Home » Intelligent Design » ID Foundations » Answering Petrushka’s assertion (and Dr Rec’s underlying claims): are ID arguments reducible to dubious analogies and after-the-fact painting of targets where arrows happened to hit??

Answering Petrushka’s assertion (and Dr Rec’s underlying claims): are ID arguments reducible to dubious analogies and after-the-fact painting of targets where arrows happened to hit??

In the Pulsars and Pauses thread, Petrushka raised a rather revealing assertion, to which MH, EA and I answered [U/d and GP just weighed in]:

P: >> I find it interesting that when it seems convenient to ID, the code is digital (and subject to being assembled by incremental accumulation). But at other times the analogy switches to objects like motors that are not digitally coded and do not reproduce with variation. >>

I have of course highlighted some key steps in the underlying pattern of thought:

(i) design thinkers think one way or another at convenience

[--> TRANS: we "cannot" happen to have either honestly arrived at views, or warrant for our views . . . ]

(ii) our arguments are based on — shudder — analogies

[--> TRANS: objectors to ID commonly fail to appreciate the difference between deductive reasoning and either classic logical induction or inference to best empirically anchored explanation, nor that inductive, empirically based reasoning is riddled with analogies so by blanket objecting to analogies, one is sawing off the branch on which s/he must sit.]

(iii) the ability to reproduce with incremental variation explains any and every thing

[ --> TRANS:  the issues that complex, multipart functional integration and resulting irreducible complexity forms islands of function that cannot credibly be reached by cumulative incremental variations per a random walk in configuration space, and that a pattern of integrated metabolic capacity and ability to replicate same (even with minor variations) using digital, symbolic code is a case in point of said irreducible complexity, are dismissed without serious consideration.]

I am actually now at the stage where my conclusion (on years of observation) is, that — for many design objectors here at UD and elsewhere — unfortunately, we are dealing with the deeply ideologised, who — absent major attitudinal change  — are unreachable by mere evidence and argument. The only mechanism I know that can trigger such a major shift in perception and attitude, is the sort of patent worldview collapse as happened at the turn of the 90′s with Marxism-Leninism.

So, let us note for record, and as a preventative for others so they will not fall into the same trap.

Now, why am I so stringent in my comments on what we are seeing?

I think a pretty good step is to clip the exchange from here on, that produced this gem and responded to it.

But first, a little context, the Ribosome in action:

The step-by-step process of protein synthesis, controlled by the digital (= discrete state) information stored in DNA

The Ribosome, assembling a protein step by step based on the instructions in the mRNA "control tape"

 

Video:

embedded by Embedded Video

YouTube DirektProtein Translation (DNA Learning Center)

(In reading the below, let us recall at all times that what is to be explained is, among other things, this digital, coded information driven algorithmic, step by step process using molecular machines in the living cell. Ask yourself, on your experience and observation, plus basic common sense and logic: what best explains algorithms, codes and related data structures and organised clusters of complex functional machines? Is there another genuinely credible explanation, and if so, why is it credible?)

Clipping from the exchanges deep in the thread:

____________

Dr Rec [DR]: >> Molecular ‘motors’ are an analogy drawn to human design.

Now you’ve taken the analogy too far.>>

JD: >> Oh? They look like motors, they function like motors, they have the same types of parts that motors have, BUT…. they aren’t motors because we know motors are designed. GOT IT!

I see 4 definitions at dictionary.com that molecular motors fit.>>

{Citing: mo·tor noun  1.a comparatively small and powerful engine, especially an internal-combustion engine in an automobile, motorboat,  or the like.2.any self-powered vehicle.3.a person or thing that imparts motion, especially a contrivance, as a steam engine, that receives and modifies energy from some natural source in order to utilize it in driving machinery.4.Also called electric motor. Electricity . a machine that converts electrical energy into mechanical energy, as an induction motor.}

ATP Synthetase -- a rotary molecular motor that makes the ATP "energy battery" molecules of the living cell, crucial to life (HT: Nobel Foundation)

The rotary, ion flow driven action of the ATP Synthetase enzyme in the mitochondria, as it makes three ATP's from ADP + Phosphate, per revolution; in engineering circles, this would be called a nanotech process unit (Source: Wiki)

MH: >> Take ATP synthase or the flagellum: these molecular motors are composed of simple machines, e.g. wheels & axles (free turning rotor which is constrained in 5 degrees of freedom by a stator imbedded in the membrane), ramps (which transform linear momentum to rotational momentum due to a flow of ions), levers (clutch mechanism to reverse direction of rotation), and screws (as the filament turns it acts as a propeller). Any machine designed and built in the macro world contains some or all of these simple machines. And please note the purpose of such is to transform one form of energy into another. In the case of ATP synthase and the flagellum, the energy of a proton gradient is converted into torque, which is used to generate chemical energy (ATP) and linear motion, respectively. Motors are a physical mechanism by which a form of potential energy is channeled and converted into a form of *useful* energy. This is exactly what we see in the cell, which means we are not speaking in analogies here. These are actual motors, in every sense of the term.

Now I would ask you: do you avoid calling these things “motors” in an effort to avoid the clear, purposeful design implications, or because you are fundamentally ignorant of what motors actually are?>>

P: >> The interesting thing is there are so many different versions of flagella, and so many genomes containing bits and pieces of the code, used for so many different purposes.

There are at least 20 different species of microbes having subunits of the flagellum code.

I find it interesting that when it seems convenient to ID, the code is digital (and subject to being assembled by incremental accumulation). But at other times the analogy switches to objects like motors that are not digitally coded and do not reproduce with variation.>>

MH: >> So what? Do you not realize that in the macro world there are single component parts that are used in a multitude of disparate systems, nuts & bolts being the most obvious example. In fact, a good engineer strives to make the hardware from system to system as standard as possible. The more variation there is in the hardware, the more headaches it causes. Copper wiring is another example, with wiring of the same gage and shielding used all over the place. Standard circuit cards, standard housings for gear boxes, standard junctions, standard belts, and the list goes on forever. Standard components is just as much a sign of design as anything, friend . . . .

Are you suggesting that the flagellum is not a motor because its components are constructed of discrete modular building blocks? If so, that’s asinine. And here’s some news for you: motors designed by humans in the macro world are reproduced also. Weird, huh? And what if the flagellum varies over time; does that plasticity make it not a motor? Nope. Still a motor. >>

KF: >> 1 –> Codes, generally speaking, use symbolic representations [whereby one thing maps to another and per a convention MEANS that], and are inherently discrete state, i.e. digital.

2 –> The DNA-> RNA –> Ribosome –> AA chain for protein system uses just such symbols, and goes through transcription, processing that allows reordering, and translation in a translation device that is also a manufacturing unit for proteins.

3 –> the fact that you find yourself resisting such patent and basic facts is revealing.

4 –> A motor is a functional, composite entity. It is made up from parts, that fit together in a certain specific way, per an exploded view wiring diagram, and when they fit together they do a job.

5 –> As has been pointed out for a long time now, that sort of 3-D exploded view can be converted into a cluster of linked strings that express the implied information, as in Autocad etc.

6 –> However, the point of a motor, is that it does a certain job, converting energy into shaft work, often but not always in rotary form. (Linear motors exist and are important.)

7 –> A lot of was and means can be used to generate the torque [power = torque * speed], but rotary motors generally have a shaft that carries the load, on the output port, and an energy converter on the input port. (Motors are classic two-port devices.)

8 –> Electrical motors work off the Lorentz force [which in turn is in large part a reflection of relativistic effects of the Coulomb force], hydraulic and pneumatic ones, off fluid flows, some motors work off expanding combustion products, etc etc.

9 –> Two of the motors in living forms seem to work off ion flows and associated barrier potentials. Quite efficiently and effectively too.

10 –> Wiki, testifying against known ideological interest:

An engine or motor is a machine designed to convert energy into useful mechanical motion.[1][2] Heat engines, including internal combustion engines and external combustion engines (such as steam engines) burn a fuel to create heat which is then used to create motion. Electric motors convert electrical energy in mechanical motion, pneumatic motors use compressed air and others, such as wind-up toys use elastic energy. In biological systems, molecular motors like myosins in muscles use chemical energy to create motion.

11 –> In short, we see here a recognition of what you are so desperate to resist: there are chemically powered, molecular scale motors in the body, here citing a linear motor, that makes muscles work.

12 –> So, there is no reason why we should suddenly cry “analogy” — shudder — when we see similar, ion powered rotary motors in the living cell.>>

EA:>> No-one is switching analogies because it is convenient. A digital code is an example of complex specified information. An integrated functional system is an example of complex specified information. There are lots of examples. No-one is switching anything.

BTW, analogies are useful and there is nothing wrong with them as far as they go in helping us think through things.

But in this case we don’t even have to analogize. The code in DNA is a digital code, it isn’t just like a digital code. Molecular motors in living cells aren’t just like motors, they are motors.>>

J: >> [To DR] If you don’t like analogies nor the design inference all YOU have to do is actually step-up and demonstrate that stochastic processes can account for what we say is designed.

OR you can continue whining.

Your choice…>>

EA: >> DrREC:

Seriously, do you think some explorer could wander up on Easter Island, and say those look natural? Or would the knowledge of statutes in human design be sufficient?

Excellent. So finally we get nearer to the heart of the matter. DrREC acknowledges that we don’t have to know the exact specification we are looking for. It is enough to have seen some similar systems. In other words, we look at a system of unknown origin and analogize to systems that we do know. This is one important aspect (though not complete) of the way we draw design inferences. We work from what we know, not from what we don’t know. We work from our understanding of cause and effect in the world, not from what we don’t know. And with those tools under our belt, we consistently and regularly infer design as the most appropriate explanation, even when we don’t know the exact specification we will find.

DrREC has no issue with this approach. He thinks it is perfectly reasonable and appropriate. He even suggests above that it is absurd to think otherwise. All correct.>>

DR: >> Funny everyone keeps coming with analogies where the design is not in question! It is almost as if they assume design, and proceed from there.

Oh, right.

The funny thing Eric can’t do it tell us what the independent specifications for protein design are.

But at any rate, there are a couple of things that went unanswered.

Despite the attempts to distract with other analogies, my post at 9.3 [ --> Cf KF at 9.3.1 . . . ]clearly demonstrates IN PRACTICE, that fsci calculations narrowly and subjectively define a design as part of estimating functional space.>>

SA2:>> As opposed to what, using examples in which design is in question? Or examples of things that don’t appear designed?

Most designed things don’t have independent specifications that one can produce or refer to. From where have you invented this requirement?

Your position seems to be that if you have this thing and you don’t know whether it was designed, comparing it to outputs of known design is an inherently invalid approach.

You also suggest that design is such a shockingly unimaginable phenomenon that it must be seen to be believed. Astoundingly, you do not apply this same skepticism to vague, unformed hypotheses of self-organization.

Living things, from the molecular level up, follow the very same patterns as any number of design technologies, except that they appear far more advanced. They do not follow any known patterns of self-organization.

You can lead a horse to water, but you can’t stop it from drinking sand. And you can’t use logic to convince someone to respect logic.>>

DR: >> Yeah. Seriously, the constant insult laced posts that go “Hey look at this human-designed object. Only a moron couldn’t tell it was deigned.” get old fast.

It also isn’t really what you guys are trying to do. You’re trying to make a design inference, based on ruling out natural possibilities through the use of improbability+specification . . . >>

{–> I flag this, as it is an unsubstantiated dismissal by definition, slipped in}

SA2: >> Was your post pre-specified?

Do you have the schematics for your computer? Can you tell me right now how every circuit was specified?

Now you’re saying that you’ll believe it if you see the specification in advance of the implementation. With a wave of the hand you have dismissed the possibility that anything of unobserved origin was designed.

Your whole pulsar tangent [which I omitted . . .  cf the thread]  is one giant strawman. No one is going about randomly trying to infer design to anything and everything for no reason. You’re arguing against the design inference by applying where it obviously doesn’t fit. That’s because you have no valid objection or alternative where it does fit.

Don’t count out, “Just look at it, it must have been designed.” No insult intended, but that’s the voice of common sense. It’s not always right, but common sense plus abundant evidence always beats a hand-waving explanation of ‘something happened, we don’t know what except that we have ruled out intelligence.’>>

DR: >> “Was your post pre-specified?”

Yes, or at least independently. By the rules english grammar and syntax.

“Do you have the schematics for your computer? Can you tell me right now how every circuit was specified?”

No, but I’m sure someone at apple does. And again, with the endless human designs. Bored now.

“Now you’re saying that you’ll believe it if you see the specification in advance of the implementation.”

Or independently. Or in any way that doesn’t draw a target around something in nature, infer that to be the specification, declare it is specified, and deduce design.

“Your whole pulsar tangent is one giant strawman. No one is going about randomly trying to infer design to anything and everything for no reason.”

SETI or NASA might be interested. I think it is right up your alley. Aren’t you design detectors?

“Don’t count out, “Just look at it, it must have been designed.”

That’s really sad for ID.>>

MH: >> Lets go back to the Voynich Manuscript. How is it that *you* don’t know what it says, or even if it says anything at all, yet *you* know for a fact that someone did it? You can just look at it and know. >>

DR: >> The Voynich Manuscript?

Where is the design detection? Are you saying it is natural, or needs to be distinguished from nature.

Some independent specifications:

1) On vellum (human product)
2) Iron ink with quill and pen (human product)
3) Conforms to manuscript and illustrations of the period

Should we continue with this absurdity?>>

SA2:  >> It’s not ID at all. It’s common sense backed up by unmistakable evidence.

ID is science, not common sense.

You’re bored? How many times have I pointed out that the very nature of extrapolation and inference requires us to reason beyond what we observe? If inference is invalid unless the subject is identical to that with which it is compared, then it is invalid in every case except when we do not need it. You’ve just invalidated the concept of inference.

Next you claim that we draw a target around everything in nature. No, we draw a target around around anything that appears to have come about by a process of arranging symbolic information that exhibits planning and foresight to arrive at a functional result. I don’t need to say more than that, such as the amazing attributes or behaviors of any living things. That a thing which reproduces and processes energy is generated from symbolic information is enough. The rest is icing on the cake, lots of it. Reducing function to abstract instructions is intelligent behavior. Yeah, humans do it, and humans are the only one’s we’ve seen do it. But it doesn’t look like humans were in on this one. If you think that somehow nullifies the obvious expression of a similar pattern, you’re free to make whatever excuses you can to deny whatever evidence you wish. But it’s still there.

To say that we draw targets around living things is to suggest that the targets weren’t already drawn. A crab is no different from the rock it sits on.

You’re wrong. Every living thing shares a profound, fundamental difference from every non-living thing. Crabs aren’t funny-shaped rocks that eat and reproduce and run away from bigger things. Every child knows that. That’s the incomprehensible, twisted aberration of reason you are forced to accept when you commit to a conclusion that is diagonally opposed to the evidence.

UB has it right. Instantiation of semiotic information transfer = intelligence. There is no alternative explanation, real, hypothetical, or imaginary. That’s a lifeline from reality. Grab it or don’t.>>

EA: >> We are showing you examples of how design is inferred. These aren’t just unrelated “analogies.” These are live examples of design inference. Set aside for a moment your philosophical bias against examples, analogies, whatever and think through this for a moment.

Under your logic, the only way we can ever know if something was designed is if we already know that what we are looking for is designed. That is entirely circular and, pardon, but frankly absurd. That would mean that it is impossible to ever discover if something is designed. Because in order to discover that, we must have already known the design we were looking for.

The fact of the matter is design is inferred all the time. The only reason you are hung up is that it happens to be in life this time, which, apparently, is philosophically unpalatable.>>

DR:>> for the umpteenth time, if it is INDEPENDENTLY specified (pi, prime numbers) in my pulsat example, that is fine.

I’ve walked through how fsci calculations specify a design post-hoc in the detection of design in explicit detail above. No one seems to want to deal with that, and has resorted to broad chest thumping rhetoric.

Don’t you just SEE the design? Lol.>>

FALSE, let us clip:

KF, 9.3.1: >> By now, it should be clear that you are imposing the a prioris, not me.

Let’s look at your:

I) Use of Durston’s, or any related metric imposes a post-hoc specification-a design in the search for design.

Look at the tables of Fits. There is an estimate based of the length, and number of sequences. But sequences of what? A post-hoc specified design

Really, now. A protein family is observed, and its variability while retaining function is used to quantify the info in the AA sequence. We have a macro-observable state that asks only: does it do job X in living systems. That is more than sufficiently independent.

The redundancy in the strings reduces the bit value from 4.32 per AA residue.

After the reduction, the number of functional bits is totted up. A comparison to threshold then tells us what you obviously do not wish to hear: a functional family that isolated in AA string config space that does a job that specific to the string sequence, is not likely to have been come upon by blind processes.

So we see a selectively hyperskeptical objectopn.

Only problem, this is the same problem as explaining functional text on blind forces.

Cicero could spot the problem c 50 BC, and so can we today, providing we are not blinkered by materialist a prioris.>>

KF, 11.1.1.4 f:  >> . . . do you understand the difference between an observation and an assumption?

Let’s take a microcontroller object program for an example.

Can you see whether the controlled device with the embedded system works? Whether it works reliably, or whether it works partially? Whether it has bugs — i.e. we can find circumstances under which it behaves unexpectedly in non-functional ways, or fails?

Can you see that we can here recognise that something is functional, and may even be able to construct some sort of metric of the degree of functionality?

Now, we observe that the microcontroller depends on certain stored strings of binary digits, and that when some are disturbed by injecting random changes it keeps on working, but beyond a certain threshold, key functions or even overall function break down.

This identifies empirically that we are in an island of function.

[As a live case in point, here at UD, last week I had the experience of discovering a "feature" of WP, i.e. if you happen to try square brackets -- like I am using here -- in a caption for a photo the post display process will fail to complete and posting of the original post, but not comments, will abort. I suspect that's because square brackets are used for certain functional tasks and I happened to half-trigger some such task, leading to an abort.]

Do you now appreciate that we can empirically detect FSCI, and in particular, digitally coded FSCI?

Do you in particular see that the concept of islands of function shaped by the constraints on — in this case — strings of algorithmically functional data elements, naturally leads to the islands of function effect?

That, where we see functional constraints in a context of complex function, this is exactly what we should EXPECT?

For, parts have to fit into a context of a Wicken-type “wiring diagram” for the whole to work, and absent the complex, mutually adapted set of elements wired on that diagram for that case, the system will wholly or partly degrade. That is, we see here the significance of functionally specific, integrated complex organisation. It is a commonplace of the technology of complex, multi-part, functionally integrated, organised systems, that function depends on fairly specific organisation, with a bit of room for tolerance, but not very much relative to the space of configurational possibilities of a set of components.

And, we may extend this fairly simply to the case where there are no explicit strings, by taking the functional diagram apart on an exploded view, and reducing the information of that 3-D representation and putting it in a data structure based on ordered, linked strings. That is what Autocad etc do. And of course the assembly process is generally based on such an exploded view model.

(Assembly of a complex functional system based on a great many parts with inevitable tolerances is in itself a complex issue, riddled with the implications of tolerances of the many components. Don’t forget the cases in the 1950′s where it was discovered that just putting a bolt in the wrong way on I think it was the F 86, could cause fatal crashes. Design for one-off success is much less complex than design for mass production. And, when we add in the issue in biology of SELF-assembly, that problem goes through the roof!)

In short, we can see how FSCO, FSCI, and irreducible complexity emerge naturally as concepts summarising a world of knowledge about complex multi-part systems.

These things are not made-up, they are instantly recognisable and understandable to anyone who has had to struggle with designing and building or simply troubleshooting and fixing complex multi-part functional systems.

BTW, this is why I can only shake my head when I hear talking points over Hoyle’s fallacy, when he posed the challenge of assembling a jumbo jet by passing a tornado through a junkyard.

Actually — and as I discussed recently here in the ID foundations series (notice the diagram of the instrument), we may take out the rhetorical flourish and focus on the challenge of assembling a D’Arsonval galvanometer movement based instrument in its cockpit. Or even the challenge of screwing together the right nut and bolt in a bowl of mixed parts, by random agitation.

And, BTW, the just linked shows how Paley long since highlighted the problem with the dismissive “analogy” argument, when in Ch 2 of his work, he pointed out the challenge of building a self-replicating watch:

Suppose, in the next place, that the person who found the watch should after some time discover that, in addition to all the properties which he had hitherto observed in it, it possessed the unexpected property of producing in the course of its movement another watch like itself – the thing is conceivable; that it contained within it a mechanism, a system of parts — a mold, for instance, or a complex adjustment of lathes, baffles, and other tools — evidently and separately calculated for this purpose . . . .
The first effect would be to increase his admiration of the contrivance, and his conviction of the consummate skill of the contriver. Whether he regarded the object of the contrivance, the distinct apparatus, the intricate, yet in many parts intelligible mechanism by which it was carried on, he would perceive in this new observation nothing but an additional reason for doing what he had already done — for referring the construction of the watch to design and to supreme art . . . . He would reflect, that though the watch before him were, in some sense, the maker of the watch, which, was fabricated in the course of its movements, yet it was in a very different sense from that in which a carpenter, for instance, is the maker of a chair — the author of its contrivance, the cause of the relation of its parts to their use.
[Emphases added. (Note: It is easy to rhetorically dismiss this argument because of the context: a work of natural theology. But, since (i) valid science can be -- and has been -- done by theologians; since (ii) the greatest of all modern scientific books (Newton's Principia) contains the General Scholium which is an essay in just such natural theology; and since (iii) an argument's weight depends on its merits, we should not yield to such “label and dismiss” tactics. It is also worth noting Newton's remarks that “thus much concerning God; to discourse of whom from the appearances of things, does certainly belong to Natural Philosophy [i.e. what we now call “science”].” )]

In short, the additionality of self replication of a functioning system is already a challenge. And Paley was of course too early by over a century to know what von Neumann worked out on his kinematic self-replicator that uses digitally stored information in a string structure to control self assembly and self replication. (Also discussed in the just linked onlookers.)

On the strength of these and related considerations, I then look at say Denton’s description (please watch the vid tour then read) of the automated multi-part functionality of the living cell:

To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometers in diameter [[so each atom in it would be “the size of a tennis ball”] and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. On the surface of the cell we would see millions of openings, like the port holes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings we would find ourselves in a world of supreme technology and bewildering complexity. We would see endless highly organized corridors and conduits branching in every direction away from the perimeter of the cell, some leading to the central memory bank in the nucleus and others to assembly plants and processing units. The nucleus itself would be a vast spherical chamber more than a kilometer in diameter, resembling a geodesic dome inside of which we would see, all neatly stacked together in ordered arrays, the miles of coiled chains of the DNA molecules. A huge range of products and raw materials would shuttle along all the manifold conduits in a highly ordered fashion to and from all the various assembly plants in the outer regions of the cell.

We would wonder at the level of control implicit in the movement of so many objects down so many seemingly endless conduits, all in perfect unison. We would see all around us, in every direction we looked, all sorts of robot-like machines . . . . We would see that nearly every feature of our own advanced machines had its analogue in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of components, error fail-safe and proof-reading devices used for quality control, assembly processes involving the principle of prefabrication and modular construction . . . . However, it would be a factory which would have one capacity not equaled in any of our own most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours . . . .

Unlike our own pseudo-automated assembly plants, where external controls are being continually applied, the cell’s manufacturing capability is entirely self-regulated . . . .

[[Denton, Michael, Evolution: A Theory in Crisis, Adler, 1986, pp. 327 – 331. This work is a classic that is still well worth reading. Emphases added. (NB: The 2009 work by Stephen Meyer of Discovery Institute, Signature in the Cell, brings this classic argument up to date. The main thesis of the book is that: "The universe is comprised of matter, energy, and the information that gives order [[better: functional organisation] to matter and energy, thereby bringing life into being. In the cell, information is carried by DNA, which functions like a software program. The signature in the cell is that of the master programmer of life.” Given the sharp response that has provoked, the onward e-book responses to attempted rebuttals, Signature of Controversy, would also be excellent, but sobering and sometimes saddening, reading.) ]

We could go on and on, but by now the point should be quite clear to all but the deeply indoctrinated.

Namely, we have every reason to see why complex, integrated functionality on many interacting parts naturally leads to islands of functional configurations in much wider spaces of possible but overwhelmingly non-functional configurations. (And, this thought exercise will rivet the point home, in a context that is closely tied to the statistical underpinnings of the second law of thermodynamics.)

Clearly, it is those who imply or assume that we have instead a vast continent of function that can be traversed incrementally step by step starting form simple beginnings that credibly get us to a metabolising, self-replicating organism, who have to empirically show their claims.

It will come as no surprise to the reasonably informed that the original of cell based life bit is neatly snipped out of the root of the tree of life, precisely because after 150 years or so of speculations on Darwin’s warm little pond full of chemicals and struck by lightning, etc, the field of study is in crisis.

Similarly, the astute onlooker will know that he general pattern of the fossil record and of today’s life forms, is that of sudden appearance, stasis, sudden disappearances and gaps, not at all the smoothly graded overall tree of life as imagined. Evidence of small scale adaptations within existing body plans has been grossly extrapolated and improperly headlined as proof of what is in fact the product of an imposed philosophical a priori, evolutionary materialism. That is why Philip Johnson’s retort to Lewontin et al was so cuttingly, stingingly apt:

For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.”

. . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. [--> those who are currently spinning toxic, atmposphere poisoning, ad homiem laced talking points about "sermons" and "preaching" and "preachers" need to pay particular heed to this . . . ] The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

So, where does this leave the little equation accused of being question-begging:

Chi_500 = I*S – 500, bits beyond the solar system threshold

1 –> The Hartley-Shannon information metric is a standard measure of info carrying capacity, here being extended to cover a case were we must meet some specificaitons, and pass a threshold of complexity.

2 –> the 500 bit threshold is sufficient to isolate the full Planck Time Quantum State [PTQS] search capacity of our solar system’s 10^57 atoms, 10^102 states in 10^17 or so seconds, to ~ 1 in 10^48 of the set of possibilities for 500 bits: 3 * 10^150.

3 –> So, before we get any further, we know that we are looking at so tiny a fractional sample that (on well-established sampling theory) ANYTHING that is not typical of the vast bulk of the distribution is utterly unlikely to be detected by a blind process.

4 –> The comparison to make this familiar is, to draw at chance or at chance plus mechanical necessity, a blind sample of size of one straw from a cubical hay-bale 3 1/2 light days across, which could have our solar system out to Pluto in it [about 1/10 the way across]. With maximal probability — all but certainty, such a sample will pick up straw.

5 –> The threshold of complexity, in short is reasonable, and if you want to challenge the solar system (our practical universe which is 98% dominated by our Sun, in which no OOL is even possible . . . ) then scale up to the observed cosmos as a whole, 1,000 bits. (The calculation for THAT hay bale would have millions of cosmi comparable to our own lurking within and we would have the same result.)

6 –> So, the only term really up for challenge is S, the dummy variable that is set to 0 as default, and if we have positive, objective reason to infer functional specificity or more broadly ability to assign observed cases E to a narrow zone T that can be INDEPENDENTLY described (i.e. the selection of T is non-arbitrary, we have a definable collection in the set theory sense and a set builder rule — or at least, a separate objective criterion for inclusion/exclusion) then it can be set to 1.

7 –> The S = 0 case, the default, is of course the blind chance plus necessity case. The assumption is that phenomena are normally accessible by chance plus necessity acting on matter and energy in space and time.

8 –> But, in light of the sort of issues discussed above (and over and over again elsewhere over the course of years . . . ), it is recognised that certain phenomena, especially FSCI and in particular dFSCI — like the posts in our thread — are in fact only reasonably accessible by intelligent direction on the gamut of our solar system or observed cosmos.

9 –> Without loss of general force, we may focus on functional specificity. We can objectively, observationally identify this, and routinely do so.

10 –> So, what the equation ends up doing is to give us an empirically testable threshold for when something is functionally specific, information-bearing and sufficiently complex that it may be inferred that it is best explained on design, not chance plus necessity.

11 –> Since this is specific and empirically testable, it cannot be a mere begging of the question, it is inviting refutation by the simple expedient of showing how chance and necessity without intelligent guidance or starting within an island of function already — that is what Genetic Algorithms do, as the infamous well-behaved fitness function so plainly shows — can give rise to FSCI.

12 –> The truth is that the talking point storm and assertions about not sufficiently rigorous definitions, etc etc etc, are all because the expression handily passes empirical tests. the entire Internet is a case in point, if you want empirical tests.

13 –> So, if this were a world in which science were done by machines programmed to be objective, the debate would long since have been over as soon as this expression and the underlying analysis were put on the table.

14 –> But, humans are not machines, and so recently the debate talking point storm has been on how this eqn is begging questions or is not sufficiently defined to suit the tastes of those committed to a priori evolutionary materialism, or how GA’s — which start inside islands of function! — show how FSCI can be had without paying for it with the hard cash of intelligence. (I won’t bother with more than mentioning the sort of hostile, hateful attack that was so plainly triggered by our blowing the MG sock-puppet campaign out of the water. Cf link here for the blow by blow on how that campaign failed.)

15 –> To all this, I simply say, the expression invites empirical test and has billions of confirmatory instances. Kindly show us a clear case that — without starting on an existing island of function — shows how FSCI, especially dFSCI (at least 500 – 1,000 bits), emerges credibly by chance and necessity, within the scope of available empirical resources.

16 –> For those not familiar with the underlying principle, I am saying that the expression is analytically warranted per a reasonable model and is directly subject to empirical test with a remarkable known degree of success, and so far no good counter-examples. So, we are inductively warranted to trust it absent convincing counter-example.

17 –> Not as question begging a prioris, but as per the standard practice of science where laws of science and scientific models are provisionally warranted and empirically reliable, not necessarily true beyond all possibility of dispute.

18 –> Indeed, that is why the laws of thermodynamics can be formulated in terms that perpetual motion machines of the first, second and third kind will not work. So far quite empirically reliable, and on reasonable models, we can see why. But, provide such a perpetual motion machine and thermodynamics would collapse.

____________

So, Dr Rec, a fill in the blanks exercise:

your empirical counter-example per actual observation is CCCCCCC, and your analytical explanation for it is WWWWWWW

If you cannot directly fill in the blanks, we have every reason to accept the Chi_500 expression on the normal terms for accepting a scientific result, no matter how uncomfortable this is for the a priori materialists.>>

EA:>>. . .  so you agree with Dembski that there is an independence requirement. We all agree.

But why on earth do you think the specification has to be known and set out beforehand?

I’ve asked this several times. Is it possible to crack a code that was previously unknown and therefore realize it was designed? All I can see from your various responses is one of two possibilities: either you are saying, yes it is possible because (i) we know it was designed in the first place (that is what it sounded like you were saying, thus my comment in 22), or (ii) we’ve seen similar systems (in other words, we analogize to our prior experience).

So which is it? Do we have to know beforehand the specification, or can we analogize to our prior experience and thus recognize the specification when it is discovered?

Let me know which of these two options you support, and then we can continue the discussion. If you support (ii) and not (i), then I apologize for having misunderstood you and withdraw my comment 22.>>

EA: >>I should add that it is funny that so much energy is being spent denying that there is specification in living cells. Specification, in terms of functional complex specified information, is really a no brainer as it relates to many cellular systems. Indeed, most Darwinists and other materialists admit the specification because it is so obviously there. What they then spend their energies on is attempting to show that the specification isn’t really that improbable (inevitability theorists), or that it comes about through some emergent process (emergent theorists), or alternatively, that while wildly improbably “evolution” can overcome it through the magic of lots of time and errors in replication (Dawkins et al.).

Don’t get me wrong, I love a good discussion about specification. Just seems funny that it is being so strenuously denied when so many evolutionists admit it as a given.>>

STRAWMAN ALERT:

DR: >> Could you provide a reference where a “Darwinist” acknowledges a specification by a designer in life? I’m really puzzled at the who the hell these “so many evolutionists admit it as a given” are.

This is almost a fourth grade playground lie you tell the kid you want to do something idiotic-everyone’s doing it. Why won’t you? All the other Darwinists are admitting design specifications…come on, just admit it….please….

“Specification, in terms of functional complex specified information, is really a no brainer”

So, in a few days, fsci has gone from being a calculation to a “no brainer” Next I’ll here the “only an idiot would deny it.” Is this science to you? Next paper, I’ll write “this is a no brainer, proof not required.”>>

EA:>> Do I have a quote from a Darwinist who says that they have analyzed cellular systems from a standpoint of design and believe the cellular systems meet the specification criteria outlined by intelligent design theorists Dembski, Meyer, and others? Of course not. They don’t use that terminology. But they do acknowledge the same point, in different words.

Starting with Darwin, who marveled at the wonderous “contrivance” of the eye, the primary goal has not been to deny that life contains complex, functionaly-integrated systems, but to argue that they can come about through natural processes.

Dawkins went so far as to define biology as the “study of complicated things that give the appearance of having been designed for a purpose.” What did he mean by that? Precisely that when we look at living systems, the appearance of design jumps out at us. Why is that; what is this appearance of design? It is because of the integrated functional complexity — precisely one of the examples of complex specified information. It is the fact that in our universal and repeated experience when we see systems like these they turn out to be designed. Dawkins isn’t arguing against the appearance of design or that such information doesn’t exist in biology (the specification); rather he argues that the appearance need not point exclusively to design because evolution can produce it through long periods of time and chance changes.

If I recall correctly, Michael Shermer is the one who has even taken to arguing in debates that, yes, life is designed, but, he adds, the design comes about without a designer, through natural processes.

Can complex specified information be calculated? Sure it can (particularly in cases where we are dealing with digital code) and there are interesting cases and good work to be done in identifying and calculating what is contained in life. But that there is a large amount of complex specified information in cells, absolutely; most everyone realizes it is there. The entire OOL enterprise is built upon trying to figure out how the complex specified information — which everyone recognizes is there — could have arisen.

The recognition that life contains digital code, symbolic representations, complex integrated functional systems is pretty universal. That is complex specified information. So, yes, most Darwinists don’t spend their energy arguing against complex specified information in life. Rather they spend their energies trying to explain how it could have arisen through purely natural causes.>>

GP:>>

I am not sure what the point of the debate is now. So, just to start, I would restate a couple of importa points here, and kindly ask you to update me about the main problems you see in the discussion here:

a) In functionally specified information, and especially dFSCI, the specification can (and indeed is) explicited “post-hoc”, from the observed information in the object. The function is defined objectively, and obviously defines a functional subset of the search space (for that specific function). However, the functional target must be computed in some way, because it includes all the sequences that confer the function, as defined.

b) In the example of a signal “writing” the digits of pi in binary code, the design inference IMO is completely justified (if the number of digits in the signal is great enough). That would be an example of dFSCI. the digits of p in binary form are a good example of dFSCI, and of “post hoc” specification.

c) Still, those who infer design in that case have the duty to seriously consider if the pattern could be generated by some law, that is by some known necessity driven system, even with possible chance contributions. In this case, as far as I know, there is no known physic system that could generate the binary code for the digits of such a fundamental mathemathical constant. So I refute a necessity explanation, at the present state of knowledge.

d) Obviously, it remains possible that some physical system, by necessity or necessity + chance, could generate that output, but, as far as I know, there is no logical reason to believe that this is true, and no empirical evidence in favor of that statement. That’s why that possibility is not at present a valid scientific explanation of the origin of our signal.>>

______________

Sometimes, it is in dialogue that we see what is really going on.

What is astonishing above, is that across the course of the discussion, DR ended up acknowledging that the issue was that we have a question of independent specification of a sufficiently complex [so, not likely on a chance based random walk] outcome. He has never acknowledged that this is precisely the set of criteria used to routinely infer to an alternative hypothesis in many cases of statistical inference testing.

And, when he has been presented with a quantification of the inference [ADDED: and an explanation of why S would be 0/1], he consistently has accused such of being mere analogies, or subjective, or painting the target after the fact.

Sorry, it is patent that what we see in the living cell is digital code fed into effecting machinery, and in a context where derangement of the code leads to loss of function in sufficiently many cases that it is quite patent that we are dealing with deeply isolated islands of function. This is instantiation, not dubious analogy.

Similarly, when  I see where those arrows just happened to hit — codes,  complex algorithms, sophisticated nanomachines, motors, etc, I think that a common sense, unbiased view would agree that such is suggestive of deliberate aiming, not of painting a target after the fact.

Thirdly, is should be quite clear that — despite all the dismissive rhetorical declarations to the contrary, in the expression for Chi_500, the default, 0, is precisely what the objectors wish [that chance and necessity explain a given phenomenon -- and pulsars FYI, DR, were so explained, so S = 0], and there is always a specific, good reason for moving it to 1 in cases that are relevant. For instance, as was given already, that square brackets block posts problem for WP, shows an island of function. So did the rocket that had to be destroyed on launch because a comma was wrong, and we definitely do see that in many living systems, variations in the code pushed through the ribosome will lead to breakdown of function. In short, the objections are specious and amount to little more than we do not like where this is pointing.

Let’s ask: your observationally anchored explanation for the origin of the codes [thus, machine language], algorithms, and organised molecular machines and systems for protein synthesis and ATP synthesis, just for starters, is XXXXXX.

(Onward, try explaining the origin of say whales, bats, echolocation etc, or human language capacity by step by step observationally anchored, FUNCTIONAL incremental changes to a relevant initial animal. And, show us some relevant concrete evidence — preferably published — that documents the observed origin of such FSCI by chance plus necessity without intelligent intervention. Hurling elephants by pointing to piles of papers behind paywalls will not do, nor will literature bluffs based on lists of papers or allusions to authors or vague summaries of claims. Give us the OBSERVATION-anchored evidence. We have a whole Internet full, as a first example, on how FSCI is routinely the product of intelligence, how we can observe that we are dealing with functionally specific information that conforms to independent things like language and context, or algorithms that have to work, etc etc. , and how we see that as a rule such functions come in islands, i.e we cannot reasonably argue that we can get to first function or leap from one island to a sufficiently distant one,  by a chance based random walk to give us high contingency, on the gamut of the solar system or the observed cosmos, once we are past 500 – 1,000 bits.)

Can you fill in the blanks on repeatable observed spontaneous chance plus necessity emergence?

If you can, S will revert to 0. But if not, we have very good reason to hold that S = 1.   END

  • Delicious
  • Facebook
  • Reddit
  • StumbleUpon
  • Twitter
  • RSS Feed

70 Responses to Answering Petrushka’s assertion (and Dr Rec’s underlying claims): are ID arguments reducible to dubious analogies and after-the-fact painting of targets where arrows happened to hit??

  1. KF:

    Thank you for trying to put some order in this chaos!

    Excellent work, as always. :)

  2. Let’s see if this helps!

  3. OK if ID arguments reducible to dubious analogies and after-the-fact painting of targets where arrows happened to hit, what the heck are “their” arguments reducible to?

    Nonsensical and unscientifc spewage.

  4. As the illustrations and vid show, dem arrows does hit some very interesting non-targets, mon!

  5. What I find most disturbing is how I initially stepped into the conversation by stating how maddening and pointless it was to argue with “brainwashed” and “incorrigible” individuals, then proceeded to argue with them with much fervor.

    I’m not sure why that is.

  6. I don’t mean to be insulting. Sometimes when I can’t drive a nail I just get a bigger hammer. The trouble is that people aren’t nails. It’s never a good approach.
    Sorry about that.

  7. Scott, I don’t recall you being insulting. Big hammer, maybe; but if you’ve ever read how Luther dealt with Erasmus (Bondage of the Will), our discourse with DrREC and P seems rather on target in regards to hammer size. And let’s not forget the words Christ had for the Pharisees (Ye fools and blind!)

  8. …both Rec and Pet stubbornly ignore the fact that there are specifications in biology that have nothing whatsoever to do with human-imputed specification, and certainly not analogies. In fact the entirety of biology is entirely dependent on them. They are the representations and protocols that make the transfer of information possible from the very start.

  9. This succinctly points out DrREC’s full and clear application of the design inference in everyday life and his absolute refusal to apply it to biology in the exact same way. Very telling. KF said the exact same thing, but it puts it in a fairly bright light with REC’s comments directly in the foreground.

  10. Wait just a minute, gpuccio. Are you sure that kairosfocus infused the order. Maybe the order just “emerged” from the chaos, you know, Kauffman style. :)

  11. Yes indeed! Luther may not have persuaded Erasmus, but he convinced many more of us how important the issue was!

  12. 12

    Thanks, Jon. “Bondage of the Will”, in my opinion, is probably one of the most important books any Christian needs to read, read and read again until it is completely absorbed.

  13. Eric:

    Well, I have inferred, some time ago, that KF is a conscious intelligent agent :) . I cannot prove that deductively however, I am afraid.

  14. And then Calvin’s “Bondage and Liberation of the Will”. You can never get too much grace.

  15. Just to introduce some argument, I would say that we should concentrate a moment on the immediate, intuitive meaning of functional specification.

    It is rather obvious that any function, however defined, needs some information to be implemented.

    Now, the concept of the function in itself can be simple: i can concieve of some molecule that accelerates a specific biochemical reaction. Let’s say I eork with that reaction in my lab, and I am bored that it is very slow, and gives very limited quantities of its final products. So I think, in my conscious imagination: how beautiful would it be if I could add something that accelerates the reactio 100 times!

    That is the desire, an intention applied to some cognitive concept, but the concept itself is very simple.

    And yet, nothing but a conscious agent could have that desire, that concept. Computers and machine have no feeling, no desire, no intent. And no cognitive representations.

    But that is not enough. To realize my intent, I have to find the information to build the enzyme. And that is not simple at all (indeed, it is so complex that we cannot still do it).

    But the point is, can I have the function if I don’t know the information? No.

    That is the essebce of FSCI. The information needed to have a function.

    The rest are technical details. But the concept is simple, powerful and fundamental. It should be obvious to anybody. The resistance to that simple concept can be explained only by a contrary intent: the concequences of that simple concept are uncomfortable for many conscious, purposeful agents in modern culture.
    ire,

  16. 16

    I have been meaning to dig into “Freedom of the Will” by Jonathan Edwards, but I feel like I should read “Resurrection of the Son of God” by Wright first. I hear it’s quite compelling. But I don’t have time for that tome at this point in my life, that’s for sure.

    And I know that grace is something that is continuous, but most of the time I find myself in the same boat as Bunyan; long stretches of fear and doubt with only occasional touches of grace and comfort.

  17. 17

    And yet, nothing but a conscious agent could have that desire, that concept. Computers and machine have no feeling, no desire, no intent. And no cognitive representations.

    Side note: I’ve been thinking about this lately… It seems to me that desire really is the essence of awareness. To have a “will” is to be a conscious agent. No desire, no awareness. So when AI folks wonder about how to make a computer self aware, what they really need to be talking about is giving the machine “desires”… but how in the world would you do that? What exactly is a desire? It seems to me that really is the essence of the soul. It’s more than just programmed responses to inputs; it’s a state in and of itself, and it is our desires from which all our actions flow.

  18. M. Holcumbrink:

    I agree with you, but indeed also cognition and meaning have no meaning out of consciousness, Indeed, I do believe that cognition and feeling, meaning and desire, are in reality two fundamental, and complementary, aspects of the consious I. Ant representatio of the self is at the same time a cognition and a feeling response to that cognition, a map of reality and at the same time an intent to react to that map.

    After all, what is the pursue of knowledge, if not a desire for truth?

  19. I don’t have a lot of time tonight, but a question to frame my response:

    Do you believe this:

    http://www.allpar.com/mopar/im.....utaway.jpg

    and this:

    http://www.ebsa.org/npbsn41/pictures/myosin.gif

    Share the same specification?

  20. 20

    DrREC, I think the first link is broken

  21. DrREC:

    In some way, copying and pasting the first link, I have reached the image.

    So, just to explain to others, the first image is a car engine, while the second should be the 3D structure of myosin.

    So, they could share a vague specification in the form of: “any machine that transforms some form of chemical energy into some form of mechanical energy”.

    That specification is a correct functional specification, according to my definition of FSCI, but is of little utility, because too generic.

    A car engine os certainly a beautiful machine, but it would be, for many reasons, useless in the ocntext of a living cell, and it’s difficult to see how it could be naturally selected by a reproductive advantage :) .

    Regarding myosin, I paste here te general characterization from Wikipedia:

    “Myosins comprise a family of ATP-dependent motor proteins and are best known for their role in muscle contraction and their involvement in a wide range of other eukaryotic motility processes. They are responsible for actin-based motility. The term was originally used to describe a group of similar ATPases found in striated and smooth muscle cells.[1] Following the discovery by Pollard and Korn of enzymes with myosin-like function in Acanthamoeba castellanii, a large number of divergent myosin genes have been discovered throughout eukaryotes. Thus, although myosin was originally thought to be restricted to muscle cells (hence, “myo”), there is no single “myosin” but rather a huge superfamily of genes whose protein products share the basic properties of actin binding, ATP hydrolysis (ATPase enzyme activity), and force transduction. Virtually all eukaryotic cells contain myosin isoforms. Some isoforms have specialized functions in certain cell types (such as muscle), while other isoforms are ubiquitous. The structure and function of myosin is strongly conserved across species, to the extent that rabbit muscle myosin II will bind to actin from an amoeba.[2]

    Domains:

    Most myosin molecules are composed of a head, neck, and tail domain.
    The head domain binds the filamentous actin, and uses ATP hydrolysis to generate force and to “walk” along the filament towards the barbed (+) end (with the exception of myosin VI, which moves towards the pointed (-) end).
    the neck domain acts as a linker and as a lever arm for transducing force generated by the catalytic motor domain. The neck domain can also serve as a binding site for myosin light chains which are distinct proteins that form part of a macromolecular complex and generally have regulatory functions.
    The tail domain generally mediates interaction with cargo molecules and/or other myosin subunits. In some cases, the tail domain may play a role in regulating motor activity.”

    So,first of all we can see that myosin is a multi-domain protein, that performs many specific functions.

    To simplify things, I suppose that we could take as main specification the function of the head domain:

    “any protein that, in a cell, binds the filamentous actin, and uses ATP hydrolysis to generate force and to “walk” along the filament”

    That is a functional definition specific enough for the cell environment in general, and that takes into account the fact that myosin is part of an irreducibly complex system, including at least actin to generate mechanical energy.

    I suppose that the car engine is not included in that definition.

    As I have said many times, the computation of FSCI depends critically on our definition. A vague and generic definition makes the computation almost impossible, and anyway useless. A specific definition allows to compute the complexity much more easily and specifically. The second definition is probably good enough to allow a computation of dFSCI for the superfamily of myosin head domain, for example by the Durston method.

    I hope that answers your question.

  22. Do they share the same specification?

    I couldn’t get to the first link, but assuming it is a car engine, as gpuccio found, then I would say not. Specification is not just a general statement of generic function (e.g., a motor, or something that moves things). It is all the information (whether digital, or embodied in the materials, physical positioning, integration of parts, and so on) needed to fully instantiate the system. Let’s say, kind of a detailed engineering description.

    gpuccio: “As I have said many times, the computation of FSCI depends critically on our definition. A vague and generic definition makes the computation almost impossible, and anyway useless. A specific definition allows to compute the complexity much more easily and specifically.”

    Well stated.

  23. Dr Rec:

    Pardon, I suggest that you take a look here, on the [augmented] two-port analysis of transduction systems, with a particular focus on cases where the output port is concerned with mechanical energy, i.e. shaft work. Of the six degrees of freedom normally available to a 3-d object [3 x translational, 3 x rotational] as a rule the system will constrain 5, leaving the desired mechanical output as a rotation of a definite axis, or a linear motion. Such a device will normally have a mounting that serves to lock out the undesired degrees of freedom. (BTW, often, this is not trivial, e.g. in rockets, this gives rise to some of the most difficult headaches, starting from the challenge of supporting a floppy and breakable broom-stick on the tip of the proverbial finger, but one that is pushing the stick up quite forcefully . . . )

    Motors can be understood in terms of [augmented] two ports, where at the input end of the device, a gated power flow is used to drive a mechanical output, rotary or linear.

    Bridging the two is a process of energy conversion, perhaps by a transduction or by a more complex, active process.

    There will of course normally be energy losses, which can be inserted into the analytical framework as coupled one-ports, etc.

    With this outline framework in mind, we may then see that the car engine or the rocket or jet engine, or the mounted electric motor, and the myosin, or the flagellum or ATP synthetase, face some very significant in-common issues and constraints, with some in-common targets.

    Myosin is of course a part of the muscular system, and so is a linear motor. It will be helpful to consider a moment on what such a motor is, perhaps with the aid of a simple case, the dynamic loudspeaker. In that case, the Lorentz force derived action is adapted to producing controlled piston-like action of a cone adapted to create sound waves. The trick of course is to have a helical coil in a ring magnet, so that the motive force is now back-forth — and coupled to the cone flexibly, not rotary. In general, as Wiki summarises for linear motors (in an electrical context):

    A linear motor is an electric motor that has had its stator and rotor “unrolled” so that instead of producing a torque (rotation) it produces a linear force along its length. The most common mode of operation is as a Lorentz-type actuator, in which the applied force is linearly proportional to the current and the magnetic field [F = q*v x B]

    Many designs have been put forward for linear motors, falling into two major categories, low-acceleration and high-acceleration linear motors. Low-acceleration linear motors are suitable for maglev trains and other ground-based transportation applications. High-acceleration linear motors are normally rather short, and are designed to accelerate an object to a very high speed, for example see the railgun.

    They are usually used for studies of hypervelocity collisions, as weapons, or as mass drivers for spacecraft propulsion. The high-acceleration motors are usually of the AC linear induction motor (LIM) design with an active three-phase winding on one side of the air-gap and a passive conductor plate on the other side. However, the direct current homopolar linear motor railgun is another high acceleration linear motor design. The low-acceleration, high speed and high power motors are usually of the linear synchronous motor (LSM) design, with an active winding on one side of the air-gap and an array of alternate-pole magnets on the other side. These magnets can be permanent magnets or energized magnets. The Transrapid Shanghai motor is an LSM . . .

    When we move to the molecular nanotech of life, we find similar devices, that face the same two-port challenges and do so quite effectively. As already highlighted:

    1: The flagellum is a rotary, reversible motor run by ion flows, with stator mounted in a membrane, a rotor coupled to a shaft and further coupled to a whip-like filament that delivers propeller action.

    2: ATP synthetase is quite similar in overall architecture, but applied to a specific case, i.e. it is a process unit that makes ATP using ion flows across a membrane in the mitochondria. The stator is mounted in the membrane, and the rotor is coupled to a subsystem that makes three ATP’s per cycle.

    3: Myosin is a key component of a linear actuator, the muscle, its basic action (clipping Wiki for a short summary) being:

    Multiple myosin II molecules generate force in skeletal muscle through a power stroke mechanism fuelled by the energy released from ATP hydrolysis.[3] The power stroke occurs at the release of phosphate from the myosin molecule after the ATP hydrolysis while myosin is tightly bound to actin. The effect of this release is a conformational change in the molecule that pulls against the actin. The release of the ADP molecule and binding of a new ATP molecule will release myosin from actin. ATP hydrolysis within the myosin will cause it to bind to actin again to repeat the cycle. The combined effect of the myriad power strokes causes the muscle to contract.

    In short, we have here molecular nanotech motors, made up from multiple, closely integrated parts, that carry out crucial tasks. Bacteria need to be able to move and flagella help them do so. Without ATP, C-chemistry cell based life would fail. And, muscular action is a key to the motility of animals.

    The challenge for objectors to the design inference is that:

    i: motors have to have that gated power flow input, to give rise to the output,

    ii: they must be properly mounted to deliver controlled motion, and

    iii: must be properly joined to a load in a way that uses transduction/energy conversion processes to achieve an end result.

    We thus see multiple, closely coupled parts working together to an evident technical goal, and implying a supportive control and energy/power flow system (with waste handling implied). Motors, in short, are inherently irreducibly complex and therefore are empirically unreachable by blind incremental accidental processes on the gamut of search resources. In short, we see here an isolated island of function problem, to explain the origin of key motors in life systems, and in the case of ATP Synthetase, this is foundational to life processes, as the polymer chemistry involved in life is so overwhelmingly endothermic.

    The only reasonable, empirical observation supported answer to this conundrum, is that such entities are just what they appear to be: elegantly designed artifacts. (Motors have but one empirically observed, analytically credible source: designers.)

    Of course, those who are insistent on a priori materialism will find a clever objection somehow, but they must be held to a key criterion of credibility: can you show on observational warrant and on analysis of the search space needle in the haystack challenges, that such a mechanism is plausible, other than by imposing question-begging materialist a prioris?

    Failing such a demonstration of why it is credible to make S = 0, we have excellent grounds to infer that S = 1 for this case, in the expression:

    Chi_500 = I*S – 500, bits beyond the threshold

    And given the required information to build and regulate the required proteins to make these nanotech motors, and to assemble the devices, we will easily run past 500 bits.

    That is, we have excellent reason to see that Chi_500 exceeds 1, i.e. to infer that the best explanation for such entities in life forms is design.

    GEM of TKI

  24. …long stretches of fear and doubt with only occasional touches of grace and comfort.

    Sometimes that’s theological, and sometimes it’s psychological. I knew a lady who managed to interpret “He will wipe every tear from their eyes” to mean she would be crying in heaven! There’s knowing, and knowing you know…

  25. 25

    To reinforce what has already been said: here is a catalog entry for a step clamp used for workholding. They are all “step clamps”, and look exactly the same geometrically when you don’t consider nominal dimensions. And when designing a fixture, the tool designer might “specify” step clamps (as opposed to some other kind of clamp) in his bill of materials. And when on the shop floor, the machinist using the fixture would “specify” the clamp by saying “Hey, hand me that step clamp.” However, the tool designer would also need to “specify” the exact dimensioning scheme in his bill of materials based on the size of his workpiece. If the workpiece is large, it will do no good so specify a very small clamp. Also, the purchaser would need to know precisely which clamp to order.

    So we see here different levels of “specification”, all valid, yet very different depending on what kind or how much information needs to be conveyed.

  26. I haven’t seen anything that actually responds to the points I’ve been making.

    Analogies linking biology with human designs fail at a number of points, but the one I think is most important is that chemistry doesn’t obey the rules of syntax that we find in language. Or the conventions found in blueprints or recipes.

    I’ve asked for anyone who can point to a theory of biological design, or even a theoretical framework that might lead to a theory of design.

    Something that would allow you to tell if one coding sequence is closer to being functional than another without running the program in a living cell. My question remains, can you tell if a sequence is one character from being functional?

    You can writes as many words as you want in admiration of the complexity of cells, but if you can’t produce a theory of design, you are not in competition with evolution. We do commercial design of pharmaceuticals using directed evolution. It is the only known practical way to design complex organic molecules.

    Making lots of variations and sieving them is the only known way to navigate functional space.

  27. P:

    I think you need to look a little closer.

    You have simply tossed out the word analogy, as if that suffices to dismiss. But in fact any analogies are quite good. In fact in the OP The Power = torque * angular velocity is a case in point from physics.

    But, it is doubtful that identifying the coded information in DNA as digital is an analogy. For, digital means, discrete state. And that is exactly what he code in question is.

    Similarly, you can see for yourself above, how a motor is by proper definition a two port device that converts a suitable energy source and power flow into shaft work and power.

    ATP synthetase and the flagellum, as well as the Myosin-Actin complex etc are motors.

    You need to face the implications of that, given just how central such things are to life function, e.g. the myosin motor is implicated in even cell division, not just muscles. ATP is of course the power battery of cellular activity.

    And, with all due respect, you are wrong, when you have a large configurational space, we do not normally navigate it by grand scale trial and error. Just the task of composing a complex message in this thread in English is a decisive counter-example. If that were by trial and error instead of insightful knowledge and skill, it would never get done.

    By knowing the intended purpose and the conventions and patterns of an information processing system, one can identify closeness to function without trial and error on the grand scale. And then some limited trials on cases known to be close to function allows debugging and implementation.

    That is how information systems are built.

    GEM of TKI

  28. PS: If you want a theory of design [ID is not that, it is a theory of inference to design (design being a fact of observation) as causal source on validated empirical signs], please cf TRIZ, as has been pointed out several times.

  29. 29

    Petrushka writes:

    You can writes as many words as you want in admiration of the complexity of cells, but if you can’t produce a theory of design, you are not in competition with evolution.

    It seems that the ideological blindness of anti-ID advocates cannot ever allow their minds to hold even the most basic and consistent corrections to their erroneous view.

    ID is not in competition with “evolution” or even “evolutionary theory”, but rather only with a specific ideological assumption that many have in regards to evolutionary theory – that everything evolution has wrought has been done without foresight or planning – IOW, blindly.

    Do Darwinists have a predictive (retrodictive) theory that demonstrates the assumed blind nature of evolutionary processes capable of doing what they are claimed to have done? Can they show how this “non-design” blindness can realistically and categorically generate any of the complex, specified, functional, interdependent systems so claimed? If not, then how is that assumption warranted?

    ID theorists do have a theory of design (in fact, several in several different fields), and it is used to infer design, to design things for various applications, and to reverse engineer other designs. ID theorists have a plethora of examples of complex, specified, functional, interdependent systems generated via various design theories (theories of language, programming, engineering, forensics, etc.) which serves as objectively-existent warrant for any intuition of or inference to design.

  30. Petrushka:

    I have answered your points many times. I will do it once more.

    Analogies linking biology with human designs fail at a number of points, but the one I think is most important is that chemistry doesn’t obey the rules of syntax that we find in language. Or the conventions found in blueprints or recipes.

    That’s quite obvious. And neither do the rules of mechanics that are used in the design of a car engine, just to go back to DrREC’s example, obey the rules of syntax. Is that an argumetn to say that the car engine is not designed?

    You can maybe find useful a distinction that you can find in the first chapters of Abel’s new book, The first gene. He says (and he is very right, IMO) that semiotic information, that is the information that conveys a message, and not only a signal, can be divided into two important subsets: Descriptive Information (DI), such as our language, whose function is to convey some specific meaning; and Prescriptive Information (PI), whose function is to implement some specific function in a material system (that’s just my way to sum it up; for the original arguments by Abel, please refer to his book).

    So, that should answer your first question. If the information in DNA does not resemble the conventions in our language, it’s not necause it is not designed, but because it is PI, just like the plans of an engine, or a computer program.

    I’ve asked for anyone who can point to a theory of biological design, or even a theoretical framework that might lead to a theory of design. Something that would allow you to tell if one coding sequence is closer to being functional than another without running the program in a living cell. My question remains, can you tell if a sequence is one character from being functional?

    Here, we need some more specifications.

    First of all, a theoretical framework for biological design obviously exists: it’s the sum of the laws that govern biochemistry. I believe we understand most of that, even if, as we know, the top down calculations are heavy (but certainly possible).

    I have also given you examples of top down calculations of proteins. One is the artificial protein Top7/1qys. Another, more theoretical, example has been kindly provided recently by DrREC.

    I agree, it’s not much. Goofy instances of a science that is just being born. But it is possible, and it will come.

    Moreover, as I have asked many times, without receiving any answer from you, why do you insist that the designer should be denied the possibility of “running the program in a living cell”? What’s the motive for that? Human programmers do run their designed code on their computers, and do that many many times before finding the right solution. Have you ever heard of debugging? I believe you have.

    So, why should the biological designer be denied what is a routine methodology in human design?

    In the same way, you seem to deny that the biological designer may use bottom up algorithms in his design. That’s nonsense. Bottom up algorithms can be an important part in a design process. How can you exclude them in advance? And why? The biological designer has even implemented a specific, autonomous bottom up algorithm of protein engineering in one of his beautiful designs, the mechanisms by which antibody affinity increases in the immune system after the primary immune response.

    IOWs, you make two very big errors:

    a) You deny that understanding of biochemical laws can lead to efficient top down protein engineering. That is false. There are difficulties, but it can be done.

    b) You affirm specific constraints for the biological designer that have no sense: that the code cannot be run in a living cell, that bottom up procedures cannot be used. That’s only a dogmatic a priori illogical position.

    My question remains, can you tell if a sequence is one character from being functional?

    If I can efficiently model the sequence, I can certainly say. Another way would be to try some analytical approach, such as deconstructing the problem into sub problems, analyzing the secondary structure, or even trying some reasonable bottom up approach, such as tryimg one aminoacid substitutions and their effect on the protein.

    Moreover, the “bad” protein can be easily synthesized. A simple analysis of the 3D structure of the “bad” protein in the lab could easily bring to important clues about what does not work in it.

    So, I don’t see your problem at all.

  31. Do Darwinists have a predictive (retrodictive) theory that demonstrates the assumed blind nature of evolutionary processes capable of doing what they are claimed to have done?

    Actualy, yes.

    A feedback system, or GA, can compute any string. Simple mathematics.

    The only issue is whether functional sequence space can be navigated with the observed change and mutation mechanisms.

    when I say there is no theory of design, I mean that ID advocates have not demonstrated or proposed any means by which the functionality of code sequences can be predicted.

    If you can’t tell what a sequence will do without trying it, the only available design mechanism is evolution.

    Feel free to be the first to prose a theory of design. I find it interesting that in the 200 years since Paley, no one except Phillip Johnson has noticed or cared that there is no theory other than directed evolution that would make design possible.

  32. Moreover, as I have asked many times, without receiving any answer from you, why do you insist that the designer should be denied the possibility of “running the program in a living cell”?

    The designer obviously does test coding sequences in living cells.

  33. a) You deny that understanding of biochemical laws can lead to efficient top down protein engineering. That is false. There are difficulties, but it can be done.

    Feel free to demonstrate this.

    You understand that I am taking the risk of being wrong in a way that that can be clearly demonstrated.

    I hope you also understand that chemistry will qlways be orders of magnitude faster than simulations of chemistry.

    I hope you also understand that chemistry is complex in the mathematical sense that small errors in initial conditions or initial parameters get magnified exponentially, which is why top down engineering will never replace evolution as the efficient method of design.

    I hope you also understand that calculating a fold, time consuming as it is, tells you next to nothing about utility.

    The bottom up approach is called evolution. You can sugar coat it by calling it directed evolution, but it still requires that functional space be connectable. If functional space is connectable, there is no need to hypothesize a director. Lenski has demonstrated that a small population can try and test all possible neighboring sequence space in just decades.

  34. 34

    Do you purposefully ignore it when you are corrected that ID is not in competition with “evolution”, but rather only with “undirected” evolution in particular cases?

  35. If efficient top down protein engineering is possible, then you would be able to determine which of a collection of coding sequences, all but one of which are randomly generated, is just one character from being functional.

    You will have a theory that predicts the utility of sequences.

    Otherwise you have the same problem that you attribute to evolution: the problem of big numbers an a sparse functional space.

    You also have the problem of knowing from first principles that life is possible. That’s an interesting problem in itself.

    I think you don’t see this problem because you assume the designer is omniscient. But it’s interesting that you think big numbers are a problem for evolution, but not for designers.

  36. If you can’t tell what a sequence will do without trying it, the only available design mechanism is evolution.

    That’s a lot of fallacy in one short sentence.

    You don’t know that you can’t tell what a sequence will do without trying it. That does not make it impossible.

    Proteins fold predictably. That is, a given DNA sequence will predictably produce the same protein which will predictably fold the same way. To assert that something which behaves with clockwork consistency is beyond prediction is absurd.

    Second, if they can’t be designed deliberately, there is no mechanism. Evolution is not a design mechanism unless deliberately employed by a designer.

    Even if a designer were to use a GA, deliberately set targets are still required. Perhaps a GA can determine how to design a specific protein. But how does the GA know what protein to design? There is no path from a single cell to a whale or a frog that can be navigated by incremental protein changes with no target. Each protein is a tiny component in a larger system, which in turn is a component in an even larger system. Individually varying proteins cannot collaborate to build systems of which they are not aware.

    If you think that is a plausible hypothesis for designing proteins, the components made from them, the components made from them, and so onward up to distinct living entities, you have the burden of stating that hypothesis and testing it. It’s absurd at face value, and it would take some rigorous application of the scientific method to change that. I happen to think that it’s a ridiculous idea, so I don’t think that any amount of serious testing will establish it.

    That’s where the premise is at. No matter how many times you confidently assert that it is an established explanation, it is not only an untested hypothesis, but an undefined hypothesis. You’re a few steps away from square one.

  37. Lenski has demonstrated that a small population can try and test all possible neighboring sequence space in just decades.

    What an odd statement. According your expectations, the “possible neighboring sequence space” should expand without limit as each neighboring sequence space allows access to even more neighboring sequence spaces.

    Testing all possible neighboring sequence spaces should take billions of years, and even then be a work in progress.

    How did Lenski do it in a few decades? How do his results compare to your expectations? How much has the available sequence space grown?

  38. I hate to break the news to you, but evolution is both an experimental science and an industrial process.

    New drugs are made by generating vast numbers of variant molecules and sieving them for function, then sieving the residue for safety and effectiveness,

    It cost the pharmaceutical industry about a billion dollars to produce one marketable molecule.

    If you don’t have a theory for predicting the utility of coding strings without testing them, then you don’t have a design process that is faster or more effective than evolution.

  39. WJM, the answer – clearly – is YES.

    (…and without the slightest bit of hesitation).

  40. Even if a designer were to use a GA, deliberately set targets are still required.

    Targets are not required for a GA, only a way to prefer one child over another. You don’t have to know where you are going or what is possible.

    Nothing in living systems sets targets. Some individuals simply have more offspring than others.

  41. Each protein is a tiny component in a larger system, which in turn is a component in an even larger system. Individually varying proteins cannot collaborate to build systems of which they are not aware.

    There’s lots of experimental evidence indicating that evolution is not aware that it is building anything. Even in simple experiments like Lenski’s evolution simply tries every neighboring variation.

  42. New drugs are made by generating vast numbers of variant molecules and sieving them for function, then sieving the residue for safety and effectiveness

    I wonder how they ‘sieve’ for function without any idea of what a useful function might be. I wonder how they sieve for safety and effectiveness with no awareness of safety or effectiveness?

    Oh, that’s right. The missing element in your passively phrased sentence (“New drugs are made“) is the scientists who make them.

    How many times will you use clear-cut examples of intelligent design to attempt to demonstrate what can be accomplished without intelligent design? It’s surreal, disconnected from reality.

  43. Targets are not required for a GA, only a way to prefer one child over another. You don’t have to know where you are going or what is possible.

    Every GA without a target demonstrates the limitations of GAs without targets. No one says you need a target.

    Even with a target, GAs require intelligent input and intelligent application of the output.

    Without a target you get – well, go ask Lenski.

  44. There’s lots of experimental evidence indicating that evolution is not aware that it is building anything.

    Who needs evidence, experimental or otherwise, to know that “evolution is not aware that it is building anything?”

    What type of experimental evidence? Someone caught evolution in the act of building something, wondered if it knew what it was building, and experimented to find out? Are you serious? I’d be impressed if someone could find the conditions in which to conduct the experiment. And then I’d question his sanity.

    Again, surreal, disconnected from reality.

  45. I wonder how they ‘sieve’ for function without any idea of what a useful function might be. I wonder how they sieve for safety and effectiveness with no awareness of safety or effectiveness?

    I’m simply saying that when industry needs biologically functional molecules, it employes the same algorithm that is embodied in fecundity and natural selection.

    There is nothing particularly new about industrializing naturally occurring processes.

    this particular instance is just a variation on selective breeding.

  46. Every GA without a target demonstrates the limitations of GAs without targets. No one says you need a target.

    GAs without targets are extremely useful and are widely used in industry.

  47. What an odd statement. According your expectations, the “possible neighboring sequence space” should expand without limit as each neighboring sequence space allows access to even more neighboring sequence spaces.

    Not in practice.

    The number of coding genes seems to have an upper limit, or at least the number doesn’t appear to expand without limit.

  48. 48
    material.infantacy

    A GA cannot be effective without evaluating fitness, imposing population generation constraints, and determining halting conditions.

    It may not have a bullseye, but a GA always has a target. Any constraints imposed on population generation, fitness evaluation, or halting constitutes a target.

  49. The fact that some individuals have more offspring is not at all like a target.

    The increased number of offspring could be the result of female choice, as in having pretty tail feathers.

    I’m not sure how halting conditions apply to living things. Could you elaborate?

  50. Petrushka:

    I think you are wrong. I think that it will be demonstrated.

    I hope you also understand that calculating a fold, time consuming as it is, tells you next to nothing about utility.

    Not true. it does not tell you everything, but not certainly “next to nothing”. Folding is the first, and probably the biggest problem to get to function.

    The bottom up approach is called evolution. You can sugar coat it by calling it directed evolution, but it still requires that functional space be connectable.

    Here you are not in best form. The bottom up approach is a method of engineering. Evolution is a word that means nothing. Of course there is evolution: new species appear, and as you know I believe in common descent.

    What we are discussing here is the cause of what you call “evolution”, and that I call the emergence of new biological information. I say that the cause is design, be it top down, bottom up, or a mix of the two. You say that the cause is a non design process of RV and NS. So, please, don’t change the state of things by playing with words with senseless statements such as:

    “The bottom up approach is called evolution. You can sugar coat it by calling it directed evolution”

    statements that mean nothing and only create confusion.

    But the really surpising statemnt is in the final part:

    You can sugar coat it by calling it directed evolution, but it still requires that functional space be connectable.

    Why? This is nonsense. Please, consider the famous Szostak result of the ATP binding protein, created by a bottom up approach. Yes, exctly the one that is usually considered as evidence that functional sequences are spontaneously present in random protein libraries, and instead is a good example of protein engineering camouflaged as ID bashing.

    In that experiment, the presence in random sequences of weak binding to ATP was transformed into a strong binding site with some functional folding by some rounds of mutational PCR followed by intelligent selection.

    That tells us two important things of why intelligent selection is infinitely more powerful than NS, a concept that you strongly refute:

    a) In intelligent selection, you know what function you want to generate, even if for the moment that function, in itself, would not be useful in the present environment. So, you can decide that you need an ATP binding protein, and you can engineer it, even if the real higher level utility of that biochemical function will be exploited only in a new and bigger context, that at present exists only in your plans, but not in the biological context you are operating on. Nothing of that is possible with NS. IOWs, IC is not a problem for planned design, while it is an unsurmountable wall to NS.

    2) The desired function can be selected even at extremely low levels. The original molecules in the Szostak experiment had very weak binding to ATP, a purely random effect that would never have been useful in any realistic biological context. But, as that function was actively wanted and recognized by the researchers, even at low level, it could be selected and amplified by bottom up “variation and intelligent selection”. With good results. (Well, the final protein was useless all the same, but at least it has a strong capacity to bind ATP :) ).

    That said, in what way does a bottom up strategy require, as you say, that “functional space be connectable”? What is connectable in Szostak’s experiment? What is connectable in antibody maturation?

    I am afraid that you are confused here. A connected space would mean that you can go through a random walk from an existing functional protein domain to another, different, unrelated protein domain, by a series of functional, naturally selectable states. That is simply not true.

    Bottom up protein engineering, instead, only requires some pre-existing function, even minimal, that can be intelligently selected, and a gradual optimization of that same function by rounds of RV and intelligent selection. That works, because an existing, recognizable function can certainly be optimized by that strategy. And there is no need to “traverse” the ocean of the search space.

    But the whole magic of the process is conscious intelligence: it’s the conscious agent that defines and recognizes the function to be developed. And it’s the conscious researcher that applies appropriate variation rates, and appropiate intelligent slection, in cycles, to get the desired result.

  51. Petrushka:

    If efficient top down protein engineering is possible, then you would be able to determine which of a collection of coding sequences, all but one of which are randomly generated, is just one character from being functional.

    Yes.

    You will have a theory that predicts the utility of sequences.

    Yes. It’s called biochemistry.

    Otherwise you have the same problem that you attribute to evolution: the problem of big numbers an a sparse functional space.

    Not if I have that theory. Not if I can anyway use bottom up engineering. Not if I can use any mix of the two. Not if I am an intelligent designer, and I have appropriate time and resources.

    You also have the problem of knowing from first principles that life is possible. That’s an interesting problem in itself.

    Yes, Interesting indeed.

    I think you don’t see this problem because you assume the designer is omniscient.

    I don’t see this problem because there is not such a problem. And yes, it is true that I believe that, in the ultimate sense, the final designer of reality can be called “omniscient”. That would only mean that he knows what he has designed.

    But here we are speaking of biological information, and biological information is not the whole of reality. It emerges in time and space, and has pecific properties that differentiate it from other apsects of reality.

    For biological information, I would say that a very, very intelligent designer could be enough. I am not sure of that, obviously. Maybe that in the end an omniscient designer is necessary even for inanimate reality. I would say that is a philosophical problem, and not one that can be easily solved.

    So, let’s leave that aspect open. I will be empirically happy with my very intelligent designer, you with your non existing (according to your philosophical views) omniscient designer.

    But it’s interesting that you think big numbers are a problem for evolution, but not for designers.

    Big numbers are certainly an unsurmountable problem for non design algorithms. They are usually a tractable problem for an intelligent designer.

  52. Petrushka:

    I don’t understand. Are you agreeing? Is that sarcasm?

  53. 53
    material.infantacy

    Hi Petrushka, I’m making no claim that NDE functions like a common GA. In context, I replied to your point,

    “GAs without targets are extremely useful and are widely used in industry.”

    This is not the case. GAs cannot operate properly without a target. Any reduction in sample space from a universal set is, by definition, a target.

    It may be argued that halting doesn’t quite fit this category, but it does require knowledge of the solution in order to be effective.

    Any constraints on population generation, or fitness assessment, constitute a target — and halting is most relevant when considering the fitness assessment.

  54. If a GA doesn’t have a target how do you know when it is finished?

    And what, exactly, would the “A” stand for? It can’t be “algorithm” because guess what? An algorithm is for finding a solution/ solutions.

  55. Petrushka: “I think you don’t see this problem because you assume the designer is omniscient.”

    Omniscience is irrelevant. We know for a fact that lots of things, even complicated things, have been engineered by less-than-omniscient designers. Why in the world would protein design require omniscience? It just doesn’t make any sense.

  56. In that experiment, the presence in random sequences of weak binding to ATP was transformed into a strong binding site with some functional folding by some rounds of mutational PCR followed by intelligent selection.

    That tells us two important things of why intelligent selection is infinitely more powerful than NS, a concept that you strongly refute:

    Artificial selection is faster when you have a specific target. Plant and animal breeding demonstrates that “intelligent” selection can achieve some targets within a human lifetime. Tame foxes are a recent example.

    Artificial selection, however, cannot see all the possible paths that might lead to reproductive success in a changing environment. The results of sexual selection offer a glimpse of how selection for a specific trait can lead to a kind of blind alley specialization which, confronted with environmental change, leads to extinction.

    “…some rounds of mutational PCR followed by intelligent selection.”

    You are describing design by evolution. The feature of evolution that is contested by ID is not whether selection is intelligent or not, by whether the source of variation has foresight.

  57. Petrushka:

    You are describing design by evolution. The feature of evolution that is contested by ID is not whether selection is intelligent or not, by whether the source of variation has foresight

    Where do you derive such an extravagant concept from? ID maintains that evolution is intelligently designed. Either it is designed top down, and the variation has foresight, or it is designed bottom up, and RV is used coupled to intelligent selection, or a mix of the two processes is used (that seems the most reasonable scenario), it is Intelligent Design just the same.

    Neo darwinism, on the contrary, is committed to the absence of design and purpose, in whatever form.

    That is the difference.

    Are you redefining ID? Bottom up protein engineering is absolutely a form of ID.

  58. Gpuccio,
    Your conception of ID is miles apart from many others’ ID. That is not surprising, given that ID has no real content, and is really just a catch-all for all manner of “God can be scientifically proven” arguments.

    The way you describe ID in the last post is mostly incoherent. And the part that is coherent is indistinguishable from regular ol’ evolution.

  59. Eric, because it’s not possible to design functional sequences without testing them to see which ones work. And to run those tests on all the possible sequences takes more computing power than is available in the universe.

  60. How do you know that it’s not possib;e to design functional sequences without testing them to see which ones work?

    And how do you know how much computing power it would take to test all of the sequences?

    And what happens if the computing was down before the universe existed- do you know how much computing power was available then?

  61. Either it is designed top down, and the variation has foresight, or it is designed bottom up, and RV is used coupled to intelligent selection, or a mix of the two processes is used…

    Well, let’s see. You have zero sightings of a top down designer and no evidence that top down design can ever be faster than simply creating and testing a bunch of variations, so the top down hypothesis lacks evidence. I will grant that finding shortcuts to protein design and the design of regulatory networks would prove me wrong about the potential for design.

    Intuitively, a top down designer would not be limited to nested hierarchies or common descent, but I suppose one mustn’t speculate about the designer’s motives.

    Selection, intelligent or otherwise, is evolution. Adam Smith would argue that feedback regulation is more effective than central planning, but selective breeding does exist, so it’s physically possible.

  62. lastyearon:

    The way you describe ID in the last post is mostly incoherent.

    Thank you. Coming from you, I take that as a compliment.

  63. Where’s DrREC?

  64. I know that at the present time the most cost effective way to design biologically active molecules is to make large batches of variants and sieve them.

    That’s the way pharmaceuticals are designed.

    I also know that Douglas Axe, who is ID friendly, has said there is no shortcut to the functionality of coding sequences.

    I am not making any claims pro or con regarding the fine tuning of the universe. I’m addressing gpuccio’s claim that design intervention has occurred thousands of times in the history of life to produce, among other things, protein domains.

    I believe your position is that ID is not anti-evolution. That doesn’t seem to be true of gpuccio. He claims that evolution cannot produce anything significant without intervention.

  65. I don’t know about others, but I’m getting pretty busy toward Christmas. At some point I will be off the air for possibly a week.

  66. Sorry about the slow reply-busy time of year.

    To reframe my point-

    Specification in the search for design is a post hoc assignment of design to what is observed.

    KF really hammers home this point: “Bacteria need to be able to move and flagella help them do so.” He’s observed some microorganisms are motile, inferred they NEED to move, and that the flagellum is the design to help them do so.

    Of course, this ignores the IMMOTILE bacteria, archaea and yeast, and the many other mechanisms of motility. Flagella-observed. Bullseye around it. Design. Case closed. So much so, that he can set his dummy variable=1, and conclude specification (design) without further investigation.

    I saw two replies to my query whether a V8 hemi and myosin share the same specification.

    Some said yes. I’m somewhat shocked. This is literally attribution of design based on the words scientists use out of convenience. We might as well say wings are designed by humans, therefore birds are designed. Is this really scientific design detection?

    The other class of replies pleaded that there is a way to independently and carefully specify a specification. But somehow the details weren’t shared. What is the ID method of determining specification independently (like pi or prime numbers, in the pulsar example). I’ve explained at length why defining a target function, then one of many sequences that might perform that sequence, applying a cut-off that specifies that sequence, and then inferring functional space from the cut off sample pool is a high-tech painting of the bullseye onto a pre-shot arrow. Is there another method?

    Lastly, I think we have a very good reason to believe natural processes can produce complex functions:

    “Cross-species analysis revealed interesting evolutionary paths of how this gene had originated from noncoding DNA sequences: insertion of repeat elements especially Alu contributed to the formation of the first coding exon and six standard splice junctions on the branch leading to humans and chimpanzees, and two subsequent substitutions in the human lineage escaped two stop codons and created an open reading frame of 194 amino acids. We experimentally verified FLJ33706′s mRNA and protein expression in the brain.”
    http://www.ploscompbiol.org/ar.....bi.1000734

    Unless you think this is design in action?

    By the way, I’m spending time with family. Could we keep replies on topic, and under a few thousand words?

  67. DrREC:

    Quich and on topic:

    Unless you think this is design in action?

    Exactly. I have quoted that paper many times as a possible model of design detection.

  68. DrREC:

    Some said yes. I’m somewhat shocked. This is literally attribution of design based on the words scientists use out of convenience. We might as well say wings are designed by humans, therefore birds are designed. Is this really scientific design detection?

    I said yes in a sense, with a detailed argumentation that you have not addressed.

    There is no doubt that both the endine and myosin transform chemical energy into mechanical energy. But, if we detail better the specification, the differences are obvious.

    What’s the problem with you? Sharing a same specifictaion has nothing to do with detecting design. We detect design if some specification that we define for an object is complex.

    Is the engine specified? Yes. We can specify it at various level of detail, but it is certainly specified. The more the specification is detailed, the greater the complexity. I am quite sure that, if the specification is precise enough, the FSCI in the engine is enough to detect design. And there is nothing strange in that, because the engine is designed.

    The same reasoning applies to myosin. Only, the final reasoning will be limited to the inference of design, because for myosin we have not independent verification, like in the case of the engine.

    So, I cannot understand what shocks you. Defining a function for an object is not painting a target post hoc: it is observing post hoc that a target exists.

    Moreover, the existence of possible specifications for an object in no way “detects design”. Only the existence of possible complex specifications detects design.

    Simple specifications are not necessarily connected to design. They can be given for objects that are not designed. A simple example will do:

    Let’s consider a cell phone, one of the new smart phones, just to be trendy.

    I can specify that object for a simple function: acting as a paperweight for my desk. That’s a function that the cell phone can easily accomplish. But it is not a complex function, and does not imply design. A simple stone of appropriate weight will do, and the stone is not designed.

    So, I hope you understand now that defining a function in no way implies design detection, as you seem to nelieve.

    But if I define the funtion: “allowing connection to other people thorugh existing networks of wireless communication, connecting to Internet, and being able to perform specific computational tasks, while weighing less that…”

    or something like that, well, that is a specification of function that does require complex information to be achieved. And the cell phone achieves that, because it is designed, and that complex information is there.

    Well, that was not quick but, I hope, pertinent.

  69. Participants and onlookers:

    Let me first express appreciation that we have had several days of quite civil discussion, and have had fairly substantial inputs from the various sides.

    I have of course lurked quietly for a little while, watching that happen.

    That is important, as too often at UD and elsewhere the discussion of design issues has been shipwrecked by poisoned distractors posed as objections.

    Now, above there is a bit of exchange over the joint specification-complexity context of the design inference.

    I fundamentally agree with GP.

    When we have functionally specific, complex organisation — which directly implies associated functionally specific, complex information — we have excellent reason to infer to design as the best explanation. For, at or beyond 500 – 1,000 bits of FSCI the sea of possible configurations cannot be subjected to a blind search that makes it reasonable to happen on unusual, specific configs by blind luck, on the gamut of the solar system or the observed cosmos.

    So, if we find an organised object that is beyond this, we are credibly looking at an artifact.

    And, the relevant specifications are based on observed function tracing to fairly specific configs. They are not painting the target around where the arrow happens to hit.

    Does anyone here reasonably expect that significant random variation of the configs of the ATP Synthetase or the flagellum, will leave it in a functional condition as a motor worth talking about? Or, does anyone here seriously believe that a motor can be cobbled together by in effect shaking a bag of parts — that happen by good luck to be well matched, like a not to a bolt! — and having them pop together in a happily functional way that fits into an environment?

    As to pointing to other bacteria, let us observe from Dr Rec:

    Of course, this ignores the IMMOTILE bacteria, archaea and yeast, and the many other mechanisms of motility. Flagella-observed. Bullseye around it. Design. Case closed. So much so, that he can set his dummy variable=1, and conclude specification (design) without further investigation.

    This is amazing.

    Let us see: a a turbojet, a turbofan jet, a pulse jet, a ram jet, a rocket, a turboprop and a piston engine all provide motility to aircraft. Can we reasonably infer from the different mechanisms involved that each of these, examined on its own merits, is not a case of FSCO/I?

    The flagellum is a case of FSCO/I. We can even estimate the information in its components by working back to the DNA involved. (Let us ignore the regulatory information for the moment, but this is plainly additional.)

    Now, that information is plainly specific, as can be seen from noting the way the motor-propellor system is organised to function. In short, despite the sarcastic dismissal, there is objective reason for seeing that S = 1 here.

    That we see sarcasm rather than a serious explanation that such a flagellum would work with significant variation and is not an island of function, is revealing.

    GEM of TKI

  70. “chemistry is complex in the mathematical sense that small errors in initial conditions or initial parameters get magnified exponentially”

    That is nonlinearity, not complexity.

Leave a Reply