. Robert Audiâs book is a pretty good starting point for those wanting to get a bit deeper into the topic.
Can you clarify what you mean by self-defeating here? What do you see as the premises in the argument, or the surrounding theory of the epistemology of theology, that lead to a contradiction?
I do not think the existence of God is a scientific question, and the design argument is not part of the natural sciences for me. The arguments both for and against Godâs existence are philosophical in nature, but science can affect the credibility of premises. For example, scientific study can help understand the extent of suffering in the world, and so affects the problem of evil, although the problem of evil is a philosophical, not scientific argument against Godâs existence. Similarly, scientific study can help understand the intelligiblity and orderliness of nature, and so affects the premises of design arguments, from the fine tuning argument to my version. Thus science can strenghten or weaken certain non-scientific reasons people have for believing or not believing in God.
Scientific study can also affect the credibility of interpretations of the Bible and other holy books, such as the YEC interpretation or geocentrism. In other words, there can be and historically has been overlap between the things discussed in science, and the things discussed in theology. This does not mean that religion is science or that religious belief needs scientific grounds, though.
Well, thatâs pretty much all I have time for this discussion 
. I will check out your replies and will be grateful for further good references, but cannot rightly justify spending more time responding to your legitimate questions or clarifying misunderstandings. Thanks again to Joshua for publishing the article, and to those who engaged with me politely.
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The distinction between my argument and the fine tuning argument is a worthy question, but itâs also one of the central points discussed in the papers by Glass and Wahlberg, as well as my response to the symposium. One underlying intuition that I am defending that the products of some complex whole (like, say, the products of an automated factory or an algorithm) can provide evidence of the designedness of that whole.
Just because I explain something in one or two sentences does not mean there is no intellectual rigor behind it, or that it can be boiled down to that. Thereâs much more to it of course - unfortunately, when Iâve linked longer, more rigorous explanations these were mostly left unread or got dismissed as philosophical babble, without recognizing that the other sideâs argument is also philosophical.
Naturalism in the sense I am using is not methodological naturalism, but philosophical/metaphysical naturalism: the worldview/assumption that nature is all there is, and no God exists. Granted that there are many variants of naturalism.
I am familiar with that paper and quote it in the book. My argument, following the line taken by Asa Gray and others, is that there is no contradiction between such evolutionary explanations and design. Both can be affirmed simultaneously as conjunctive explanations, as answering different explanatory questions, or as functioning on different levels.
For the argument, God fine tuning nature to make evolution possible is sufficient, although outside the argument, I believe much more divine action takes place. One intuition that I defend is that a cosmos specifically set up by a purposeful Creator to produce evolution of this type is more likely to result in the evolution of such structures, than a cosmos that is not ordered for that purpose. In his paper, Glass wants to push me to argue for more direct divine action in the evolutionary process - his argument there is that divine direction of mutations can make certain valuable evolutionary outcomes more epistemically probable, even without arguing that such outcomes are impossible without God directing mutations.
Thereâs a bunch of good literature explicating/responding to the problem of divine action and chance, such this open access volume.
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Mercer:
It seems we both feel misrepresented in this discussion then. It seems to me you have not provided a critique of my arguments at all, only a critique of Axe and a critique of what you imagined I was saying, rather than what I actually argued. You seem to be operating with an extreme hermeneutic of suspicion here.
I did read Axeâs original paper as well, but itâs quite old already - I rather wanted to cite the more recent stuff, and am happy to leave to leave the critique of the contents of the papers to scientists. As a theologian/philosopher, rather than criticizing some peer reviewed scientific paperâs methodology directly, I will typically rather opt to see how the papers are cited in other peer reviewed papers, see other papers on the same topic, and then criticize and contextualize the argument by reference to other peer reviewed papers. My judgment when writing the book was that this was sufficient in the case of Axeâs paper - as there is a wide range of estimates for the prevalence of functional proteins in the literature regardless, and Axeâs paper as one data point is not significant for the conclusions of that section.
I also did not conflate activity and stability in the book or here, but distinguished them. The point that âfunction in virtually all but strictly structural cases requires some instabilityâ is not contradicted by what I wrote, nor would mentioning it have changed the conclusions of that section. It seems to me that you have not provided a scientific criticism of anything I argued, but simply further criticisms of Axeâs paper and Meyerâs use of it.
I am always grateful for more technical help, so perhaps I will try my luck with some questions if I have some in the future. The first one is the kind of paper that I as a non-biologist would miss in a literature search focusing on the prevalence of functional proteins or direct refutation of Axe, since these terms are not mentioned in the paper. I did see the PS thread discussing how their methodology finding so many functional variants would be unexpected based on Axeâs figures, with a long discussion between Ann Gauger and yourselves, though.
Can you clarify your question more? Do you want me to unpack more on why I think a purposeful, good creator setting up evolution makes it less surprising to have biological organisms containing apparently purposeful order emerge, as compared to a world where there is no creator to set up the evolutionary process in that way? Or are you asking me to argue more for the epistemic improbability of these things on atheism? I am trying to see if you are getting at some objection I have not already addressed in the literature. This is just for future work unfortunately - I do not have the time to write those arguments in long form here, and one-sentence explanations have already proven less than helpful in this discussion.
The teaching semester is starting next week, and with that, I have pretty much used up all the time I had available for the discussion. I will do one more round of replies to hopefully clear up some misunderstandings, and ask further questions about things that might be helpful to me.
Thanks for everyone who has engaged politely with the papers and/or provided good information. I was hoping for more of that kind of discussion, but communication across ideological differences and getting people to understand a style of design argument that differs from Intelligent Design proved difficult, as expected. When I provided papers with explanations of the arguments in terms of up-to-date philosophy of science and philosophy of religion, using terms like conjunctive explanation, that was dismissed as philosophical babble or not read at all. But then if I provide short answers in colloquial language, that will of course be termed not rigorous.
But now to final short replies to everyone.
Thanks Art!
I am interested in reading more critique of Dentonâs paper and later book on structuralism - his work has not gotten much nearly as much critical attention as that of Meyer and Axe. Could you point me to some of what you consider the best critiquer of that paper and/or his ideas generally? I did not see a mention of Denton in the linked discussion.
Also, how would you assess other similar arguments, such as Andreas Wagnerâs claim about a metaphorical âlibrary of formsâ underlying evolution. I reference Pigliucci critique of this, but I am interested in your take.
Or what about Ahnertâs claim that âthe accessibility of phenotypes may be just as important a determinant of evolutionary outcomes as the pressures of natural selection.â Interested in your take on this.
Would using Artâs 2007 article as commentary of the 2004 article really have been that bad? I did not see anyone here arguing that Artâs critique of Axe has aged poorly - just that there are now additional reasons in addition to what he says. Please clarify if Iâve misunderstood. In any case, I do use more recent references in the book though. And there is actually plenty of progress in philosophy and theology, hereâs a cool paper on the topic.
Before this discussion, I would have been moderately interested in reading your critique of Meyerâs arguments, in addition to the Meyer-critiques Iâve already read and reference. Unfortunately, while I remain confident that you know your science, this engagement has made me less confident that you will fairly and accurately represent those you disagree with. The end result is that I am still mildly interested though - so please do write something on this or link to an existing discussion. I will likely read, though I do not have time to participate further.
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Yes.
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Two questions come out of this. One concerns a commitment to clarity on sufficiency. While it is possible the creator set up the factory, hit the green button, and then left for all time, I am not clear if under your Biological Design Argument whether our not He occasionally returns to make adjustments and maintain with an oil can. If He does, that sounds indistinguishable from, for example, Beheâs position.
On the other hand, the relationship to fine tuning is close enough that the alternative responses to fine tuning fully apply. Divine teleology could supply account, but an infinite multiplicity of universes would also satisfy. The responses to fine tuning appropriately and completely address the BDA. We could just find ourselves in a universe which happens to have the settings where we respond with wonder and faith to what we aesthetically or subjectively perceive as beauty and design.
So far, the BDA seems to occupy a very murky and narrow penumbra between fine tuning and full on ID.
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