Carnivalia, and an open thread

Behe has a new book; it's awful; Film at 11.

Loch Ness monster on a rampage

Loch Ness monster on a rampage

LOL Did you actually SEE the footage? I blogged it yesterday, there are links to the BBC video of the interview and the actual footage. I remain unimpressed.

I have not seen the footage. Has it made its way to YouTube yet?

Please excuse the self-serving nature of this but here is a five part logicical argument I posted on Telic Thoughts...
http://telicthoughts.com/id-and-consciousness/#comment-109699

I am an Atheist and, according to many TTers, an "ID Critic". Here in Pharyngula, I have been called a "Quantum Quack".

It looks like the Penrose/Hameroff model is the Red-headed step child everyone wants to ignore and hope will go away.

TT's MikeGene responded to my prodding for a reaction with...

They are interesting and thought provoking; I gave you the thread, didn't I? Why not see if PZ will provide you the same opportunity?

So, Dr. Myers, I thought I would give you an opportunaty to react.

React? To what? Penrose-Hameroff are babbling nonsense that has no connection at all to what we know about how the brain works. Quantum effects in microtubules are going to be inconsequential relative to ion fluxes and chemical changes in membrane properties and channels, and there is no explained mechanism to regulate quantum effects. It's like trying to explain the tides by speculating about the dabbling of gnats in estuaries.

The people who talk about this stuff usually seem to have absolutely no knowledge of neuroscience. Talk to me again when you've read Kandel and can explain what quantum fluxes in microtubules adds to our understanding of how neurons work, because none of the stuff you've said or linked to on TT shows any understanding of the basics.

When you have, physicists, neuroscientists, mathmeticians and biologists telling you it doesn't make any sense.

You might want to consider that you're probably NOT onto something.

I gored the spelling of mathematicians. I apologize to the maths guys.

Hi PZ Myers,

Thank you for responding.

I have no doubt that you know more about microtubules than I do. I will have to trust that you know more about them than Dr. Hameroff. I have a little more difficulty in trusting that you know more about Quantum Physics and mathematics than Penrose.

All I can do is my best. I am reading both sides of the issue and I grant you the details on Hameroff's presumptions about neurons are shaky at best.

I will read up on Kandel and "get back to you". Please note, I said very little about microtubules in my TT comments.

It is Penrose's ideas about the possibility of non-algorithmic processes in nature that intrigue me the most.

Are you certain Penrose has nothing to offer to the field of biology?

Quantum effects in microtubules are going to be inconsequential relative to ion fluxes and chemical changes in membrane properties and channels [...] The people who talk about this stuff usually seem to have absolutely no knowledge of neuroscience.

Those people also usually seem to have absolutely no knowledge of physics.

Mainstream physicists are frankly tired about the amount of quantum woo flung around as so much poop, and Max Tegmark even took the time off from cosmology to write a paper showing why Penrose's and similar ideas simply doesn't work as stated.

Based on a calculation of neural decoherence rates, we argue that that the degrees of freedom of the human brain that relate to cognitive processes should be thought of as a classical rather than quantum system, i.e., that there is nothing fundamentally wrong with the current classical approach to neural network simulations. We find that the decoherence timescales ~10^{-13}-10^{-20} seconds are typically much shorter than the relevant dynamical timescales (~0.001-0.1 seconds), both for regular neuron firing and for kink-like polarization excitations in microtubules. This conclusion disagrees with suggestions by Penrose and others that the brain acts as a quantum computer, and that quantum coherence is related to consciousness in a fundamental way. [ Bold added; http://arxiv.org/abs/quant-ph/9907009 ]

(And he has followup papers at http://space.mit.edu/home/tegmark/brain1.html where he answer some critics.)

In short, quantum coherence effects disappears way too fast to couple to other effects in the brain and make a difference in function. Even on the smallest structures imaginable having any function at all.

The picture of lack of physics knowledge is specifically strengthened when the referenced comments on Telic Thoughts discuss "randomness" without defining it. Randomness has no specific definition in physics, so it could be equi-probability, non-predictability, non-determinism, ... Here it is confused with pseudorandomness, at which point I lost interest in reading further.

Unfortunately Thought Provoker doesn't provoke any thoughts. Actually, I think Quantum Quack may be too charitable here, because some of those can like Penrose make some interesting observations amidst the woo.

Seems that I was too harsh on Thought Provoker who now shows a willingness to consider the matter. I can't say that any specific claim of mine is wrong, but it puts a new angle on the proficiency. One must learn to walk before running.

Good luck on your studies, TP, and FWIW AFAIK Tegmark's paper is the current answer from the physics consensus to Penrose et al; I'm not aware of any valid criticism of it.

New astronomy and space podcast. From Chris Lintott (BBC Sky at Night) and Harriet Scott (Heart FM radio). Sould be interesting as it develops.

http://www.livingspaceonline.com/?p=5

Um, I am reminded of PZ's "three comments before flinging mud". Speaking of studies, it seems I am a slow learner. :-|

On another topic, PZ or others, do you have any comments about the hox-genes-in-paddlefish article? I'm linking to Glen Laden's post about it; he links to a press release. Apparently, paddlefish have two sets of hox genes and one of them was re-purposed to produce wrist or ankle bones for early tetrapods. Zebrafish have one set, if I read the press release correctly. The paper is published in the May 24, 2007, issue of Nature: "An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish," by Marcus Davis, Randall Dahn, and Neil Shubin. It provides evidence to confirm "Accepted theory among scientists... that the pattern of Hox gene expression seen in zebrafish represents the primitive condition for the fin in any vertebrate, and the group leading to tetrapods elaborated on this Hox expression by adding a second phase and added to the skeletal pattern."

Just a cute picture, squid related.

Hi Torbjörn Larsson,

Seems that I was too harsh on Thought Provoker who now shows a willingness to consider the matter.

You thought THAT was harsh? ;)

I have been been an ID pest since the Dover trial. It would take more than that to make even a small dent.

Good luck on your studies, TP, and FWIW AFAIK Tegmark's paper is the current answer from the physics consensus to Penrose et al; I'm not aware of any valid criticism of it.

Thank You. I had already looked into the Tegmark paper. I thought is was more damaging to Hameroff than Penrose. However, I will look again.

I will also rereview what I thought were "valid" answers to Tegmark.

Here are videos from Beyond Belief 2006. Hameroff presents on Sunday, November 5, Session 4. Stick around, or fast forward through his talk, and see how the Q&A session goes. Nobody is buying this.

Daniel Dennett, in his book Darwin's Dangerous Idea, addresses whether Penrose has made any contribution to biology, which is definitely is not Penrose's field of expertise.

video of the interview of the "monster hunter" who took the footage of the "loch ness monster" and actual footage available HERE ON THE BBC SITE the two videos you are looking for are What's that? Is it a monster? and Is it Nessie... or just an otter?. Enjoy ;)

The Mind Outside The Brain (Part 1)

Deepak Chopra - June 01, 2007

"By now everyone is familiar with advances in brain imaging and the fascinating insights being produced in many areas of brain research. Much less known are advances in locating the mind outside the brain. Long considered paranormal and therefore easy to dismiss, the reality of many phenomena is being verified. For a long time there has been a popular belief in ESP, clairvoyance, and related abilities. I thought it would be interesting to devote a series of posts to some intriguing studies, but more importantly, there is a major discovery waiting around the corner. Science is about to realize that intelligence is a field effect and that this "mind field" surrounds us on all sides, like the earth's magnetic field. It is thanks to the mind field that our brains are able to think and also to connect with other minds, not by physical means but invisibly, the way one magnet is connected to every other on earth."

"The latest findings, which got wide publicity in the media, have to do with our ability to sense what is going to happen in the future. "Is this REALLY proof that man can see into the future?" (http://www.dailymail.co.uk/pages/live/articles/technology/technology.ht…)
London's Daily Mail reports on a Dutch professor of psychology, Dr. Dick Bierman, who is using real-time brain scans to see if people sense things before they happen. "Sense" is different from "envision." Bierman is working with "presentiment," the physical or emotional feeling that something unusual is about to happen. Anecdotally, presentiments have been associated with many if not most great disasters. Some people didn't go to work at the World Trade Center on 9/11 because they felt suddenly sick or uneasy."

How far does this phenomenon extend, and what is its deeper significance?

http://www.huffingtonpost.com/deepak-chopra/the-mind-outside-the-body_b…

"Is this REALLY proof that man can see into the future?"

http://www.dailymail.co.uk/pages/live/articles/technology/technology.ht…

The paper is published in the May 24, 2007, issue of Nature: "An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish," by Marcus Davis, Randall Dahn, and Neil Shubin. It provides evidence to confirm "Accepted theory among scientists... that the pattern of Hox gene expression seen in zebrafish represents the primitive condition for the fin in any vertebrate, and the group leading to tetrapods elaborated on this Hox expression by adding a second phase and added to the skeletal pattern."

Not quite, it disconfirms the previously accepted theory! Both paddlefish and tetrapods were found to have 2 phases which is likely to be the primitive condition.

Monado:

I tried to raise the issue on another thread, since it is interesting in that it shows another model organism that may be special. Though as windy notes, the authors shows (or at least speculates in the press release) that the paddle fish pattern may be the more basic one, being lost in some cases.

Just as tetrapods went off and did something crazy with their fin by adding to it, zebra fish went off and did something crazy by losing part of their fin. So the innovation here is about a pattern of loss of gene activity [for the zebrafish] and not a pattern of acquisition [for tetrapods].

Also I am reminded of PZ's posts on Drosophila and similar specialty, there IIRC probably caused by fast growth. Could it be a similar case? Or did it happen anyway? It may be harder or impossible to sort out.

Thought Provoker:

You thought THAT was harsh? ;)

Well, too harsh anyway. I am a sucker for people who tries to learn new stuff or at least reconsider old knowledge. What can I say, it is probably my inner academic. :-)

I am glad you have enough skin to take other mistakes.

"other mistakes" - others mistakes.

Anecdotally, presentiments have been associated with many if not most great disasters. Some people didn't go to work at the World Trade Center on 9/11 because they felt suddenly sick or uneasy.

And I didn't go to work one day this past winter because I thought I was coming down with the flu.

Nobody crashed a plane into Cambridge, Massachusetts that day.

This is one of those times when I wish I could be calm, fatherly and Saganesque. But no, all my brain does is scream, "Fucking credulous imbecile newspapers telling lies to people who pay dearly for the privilege. Fucking iron heel of stupidity grinding down every chance we'll ever get of a noble destiny or even common decency. Fucking leeches giving false hope to people who desperately need the real thing. Motherfucking Deepak Chopra!"

(Spider Jerusalem is my co-pilot.)

If we were to judge by his Turing arguments, we'd have to conclude that Penrose didn't even understand the math. If there wasn't extensive and compelling evidence that he's a polymath, we'd reject him as a complete fool.

Which goes to show: no person is so smart that they're beyond being stupid.

the authors shows (or at least speculates in the press release) that the paddle fish pattern may be the more basic one

Should have read that release again, (or, better, the paper, :-) since it states clearly that the paddle fish is to be considered as a proxy for a more primitive fish.

"It is Penrose's ideas about the possibility of non-algorithmic processes in nature that intrigue me the most."

However fascinating they may be, they're entirely conjectural. Penrose's idea is basically that we'll discover these non-algorithmic effects in a future theory of quantum gravity. That sort of speculation would be baseless if not for his utterly faulty arguments from Goedel's incompleteness result.

Penrose may be a brilliant mathematician and physicist, but his ideas on AI and brain function are woo.

Hi All,

It is the Quantum Quack again.

I wasn't surprised that PZ's "read Kandel" was his way of telling me to go learn the basics. Both sides of the argument are quoting Kandel. At this point, I am not overly worried about whether or not the brain is too noisy or too hot. I am more focused on Penrose.

For the part I am interested in Tegmark supports Penrose's specific gravity theories. Tegmark just disagrees that it will work on Tubular Dimers the way Hameroff says it will.
Tyler DiPietro wrote...

However fascinating they may be, they're entirely conjectural. Penrose's idea is basically that we'll discover these non-algorithmic effects in a future theory of quantum gravity. That sort of speculation would be baseless if not for his utterly faulty arguments from Goedel's incompleteness result.

Penrose may be a brilliant mathematician and physicist, but his ideas on AI ... are woo.

This is the part I am having problems seeing where Penrose is making a weak argument. It seems to me that the Goedel's incompleteness theorem means something. I understand Penrose has made the argument against Strong AI based on the logic found here...
http://planetmath.org/encyclopedia/StrongAIThesis.html

Appealing to weak AI is fine, but that is an admission that existence of non-algorithmic processes is possible.

I understand Penrose to be saying that means the possibility is not metaphysical but real.

I find his example of the Penrose Tilings compelling. Penrose, himself, figures out the two shapes and associated rules that fulfill the aperiodic tiling problem. Ten years later, it shows up in a crystal formation thought impossible by mineralogists.

Penrose says the solution to the aperiodic tiling problem can not be solved algorithmically for the general case.

Is he correct?

If he is, why is it such a stretch to think it is a reasonable presumption that if non-algorithmic processes are possible quasicrystals might be due to a non-algorithmic process?

Provoking Thought.

TP,

There are tow obvious problems with the argument your cite makes.

1. It makes the assumption that our minds must be "consistent algorithms" to make strong AI possible. The problem is that Goedel's incompleteness result does not apply to "consistent algorithms" but a consistent fixed formal system powerful enough to state basic arithmetical truths about the natural numbers. In fact, I'd like more info on how "inconsistent algorithm" is defined. Conjecturally, it could apply to approximation algorithms for problems in the class NP for which there are no known polynomial time solutions, but that would be more accurately called an "inconsistent problem" IMO. The idea of an "inconsistent algorithm" sounds incoherent almost on it's face. But I need more info.

2. We don't have to accept the consistency requirement for a strong AI. One of the aspects of the argument that I'm never seen AI opponents adequately justify is why a computer emulating a mind would have to work in a fixed formal system, a la ZFC.

As for the Penrose tiling problem is interesting, but I would say that an intractable problem doesn't prove Penrose's case. The problems in the class NP but not in P (assuming P is a proper subset of NP, which itself has of course not yet been proven) could very well be intractable. What Penrose relies on in not the existence of intractable problems but the brain being able to solve those problems. And in that, he's hardly proven his case. I find his Goedel argument faulty for the reasons outlined above.

One other thought: one aspect of aperiodic tilings is that they can use prototiles that are periodic locally but force a global pattern that is aperiodic. This relates to the problem is that the "mind" doesn't itself have to be an algorithm but rather a peripheral effect of other working algorithms. Something to consider.

Hi Tyler,

You wrote...

the Penrose tiling problem is interesting, but I would say that an intractable problem doesn't prove Penrose's case. The problems in the class NP but not in P (assuming P is a proper subset of NP, which itself has of course not yet been proven) could very well be intractable. What Penrose relies on in not the existence of intractable problems but the brain being able to solve those problems. And in that, he's hardly proven his case. I find his Goedel argument faulty for the reasons outlined above.

Thank you for responding. Other than your disagreement with the Goedel argument, I think you and Penrose are in basic agreement.

Of course Penrose can't prove what he thinks in unprovable. He can only show "interesting" examples. And, yes, I realiZe how this sounds like familiar "woo".

This should not be surprising considering that I started with the ID "argument". Penrose is thinking past his Specific Gravity hypothesis and looking into possible implications assuming it is correct. The self collapse of quantum states is being scientifically accepted (e.g. Tegmark) as a given. Unlike other "woo", quantum waveform collapse is scientifically testable and is being tested.

It may be unpopular, but "quatum weirdness" properties like non-locality and non-algorithmic may be reality.

This is the part I am having problems seeing where Penrose is making a weak argument. It seems to me that the Goedel's incompleteness theorem means something.

Of course it means something. That "something" has nothing to do with what Penrose thinks it implies.

In what meaningful way is quantum behavior "non-algorithmic"? I can certainly deduce key properties of a quantum phenomenon using an algorithmic approach: solve the Schroedinger Equation for the given potential, square the wavefunction to get a probability, etc.

Other than your disagreement with the Goedel argument, I think you and Penrose are in basic agreement.

Except for the central premise of the argument, everybody agrees. How wonderful.

Unlike other "woo", quantum waveform collapse is scientifically testable and is being tested.

The "collapse of the wavefunction" is the very opposite of woo. It is a central postulate in a well-verified description of the physical world. In a way, wavefunction collapse is like sex: we know it has to happen, but why it does or does not occur under particular circumstances is a question worth exploring further.

From Thoughts from Kansas:

Creekstone Farms wants to test every steer they slaughter for mad cow disease. The USDA, under pressure from larger meatpackers, says they can't

Hi Black Stacey, you wrote...

The "collapse of the wavefunction" is the very opposite of woo. It is a central postulate in a well-verified description of the physical world.

I agree with you, but others don't. They claim it is only metaphysical hand waving and not real. I suspect some of them don't like the dominoes they see lined up. Here is wikipedia's version of the dominoes falling. The first domino...

The threshold for Penrose OR is given by the indeterminacy principle E=ħ/t, where E is the gravitational self-energy (i.e. the degree of spacetime separation given by the superpositioned mass), ħ is Planck's constant over 2π, and t is the time until OR occurs. Thus the larger the superposition, the faster it will undergo OR, and vice versa. Small superpositions, e.g. an electron separated from itself, if isolated from environment would require 10 million years to reach OR threshold. An isolated one kilogram object (e.g. Schrodinger's cat) would reach OR threshold in only 10-37 seconds. Penrose OR is currently being tested.

Ok so far? Good, the next domino...

An essential feature of Penrose OR is that the choice of states when OR occurs is selected neither randomly (as are choices following measurement or decoherence) nor completely algorithmically. Rather, states are selected by a "non-computable" influence involving information embedded in the fundamental level of spacetime geometry at the Planck scale.

Getting nervous yet? The next domino...

Penrose argued that quantum computation which terminated not by measurement, but by his version of objective reduction, constituted consciousness (allowing Platonic non-computable influences). Penrose had no definite biological qubits for such quantum computation by OR, except to suggest the possibility of superpositions of neurons both "firing and not firing"

Is the "woo" detector going off yet? Hameroff helps with the next domino...

For biological qubits, Penrose and Hameroff chose conformational states of the tubulin subunit proteins in microtubules. Tubulin qubits would interact and compute by entanglement with other tubulin qubits in microtubules in the same and different neurons.

Of course, this is where Penrose is out of his element and Hameroff doesn't have enough reputation or evidence to counter the loud skeptics.

Right now I am trying to verify the second domino. Is the waveform collapse algorithmically incomplete and non-random? It might help explain the formation of quasicrystals as Penrose has argued.

For the part I am interested in Tegmark supports Penrose's specific gravity theories.

Um, how did we get from quantum mechanics to gravity theories? Are you discussing Penrose's twistor suggestions for quantum gravity? What this has to do with the brain eludes me.

As I noted Tegmark's analysis shows that quantum coherence effects disappears way too fast to couple to other effects in the brain and make a difference in function. This covers Penrose's quantum ideas on brains.

It seems to me that the Goedel's incompleteness theorem means something.

Gödel's incompleteness theorems has nothing to do with physics. All they say is that formal systems can be complemented if we want or need, with theorems that we discover we can't prove. In effect, formal systems have enough power to describe anything we want them to.

However, ordinary arithmetic (Peano's axiom) are enough to do physics. The map is not the territory.

"quatum weirdness" properties like non-locality and non-algorithmic may be reality

We know that quantum theory is non-local. What is forbidden is local hidden variables, what is shown is non-local correlations. The same goes for collapse, it exists. Further, there are currently many interpretations that are compatible with experiments, and we can't distinguish between them.

Really, it seems to me that you throw in any catch word you can to support your argument, which basically is an argument from ignorance: "I can't understand how the brain works classically". (Which btw makes it rather boring to discuss at length, if you concede one point you just add a new one.)

Well, biologists can.

Quantum effects in microtubules are going to be inconsequential relative to ion fluxes and chemical changes in membrane properties and channels [...] The people who talk about this stuff usually seem to have absolutely no knowledge of neuroscience.

Those people also usually seem to have absolutely no knowledge of physics.

Mainstream physicists are frankly tired about the amount of quantum woo flung around as so much poop, and Max Tegmark even took the time off from cosmology to write a paper showing why Penrose's and similar ideas simply doesn't work as stated.

Based on a calculation of neural decoherence rates, we argue that that the degrees of freedom of the human brain that relate to cognitive processes should be thought of as a classical rather than quantum system, i.e., that there is nothing fundamentally wrong with the current classical approach to neural network simulations. We find that the decoherence timescales ~10^{-13}-10^{-20} seconds are typically much shorter than the relevant dynamical timescales (~0.001-0.1 seconds), both for regular neuron firing and for kink-like polarization excitations in microtubules. This conclusion disagrees with suggestions by Penrose and others that the brain acts as a quantum computer, and that quantum coherence is related to consciousness in a fundamental way. [ Bold added; http://arxiv.org/abs/quant-ph/9907009 ]

(And he has followup papers at http://space.mit.edu/home/tegmark/brain1.html where he answer some critics.)

In short, quantum coherence effects disappears way too fast to couple to other effects in the brain and make a difference in function. Even on the smallest structures imaginable having any function at all.

The picture of lack of physics knowledge is specifically strengthened when the referenced comments on Telic Thoughts discuss "randomness" without defining it. Randomness has no specific definition in physics, so it could be equi-probability, non-predictability, non-determinism, ... Here it is confused with pseudorandomness, at which point I lost interest in reading further.

Unfortunately Thought Provoker doesn't provoke any thoughts. Actually, I think Quantum Quack may be too charitable here, because some of those can like Penrose make some interesting observations amidst the woo.

Seems that I was too harsh on Thought Provoker who now shows a willingness to consider the matter. I can't say that any specific claim of mine is wrong, but it puts a new angle on the proficiency. One must learn to walk before running.

Good luck on your studies, TP, and FWIW AFAIK Tegmark's paper is the current answer from the physics consensus to Penrose et al; I'm not aware of any valid criticism of it.

Um, I am reminded of PZ's "three comments before flinging mud". Speaking of studies, it seems I am a slow learner. :-|

Monado:

I tried to raise the issue on another thread, since it is interesting in that it shows another model organism that may be special. Though as windy notes, the authors shows (or at least speculates in the press release) that the paddle fish pattern may be the more basic one, being lost in some cases.

Just as tetrapods went off and did something crazy with their fin by adding to it, zebra fish went off and did something crazy by losing part of their fin. So the innovation here is about a pattern of loss of gene activity [for the zebrafish] and not a pattern of acquisition [for tetrapods].

Also I am reminded of PZ's posts on Drosophila and similar specialty, there IIRC probably caused by fast growth. Could it be a similar case? Or did it happen anyway? It may be harder or impossible to sort out.

Thought Provoker:

You thought THAT was harsh? ;)

Well, too harsh anyway. I am a sucker for people who tries to learn new stuff or at least reconsider old knowledge. What can I say, it is probably my inner academic. :-)

I am glad you have enough skin to take other mistakes.

"other mistakes" - others mistakes.

the authors shows (or at least speculates in the press release) that the paddle fish pattern may be the more basic one

Should have read that release again, (or, better, the paper, :-) since it states clearly that the paddle fish is to be considered as a proxy for a more primitive fish.

For the part I am interested in Tegmark supports Penrose's specific gravity theories.

Um, how did we get from quantum mechanics to gravity theories? Are you discussing Penrose's twistor suggestions for quantum gravity? What this has to do with the brain eludes me.

As I noted Tegmark's analysis shows that quantum coherence effects disappears way too fast to couple to other effects in the brain and make a difference in function. This covers Penrose's quantum ideas on brains.

It seems to me that the Goedel's incompleteness theorem means something.

Gödel's incompleteness theorems has nothing to do with physics. All they say is that formal systems can be complemented if we want or need, with theorems that we discover we can't prove. In effect, formal systems have enough power to describe anything we want them to.

However, ordinary arithmetic (Peano's axiom) are enough to do physics. The map is not the territory.

"quatum weirdness" properties like non-locality and non-algorithmic may be reality

We know that quantum theory is non-local. What is forbidden is local hidden variables, what is shown is non-local correlations. The same goes for collapse, it exists. Further, there are currently many interpretations that are compatible with experiments, and we can't distinguish between them.

Really, it seems to me that you throw in any catch word you can to support your argument, which basically is an argument from ignorance: "I can't understand how the brain works classically". (Which btw makes it rather boring to discuss at length, if you concede one point you just add a new one.)

Well, biologists can.