Monday, April 24, 2017

Programming Intelligence

Consider the use of cellular automata not simply, for artificial life, but for artificial intelligence.

How much programming does a cell need to develop into an animal of a given intelligence?

Saturday, April 22, 2017

PZ Myers' Potty Mouth Proves Behe Right (or Mushroom Stories)

Years ago, in a court opinion stolen straight from the ACLU's amicus brief, Judge Jones the III claimed that ID could not be science because the ID scientists had not yet done the work in the lab of showing by experiment what natural selection could not do. 

Later Michael Behe would criticize Judge Jones' opinion on the grounds (among others) that that sort of lab work, while important, would produce results which would be simply be dismissed by critics as a failure to find the right conditions for evolution.
(13)  As a further example, the test for ID proposed by both Professors Behe and Minnich is to grow the bacterial flagellum in the laboratory; however, no-one inside or outside of the IDM, including those who propose the test, has conducted it. (P-718; 18:125-27 (Behe); 22:102-06 (Behe)). 
If I conducted such an experiment and no flagellum were evolved, what Darwinist would believe me? What Darwinist would take that as evidence for my claims that Darwinism is wrong and ID is right?

Prophetic!  Douglas Axe and Anne Gauger worked out just such an experiment, and only a prophet could have anticipated the response by the true believers in adaptationism.
Myers' argument gone to pot

At Panda's Thumb, P.Z. Myers dismisses Axe and Gauger's results as having a flawed protocol and points to a paper criticized in their work as succeeding where they failed:

Gauger and Axe are saying, "Ooh, we sh** in a pot and we couldn't even get mushrooms to grow in it,". . .
Meanwhile, the paper P.Z. Myers swoons over is about postulating lineages from an ancestral lineage.  How?  By working against natural selection and de-optimizing the effectiveness of the proteins.  (Note: Inventing a story about the improbable way the mushrooms must have grown is not the same as growing the mushrooms.)  Why did the proteins get just the changes that would make them sub-optimal in the right (pre-adaptational) way without breaking them, but preparing them?  Wouldn't the sub-optimality have made the organisms targeted for removal from the gene pool?  I know, I know... only an evolution denier would see a problem with that.  But why does natural selection stop doing its job precisely when Evolution needs it to? 

Paul Nelson's "Outrageous Lies"

Demonizing anyone advancing a teleological point of view is something that the neo-Darwinist research program has accomplished well.  Keep the debate focused on your opponents, and make your opponents look bad. 

Ed Brayton on ScienceBlogs claims to have found more evidence of "lying for Jesus":

Keith Miller said absolutely nothing that even remotely resembles what Nelson claims. Nelson, much to my surprise, was telling a baldfaced lie in order to make Keith Miller look foolish . . .  So not only did Miller not deny that a thief had stolen the items from his car . . . he explicitly agreed that a thief had stolen them. Nor did he claim that a “natural regularity” occurred. What he did dispute is the notion that human actions are somehow outside of the sphere of natural explanations.
Paul Nelson, apparently for comic effect, innocently if carelessly, states that Keith Miller (not to be confused with Kenneth Miller) would not phone the police if a thief broke into his car, since there is nothing about the evidence of the act---no inherent property of purposeful intent distinguishing it from any other natural cause--and, as Miller himself seems to explain this makes sense since a thief is just another bit of the natural world.  

Friday, April 21, 2017

Is Evolution 2.0 Question-Begging?

Oh, ok. So you're gonna make a lot of money, right? 
Right. It's not yours? 
Uh...Well, it becomes ours. 
How is that not stealing?
... Uh, I'm not explaining this very well.

How did evolution come about?  Well, you see, first there were cells that became smart enough to evolve and then they evolved to become even smarter at evolving.  Until they're super-smart!  See?  ... Hmmm.  This sounds awfully familiar.  
I fully understand that how cells got to be so smart is a HUGE unanswered question. I agree that information always infers intelligent agents. And perhaps God is the answer. But my position is that living things are agents too and we can and should trace the progress from one evolutionary step to the next. I invite you to consider that the capacity cells have to evolve is a far more impressive miracle than, say, God beaming Zebras on to the savanna Star-Trek style where they suddenly appear eating grass.
It's not simply A huge unanswered question.  It is THE critical problem in terms of this "third way" approach having any real explanatory value in terms of purportedly supplying the completely naturalistic account for life that scientists have been purporting neo-Darwinism to be.  When you find a robot factory in the woods, is its presence there explained by the "fact" that the robots seem super-sophisticated?  It isn't explained by attributing intelligence to the obviously sophisticated factory.  It isn't even explained by attributing intelligence to the woods themselves.    

Tuesday, April 18, 2017

Does Perry Marshall Mispresent Intelligent Design?

The challenge continues to understand Perry Marshall's quasi-ID point of view.  It is almost as if Marshall is saying that rarefied design is philosophical proof of God's existence but of necessity there can be no be scientific proof of actual design because scientists "can't get a paycheck" with that sort of thing.  (While I disagree with Marshall on this point, I think he's hit upon something important: who, ultimately, is paying for the science--e.g. Joe Taxpayer--and what sort of science would they like their money spent on?)

At any rate, a possible elucidation of Marshall's antipathy toward the ID movement shows up in a response to a commenter's opinion about whether it makes more sense to attribute the intelligence to the evolving cells than to an "omniscient" designer's influence.  Marshall effuses

Saturday, April 15, 2017

A Response to Perry Marshall

Part of my response (in moderator limbo since the first week of April) to Perry Marshall's explanation is below.  Marshall seems to argue on his blog that unless we attribute/limit all the intelligent design in macroevolutionary diversity to intelligence that is in the evolving organisms themselves, the recognition of intelligent design becomes a science-stopping God-of-the-gaps philosophy of science.
It is hard to understand your position in a way because sometimes you seem to making a design argument, and sometimes you seem to be arguing like Ken Miller that any influence God has had on history must somehow be undetectable. [Note: Actually, this is probably more like a BioLogos argument; Miller might argue that God refused to interfere with history altogether before Biblical events.] Near as I can tell, your version of a 3rd way is an attempt to keep theists from disengaging from the facts and/or basing their faith on certain scientific mysteries remaining mysteries. I can sympathize with that. In some ways you seem to be saying that the evidence for intelligent design stands regardless of the time frame that the information is put into the system. A lot of ID people would be on board with you there—except that most wouldn’t _require_ that the information be limited to the law-like behaviors of the universe and have specific evidential reasons (which you and others may disagree with) for rejecting that limitation.

Whether there is a coherent 3rd way depends on precisely what _is_ being added to the table and whether it is something more than a porridge of what is already on the table. It depends on whether one is proposing some sort of law that explains how watch-innovating factories are plausible (not merely possible) with no guiding influence. The reference to the Biocentrism book makes me suspect that the third thing being put on the table is a conscious universe akin to the thoughts of Thomas Nagel or Rupert Sheldrake, but somehow more dependent (in an unclear way) on material mechanisms. The problem with Sheldrake’s ideas (aside from the lack of academic engagement) is that they don’t present anything more clear than I have so far heard about the third way, although some of the things you’ve written sound like a front-loaded ID position. Positing a consciousness in cells and then arguing that cells can perform macroevolution over deep time because they are conscious, creative geniuses — if that is the hypothesis — is an intriguing hypothesis but seems like another extraordinary claim in need of extraordinary evidence.  If the “weak version” of 3rd Way is that “consciousness needs to be considered as a fundamental part of the problem and not merely epiphenomenal” then that much is easy to agree with. If one is applying the same sort of “in[de]finite departure” extrapolation to cell intelligence (as has been applied to mutation), that is the thing to be proved and that potential explanation has its own problems.

Saturday, April 8, 2017

Significantly more complex V-ATPase

From PLOS One.  Discussed in more detail here
Two very distinct mechanisms, which most likely evolved independently, are employed for ATP-driven H+ pumps: the rotary mechanism of the V-ATPase and the alternating access mechanism used by the P-ATPases (Fig 1). The significantly more complex V-ATPase consists of 25–39 protein chains compared to a monomeric or homodimeric polypeptide for the P-ATPase. The operating mechanism for the V-ATPase is also more elaborate consisting of an electric motor-like rotary mechanism. In contrast, the P-ATPase operates by switching between two (E1 and E2) conformations similar to most allosteric mechanisms.
How do we measure "significantly more complex" in terms of bits? 
Mechanism is discussed in more detail here

Sunday, April 2, 2017

P.Z. Myers and the Bridge Hands Fallacy

In P.Z. Myers' universe all improbable outcomes are equally meaningless.  He states:
If I played bridge very, very fast, dealing out one hand every minute, that means I'd still have to wait 1.1 million years to get any particular hand you might specify ahead of time…and my life expectancy is only on the order of 102 years. Therefore, bridge is impossible. Similarly, if you add up all the nucleotide differences between me and my cousin, the likelihoods of these particular individuals is infinitesimally small…but so what? We're here.
No more unlikely than other hands
If I were to flip a coin 100 times, and the resulting pattern of coin flips exhibited inordinately high randomness deficiency, I could argue that the resulting pattern was no more special than a bit sequence with Kolmogorov complexity K(x) > 92 bits.  Using Myers' logic, that is.

But that would completely miss the point of what randomness deficiency is.  Myers is essentially arguing that since all microstates in a 'gas in a box' are equally unlikely, there isn't anything unusual about ending up in an improbable macrostate (like say, all the gas particles consolidated in one small corner of the box) since that particular microstate is no more unlikely that any of the quadrillions less special microstates.

If I am handed a Rubik's cube in a scrambled state, and I give it 20 turns and find it completely unscrambled, in Myers' world since this unscrambled state is just as likely to be generated as any other cube configuration, most of which are very disordered, we shouldn't be that amazed if the outcome is one of those highly ordered states.

Wait, you may say, don't highly unlikely coincidences happen all the time?  Sure they do.  If you expand your sample space to the space of all events, then there are myriads of ways to be surprised by coincidences--but then the bits of information needed to describe/prescribe exactly which of these quintillions of ways to be surprised was/will be instantiated approaches the logarithm of all the possible ways.   It's a one-in-septillion chance to be surprised in any one way, but you've bought a septillion lottery tickets by being willing to be surprised by any one of them.  But there will still be some limit to the number of lottery tickets even if one's 'universe of discourse' is the known physical universe.  As one approaches the limit of the Universal Plausibility Bound, one starts to exhaust the universe's capacity for producing accidental coincidences.  As the randomness deficiency approaches 450-500 bits, the sequence starts to be inexplicable in terms of chance alone, even with helpful distributions.

See Richard Dawkins below argue that coincidences are meaningless, in a very similar manner to P.Z. Myers, and consider why in a world in which "biology is the study of things that appear to be designed" it is important to be able to dismiss all incredible coincidences.  Are all coincidences meaningless, or do we generally need to apply reason to separate meaningless coincidences from meaningful coincidences?