February 19, 2008

K.D. Kalinsky

(Note from Denyse: An ID theorist asked me to publish this essay on detecting design in nature. It is exactly as the scientist gave it to me except that

– I have linked the sections for easier Web handling

– all the notes have been moved to the end.

– I don’t see a font choice for superscripts or subscripts in Blogger, so have decided to enclose the element that would be super or subscripted in two periods. In the number 10.-64. assume that .-64. Is a superscript. In the equation, P.f. = M(E.x.)/N, assume that .f. and .x. are subscripts.

A .pdf version of his paper exists but is not on line as of this writing, so far as I know. I am glad to publish non-abusive comments that focus on the paper at the Post-Darwinist, but feel free to discuss it here as well.)

Next: Introduction

Sections:

I. Introduction

II. Defining some terms and concepts

III. The role of intelligent design in science

IV. Functional Information

V. Application to Biological Life

VI. Conclusion

End Notes

Denyse – the usual way of showing super- and sub-scripts in text is to use ^ and _ respectively, so 10^2 = 100.

From here, it’s only a short step to using LaTeX. 🙂

Bob

Thought provoking article. Following are some thoughts:

1) Re: Intelligent Design: an effect that requires a mind.

It would help to distinguish between primary and secondary causes. e.g.,

Is a computer a secondary cause that requires a mind as the primary cause?

Is a human mind a primary or secondary cause?

(Or possibly address this in a subsequent paper.)

2) Recommend describing or defining “functional information”. Are you using the same definition of Hazen et al.?

e.g.

3) Provide reference to 500 million years referred to in:

“If we suppose that the entire set of 10.47. proteins reorganized once per year over a 500 million year interval (about the estimated time period for pre-biotic evolution),”

4) Address the objection of panspermia, that the formation happened elsewhere and was transported to earth.

5) The earth made of proteins appears much higher

Suggest describing taking the full volume of ocean half full of proteins as a possible amount of protein, and then rounding that up to the full earth with citation.

6) The once per year rearrangement may sound slow.

Compare taking the fastest rate of chemical rearrangement in water.

(Possibly round up to inverse Plank time as the fastest possible rate.)

7) Endnotes:

For a posted version, suggest providing links to articles were available on the web: e.g.

http://www.pnas.org/cgi/conten.....ppl_1/8574

Functional information and the emergence of biocomplexity

PS I second Bob O’H. The ^ and _ marks would be much easier to understand.

PPS Maybe refer to the cooling and the period of time needed to preserve organic molecules, RNA and then DNA, then round that up.

A cautious and very sharp paper. I love how the paper remains focused and does not discuss irrelevant side issues.

I third the recommendation of ^ and _.

I like the approach of this paper and the almost muted points it makes. This is what an ID paper should read like, in my opinion.

Very nice indeed

This may turn out to be the short step that leaves your mark on parodistic web pages.

A really excellent paper, but from the devil’s advocate position I think the Darwinists might object that at least in the protein folding domain and protein total amino acid sequence cases there are actually the usual hypothesized intermediate steps for the targets of the fitness functions, which pose individually very much lower functional bit requirements. For example, he estimates the functional information required for the average 300 amino acid protein to be around 700 bits of information, and establishes this as the goal for the natural process. The objection might be that in reality the process at any point would already have a partially or minimally functional protein. Would the fitness function only need to select for a slightly reconfigured amino acid sequence (fewer bits of information), not the entire sequence?

Great article.

But I sometimes wonder why we’re so obsessed with presenting the argument from design at molecular and cosmic levels, ignoring all the things that any fool – or should I say, anyone

buta fool – can see.Don’t get me wrong – I think it’s awe-inspiring that bacteria are like little motor boats. And I’m grateful to Michael Behe and his friends for pointing that out. But is it only people with big microscopes who can spot design in the universe? I think not. The “dirt, water, seed, sun… look, a tree!” sequence is enough for most of us. We’re persuaded long before we start counting teeth on the gears in Paley’s watch.

Anyway, here’s the argument from specified and irreducible complexity as a first-century writer put it (while discussing something else, by the way, as if it was an trivial thing): “Every house is built by some man; but He who built all things is God” (Hebrews 3:4). If that doesn’t convince someone, all the formulae in the world won’t do the job either.

We’re not going to get blind men to see color by telling them the exact wavelength where red turns to orange.

Thanks. I’ll give it a look.

Like me, it must strike others here that the obvious has become to many so obscure by their brains being educated out of their minds, that it take this level of elucidation to hopefully return it to sanity…

Thank you very much..

Hey alan,

Could you send me an email via my site (click my link)…I have a question for you (off-topic to UD)

Atom

Great, very great article!

I believe that the mathenatical treatment here is especially simple, correct and clear (although a correct typographic notation would certainly help…). The mathematical reasoning is, in my opinion, flawless. Indeed, it has the special advantage of taking full account of what an evolutionary fitness function can do, and of what it can’t do, which is one of the equivocal tricks of darwinist reasoning.

Indeed, such an article is effective in showing without any doubt the obvious, because it seems that the obvious is not obvious to many.

I am particularly happy that the author correctly remains loyal to the principle that scientific knowledge is never ultimate, and never gives “proof” of anything, an elementar concept of epistemology which seems particularly unpopular at present. So, Mr. (Dr, Prof.?) Kalinski (if that’s the mane of the author), please receive all my compliments and esteem, for the article in general, and for never presenting your evaluations as a “fact”!

The only point I had some technical problems with is the specific use of the term “natural selection” in the article, which is evidently used in a wider sense than the traditional one of “blind, mechanical selection”. I think that point needs better clarification, but in no way it affects the general reasoning.

One last observation: we are witnessing, in scientific literature, an increasing number of research studies about protein intelligent engineering by targeted random search plus intelligent fitness measure, as I have already dicussed in a couple of posts. That is a precious occasion of confirming these calculations the other way, that is verifying what happens when we try to climb “Mt. Improbable” in an intelligent way, but imitating some of the processes of “natural” selection. I am sure that, even in that experimental context, the whole corpus of the ID model and calculations is going to be unequivocally confirmed. And that will be the coup de grace, I hope, for the fairy tales of the darwinian model.

alan (#10):

I apologize that I have “plagiarized” your comment about the obvious. Indeed, I had not yet read your post when I wrote mine. It seems that we had the same spontaneous reaction to this wonderful article…

Anyway, I hope you are not going to oblige me to “retract”… 🙂

Hmmm. I guess you won’t be surprised to hear that I’m not so effusive. 🙂

I tried to post something on Part IV at Post-Darwinist, but for whatever reason it didn’t get through. So, here’s an updated version.

From (1) and the first (2), I(Ex) = -log Pf.

From (3) and the second (2), Inat = -log Pf.

So, the inequality in (4) [I(Ex) > Inat] can never hold. The only way I can make sense of this is if they are different Pf’s, in which case the author should be made to stand in a corner and recite

How to Solve Itas punishment for poor notation.But if the Pfs are different, which one isn’t Pf?

If I(Ex) is calculated with Pf, then this is

saying that intelligence is more likely only if the search is worse than blind chance. That gives natural processes a pretty low barrier to cross.

If Inat is calculated with Pf, then it’s saying that intelligence is inferred if there is any active information (to use terminology we should all be familiar with).

Of course, it’s also possible that the author meant something else – until the maths is sorted out, I would have to reserve judgement.

Bob

P.S. Some tags don’t work in Blogger, but work fine here.

Oh, the tags work fine in the preview, but not once the text is submitted. Oh well.

Bob

Let me get this straight; so the author is admitting the possibility that a system could evolve provided the right fitness function or fitness/landscape is applied. Hence we are now back to the general but very abstract question about whether the physical regime possesses a kind of ratchet of morphological stability that allows evolution to lock in morphologies at a variety of progressive levels. From a theistic point of view it is impossible to rule this out as a possible feature of our world. If our world has this mathematical evolvability it will, in fact, be a rather subtle feature, because it effectively solves a kind ‘meta problem’; it is a feature that facilitates evolution. Meta problems, as Godel discovered, are always more difficult to solve. If ‘evolvability’ were a feature of our world, it would be difficult to conceive the enormous number of possibilities that must be exhausted by some kind of meta-evolutionary (or second-order evolutionary) process for itself to have ‘evolved’. Nevertheless, as far as I can see, the author is admitting at least the possibility of a position that is now very close to the conventional ‘first-order’ evolutionary one. As a theist I would agree with the author that information content in this case is now regressed to the physical meta-system that incases first order evolution.

So, is this paper admitting that irreducible complexity may not so much be found at the biological structure level but in the abstract physical regime that constrains biological realities? Although I myself am not adverse to this notion, it would no doubt be hotly a contended between theists and atheists – a battle fought in a much more logically highfalutin and abstract realm than contentions over the probability of the molecular engineering of particular structures; for like the laws of physics, the conceivable structures of morphospace have a platonic/conceptual status rather than flesh and blood existence! However, down at the earthy particulars of biological realities, this rendition of ID is not so different from conventional first order evolution.

Talking about earthy realities: Denyse this might be your lucky day: Prof Larry Moran might give you a kiss for all this; but judging from what he gets up to with Parisian statues you might get something else as well, so watch your back.

Hey Bob O’H,

You wrote:

From my single reading of the paper, the author seemed to make it clear that I

natneeds to take into account R, the number of tries nature has to solve the problem, whereas the intrinsic difficulty of the problem has no reference to number of attempts. In this way, if the nature, given a number of tries can only generate M bits of functional information, and N is the amount of functional information needed to have a reasonable change of solving the problem, and N >> M, then we say nature will probably not be able to solve the problem in that many attempts.So the Pf’s would need to be different, since one would take into account R, where as the other would not.

More specifically, if we have:

P

f= 1-(1-0.5)^1/RThen when P

f= M(E_x)/N (in other words, when we have equality with our intrinsic problem probability), we get:M(E_x)/N = 1-(1-0.5)^1/R

Since we know what is on the left and can calculate, we can solve for R, which tells us how many attempts we need to have at least a 0.5 chance of solving the problem. If we want to change it to a .10 chance, we get a different value for R.

So the author is using P

ffrom the original equation to derive a new equation (once he/she plugs in the value for 0.5 chance of solving the problem), and so Pfwill only equal the original Pffor one R value.If we find R << R_needed, then the author’s inequality will hold.

{DH corrected per Atom #39}

Rats, make E^x read E_x.

{DH did that fix #18?}

Right. And at that point I(E_x) = I_nat, so the inequality can never hold. We need some indication that the P_f’s are different, or the argument should have been developed in terms of the inequality from the start.

I think it’s time to break the Polya out.

Bob

Thanks DH, yes, it did fix it.

{DH Try clicking on the “e” below you username on the left to see if you can go back in and edit your posts.}

Bob, go easy on ’em. 🙂

…but in more seriousness…

I think the reason is because the P

f‘s arenotyet different, as long as we haven’t stated what R is. They may be different, they may be the same.So the author was starting with the assumption that they are the same and then coming up with an equation that makes R the free variable. As you change R, you change P

f. If you don’t change R, you don’t change Pf.So yeah, I guess the author could have made that clearer, but I don’t think the author was in error.

What do you think?

“What do you think?” – Atom

I think that even if you get your R’s and P

f‘s straightened around to Bob’s satisfaction, it won’t change his mind. He doesn’twantto believe.If they may be different, then they are not representing the same number, so they should be different. It is an error, but an error of notation.

I notice nobody has tried to answer the rest of my criticism. I’ve got more, too. 🙂

Bob

Bob,

In the derivation you first begin with the same P

f, then find an equation with R, and then get the new equation (which you drop reference to Pfin, instead just using the form with R, which could change values), which is exactly what the author did. Only when you tried to go back and see how he/she derived the equation did you say “Hey, when R a certain value then I_ex and I_nat are the same!” But that is the point…they are the same for the initial case we use to derive the general equation, but if we find empircally that R_actual is actually different from R_initial, then we get an inequality.It isn’t something worth belaboring, you should just accept that the notation was confusing, but not incorrect for what the author was doing.

Anyway, for the rest of your criticism, what is it? It seemed tied up to your notation confusion, so I thought it was the same.

The rest of the paper flows from that derivation. If the number of attempts that are possible (R_actual) are much less than the attempts needed (R_needed, the value at which I_nat = I_ex, or even better, I_nat > I_ex), then it is likely that chance is not capable of producing the necessary functional information.

Atom