Biological Information and Intelligent Design: Meyer, Yarus, and the Direct Templating Hypothesis

That’s not how science works. It’s about testing one’s own hypotheses, not making demands of people who do actual science.

BTW, I’m very confident that Swamidass isn’t assuming anything. On what basis did you make such an accusation?

So you seem to be getting very emotional here @eddie. Not sure what to make of that. Just because we disagree on the science does not mean the conversation needs to be charged. Clearly, we are striking close to home.

So, the first definition of IC (which I will refer to as IC1) that Behe gives is about 1996 in Black Box:

A single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning
-Darwin’s Black Box

This matches Demski’s definition (also IC1):

A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system’s basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system.[

The true brilliance of Behe’s first IC definition is that it is 100% objective and can be directly measured in a biological system. It is a real, directly observable feature of any system.

So, his first argument is that IC1 systems are impossible to evolve. The thing is, this is directly falsifiable in the lab. In fact, a single protein protein interaction CAN in fact produce a IC1 system. This is so obviously observable that Behe no longer even makes the argument the way. Most biologists agree that IC1 exists throughout biology, and that evolution can produce IC1 systems. Case in point is the flagellum, which several people have demonstrated has several plausible selectable intermediates (despite your loud protests). We all agree that it is an IC1 system, and are also convinced that evolution can produce IC1 systems by both directed and indirect means.

Now that his first argument (IC1 systems cannot evolve) has been demonstrated experimentally (directly btw) to be false, we can throw that in the dust bin and move two his new IC2 definition. The second definition of IC (which I will refer to as IC2) that Behe gives is in 2000 and carried through to his current argument:

An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.
http://www.discovery.org/a/442

Now this definition suffers greatly compared to IC1, because it is not longer objective and directly measureable. Instead, we need to understand something of the evolutionary pathway, which is not directly observable.

Still, for the IC2, most knowledgeable scientists agree that IC2 systems exist in nature too. Similar to IC1 systems, we are convinced that evolution can evolve IC2 systems also. Embedded in this definition is an important straw man. He writes “one or more unselected steps.” Here, into the IC2 definition is being smuggled a strict enforcement of “Darwinian” evolution. Now, anyone following biology at a basic level of competence knows that strict-Darwinian evolution was falsified a long time ago, in the 1970s. We now know that a large proportion of changes are near neutral or even slightly deleterious in the short term. So this dominant pathway of change is intrinsically ruled out by Behe’s definition.

So, with that in mind, it is correct to say that modern biology agrees that IC2 systems appear throughout biology, because we thinking neutral mutations are often the evolutionary path to the systems we see, and they are not selected. Of course, this is all beside the point, because we are convinced the evolution can evolve IC2 systems too.

Now, we could define a new version of IC (IC3 if you humor me here) that allows for all changes by natural mechanisms. How might that fair? Unfortunately, this definition is even more unhinged from objective evaluation than IC2. We have moved entirely away from the concrete brilliance of IC1, to a fundamentally theoretical classification that is not directly testable in any way.

Well, no one has yet demonstrated that any system in biology is IC3. The claim that IC1 = IC3 is clearly false. So is the claim that IC2 = IC3. But how do we demonstrate that a biological system is IC3, and not just IC1 or IC2? No one knows. No one has proposed a way of doing so in a way that seems remotely plausible to anyone outside the “already convinced” ID crowd. Instead we have a lot of sloppy arguments that somehow treat all classes as if they are the same thing.

Honestly, i do not know how to solve this problem. But I am not an ID advocate, so that isn’t my job. The fundamental problem for IC arguments is that biologists already agree that IC1 and IC2 systems exist, and we have even demonstrated their evolution directly in the laboratory.

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You clearly did not read the article or watch the video. There were several selectable steps proposed.

So to be clear. The argument unfolds this way:

  1. ID advocate points to flagellum and says there are no conceivable intermediate steps.
  2. Scientists point out that there are several conceivable intermediate steps.
  3. ID advocate calls the sequence an unproven fairy tale.
  4. Scientists reply that whether it happened this way or not, this demonstrates that your claim #1 is false. There are conceivable intermediates.
  5. ID advocate demands: prove that that is exactly what happened.
  6. Scientists explain, we never claimed that is exactly what happened. Though guess, what we have some evidence that some of this is what happened.
  7. ID advocate wants more evidence.
  8. Scientist provides more evidence.
  9. Return to #7.

Well, I find this argument boring and predictable. It is literally exactly what happened in the Dover trial, and it is replaying here almost exactly in this thread. I’ve already proven the first claim #1 is false. That is the entire ID argument. So I’m done.

This is an oversimplification. Some of these intermediate steps are visible in actual organisms today, but not always. Remember, we are talking about something that happened in the very very distant past, so direct evidence like that is expected to be spotty.

Another case is more interesting, the evolution of the eye. Most people agree that eyes are more complicated than flagellum and that they are irreducibly complex. Turns out that we have almost all the intermediates in extant species. You can see a clear smooth sequence of intermediate states. If that is true for the eye (which is objectively more complex than the flagellum), I’m inclined to believe this to be true about the flagellum.

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As Swamidass has patiently explained to you, there do not have to be selectable gains at every step. It’s that non-Darwinian part of evolution that you don’t seem to grasp.[quote=“Eddie, post:41, topic:5784”]
“ID hypothesis” is irrelevant here. Whether ID is true or not, the onus is on you to build the bacterial flagellum for me from scratch, before my eyes, showing me plausible, selectable intermediate stages. Otherwise, I am under no intellectual obligation to believe that the flagellum could have been created by neo-Darwinian mechanisms.
[/quote]
There is no onus on Dennis.

The onus is on you to test your own ID hypothesis.

That’s why “ID hypothesis” is highly relevant. You and Behe are rejecting the most fundamental aspect of science when you deny the reality of hypothesis testing, which is anything but getting pseudonymous commenters to believe you by jumping through absurd rhetorical hoops.

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I guess I may be trying to untangle the arguments centered on ID/notID, from examples which are thought to illustrate or show evolution (chance variation with natural selection) - I had at some time, tried to follow the argument(s) regarding eyes, but I confess I gave up when I came across an example where fish at great depths are reported to have thick lens made out of crystalline calcium compound(s) (it may be a crystalline calcium sulphate, but I cannot recall all the details).

At the moment I am struggling with the concept of genes, and as I indicated in a previous post, there is controversy on the notion of distinct genes, or various portions of DNA performing a variety of functions.

I suppose I am glad that scientists such as yourself are comfortable with ToE as it impacts on the biological sciences - as a somewhat interested scientist, I keep finding more and more difficulties as I search the literature and wade through PoS discussions related to biology.

It seems to me that variety is ubiquitous in the bio-world, but rationalising this as some sort of fitness criteria is woefully inadequate.

… or maybe, indeed, outside the proper business of science. Is natural selection a regularity in nature, or a near-infinite series of mostly incalculable contingencies?

If the former, its results ought to be predictable according to scientifically determinable laws (as opposed to laws that predict how a feature or gene will behave, assuming it has been selected.)

If selection cannot be reduced to laws (ie it is not a lawlike process), then it would seem science can only (in the main) observe it in the same way that one can observe historical events, such as the results of wars or elections, without being able to formulate laws of history that explain reliably who will win any particular struggle and why.

One can, after all, make a pretty good theory that the winners of wars will always write the history-books, but that doesn’t make winning wars a scientifically predictable process.

This, of course, ignores the preponderance of near-neutral changes in current theory, in which survival is simply the result of not perishing - even more contingent and non-lawlike. But do we really make natural selection, in its pure adaptive sense, non-random by saying something as vague as “it always selects the fittest”? Is warfare lawlike because the best team (defined entirely by its winning, whether by nuclear arms, a meteorite strike on the enemy or a vision of angels) always wins? No - war may not be truly (ontologically) random, but it is contingent and therefore not amenable to scientific explanation (and therefore, actually, random as far as science is concerned).

If science is the study of the repeatable, what makes natural selection any more a scientific process, than is contingent history - which is as much as to say a product of providence?

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Your discussion, Jon, reminds me of Asimov’s “Foundation Series” trilogy (I think it was) that I enjoyed years ago. Was it Harry Seldon in there who had figured out how to predict the galaxy’s future with his socio-political-“whatever all else” equations? (I can’t remember the phrases used). But in any case in the novel he, even from his grave, appears to “run” the show with his accurate predictions and sage pre-recorded advice to the particular group of people (“foundation”) that considered him a prophet. Then it all falls apart when somebody was born with an extraordinary --and therefore unpredictable genetic ability who then influenced history so that Seldon’s predictions got derailed.

It all seems so naively quaint now in light of chaos theory and QM developments (that Asimov would have known about – though it would have been fresher in his day). That every subatomic movement will ramp its way up into contingencies of the highest order in very little time leaves any trace of long-term predictive possibility in shambles.

So I guess on your reading then, we are left with the conjecture that natural selection must remain a vague concept, the results of which are beyond science – at least in its particulars.

That’s right, @Jon_Garvey, the most difficult part of the theory of evolution is the inability to properly define fitness, and to predict the course of natural selection. It has often been pointed out that “survival of the fittest” is a tautology, since which phenotype is the fittest is often determined by which one survives. These difficulties make evolution resistant to the kind of mathematical law construction that characterize physics, and a few areas of biology like population genetics.

But does this put Darwinian evolution outside of science? I dont think so. Natural selection is demonstrable in both laboratory experiments and field observations, it can be inferred from fossils and comparisons of related species (as Darwin did), and is clearly a true phenomenon. Yes, it is highly contingent, and the war analogy is a good one, but wars are in fact won or lost, and historians are able with quite a bit of analysis and effort to tease out the causes of the relevant events.

I know quite a few non-biological scientists who dismiss biology as a science because of its resistance to mathematical treatment, and I would love to be able to see many more laws in biology. But maybe physics and chemistry were the easy stuff, and the rules for biology are quite different.

A recent blog post of mine was titled "The Reasonable Ineffectiveness of Mathematics in Biology" in which you posted a similar comment related to biology being more akin to history or philosophy, and I agreed with you in the sense that as we go deeper into the science of biology, we might very well find ourselves needing to use entirely new tools apart from mathematics. What these new tools will look like is anyone’s guess.

But, we are off topic, something that often happens with me, and for which I apologize. By way of bringing things back, I would say that the mathematical imprecision of the theory of evolution does nothing to promote some of the Intelligent Design proposals. The use of probability theory in the early days by Dembski and others was notoriously unconvincing. I think its clear that both mathematical and engineering idea and analogies just do not work for biology, and I am glad that most ID advocates seem to have dropped that approach.

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This post was flagged by the community and is temporarily hidden.

I can accept contingency and speculation as part of the science enterprise, and if biologist need a qualitative notion, such as selection, as part of their paradigm, so be it.

My concern has been focussed on the teaching that evolution is God-ordained. That is simply wrong and I am astonished that people cannot, or do not want to, see the distinction.

Evolution as a theory that has undergone many steps in its evolution (intentional pun :smirk: ) is, and has been, a primitive semantic paradigm of biology. Another treatment of PoS points out that often in the natural sciences (and other areas), justification may be provided on the basis that “we cannot come up with anything better”. Great distinction is also understood between speculation and fact, and if a field cannot provide verification for whatever reason (takes too long, happened in the distant past, too complicated for detailed experimentation, etc,) this too is part and parcel of that paradigm.

Again I restate, such matters and outlooks have been part of the science enterprise - but these matters show ToE lacks the weight of “God-ordained”.

Merv

Ah! Hari Seldon and psychohistory, put off course by the mutant Mule. As you say, in reality it would have been put off course by every turn of human choice, not to mention every chance mutation affecting events for millennia before The Mule. The experience of a century of “scientific” ideologies with theories of history like Marxism has shown that history is not reducible to statistical laws, and that is why history is not included in the sciences.

And that would be my reply to Sy: there is no need to doubt the existence of natural selection to suggest that it is a philosophical or historical, not a scientific, concept. In history, historians’ analysis of causes is recognised to be partial in both the numerical and ideological senses of the word: history is constantly re-written to reflect new insights and (more crucially) new prejudices. And it is increasingly speculative the less documentation remains to us. Scientific substitutes for history like archaeology can give us no more than a few bones on which to impose modern imagination.

And the lessons of history are never more than provisionally applicable to the future: even the historical equivalent of slam dunk natural selection like “white polar bears are adapted to snow” - such as “The allies were bound to win World War II because they used nuclear weapons first” - was immediately negated for the future by the doctrine of Mutually Assured Destruction.

Likewise the labour-intensive efforts that seem to have shown that the melanotic form of the peppered moth actually was genuinely selected during the industrial revolution still leaves the question of why hundreds of other insect species survived without becoming darker - the observation leads to no general law, and therefore puts chance (in its scientific definition of “unpredictability”) back in the driver’s seat of selection.

The bottom line is still, “How much can science (as opposed to philosophy) actually say about contingent events?” And that is relevant to the thread because chance is never a scientific explanation, but an admission of ignorance, for which design is the default explanation theologically.

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@DennisVenema

No argument is sound when it is built on a false assumption. DNA is a natural code which is not arbitrary.

The best example of this is the Apache Code Talkers of World War II. They could speak by radio on the battle field because their language was unique and unwritten.

People often point that out, but they’re mistaken when they do. Tautologies are always true. When a new mutation creates a fitter phenotype (and thus a fitter genotype(*)), the fitter phenotype usually does not survive, as I’m sure you know. So survival of the fittest can’t be a tautology.

(*) Usually, that is. This can get a little tricky depending on exactly how you define the fitness of a genotype and a phenotype.

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That’s the rub, surely: the definition of “fitness” is normally related to differential survival/reproduction. If it isn’t, it’s hard to think of any scientific definition that allows fitness to equate to non-survival. It becomes a bit “Arminian” - “This trait would have been successful if only it hadn’t failed through bad luck.” On what measure? Virtually any trait, including loss of function, can increase survival of the phenotype, in the right circumstances.

To define fitness apart from measuring reproductibe success would seem to require a complete knowledge of each and every circumstance relevant to the organism and its environment, and then to make a value judgement about the value of the trait in question - which would require being God. You surely can’t usefully define a supposedly scientific term like “fitness” on the basis of what an omniscient being would deem advantageous!

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It is defined as the expected, not actual, reproductive success of the trait in question. (Either the absolute success, or success relative to an alternative trait – one can define both absolute and relative fitness.)

Measuring fitness is quite a different thing than fitness itself, and you seem to be confusing them. The fitness of a trait is how reproductively successful it would be if you could generate identical populations many times and measure its average success. Any particular history of reproductive success provides an estimate – a measurement – of the fitness; it isn’t the fitness itself. In the case of a trait at an appreciable frequency in a very large population, like a lab flask of bacteria, the actual history provides a very good estimate of the real fitness. For a new mutation or for a small population, the actual history provides a very noisy measurement.

I’m pretty sure that’s false and it’s certainly irrelevant. False, because I think most possible traits are unconditionally deleterious or (often) nonviable. Irrelevant because fitness is defined on a particular genetic background and in a particular environment. It’s perfectly well understood that the same trait may be beneficial in one environment or on one genetic background and deleterious in another situation.

Again, you’re confusing the fitness itself with accurate measurement of the fitness. Just because I sometimes have no good way of measuring something doesn’t make that something a scientifically useless concept. According to statistical mechanics, the temperature of the air around me is a measure of the average kinetic energy of all of the gas molecules in it. Calculating that average would seem to require a complete knowledge of the velocity of each and every one of septillions of molecules, which is utterly impossible. And yet “momentum” continues to be useful scientific concept anyway, as does the microscopic definition of temperature.

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“Survival of the Fittest” can be measured in an equation, where everything is held equal except as few variables as possible. What is being measured? The absolute number of offspring (over time) vs. the percentage of offspring as a ratio of total offspring produced in the population (over time).

Like offspring produced over time is just like cash disbursements being generated by an investment project … some years are big… some years are low … but the Net Present Value of all these cash outflows can be quantified - - and compared against other projects.

In measuring survival of the fittest - - or really, Natural Selection (still a much better phrase, even though I’m defending survival of the fittest at the moment!) - - each Ancestor represents a PROJECT … and each new descendant (over time) is a variable cash flow.

These various rates of offspring over time can be quantified, and compared back to Year Zero (whatever year you want to make zero).

Assuming you run the experiment (or study) long enough, you can generate statistically significant results … and literally Quantify the most fit individuals!

Ancestors

Of course, but my point was that saying survival of the fittest is a tautology does not remove natural selection from the realm of science. I was not agreeing with the saying. But while the distinction you make between expected and actual measured fitness is valid, it doesnt really answer @Jon_Garvey’s point about predictability of the fitness of any particular phenotype apart from a priori knowledge of the contingent factors interacting with the phenotype. In other words the use of expected fitness in population genetics equations is a theoretical construct that is very useful, but does not address this point of predictability. At least that I can see.

I am uncertain that your description is correct. Temperature is a concept of heat, and devices have been constructed to obtain accurate measurements and these have been standardised. We may seek a theory to equate temperature of any substance, including a gas in an enclosed space, and this takes us to the nature of the particular substance. If we find a theory of gases that is superior to the kinetic theory you refer to, the measurements will not change nor be modified. Also science may deal with different molecular concepts; for example as we approach absolute zero, molecules exhibit differing behaviour.

It sounds as if you conflate NS with something that is measured (even as an approximation) and at other times as an explanation for observations in your field (populations and variations related to their behaviour in niche environment spaces). It is this that makes NS an arbitrary notion that kicks in when one may be unable to account for all of the data, or imo, when there is a lack reproducible data.

Discussions of genotype, and subsequent inferences of a phenotype, become even more obscure to my way of thinking (as a non-biologist), since even the concept of a gene is debated.

When we say God creates and sustains His creation, we refer to the entire creation, and we should treat biology as a portion within that larger framework. Semantics in ToE strike me more as statements of belief specific to biology - or as @Jon_Garvey argues, more of a philosophical commitment, instead of a testable scientific theory.

Steve

This is very largely my point. The scientific aspect of natural selection is the quantifiable (and hence predictable) statistical aggregate of its effects - measured by reproductive success; just as the gas laws quantify the unquantifiable.

The individual movements of molecules in gas, or the individually conceivable usefulness of traits, or alleles, which in fact perish, or are linked inextricably to deleterious traits, or dependent on other variable traits, or all the other confounding factors that make them unmeasurable … these are conceptually useful to science, but are not science themselves, on the very basis that they must be conjectured, not measured. And Brownian motion is a lot easier to conceptualise than the nebulous concept of “fitness” in the abstract.

Statistical predictions about human populations make an assumption, perhaps, that individuals are acting for certain reasons (self interest, for example), but the science is entirely in the statistical pattern. True, you could isolate an individual and examine his motivations in lab conditions, as social psychologists do (perhaps the equivalent of fitness studies like Lenski’s), but then you’re observing an abstracted contingency, not behaviour in the real world. It may confirm that individual human behaviour (like natural selection) exists, but not what fitness is beyond the statistical proxy of reproductive success.

It’s analogous to the idea that scientific laws are the same in all times and places - it’s conceptually useful to science, but a philosophical assumption that is not, itself, part of science.

I probably erred in my last post: it’s less Arminian and more Molinist: “How would X behave if the world were other than it is.” Or if we could do measurements that we can’t, in fact, do. And although in a brief comment I neglected the role of the utterly deleterious trait (unfit = dead), it’s still paradoxical to be working on a concept about traits that are selected by real environments, which can only be examined by mentally abstracting them from real environments to hypothetical conditions that can’t be actualised.

This would be less strange if one were dealing with something one believes to be specific and constant, though unmeasurable, such as the movements of molecules. But “fitness” is an interaction between constantly changing actual variations and a constantly changing actual environment. In other words, it’s contingent in every way, can’t be measured, and has no concrete existence other than a teleological estimate of potential value. Just like history.

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