Thursday, October 17, 2013

to add or not add; that is the question

The following does not seem to me an atypical statement in related topics:
CRCs are so called because the check (data verification) value is a redundancy (it expands the message without adding information) and the algorithm is based on cyclic codes.  [emphasis mine]
To the ones who talk about "adding information," this is not a meaningless distinction.  There are some functions of a collection of bits that may be considered strictly as functions of those bits and other functions that compute a function of  those bits with some other data built-in to the function itself.

So why, when it comes to biology, do some people pretend statements about conservation of information are meaningless?

Sunday, October 13, 2013

The Whistling Herring

 "He eteĆ¾ no ffyssh But heryng red."

The dialogue's not perfectly accurate but is more or less the MirrorMask version of an old Yiddish joke:
What’s green, hangs on a wall, and whistles?
Gryphon: I give up, I think, no wait, wait… Fine. What’s the answer?
Helena: Okay. It’s a herring.
Gryphon: But a herring isn’t green.
Helena: You can paint it green.
Gryphon: But a herring doesn’t hang on a wall.
Helena: You can nail it to a wall.
Gryphon: But a herring doesn’t whistle!
Helena: Oh, come on. I just put that in to stop it from being too obvious.
This puts me in mind of Dembski's tractability condition.  (In more recent developments of algorithmic specified complexity, the tractability condition is built in as a feature of randomness deficiency.)  Even if it's true that a herring can be green because of paint, and even if it can be made to hang on a wall, the effect is to include anything that can be painted green and hung on a wall.  These increase the specificational resources of the target space so that it's no longer specific.  I can paint a squirrel green and stick it on the wall.  Or a carrot.  Or a handkerchief.  Which is precisely the joke. Once I include things that aren't normally, typically green, as well as things that don't typically, normally hang on a wall, the riddle becomes intractable.   

Saturday, October 12, 2013

The Coexistence of Sound and Bad Adaptations

From Pierre-P. Grasse's Evolution of Living Organisms:
Rabaud's study of cases like Tipula led him to confuse finality with utility Had he referred to paleontology he would have realized that the two concepts do not [always] coincide.  An end may be useful, useless, or indifferent.  The evolutionary trend may be good, bad, or  neutral for the succeeding line.  Evolution is indifferent to the survival or demise of the species.  Faulty evolution is littered with the bones of its victims.  The coexistence of a sound adaptation and a bad one, of useful, indifferent, or harmful characteristics, is one of the facts that demonstrate that the last word does not lie with selection in the world of living things.
Do Grasse's examples reveal something about the noise threshold of natural selection?   Or do they more often than not reveal that we are too ignorant to recognize what features selection is responding to?

If an apparently better adapted snail is outpopulated by another snail in its own environment, are we too ignorant to be making meaningful speculations about the selectionist history of a prehistoric taxon? or are we mostly in the dark about what each organism brings to the table (again, generally in the dark about the features at selection's disposal)?

Many adaptationists would say, "But of course, we must be temporarily ignorant about the adaptations upon which selection is acting!"  And most of those who would heroically defend science from "Darwin deniers" would nod their heads vigorously at this, as a reasonable (and useful!) defense against the ever-present dangers of provincial antiscience.  In other (i.e. non-political) forums, they might just as well argue that Grasse is citing meaningful evidence for the prevalence of neutral mutations -- which has its own usefulness for protecting Darwinism.

Or they might argue there is really nothing significant about it either way since it could be evidence for either neutrality or for our ignorance or anything in between, underdetermined as it is.  That is, the meaning of these examples depends entirely on which pro-selection argument it seems to be good for in a given context.

Thursday, October 3, 2013

Lynn Margulis is a secular creationist too!

Jerry Coyne goes all anticreationist in branding Lynn Margulis as a secular creationist.

Coyne disapproves of Margulis's book Acquiring Genomes, to make an understaement, but what seems to have earned his disapproval is simply that Margulis' saw any need for any explanation.  In order for her to see any explanatory gap (Altenburg 16, anyone?), she had to be completely ignorant of all the advances in evolutionary speculation over the last 30 years.

You don't need to look any further, of course, than the title of the article:  By "dissing" neo-Darwinism, Margulis has dissed evolution.  Typical anticreationist fare.

Once again, macroevolution is a simple consequence of population genetics, not so simple that one has to be knowledgeable about a great many articles (the very many exciting scholarship to which Coyne alludes) in order to appreciate just how macroevolution has been explained to the satisfaction of neo-Darwinists.

Coyne seems to have missed (or "dissed") that Margulis' endosymbiotic theory ideas have caught on and become much more mainstream in evolutionary science.  If, as recent and sketchy jurisprudence has it, science is what scientists do, Margulis' "crazy" ideas, as he puts it, have wormed their way into science without his approval.  The explanatory gap is illusory, in Coyne's opinion.

Personally, I think there are some serious problems with Margulis' ideas with regard to the specific explanandum of generating novelty, but I believe she's very right about the explanatory gap:
This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create.
After quoting the above, Coyne completely dances around Margulis' insight that selection is severely constrained and that natural selection is not omnipotent.

Coyne also defends his old friend Richard Lewontin. I think it may well be possible that Margulis remembers Lewontin's words in a more unflattering light than he said them (and I don't see a complete retraction there from Lewontin) but I think Lewontin more than likely said something akin to what Richard Feynman recounts in his Cargo Cult Science speech:
For example, I was a little surprised when I was talking to a friend who was going to go on the radio. He does work on cosmology and astronomy, and he wondered how he would explain what the applications of his work were. "Well," I said, "there aren't any." He said, "Yes, but then we won't get support for more research of this kind." I think that's kind of dishonest. If you're representing yourself as a scientist, then you should explain to the layman what you're doing-- and if they don't support you under those circumstances, then that's their decision.
Unlike Feynman's friend, Margulis did not claim that Lewontin mischaracterized his work but was honest about it.  Lewontin has since clarified that Margulis' recollection made it sound like Lewontin's work with disappointing formulas was so he could get grant money for himself where as it was to get money to “run an institution”: to “fund a group of creative people to do what they want.”  Once again the selfish gene has led to altruism.  I think maybe Coyne's overstated umbrage over Lewontin's alleged hucksterism disguises that he is reacting to Margulis getting dangerously close to the fact that there is big money in overflated claims of what has actually been explained, and neo-Darwinism has been a TROUGH.

Are all the papers on evolutionary biology written by hobbyists?  It takes money for people to spend their working life speculating on historical contingencies of how one organism changed into another during such and such an epoch and speculating on what natural selection may explain.  Whence cometh the money?   How might the money flow be affected by perceptions that evolutionary biology might be making popular evolutionary views more elaborate and more consistent with what it known about how organisms work, but not necessarily deepening our understanding of how organisms work?  Once you stop defining the deepening of knowledge in terms of refining "biology's unifying principle," it may be that our understanding is actually being stunted by so much number-crunching in the service of idle speculation.

I'll add here that Jerry Coyne also has a beef with secular creationist Mary Midgely, and anyone who undermines the popular credibility of the Modern Synthesis.  So if you want to know how the Modern Synthesis is falling apart, find out what Bilbo Baggins, er... I mean, Jerry Coyne hates.  Look up all the people he tries to discredit, and you will have an idea what's going on.   In tune with Thomas Nagel's "dangerous sympathy" for Darwin skeptics, Coyne thinks that Margulis may be "worse for science than creationists [Coyne probably has ID proponents in mind here], since her scientific credibility remains high." Actually, an anticreationist usually doesn't mind people doubting Darwinism as long as (a) they are in the minority (among tax-payers and grant-funders) and (b) they can all be denied "scientific credibility."  

Wednesday, October 2, 2013

The Cost of Combining the Results to Subproblems

Something to consider:  Recurrence relations must take into account the cost not only of solving subproblems but the combining the results.

One of the weaknesses in Elsberry and Shallit's essay is the short shrift they give to the arrangement of words within a sentence -- particularly in regard to the Weasel simulation.  In fact, it is so such a salient point that you wonder how anyone with a computer science background (namely Shallit) can be so blind to it.  E and S actually argue that, considering the random formation of separate words to a sentence as the solutions of the subproblems, the cost of getting them to link at precisely the right places into the correctly ordered sentences is trivial.  Of course, given their treatment of the problem mathematically, they are considering the spaces joining the words as no different from the characters in the words themselves.  Developing the "ks it" string is no different from developing the string "think", since the interrelationships between adjacent characters do not matter to the simulation at all.

If I have complete subassembly items of a jet plane, what is the information cost of  defining how they are put together -- or alternatively, what it is the computational cost of trial-and-error fitting together of components of the plane until it is assembled in a working fashion, in the absence of that information?

Even in "embarrassing parallel" problems, how much forethought or arranging needs to be put into how to put together the results of the distributed computation?   Considering natural selection as a computational problem, what is the cost of massively parallelizing?  Well, there is a definite cost to having too many mutations at one time.  This reduces the bandwidth and makes for an "embarrassing" amount of redundancy.  Now, a mutations themselves are distributed over a large population, and with a large population you can experiment here and there.   Mutational experiments can then combine without destabilizing the species.  However, this makes it very, very difficult for two mutations  needed to combine for a special result to combine in one special hybrid individual.  If the two mutations are not quite "neutral enough" they will likely never meet up.  Then, you say, small populations are often somewhat isolated.  Maybe it is this isolation, a "founder effect" and such that affords the complementary mutations a chance to find each other.  But then it is fortuitous for them both to occurred in the same small population.  Then, you say, it is some special combination of small populations occassionally.  This final retreat is rather like a shell game, I think.  In the end, if there is some ideal combination of ideal gene flow between ideally sized local populations, isn't this itself a deus machina?

But then, isn't that evolutionary science?  Speculating what remarkable conditions would be needed for natural selection to have done it, and then asserting then that this remarkable set of conditions is indeed what was the case, since we know that natural selection has brought it about?

This reminds me of the "fortuitous tree"...

Tuesday, October 1, 2013

Anticreationism from Stephen Jay Gould

In his Non-Overlapping Magisteria (I can't help but think of this phrase when watching The Golden Compass) Stephen Jay Gould claims "creationism" -- and one naturally thinks he has in mind specifically what he heroically opposed in McLean vs. Arkansas -- "a splinter movement (unfortunately rather more of a beam these days) of Protestant fundamentalists who believe that every word of the Bible must be literally true."

Phillip Johnson considered this proposed treaty between "magisteria" as disingenuous.  While I won't speculate here about Gould's motives, I do think most of the reasoning behind the idea of non-overlapping magisteria (which despite Gould's framing of the problem surely wasn't first thought of by him) does seem a little disingenuous to me.

More importantly though, you'll notice that whomever the initial supporters/advocates were in this land where Protestant fundamentalism is more than a mere footnote in its history, ID advocates (including those that advocate against this outlawing of ID) include more than Protestant fundamentalists.  As far as I know, neither Michael Behe nor Jonathan Wells nor David Berlinski nor David Klinghoffer nor Richard Sternberg are Protestant fundamentalists.

It's important to realize, however, that anticreationists believe that if the intelligent design movement evolved out of the creation science movement to any significant degree (Of Pandas and People is the important missing link fossil for the Barbara Forrests) then it has to classified as the same movement with the same pros and cons, the same limitations and problems, with all the same ideological grounds.   All one has to do is look into Eugenie Scott's treatment of Richard Sternberg to see this.  Or to look into the latest edition of Why People Believe Weird Things to see how Michael Shermer has updated his section on creationism to mention "intelligent design" as a new form of creationism and most of his criticisms of creationism have no bearing at all on intelligent design.  (I believe the ones that do have some sort of bearing are --as stated--strawman arguments or weakly applied to ID, but they could at least be developed in some way; the others are complete non sequiturs.)  But it's important to take evolutionist Michael Behe and pin a Duane Gish nametag to his chest and continue the debate from there.

Otherwise, what is the point of trying to discredit intelligent design with the guilt by association argument.  Association with Protestant fundamentalism.  If most people who find the courage to speak out against a sketchy scientific program -- in the face of great risk to their careers -- happen to do so because of a matter of faith, why does that become legal grounds for invalidating a cause?
Justice Scalia has a reputation for throwing attorneys off-balance with elaborate hypothetical questions. True to form, he posed for Topkis a long hypothetical question—for the purpose, presumably, of demonstrating that a law could have a religious motivation and yet be constitutional. “Let’s assume,” he began, “that there is an ancient history professor…who has been teaching that the Roman Empire did not extend to the southern shore of the Mediterranean in the first century A.D. And let’s assume a group of Protestants who are concerned about that fact, inasmuch as it makes it seem that the Biblical story of the crucifixion has [the] thing a bit wrong.” Concluding his story, Scalia tells Topkis that the upset students march “to the principal of the school, and say, ‘This history teacher is teaching what is just falsehood.’ And the principal says, ‘Gee, you’re right.’ And he goes and directs the teacher to teach that Rome was on the southern shore of the Mediterranean in the first century A.D.” The principal’s order was “clearly” religiously motivated, Scalia asserted, but wouldn’t it also, he asked, be constitutional?
Sometimes the only ones that will put up much of a fight are those who have a big stake in the outcome.  In spite of our First Amendment (and ironically, using an odd interpretation of it), those who have such a stake are often denied a voice precisely because of that stake.  Hmmm.

I think skepticism against Darwinism is nonetheless gaining momentum outside the Protestant faithful.  Thomas Nagel, a leading atheist philosopher, has joined the ranks of the secular creationists:
I realize that such doubts [about Darwinian naturalism] will strike many people as outrageous, but that is because almost everyone in our secular culture has been browbeaten into regarding the reductive research program as sacrosanct, on the ground that anything else would not be science.
No kidding.  In his Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False, Nagel has joined this mystical splinter cult of Protestant fundamentalism. He's even made given a "pernicious" and "dangerous" commendation to some of the intelligent design advocates at Discovery Institute.  One of the many who pretend to not be a Protestant fundamentalist in order to "mainstream" a thinly disguised form of Biblical literalism.

Can you say "bugaboo," kids?  I knew you could.  

Coyne also bizarrely characterizes Berlinski as a “creationist,” and a “defender” of Intelligent Design theory. In fact, he is neither. The notion that Berlinski is a “creationist” is nothing short of laughable and while “sympathetic” to ID, he is by no means an advocate of the theory, much to the chagrin of his colleagues at the Discovery Institute. 
Moshe Averick