Doug Axe now replies to James Shapiro: Can we let the science decide?

_{Denyse O'Leary

January 18, 2012

Darwinism, Evolution, Intelligent Design}

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Readers will recall James Shapiro, author of Evolution: A View from the 21st Century. Bill Dembski asked him, based on his observations, Why aren’t you a design theorist?

Which, in the context, is somewhat like asking, “Well, if you agree with me about how badly things are run down at City Hall, will you join Citizens for Municipal Reform?”

Well, Shapiro replied, giving his objections, and now Biologic Institute’s Doug Axe has replied to Shapiro here:

I think we all agree that science should be the arbiter here. Naturalism and ID both make testable claims about how things happen in the real world, so it ought to be possible to evaluate these positions by evaluating their respective claims.

If crutches are devices for propping up lame positions, then I completely agree that they should go, but let’s be careful to call a crutch a crutch. As an ID proponent, I’ve put forward the scientific case for thinking that the thousands of distinct structures that enable protein molecules to perform their specific tasks inside cells cannot have arisen in a Darwinian way. Moreover, the facts of this problem seem to preclude any naturalistic solution, Darwinian or not.

Shapiro is looking for a no-Darwin but no-intelligence solution. Does it exist?

Also, Axe’s senior scientist Ann Gauger offer some thoughts on Dembski’s questions here.

0 to 60 quick, on Shapiro:

Antibiotic resistance: The non-Darwin truth

“Four kinds of rapid, multi-character evolutionary changes Darwin could not have imagined”

“Key non-Darwinian Evolutionary Scientists in the 20th Century”

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Comments

"Only GOD could be the intelligent agent behind the complex genetic code." I think there's an ixnay on admitting the Godnay is the Designernay herenay.... Hilariously to those of us amused each time someone tries to argue ID isn't a flimsy creationist front, against historical, current funding and logical considerations. Your politicians even call it "intelligent design creationism"DrREC_{January 19, 2012
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Thank you for your reply Chas. But it requires no faith to consider history to have unrolled according to principles we can investigate now, any more than it requires faith to consider it plausible that the Normans came from France rather than from outer space. And the better one understands the fundamentals of the process, the better placed one is to evaluate its plausibility. It DOES require faith Chas, because you're talking about a historical science, not an empirical one. Like I showed in my original post, even Jerry Coyne admits that. Darwinism is a worldview, a religion if you will, not a scientific theory. When ANYTHING and EVERYTHING is attributed to it no matter how contradictory to previous predictions and claims, that proves the 'theory' is UNfalsifiable. Now, if you wish to believe in it, that's your right. I firmly believe God gave us free will (contrary to atheists' claims that we have no free will) and that you have the right to believe as you choose. The problem is, you are not promoting a scientific theory, but rather your materialistic faith. As I asked before, at what point would you ever concede there MUST be a supernatural first cause for nature/the natural? If you say never, then you are ignoring the known scientific principles we have, in exchange for faith that one day, all the mysteries will be explained by purely naturalistic means. The design inference, however, requires introduction of an exceptional cause. We can see design in action, among entities that are the end result of some historic process. We use that inference to pass that same quality back into the historic process itself. And that, to me, requires the leap of faith – faith I do not possess, that an entity capable of such interference can even have existed, let alone performed the interactions necessary to overcome the assumed barriers to complexity. The same applies to space aliens as to deities. Tell that to seti and the other 'scientific' journals that allow e't's to be postulated, but not GOD. ;-) But to get back to the point, what you're doing is saying GOD wouldn't do this or that, ergo God can't exist. That's not a logical position my friend. Why couldn't the GOD of the Bible exist and do what the Bible claims He did/does? Only GOD, someone outside the laws of physics, could be the cause of them. God is eternal, and UNcaused...that's why He's GOD. Just because you may not be able to fully comprehend Him (none of us can) doesn't mean His existence is improbable. Only GOD could be the intelligent agent behind the complex genetic code. The living cell is a complex, biological machine that rivals computer OS in terms of information. If you wouldn't believe the information in Windows 7 came into existence by itself, why would you believe the information in a living cell did? We can use the same experience and knowledge that tell us the information in Windows 7 had an intelligent creator, to deduce the information in the living cell had a creator. All I'm asking is that you use the same logic and intelligence that tells you the faces on Mt Rushmore were not caused by erosion slowly over time, to realize the living cell is not the product of blind, random chance. And, as an aside, I do wish people would stop asserting that somehow atheists have some fundamental need, ideological or whatever, to see evolution as true. Their confidence in it (faith, if you will) is rational, and would be overthrown by rational considerations. I have to disagree. It was Richard Dawkins who said: An atheist before Darwin could have said, following Hume: "I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one." I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist. -- Richard Dawkins, The Blind Watchmaker (1986), page 6 Atheists NEED darwinism, which is why they fight so hard to prevent it form being criticized, and having dissenting opinions heard. Take careBlue_Savannah_{January 19, 2012
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The most parsimonious explanation is: "I don't know." Everything else is playing the Texas Shaprshooter fallacy over billions of years of rock strata. And it's not simply that the historical narrative of Evolution is a creation myth. It's a creation myth that rests its laurels on ad-hoc hypothesizing and positivism as its proof that it is the One-True-Truth behind the creation of man. If you want parsimonious religious frameworks then there are plenty to choose from that have far better apologetics in place than Darwinism. If you want parsimonious scientific theories, then get back to me when we start performing experiments on the lab-table.Maus_{January 19, 2012
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Elizabeth: And by “intrinsic design process” I mean the evolutionary algorithm itself – the tendency of things that replicate with heritable variance in reproductive success to adapt to their environment. Shapiro essentially is talking about that algorithm at population level – the evolution of evolvability. Which you could state as the tendency of populations that are maximally adaptive (have optimal rates and types of variance production for instance, or optimal epigenetic mechanisms) to persist over time, resulting in extant populations being those consisting of organisms who have heritable mechanisms that tend to result in successful population adaptation. Wow! When you start that way, I have only two options: either become aggressive and spend a lot of time trying to show you, without succeeding, that what you are saying is senseless, or leave you at your opinions. As today we suceeded in agreeing on one thing, I will take the second option :)gpuccio_{January 19, 2012
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Dr Liddle, What "just occurs" (borrowing your terminology) cannot be shown to prefer one scenario over another to achieve a goal. Agent-based choice between naturally occurring scenarios is the only thing that can cause control to happen. I define control as a formally describable process that drives a system through a sequence of states towards improved utility (function). Empirically, control per se always requires a layer on top of physical reality. Particular mechanisms of control are necessarily instantiated into physicality, but physicality alone cannot be sufficient to understand the semantics of information. There are simply no observations which would give grounds to the belief that control can crystallise from chaos. So control is irreducible to physicality. Think of the TCP/IP stack of protocols for communication between computers. Control is first defined conceptually at the top (application layer) and then realised all the way down to network layer and finally to physical layer of electric/optic circuitry. Semantics is given by the encoding/decoding protocols, i.e. via a non-physical entity. In no way is it possible to think of anything like a scenario where the meaning of communication can emerge at the level of voltage jumps in the connecting cable. We note on massive observation that meaning or control cannot crystallise. Agent-based choice is at the heart of any algorithm. Why is control inherent in what "just occurs" in the cell or complex artefacts and, at the same time, not inherent in what "just occurs" in other scenarios? When you answer this question for yourself, you will see that formalism or semantics cannot emerge in "just-occurring" scenarios but always need agency. Whenever we are able to detect formal function, the detection is an empirically warranted pointer of design.Eugene S_{January 19, 2012
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OK so according to Shubin he was NOT looking for a transitional form, rather he was looking for evidence of the transition which HE said would be between two data points-> fish and no tetrapods and fish and tetrapods. Unfortunately Tiktaalik was found in strata in which both fish and tetrapods existed.Joe_{January 19, 2012
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Misposted reply to Blue Savannah at 6!Chas D_{January 19, 2012
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Geez you just can't do anything for yourself- It has to look like a transitional form, meaning is has characteristics of the alleged ancestor and the alleged descenents:
Fossils or organisms that show the intermediate states between an ancestral form and that of its descendants are referred to as transitional forms.- UBerkley
That means it looks like a transitional form.Joe_{January 19, 2012
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Yet darwinian evolution is beyond reproach. Why? How is your faith in it, different from my faith in a creator?
The darwinian paradigm is based upon actions that we can see having an effect on the very entities in which we are interested - biological organisms. The competition of replicators in a finite world is almost axiomatic - of course if more organisms are born than can possibly survive, there will be concentration of fitter variants. Whether this simple fact can or cannot have led to current organismal diversity is a challenge to one's conceptions of plausibility, and one cannot put one's own conceptions as superior to another's, in either direction. Still ... I have absolutely no trouble with conceiving the process in action, sweeping right through barriers that others perceive - and all too often, these perceptions are quite clearly rooted in a misperception of what evolution actually says. Trying to deal with those misperceptions wins one no friends, since one is dealing with something rather central to the opponent's worldview***, rather than someone keen to learn more. Evolution has the satisfying character that no causes are introduced that we cannot observe in action, or model based upon known principles. If you think that the proposition is implausible, fair enough. But it requires no faith to consider history to have unrolled according to principles we can investigate now, any more than it requires faith to consider it plausible that the Normans came from France rather than from outer space. And the better one understands the fundamentals of the process, the better placed one is to evaluate its plausibility. The design inference, however, requires introduction of an exceptional cause. We can see design in action, among entities that are the end result of some historic process. We use that inference to pass that same quality back into the historic process itself. And that, to me, requires the leap of faith - faith I do not possess, that an entity capable of such interference can even have existed, let alone performed the interactions necessary to overcome the assumed barriers to complexity. The same applies to space aliens as to deities. *** And, as an aside, I do wish people would stop asserting that somehow atheists have some fundamental need, ideological or whatever, to see evolution as true. Their confidence in it (faith, if you will) is rational, and would be overthrown by rational considerations. That's not to say that alternatives are irrational, but analogies that other people find convincing are not convincing to me. My 'commitment' to atheism is about equivalent to my commitment to not supporting a particular, or any, football team. I'm just not that interested. It needs no support from biology.Chas D_{January 19, 2012
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And what are the criteria for "transitional form" Joe?Elizabeth Liddle_{January 19, 2012
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Yes it does- just look at the criteria for "transitional form". And you have no idea what Shubin said- you obviously have reading comprehension issues.Joe_{January 19, 2012
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Also “transitional foem” boils down to nothing more than “it looks like a transitional to me”.
No, it doesn't. That's probably why you've misunderstood Shubin.Elizabeth Liddle_{January 19, 2012
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Dr Liddle, This is equivalent to the untenable position of emerging formalism and semantics. Unguided evolution can at best modify what it’s given. It has no capacity to produce sufficient novelty. There is no ‘magic’ inside RV + NS.
There doesn't have to be "magic" to produce novelty. And I simply dispute your other assertions!
Emergence is just a rhetorical device. Nothing of the sort has ever been detected in nature (apart from life, which is the point in question, and complex enough artefacts).
It's certainly a word, and so, in that sense, is a "rhetorical device". I'd say, rather, that it is a useful concept, and if we describe it simply as properties of a whole that are not possessed by its parts, then it is "detected" in nature all the time. We would be unable to make sense of the world were it not so.
In nature, there are no algorithms, nor ever can be. Simply because physical reality is inert to utility.
This makes no sense to me. Clearly there are only things called "algorithms" if there are people to call things "algorithms". "Algorithm" in other words is an attribute we assign to systems with certain properties that we call "algorithmic". And there are many processes in nature that display those properties, I would argue, not all of them even organic. Any sorting systems is "algorithmic". And evolutionary processes certainly are, because we can actually model them as computer algorithms!
Algorithm is a formal process which assumes a formal language, semantics and a way to steer system states towards improving utility (i.e. control). Algorithms therefore cannot explain the emergence of semantics.
Well, the expression of an algorithm may require a semantic language (at least at high level). But the essence of an algorithmic process, surely, is that what happens next is contingent on what happened before - the "if...then" statement in a computer algorithm. But it doesn't have be expressed symbolically, it can just occur. "WHILE stones exist IF stone weight > W AND velocity < V, THEN drop stone, ELSE roll it back" is just a human-language way of expressing the intrinsic rule by which, for example, stones along a beach may be systematically graded small to large. Chesil BeachElizabeth Liddle_{January 19, 2012
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I think it was the egg. I believe you think so too (correct me if I am wrong). And so?Eugene S_{January 19, 2012
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2.2.1. Champignon, Could I also add my two pence. I hope UprightBiped will allow me to intervene. I think that the answer to your question is 'yes'. A simpler example is a random correction of an error (such as a double negation, one after the other, or a sequence of two mutations where the second cancels the first). These are examples where an increase of information happens by chance. However, acknowledging that this can happen is not the same as acknowledging that this is the way functional information emerges. Do you think that the two are equivalent: 1) I can walk; 2) Since I can physically walk, I can walk to the Moon? Empirically, we can see that whenever there is a high enough quantity of functional info, it is as a result of intelligent agency. As has been noted, this is not a logical necessity proof, but an empirical observation based on data available today. Empirically, as soon as we detect formal function, control, semantics, we are looking at artefacts. In other words, one can engage in all sort of Darwinian explanations but by far probabilistically the best (in terms of Newton, Occam and Bayes) will be choice contingency (design).Eugene S_{January 19, 2012
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Shubin: Let’s return to our problem of how to find relatives of the first fish to walk on land. In our grouping scheme, these creatures are somewhere between the “Everythungs” and the “Everythings with limbs”. Map this to what we know of the rocks, and there is strong geological evidence that the period from 380 million to 365 million years ago is the critical time. The younger rocks in that range, those about 360 million years old, include diverse kinds of fossilized animals that we would recognize as amphibians or reptiles. My colleague Jenny Clark at Cambridge University and others have uncovered amphibians from rocks in Greenland that are about 365 million years old. With their necks, their ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find whole fish that look like, well, fish. They have fins. conical heads, and scales; and they have no necks. Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.- Neil Subin pages 9-10 Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals. What part of that don't you understand? The problem is the transition took place millions of years earlier. So no he shouldn't be looking for evidence of the transition between fish and tetrapods in rocks about 375 million years old. The transition took place before that. IOW you evos don't know what you are talking about and it shows.Joe_{January 19, 2012
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Elizabeth you are confused. He was NOT looking for tetrapods. He said he was looking for the TRANSITION between fish and tetrapods which occured much earlier than the strata he found Tiktaalik. And yes his prediction was that the transition between fish and tetrapods would be found in strata after fish and BEFORE tetrapods. That is what Shubin said. It is stupid to go looking for evidence of a transition many millions of years AFTER the transition took place. Also "transitional foem" boils down to nothing more than "it looks like a transitional to me". Also given the new data there would be no reason to look for the transition where he did. But obvioulsy you cannot grasp any of that.Joe_{January 19, 2012
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I answered Nick's question. Eiethr respond to that or bug off.Joe_{January 19, 2012
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Pick any one (from each word) and tell us how Darwinism fits it. Good luck...Joe_{January 19, 2012
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Spot on.Eugene S_{January 19, 2012
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Dr Liddle, This is equivalent to the untenable position of emerging formalism and semantics. Unguided evolution can at best modify what it's given. It has no capacity to produce sufficient novelty. There is no 'magic' inside RV + NS. Emergence is just a rhetorical device. Nothing of the sort has ever been detected in nature (apart from life, which is the point in question, and complex enough artefacts). In nature, there are no algorithms, nor ever can be. Simply because physical reality is inert to utility. Algorithm is a formal process which assumes a formal language, semantics and a way to steer system states towards improving utility (i.e. control). Algorithms therefore cannot explain the emergence of semantics.Eugene S_{January 19, 2012
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No, he is not "looking desperately". And by "intrinsic design process" I mean the evolutionary algorithm itself - the tendency of things that replicate with heritable variance in reproductive success to adapt to their environment. Shapiro essentially is talking about that algorithm at population level - the evolution of evolvability. Which you could state as the tendency of populations that are maximally adaptive (have optimal rates and types of variance production for instance, or optimal epigenetic mechanisms) to persist over time, resulting in extant populations being those consisting of organisms who have heritable mechanisms that tend to result in successful population adaptation. It's an extension of the Darwinian system, not an alternative to it.Elizabeth Liddle_{January 19, 2012
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Elizabeth: It may suggest that, but it will never be scientifically supported, because there is no "third way" (just my opinion :) ). The research remains valid, and it supports ID. Shapiro is just looking desperately for a way out of the simple fact that all he knows and all he finds supports ID. But he will not find that way. In the meantime, as he is a good and honest scientist, his research is contributing both data and concepts that are certainly useful. By the way, could you explain simply what you (or Shapiro) really mean by "intrinsic design process"? Just curious.gpuccio_{January 19, 2012
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Here's my questions to atheists: 1. At what point would you accept that the universe or nature had a supernatural first cause, or would you always just hope/believe that one day, perhaps long after you're gone, an answer will be found that supports a materialistic explanation? Isn't that FAITH?? For example, let's say GOD created the universe, how would you ever realize THAT if you continue to reject that possibility from the start? You say the supernatural is not science, but you accept other things that cannot be verified by our scientific methods, such as the belief that all life is the sole product of darwinian evolution. Even uber-darwinist Jerry Coyne admitted: In science's pecking order, evolutionary biology lurks somewhere near the bottom, far closer to phrenology than to physics. For evolutionary biology is a historical science, laden with history's inevitable imponderables. We evolutionary biologists cannot generate a Cretaceous Park to observe exactly what killed the dinosaurs; and, unlike "harder" scientists, we usually cannot resolve issues with a simple experiment, such as adding tube A to tube B and noting the color of the mixture. Of Vice and Men The New Republic April 3 2000 p.27 Yet darwinian evolution is beyond reproach. Why? How is your faith in it, different from my faith in a creator? (Aside from the fact logical deduction of the evidence points to a creator) 2. Why is ANY possibility allowed, EXCEPT God? Extraterrestrials, a multiverse, etc are both allowed to be promoted as 'science' yet there's no evidence for either. There's also no evidence our 'scientific' methods would be able to determine an extraterrestrial or a multiverse, yet both are put forward as possibilities...but not GOD. Why? Thank youBlue_Savannah_{January 19, 2012
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But his research completely undermines ID's central thesis! It suggests that the design processes that give rise to functional organisms are intrinsic, not the result of external design and implementation.Elizabeth Liddle_{January 19, 2012
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So why can't you produce the definitions you are using? How else are we to know which of several dictionary definitions is the one you mean? Here is Merriam-Webster:
Definition of SCIENCE 1 : the state of knowing : knowledge as distinguished from ignorance or misunderstanding 2 a : a department of systematized knowledge as an object of study [the science of theology] b : something (as a sport or technique) that may be studied or learned like systematized knowledge [have it down to a science] 3 a : knowledge or a system of knowledge covering general truths or the operation of general laws especially as obtained and tested through scientific method b : such knowledge or such a system of knowledge concerned with the physical world and its phenomena : natural science 4 : a system or method reconciling practical ends with scientific laws [cooking is both a science and an art] 5 capitalized : christian science

Definition of THEORY 1 : the analysis of a set of facts in their relation to one another 2 : abstract thought : speculation 3 : the general or abstract principles of a body of fact, a science, or an art [music theory] 4 a : a belief, policy, or procedure proposed or followed as the basis of action [her method is based on the theory that all children want to learn] b : an ideal or hypothetical set of facts, principles, or circumstances —often used in the phrase in theory [in theory, we have always advocated freedom for all] 5 : a plausible or scientifically acceptable general principle or body of principles offered to explain phenomena [the wave theory of light] 6 a : a hypothesis assumed for the sake of argument or investigation b : an unproved assumption : conjecture c : a body of theorems presenting a concise systematic view of a subject [theory of equations]
Which of these do you regard as "standard"?Elizabeth Liddle_{January 19, 2012
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I would just say that IMO Shapiro can go on with his cognitive attitude, and go on making good science. Unless he can really show a "third way" (and I don't think he can), all he does is definitely in favour of ID. That's very fine with me. It's important to have people who make good ID research outside of ID.gpuccio_{January 19, 2012
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I mean "transitional" of course in the sense of "showing features of both earlier and later organisms, not as in "animals that are both descended from Silurian fish and directly ancestral to all modern tetrapods".Elizabeth Liddle_{January 19, 2012
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No, it means that he was correct, for correct reasons, in his prediction that he would find tetrapods in that stratum in that place. We know know that other tetrapods also lived earlier. But his prediction was not that "the first tetrapods will be found in Greenland" but that "tetrapods showing transitional characteristics are likely to be found in Greenland". And he was absolutely correct.Elizabeth Liddle_{January 19, 2012
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Joe, it is no use. We know empirically how people from the other camp can twist definitions they said were taken from a dictionary.Eugene S_{January 19, 2012
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