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  Topic: The Magic of Intelligent Design, A repost from Telic Thoughts< Next Oldest | Next Newest >  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Oct. 14 2007,22:59   

Hi Creeky Belly,

You wrote...
 
Quote
...but decoherence times are much different for this quantum interaction than for say, spin states. I don't think you can just side-step this issue and say you're not worried, there's some real considerations that need to be made when you talk about exactly what is being entangled. Coherence times across molecules run the risk of quickly going into a mixed state (no interference), which is why not everything is connected in a quantum sense. I guess what I'm really trying to say is, I don't really care if you can accept that molecules don't have trouble staying in a coherent state, the evidence is on my side that they have short times at room temperature.

This is why I broke things up into more manageable sub-topics.  I don't understand your fundamental objection to presuming long quantum coherence times for isolated biomolecules.  Here are the two states of tublin dimers...

The peanut-shaped tubulin dimer switches between two conformations in which the alpha monomer flexes 30 degrees from vertical alignment with the beta monomer. These are referred to as open and closed states (Figure 8, Melki et al 1989, Hoenger and Milligan 1997, Ravelli et al 2004). link

Here is the Ravelli 2004 paper showing the two different tubulin dimer configurations.  Ravelli used the terms "curved" and "straight" instead of "open" and "closed".

If I am understanding things correctly.  There isn't much of a question that tubulin dimers exhibit two distinct states.  This appears to be a scientific observation.  What is being questioned is whether superposition of this bend is possible/likely if the tubulin dimers are appropriately isolated.

Not to take too much advantage of your DNA concession, but DNA superposition would be of a similar nature.  We aren't talking spinning electrons here.  We are talking about the physical orientations of biomolecules.

Just look at the pictures in the Ravelli paper.  It just isn't that big of a difference.

Bed Time.  Will comment more tomorrow.

  
creeky belly



Posts: 205
Joined: June 2006

(Permalink) Posted: Oct. 14 2007,23:52   

Quote
If I am understanding things correctly.  There isn't much of a question that tubulin dimers exhibit two distinct states.  This appears to be a scientific observation.  What is being questioned is whether superposition of this bend is possible/likely if the tubulin dimers are appropriately isolated.

Not to take too much advantage of your DNA concession, but DNA superposition would be of a similar nature.  We aren't talking spinning electrons here.  We are talking about the physical orientations of biomolecules.

Maybe I missed something in these papers, but nowhere do I see any discussion of superposition or coherence. There's no evidence that these bends constitute a well defined quantum state.

Never did I say that I thought DNA could maintain coherence, only that it could exhibit and use quantum effects. I believe that's part of the transcription error process, and ultimately the source of the random mutation aspect of evolution.

Again, this needs to be settled in the lab, and since I'm already tied up with another science project, you should get Hameroff to pursue it. Otherwise, we're at an impass, and I don't know how fruitful the rest of the conversations will be. It's nice to think that evolution took advantage of such a powerful tool like quantum computation, but until we can discover the mechanisms and figure out if some glaring barriers are overcome, the point is moot.

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Oct. 15 2007,05:06   

In all of this the first thought I have is that these effects should show up in an MRI machine. I might be wrong, but AFAIK, they don't.

Incidentally, I have no problem with "macroscopic" quantum effects in isolated systems (fullerenes, single molecules etc) or photosynthesis or even DNA (although I'd like to see what specific claims were being made first)  in principle. I also don't have too much issue with really "macroscopic" quantum phenomena, subject as they are to low probability etc (one of the fundamental aspects of the decoherence problem IIRC). My point is that microtubles are big enough and unisolated enough (i.e. they are surrounded by wet, noisy stuff) that any quantum effect should be stark staringly obvious and if we are talking about 25ms timescales, certainly observable by resonance techniques.

I might be wrong, but that is my first impression. IANA quantum physicist however!

Louis

--------------
Bye.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Oct. 15 2007,10:08   

Hi Louis,

You wrote...
   
Quote
In all of this the first thought I have is that these effects should show up in an MRI machine. I might be wrong, but AFAIK, they don't.

Welcome to the frustrating world of Quantum Physics and its measurement problem.

In the opening post of this thread I described my version of the GHZ states (special coins) but pointed out that no peeking was allowed.  This wasn’t a trivial note.  The nature of Quantum Physics is very strict on the no-peeking rule.

Experimenters have been trying to catch particles in the act of going through two slits in superposition for decades.   They have tried every non-evasive trick in the book with no luck.  They have even tried waiting until after the particles have already gone through the slits and it didn’t work.  Google “wheeler quantum delayed choice” and browse the entries.

We are building quantum computers and secured communication devices on the presumption that superposition is a reality even though we have never had it “show up” on countless experimental attempts to get it to do so.

I will attempt in the future to provide further explanations of Hameroff’s description of how tubulin dimers are kept isolated.  However, real life is keeping me quite busy lately.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Oct. 15 2007,11:19   

Hi, TP.

Sorry to have been absent from the conversation. Real life intervened.

Anyway, your last several posts are emblematic of the problems this discussion has suffered from the beginning: reckless extrapolation, misrepresentation of data, assuming facts that aren't established, etc.

 
Quote (Thought Provoker @ Oct. 13 2007,14:36)
Before we review the evidence of living things directly using quantum physics, we need to discuss the concept of decoherence.


As has been stated repeatedly, we know living things use quantum physics. Evidence that photosynthetic complexes use quantum tunneling is not sufficient to support a claim that living things use quantum superpositions of entire proteins to perform quantum calculations. Based on what you've provided to date, as well as everything I've read from Hameroff, Patel, etc., that evidence is entirely lacking. It's pure speculation.

Not that there's anything wrong with speculation per se. But it's ludicrous to use such abject speculation as a basis for claiming that quantum computation in microtubules is the likely basis for consciousness. Absolutely ludicrous.

 
Quote (Thought Provoker @ Oct. 13 2007,14:36)
It is reasonable to presume that tubulins are capable of being in quantum position since similar sized fluorofullerenes exhibit quantum behavior.


No, it isn't! It's ludicrous to presume that a 1634 amu fluorofullerene exhibiting wave-like behavior in a carefully isolated system means that a 110,000 alpha/beta tubulin heterodimer is capable of quantum superposition in any useful sense in the midst of a living cell.

Did you note how the authors boasted that their fluorofullerene was twice as massive as the previous largest molecule to show such effects? Twice. Yet you want to presume similar effects in a molecule more than sixty-seven times larger! In a cell, yet.

 
Quote (Thought Provoker @ Oct. 13 2007,14:36)
DNA provides another possible example of life directly using quantum effects. Patel is refining the model (Grover's algorithm) of the search function inherent in the DNA...


Patel's model is pure speculation, as well as almost certainly wrong. He wants to claim that the cell uses a quantum search function during DNA replication. For that, he needs some sort of superposition of the four different bases, during the "search" to determine which base should be added next.

His original idea was that enzymes would somehow rapidly "cut and paste" functional groups to create an effective superposition of A, G, C, and T. From a biochemical, molecular, and enzymatic perspective, that is just laughable.

Now he apparently realizes that idea is dead wrong, so he's 'refining' the model. But he hasn't even developed a complete model yet, much less provided a realistic link to the known biochemistry of DNA replication.

So, to use Patel's 'model' as a "possible example of life directly using quantum effects" is just more wild extrapolation.

In reality, quantum superposition a la Patel almost certainly plays no role at all in selecting bases during DNA replication. But even on the remote chance that it did, it still wouldn't mean DNA is a quantum computer in any useful sense. At most, DNA would be 'quantum computing' which base to pair with the opposite strand. Big deal.

Quote (Thought Provoker @ Oct. 14 2007,22:59)
I don't understand your fundamental objection to presuming long quantum coherence times for isolated biomolecules.  Here are the two states of tublin dimers...

The peanut-shaped tubulin dimer switches between two conformations in which the alpha monomer flexes 30 degrees from vertical alignment with the beta monomer. These are referred to as open and closed states (Figure 8, Melki et al 1989, Hoenger and Milligan 1997, Ravelli et al 2004).

Here is the Ravelli 2004 paper showing the two different tubulin dimer configurations.  Ravelli used the terms "curved" and "straight" instead of "open" and "closed".


This is a good example of why I am highly skeptical of Hameroff. Note how he states without qualification that the tubulin dimer switches between two conformations. He even cites three papers to support his claim.

However, when you actually read the papers, things aren't quite as simple. Melki proposes a curved state that occurs in subunits that are not part of an intact microtubule. Hoenger and Ravelli each show curvature cause by other molecules binding to tubulin (kinesin and ncd for Hoenger; colchicine and RB3 for Ravelli). Ravelli even states:

Quote (Ravelli @ et al.)
It shows the interaction of RB3-SLD with two tubulin heterodimers in a curved complex capped by the SLD amino-terminal domain, which prevents the incorporation of the complexed tubulin into microtubules.


So, what we really have is a series of reference showing that tubulin can adopt curved structures when it is not part of a microtubule. Yet Hameroff is quite happy to cite them as evidence that tubulin can switch between states within a microtubule. That's disingenuous. And, as we discussed on the previous thread, overstating the evidence is a recurring theme with Hameroff.

It's fun to play "what if" and wonder if there's some connection between consciousness and quantum effects. There's nothing wrong with imagining wild hypothetical scenarios where this might even be true. But it's silly to pretend that such imaginings make it likely, and it's self-deceptive to think that wild extrapolations of known observations constitute evidence.

  
Jim_Wynne



Posts: 1208
Joined: June 2006

(Permalink) Posted: Oct. 15 2007,11:44   

Quote (Thought Provoker @ Oct. 15 2007,10:08)
Welcome to the frustrating world of Quantum Physics and its measurement problem.

Damn, I was hoping that an actual physicist would answer the door. I must be on the wrong floor. This seems to be Being Hit on the Head Lessons.

--------------
Evolution is not about laws but about randomness on happanchance.--Robert Byers, at PT

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Oct. 15 2007,13:24   

Quote (Thought Provoker @ Oct. 15 2007,16:08)
Hi Louis,

You wrote...
   
Quote
In all of this the first thought I have is that these effects should show up in an MRI machine. I might be wrong, but AFAIK, they don't.

Welcome to the frustrating world of Quantum Physics and its measurement problem.

In the opening post of this thread I described my version of the GHZ states (special coins) but pointed out that no peeking was allowed.  This wasn’t a trivial note.  The nature of Quantum Physics is very strict on the no-peeking rule.

Experimenters have been trying to catch particles in the act of going through two slits in superposition for decades.   They have tried every non-evasive trick in the book with no luck.  They have even tried waiting until after the particles have already gone through the slits and it didn’t work.  Google “wheeler quantum delayed choice” and browse the entries.

We are building quantum computers and secured communication devices on the presumption that superposition is a reality even though we have never had it “show up” on countless experimental attempts to get it to do so.

I will attempt in the future to provide further explanations of Hameroff’s description of how tubulin dimers are kept isolated.  However, real life is keeping me quite busy lately.

TP,

Erm, when I said I wasn't a quantum physicist I didn't mean I was someone who didn't know about the double slit experiments and superpositions (to name two examples). But no matter.

The reason I mentioned an MRI machine is precisely BECAUSE of the sensitivity to quantum states that such techniques detect. Take the simple example of the NMR spectra of tertiary amines, we can see the effect of nuclear inversion in nitrogen (which proceeds by tunnelling) on the NMR spectrum. More complicated examples would invlove things like the nuclear Overhauser effect in which we can detect interactions between atoms through space (as opposed to through bonds). In other words we can see if some atoms are near each other in space even if we can't detect interactions between those atoms through the bonding system of the molecule. These quantum effects make detectable signals/signal changes in the NMR, none of them involve "peaking into the box" in the manner you describe.

I'm not denying the existance of superpositions or questioning quantum mechanics (very far from it) I am saying that it seems from what you are saying about quantum effects in microtubules that these things are on the orders of magnitiude of time and size that they would easily be detectable by NMR/MRI. I'm wondering why they haven't been...and "no one can see a superposition" isn't an answer because the question doesn't involve looking for a superposition of states, it involves looking for the effects/decoherence of those superpositions. What you're proposing would be detectable by NMR/MRI, you'd see redundant signals derived from the decohered superpositions. Again, AFAIK we don't. That's a fatal flaw for your claims.

As others have noticed a large number of the phenomena you are referencing are observed under very specific physical conditions. Extending these to the brain simply doesn't work because those conditions aren't present in the brain. We know quantum effects happen in "day to day" chemistry (the whole lot is predicated on it actually) but the claims your making seem to be a little extended beyond the data we have. Again, to reiterate, no one is denying quantum effects in chemistry/biochemistry and no one is saying that we'd have to "do the impossible" and see the cat in the alive/dead superposition.

Cheers

Louis

--------------
Bye.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Oct. 15 2007,13:51   

Hi qetzal,

Thank you for your comment.  You provided some very good points that will take some time for me to respond to.

You correctly pointed out that a tubulin dimer is made up of two tubulin monomers.  This makes for a total mass of 110K amu.

I am adjusting my thinking accordingly.

I will try to respond more fully later.

  
C.J.O'Brien



Posts: 395
Joined: Aug. 2005

(Permalink) Posted: Oct. 15 2007,14:07   

Louis:
Quote
We know quantum effects happen in "day to day" chemistry (the whole lot is predicated on it actually)

A problem I see here is a conflation of two concepts: One is what I'll call "quantum-scale effects," the other is "quantum effects." The former is what Louis is talking about here. It is trivially true that all of nature is ultimately "reducible" to quantum-scale phenomena. What is at issue is whether a description at this level is useful or illuminating. Theoretically, a baseball game  could be described as a series of quantum-scale events. But could you get the kind of information from that description that you can easily get from a good-ol' fashioned box score? No, because it's the wrong level of analysis.

"Quantum effects," on the other hand, are those that become manifest in highly contrived experimental set-ups, and there's no particular justification for appealing to them in a given macroscopic system. Now, if baseballs had the habit of occasionally "tunneling" through the right-field fence, it would be a different story. But for effects that won't happen, by probability, in several million lifetimes of the universe, I say you can safely ignore them as foundational explanatory concepts for systems with viable macroscopic explanations.

--------------
The is the beauty of being me- anything that any man does I can understand.
--Joe G

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Oct. 15 2007,14:41   

Hi Louis,

I am not sure what you are looking for here.  Qetzal brought up the suggestion that the tubulin dimers are always in a given state when assembled as microtubules.  I am looking into that.

Is that what you are talking about?

The interference pattern of the double slit experiment is the indirect evidence of superposition.  Dr. Hameroff suggests that the gamma EEG frequency (30Hz to 80Hz) could be the indirect evidence of tubulin superposition.

I am honestly trying to understand what kind of evidence you think an MRI would be able to detect.  I understand, the existence of Gamma EEG waves correspond to the existence of consciousness (a lack of consciousness means a lack of Gamma EEG and visa-versa).  I am presuming neurologists are looking hard for the fundamental source of Gamma EEG waves using MRI along with every other state-of-the-art instrument that is available.

Is there a better hypothesis for the source of Gamma waves?

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Oct. 15 2007,14:49   

Quote (Thought Provoker @ Oct. 15 2007,13:51)
Hi qetzal,

Thank you for your comment.  You provided some very good points that will take some time for me to respond to.

You correctly pointed out that a tubulin dimer is made up of two tubulin monomers.  This makes for a total mass of 110K amu.

I am adjusting my thinking accordingly.

I think you're missing the much bigger point.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Oct. 15 2007,15:34   

Hi Jam,

"No, I'm not!"

(blame Jim Wynne)

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Oct. 15 2007,20:34   

Hi qetzal,

You wrote...
     
Quote
So, what we really have is a series of reference showing that tubulin can adopt curved structures when it is not part of a microtubule.

After doing some digging I have found that it is generally accepted that intact microtubules contain both configurations of tubulin.  The Alpha tubulin monomer binds with GTP.  The Beta tubulin monomer binds with either GTP or GDP.  If Beta monomer binds with GDP the tubulin dimer is curved.

A microtubule with curved tubulin dimers on the end cap will start falling apart with the curved tubulins becoming loose.  Therefore the end caps of intact microtubules have straight tubulin dimers.  However, the middle section can, and does, contain curved dimers.

Here is a fairly easy to read paper from Mershin, Kolomenski, Schuessler and Nanopoulos titled...

Tubulin dipole moment, dielectric constant and quantum behavior: computer simulations, experimental results and suggestions.

It explains the GDP and GTP binding.  The paper also includes this in its discussion section...
Regardless of whether it turns out that tubulin and MTs are purely classical systems or they have a quantum nature, the excitation and detection of the theory-suggested ’flip waves’ would be an important step towards understanding the role that tubulin and MTs can play as binary switches and networks respectively, both in naturally occurring systems such as living cells as well as in synthesized structures. Note that the energy needed for a tubulin conformational change or ’flip’ is roughly 200 times lower than a conventional silicon-based binary switch, making laser-pulse induced switching feasible. This conformational change energy is also about 30 times larger than thermal noise at room temperature, making the system reasonably resilient to thermal noise.

And its summary section...
Theoretical efforts by us and others have strongly suggested that tubulin is near the "front lines" of intracellular information manipulation and storage. Our group has performed preliminary measurements on tubulin in an effort to supply experimentally determined parameters (such as the refractive index, polarizability and dipole moment) to apply to the various models of tubulin.
...
We used computer simulation to calculate the electric dipole moments of the two tubulin monomers and dimer and found those to be |p?|=552D, |p?|= 1193D and |p??|=1740D respectively. We used refractometry to corroborate our previous SPR-derived result (equation(1)) for ?n/?c ~1.800ml/mg. The refractive index of tubulin was found to be ntub ~2.90 (3) and that gives the high frequency tubulin dielectric constant at ?tub ~8.41 (4). In addition, the highfrequency polarizability was found to be ?tub ~ 2.1x 10-33 C m2/V(5). Several methods were described to determine the low-frequency DC-p as well as to check for both coherence and entanglement among tubulin dimer dipole states. An experiment was suggested whereby using a perforated metal chip layered with a network of aligned MTs, and employing entangled photons in the SPR-exciting laser beam, it can be determined whether surface plasmons interacting with MTs can stay entangled and whether this entanglement can be propagated and conserved by the biomolecules.


In its conclusion...
The electric and energy-transduction properties of tubulin and the polymers it forms are important not only because of the role these play in intracellular protein interactions but also because it may well be that nature has already provided us with suitable nanowires, switches or even logic gates. Beyond the obvious benefit to the credibility or otherwise of the various "quantum brain models", determining the dipole moment of tubulin and its dynamics will further our understanding of tubulin and other similar proteins (such as actin) and will shed light on whether we can use these as the basis of biomolecular electronic circuits of even quantum information processing.
Tubulin, microtubules and the dynamic cytoskeleton are fascinating systems and in their structure and function contain the clues on how to imitate nature in artificially fabricated biomolecular information processing devices paving the way for biobits and perhaps even bioqubits.


While this paper presented a specific positive picture of the Orch OR model, it is just one of many talking about the different types of tubulin dimers that make up microtubules.  Early papers talked about one type for the ends and the other type for the middle, but it was clear it is generally assumed both types are present in an intact microtubule.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Oct. 15 2007,21:55   

Hi TP,

Thanks for the reply (and especially for the Python link!), but I think perhaps you did miss the overall point.

Regarding tubulin:

I wasn't claiming that tubulin dimers don't exist in two (or more) states while part of a microtubule. My point was that Hameroff claimed they clearly did, but the references he cited didn't support his claim. It's poor scholarship to claim that tubulins can be straight or curved in microtubules, and cite references that only show curved states outside tubulins.

Hameroff should have done one of two things. Either cite references that support two states within microtubules, or say that there might be two states within microtubules.

If that was the only case where Hameroff appeared to overstate the evidence, I wouldn't gripe. Unfortunately, it's not. Hopefully you recall that we discussed this on the previous thread. From everything I see, Hameroff shows a recurring pattern of claiming things are a certain way (that coincidentally fits with his hypothesis), when the available or presented data only shows that things could be that way.

People who do that repeatedly don't get the benefit of the doubt from me.

Which leads us the the real issue. I'm not really interested in disputing specific factual claims like "tubulins exist in two or more states in microtubules." That was given as just one example of the fundamental problem.

What I'm really objecting to is the overall rhetorical approach of overstated evidence, unreasonable extrapolation, unwarranted presumptions, and unsupportable claims of likelihood.

You keep citing Hameroff as if he's all but proven quantum superposition in microtubules. The fact is, that's entirely speculative. Your latest cite is more of the same - claims that tubulins might exhibit quantum coherence, along with designs of experiments that might test those claims, but no actual data.

You repeatedly cite Patel as evidence that DNA is 'likely to be' a quantum computer. In fact, Patel is almost certainly wrong, and even if his general idea has some grain of truth, the computing power he's attempting to claim is trivial. How much computation is involved in deciding if A, G, C, or T should be added opposite a given base during DNA replication?

You've cited the photosynthesis study ad nauseum, but the fact is that it has almost no relevance to what you're really trying to show.

I respectfully suggest you admit to yourself the following truth: quantum computing by microtubules may be an interesting speculation, and it may fit well with your belief in quantum interconnectedness, but at present it is virtually pure speculation. The data that's been cited so far doesn't begin to provide actual support for this claim. And until someone gets around to actually performing experiments that directly test these claims, they will remain pure speculation.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Oct. 15 2007,22:48   

Hi qetzal,

You know I am an engineer and not a scientist, right?

That being said.  In 1951, two inexperienced young scientists put together a highly speculative model for the genetics.  The model was humiliatingly wrong.  The two were chastised and told to quit working on it.  However, they were stubborn and after "borrowing" data obtained by more experienced scientists, they got lucky and this time the model they put together resulted in them eventually being awarded the Nobel Prize.

The two scientists, of course, were Watson and Crick and the model was DNA’s double helix.

Stuart Hameroff is 60 years old.  He has been working on this for his entire professional life.  Do you think he really cares whether or not you give him "the benefit of the doubt"?

Sir Rodger Penrose probably cares even less.

Jack A. Tuszynski, Avner Priel, Arnolt J. Ramos, Horacio F. Cantiello, Nancy J. Woolf, Vahid Rezania, Michael Hendzel and others might care.  They are the ones doing the experiments.

I find Orch OR interesting for a couple of reasons.  First of all, it makes for a good hypothetical in the ID/Darwin debates.  Would either side accept this as a reasonable hypothesis?

Second, it is thought provoking both for others and for myself.

Third, it feels right.  The details aren't as important as the fact that things fit together.  Too many questions have gone unanswered for too long.  Orch OR goes a long way to answering the big ones.

Besides, SteveStory said he was looking to provide you guys with something more substantial than the cotton candy opponents you a used to dealing with.

Now if you would rather argue with AfDave....  
:D

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Oct. 16 2007,00:24   

Quote (Thought Provoker @ Oct. 15 2007,22:48)
Hi qetzal,

You know I am an engineer and not a scientist, right?

That being said.  In 1951, two inexperienced young scientists put together a highly speculative model for the genetics.  The model was humiliatingly wrong.  The two were chastised and told to quit working on it.  However, they were stubborn and after "borrowing" data obtained by more experienced scientists, they got lucky and this time the model they put together resulted in them eventually being awarded the Nobel Prize.

The two scientists, of course, were Watson and Crick and the model was DNA’s double helix.

Nice tale. Points for using Watson and Crick instead of Galileo.

Here's another. Once upon a time, there was a brilliant chemist, biochemist, crystallographer, and molecular biologist, all wrapped up in one. He was a pioneer in quantum mechanical treatments of chemistry. He won the Nobel Prize for his work on the nature of chemical bonds. Later, he won the Nobel Peace Prize for his efforts against nuclear testing. He's the only person to be the sole recipient of two Nobels.

The scientist, of course, is Linus Pauling. The list of fundamental discoveries that he made is mind-boggling. And after decades of brilliant accomplishment, do you know what idea he championed at the end of his career? Orthomolecular medicine - the idea that mega-doses of vitamin C could cure colds and cancer. He became so thoroughly enamored of this idea that he apparently forgot the #1 rule in science: data rules.

He was convinced he was right. Thus, anecdotal data that fit his convictions was offered as proof. Data that contradicted him was dismissed as the result of incompetence or even fraud.

I saw him give a talk on vitamin C when I was in grad school. It was quite sad.

The lesson? Ideas in science aren't judged on the people who propose them. They're judged on the data that supports them.

 
Quote
Stuart Hameroff is 60 years old.  He has been working on this for his entire professional life.  Do you think he really cares whether or not you give him "the benefit of the doubt"?

Sir Rodger Penrose probably cares even less.

I don't expect either of them to care what I think. As scientists, I *do* expect them to care about basic scientific principles, such as providing data to support your hypotheses, and fairly distinguishing fact from conjecture.

   
Quote
Jack A. Tuszynski, Avner Priel, Arnolt J. Ramos, Horacio F. Cantiello, Nancy J. Woolf, Vahid Rezania, Michael Hendzel and others might care.  They are the ones doing the experiments.


Great! Let's see some of their results! I'm quite tired of the hand-waving and speculation. What do their experiments actually show?

   
Quote
I find Orch OR interesting for a couple of reasons.  First of all, it makes for a good hypothetical in the ID/Darwin debates.  Would either side accept this as a reasonable hypothesis?


I get the impression that you see this as partly a philosophical debate. Personally, I couldn't care less about the philosophy. I accept the ToE because it's supported by evidence and accurately predicts what we see. I reject ID because it isn't, and it doesn't.

If you show me that Orch OR accurately predicts things that conventional models don't, I'll be much more interested. Until then...

Quote
Second, it is thought provoking both for others and for myself.


Yeah, it's been a more interesting discussion than the typical ID bilge. But for me, it's now pretty tapped out (absent some data...?).

Quote
Third, it feels right.  The details aren't as important as the fact that things fit together.  Too many questions have gone unanswered for too long.  Orch OR goes a long way to answering the big ones.


Hand-waving doesn't really answer any questions. In fact, it's usually just a way to avoid really answering, so we can pretend that the answers we like are true.

If anyone can show that Orch OR accurately predicts things that other models can't, then it will be fair to say that it answers questions. Until then, it's just castles in the air.

   
Quote
Besides, SteveStory said he was looking to provide you guys with something more substantial than the cotton candy opponents you a used to dealing with.

Now if you would rather argue with AfDave....  
:D


AFDave?!! OK, Uncle! You win!

;-)

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Oct. 16 2007,13:26   

Hi qetzal,

Please pardon me for threatening you with AfDave but the point was to put things into perspective.  I'm just an engineer trying to make sense of things.  That, and having some fun being a quasi-troll.

You wrote...
     
Quote
I get the impression that you see this as partly a philosophical debate. Personally, I couldn't care less about the philosophy. I accept the ToE because it's supported by evidence and accurately predicts what we see. I reject ID because it isn't, and it doesn't.

If you show me that Orch OR accurately predicts things that conventional models don't, I'll be much more interested. Until then...

It is the "until then..." where the philosophical battle takes place.  What are the default presumptions?  I am not challenging established ToE principles, neither is Mike Gene.

What is your presumed answer for the GHZ states described in the opening post to this thread?

What is your presumed answer for the source of Gamma EEG waves?

What is your presumed answer for how single-celled organisms can avoid obstacles, find food and engage in sex?

I suggest that many have a philosophical bias towards explanations that presume solid matter is operating in a universe of Euclidean Geometry where time always marches forward like a frame by frame movie (i.e. “Materialism”).

“Materialism” is a philosophical outlook.  I think it is outdated considering what we know from quantum physics.  The Many Worlds interpretation is a desperate attempt to hang on to the security blanket of presuming solid particles actually exist.

I am not suggesting God or even Intelligent Designer(s) should be presumed.  A lot of people have complained that my philosophical leaning is “Naturalism” which, to some, is just as bad as “Materialism”.

We can’t escape our biases.  We all have them.  But I suggest in this case, you might be attempting to presume a biased position that you have no right to claim as the default ("conventional models").

I am an engineer putting together my model.  You put together yours and we will compare them.  Ok?

  
creeky belly



Posts: 205
Joined: June 2006

(Permalink) Posted: Oct. 16 2007,15:14   

Quote
“Materialism” is a philosophical outlook.  I think it is outdated considering what we know from quantum physics.  The Many Worlds interpretation is a desperate attempt to hang on to the security blanket of presuming solid particles actually exist.

I am not suggesting God or even Intelligent Designer(s) should be presumed.  A lot of people have complained that my philosophical leaning is “Naturalism” which, to some, is just as bad as “Materialism”.

We can’t escape our biases.  We all have them.  But I suggest in this case, you might be attempting to presume a biased position that you have no right to claim as the default ("conventional models").

I am an engineer putting together my model.  You put together yours and we will compare them.  Ok?

Materialistic in what sense? The fact that most of the universe is not in a coherent quantum state and can be treated classically? Not everything is interconnected in a quantum sense like you suggest, we've been over this many times. If things were connected in this way, our daily experience would be something quite enigmatic. In physics we don't say that solid particles exist, we typically talk about solids, liquids, gases, and plasmas, all with distinct properties as a macroscopic distribution of quantum perturbations. They have an effective interaction range, and depending on the interaction, it will have some unit of mass or charge. Being solid is a product of lattice structure, and I don't know a single scientist who would claim that a single particle has to be a billiard ball. There is a reason they don't have to be coherent, which you always seem to skip over.

We have many experiments that show the difficulty of keeping coherent quantum states at in a thermally noisy environment. The onus is on you to show through experimentation that microtubles (or dimers) 1) have well defined quantum states, 2) long coherence times, 3) perform quantum computation, and 4) are the source of consciousness. The experiments for 1-3 are straightforward, and should be performed by Hameroff (currently non-active experimentally), or the Dibit group (need more specific interactions). I leave 4) to you to dispute through metaphysics if you wish, but I have no reason to accept the premise until 1-3 are satisfied.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Oct. 16 2007,15:55   

Hi TP,

You wrote:

   
Quote (Thought Provoker @ Oct. 16 2007,13:26)
Hi qetzal,

Please pardon me for threatening you with AfDave but the point was to put things into perspective.  I'm just an engineer trying to make sense of things.  That, and having some fun being a quasi-troll.

You wrote...
         
Quote
I get the impression that you see this as partly a philosophical debate. Personally, I couldn't care less about the philosophy. I accept the ToE because it's supported by evidence and accurately predicts what we see. I reject ID because it isn't, and it doesn't.

If you show me that Orch OR accurately predicts things that conventional models don't, I'll be much more interested. Until then...

It is the "until then..." where the philosophical battle takes place. What are the default presumptions?  I am not challenging established ToE principles, neither is Mike Gene.


OK, in retrospect, I realize my comment actually does relate to my philosophy. Let me clarify.

I don't care about the implications of ToE, ID, or your Third Choice (TC) vis-a-vis philosophies like materialism, naturalism, teleology, etc. My philosophical bias is for models that accurately predict empirical observations. Those models can be materialistic or non-materialisic, teleologic or non-teleologic. I don't much care about that, as long as they are accurate and predictive.

So, I don't reject ID because it implies the universe is teleologic. I reject it (in most forms) because it either makes no predictions or wrong predictions.

I'm highly skeptical of your proposals because I see little evidence to support them, and I don't see that they predict reality better than ToE and other, more conventional models. At least, not in those cases where I know the conventional models well enough to judge.

If, however, you showed me that your models (&/or Hameroff's, Penrose's, Patel's, etc.) predict observation in ways that other models can't, I will happily re-consider the validity of your models. The same goes for ID. (Of course, I'm looking for useful predictions. We can debate what that means, but typical ID claims like "Stuff is complex" and "Darwinism can't explain X" don't make the grade.)

   
Quote
What is your presumed answer for the GHZ states described in the opening post to this thread?


What do you mean? To the extent that I understand it, I accept that quantum entanglement occurs under certain conditions. If GHZ accurately describes how that operates, I'm fine with it.

   
Quote
What is your presumed answer for the source of Gamma EEG waves?


Well, I'm not a neurologist, so I don't have a presumed answer. Which doesn't mean there isn't a perfectly good explanation, just that I don't know it, and I'm not interested enough to look it up.

   
Quote
What is your presumed answer for how single-celled organisms can avoid obstacles, find food and engage in sex?


OK, this is closer to my expertise. Let's take finding food. This is an example of chemotaxis - movement in response to a chemical gradient. Bacteria typically swim towards chemoattractants (incl. food), and away from chemorepellants (e.g. harmful compounds). They can do this by mixing two kinds of swimming: runs and tumbles. Runs are relatively long periods of roughly straight line movement. Tumbles are short periods where the cell randomly re-orients.

When bacteria move up an attractant gradient, they are seen to have longer runs and fewer tumbles. When they get 'off course' (i.e. if they're not moving up the gradient any more), they're more likely to tumble and change direction. Changing the duration of runs and the frequency of tumbles like this lets them take a so-called random walk approach towards the source of the attractant. As long as they're moving in the right direction, they tend to keep going. If they go in the wrong direction, they're more likely to stop and try a different direction.

Note - when they change direction, they don't automatically re-orient towards the source. Re-orientation is (apparently) random. If, by chance, they end up pointing in the right direction, they'll keep going. Otherwise, they'll soon change direction again.

Note also - once they reach the food source, they're at the maximum point of attractant concentration. Any direction they move is away from the gradient. So, they minimize the length of their runs, and tumble frequently. In this way, the just sort of mill about in the region of highest food concentration.

So, how do they control runs and tumbles? They have receptors on the surface that bind attractants (and repellants). Binding causes a conformational change in the receptor, which extends through the membrane to the inside of the cell. The altered receptor interacts with other proteins. This changes the level of phosphorylation on a protein called CheY. When CheY is phosphorylated, it binds to certain flagellar proteins. This causes the flagella to rotate clockwise. Because of the unsymmetrical shape of the flagella, CW rotation causes tumbling.

When CheY is un-phosphorylated, it doesn't bind the flagellar proteins. In that case, the flagella rotate counterclockwise. Again, because of flagellar shape, CCW rotation causes runs.

Here is a review that provides more detail (see first section).

Note that nothing in this whole scheme requires any quantum superposition of proteins, or quantum calculation by the cell's DNA or tubulin-like proteins. There's no need to invoke any ill-defined awareness in the cells, quantum interconnectedness, or retrocausation. If someone can show how those things increase the accuracy of the model, great. At present, however, they don't appear to be relevant.

 
Quote
I suggest that many have a philosophical bias towards explanations that presume solid matter is operating in a universe of Euclidean Geometry where time always marches forward like a frame by frame movie (i.e. “Materialism”).

Perhaps, but I don't. My bias is against models that don't increase our explanatory power, and don't increase our ability to predict observations. As an aside, I think your definition of Materialism is rather different than the usual one.

 
Quote
“Materialism” is a philosophical outlook.  I think it is outdated considering what we know from quantum physics.  The Many Worlds interpretation is a desperate attempt to hang on to the security blanket of presuming solid particles actually exist.

I am not suggesting God or even Intelligent Designer(s) should be presumed.  A lot of people have complained that my philosophical leaning is “Naturalism” which, to some, is just as bad as “Materialism”.

We can’t escape our biases.  We all have them.  But I suggest in this case, you might be attempting to presume a biased position that you have no right to claim should be considered the default ("conventional models").


Well, hopefully I've at least clarified what my philosophical position is. I'm not saying it's objectively right, or that you should adopt it as well. However, I will say that it's more or less a default position for science.

 
Quote
I am an engineer putting together my model.  You put together yours and we will compare them.  Ok?


Depends. A model for what? There's a model that I currently accept for how bacteria find food. (At least, that's one way they do it; there are undoubtedly others.) If you have an alternative, we can discuss how it they compare.

However, if you're looking for my proposed model of consciousness, I don't have one. That doesn't mean I have to accept yours or Hameroff's. I'm perfectly content with the fact that we don't have an adequate model for consciousness yet.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Oct. 16 2007,16:10   

Hi Creek Belly,

You wrote...
Quote
Materialistic in what sense? The fact that most of the universe is not in a coherent quantum state and can be treated classically?


Treating it "classically" is your philosophical bias.  Thinking of things as solid object existing in a specific location in Euclidean Space where the frame by frame movie is always moving forward in time is a biased view point.

This view isn't consistent with scientific observations.

You might as well be saying that we must treat the world as flat except under special circumstances where its "roundness" manifests itself.

Quote
The onus is on you to show through experimentation that...


I disagree, absent a default explanation, all I have to do is present a consistent model for testing.

You present your model, I present mine.  We compare.

What does your model say about single-celled organisms avoiding obstacles, finding food and engaging in sex?

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Oct. 16 2007,16:39   

Hi qetzal,

You did as I asked.  You offered an explaination for finding food.  I like your explaination better.

I learned something.

Thanks.

However, your GHZ states explaination wasn't as good and neither of us are neurologists.  I am looking looking into understanding gamma brain waves better than I do.

I will post what I find.

  
creeky belly



Posts: 205
Joined: June 2006

(Permalink) Posted: Oct. 16 2007,16:57   

Quote
Treating it "classically" is your philosophical bias.  Thinking of things as solid object existing in a specific location in Euclidean Space where the frame by frame movie is always moving forward in time is a biased view point.

This view isn't consistent with scientific observations.

You might as well be saying that we must treat the world as flat except under special circumstances where its "roundness" manifests itself.

Classical is not always Euclidean; hyperbolic geometry falls out of special/general relativity which are classical equations. I define classical as not exhibiting wave interference behavior, which happens at larger scales. That is a fact. You can set your watch to it. At the classical level, the quantum "interconnectedness" is lost or equivalent to classical treatment. It's only a philosophical bias if you look at the entire world this way, like you do with quantum effects.

 
Quote
I disagree, absent a default explanation, all I have to do is present a consistent model for testing.

You present your model, I present mine.  We compare.

What does your model say about single-celled organisms avoiding obstacles, finding food and engaging in sex?

My model says that due to the thermal activity and decoherence times of coupled molecular structures, the likelihood that quantum computing takes place in the brain is negligible. Microtubules (or tubulin dimers) do not exhibit well defined quantum states, and thus will constitute a classical arrangement of matter. Any interference that might occur in such a system will decohere in a time insufficient to perform quantum calculations. Since your experiment has not been tested, and mine has been backed up by years of peer-reviewed research, you are in a poor position to dispute. Thus, you need to perform the experiment to show that this model is not consistent with what actually goes on in the brain, or microtubules, or tubulin dimers, whatever.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Oct. 16 2007,17:17   

Hi Creek Belly,

You wrote...
 
Quote
That is a fact. You can set your watch to it.

LOL  Minkowskian Geometry is reality.  You can unset your watch by it. link

qetzel did a good job on the finding food explaination.

Why don't you give a shot at explaining the GHZ states problem.

I say it isn't a problem once you accept Minkowskian Geometry's...

dL^2 = dx^2 + dy^2 + dz^2 – dt^2

...is reality.  Quantum effects are interconnected.

All quantum effects are interconnected, in the GHZ states the interconnectedness is detectable, in "classical" situations it is not.

That is my explaination.  What's yours?

  
creeky belly



Posts: 205
Joined: June 2006

(Permalink) Posted: Oct. 16 2007,17:47   

Quote
I say it isn't a problem once you accept Minkowskian Geometry's...

dL^2 = dx^2 + dy^2 + dz^2 – dt^2

...is reality.  Quantum effects are interconnected.

All quantum effects are interconnected, in the GHZ states the interconnectedness is detectable, in "classical" situations it is not.

That is my explaination.  What's yours?

Minkowskian geometry is hyperbolic geometry. Coherent quantum systems are in pure states. Decoherent quantum systems are mixed states, classical states that lack interference. What's the problem? Maybe I don't know understand what you mean by "interconnected". Do you mean entangled, in the same light cone? The former is certainly not true.

The GHZ is a basis measurement problem, by measuring in X and Z angular momentum for a spin 1/2 system, and by taking one of three entangled qubits (in the superposition |000> + |111>) you can beat classical expectation values with interference. Again, for a coherent, entangled state, not for every quantum effect. You can have a pure quantum state that is not entangled, and will therefore not be interconnected.  Look at the state |001> + |011>. A pure state? Yes. Entangled? No. The effect of measuring one of the bits will not affect the measurement of the others (in the same basis) which is the whole reason the GHZ game works.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Oct. 16 2007,19:45   

You wrote...  
Quote
Maybe I don't know understand what you mean by "interconnected". Do you mean entangled, in the same light cone? The former is certainly not true.

Quantum effects are interconnected because quantum effects are patterns in the single space-time wavefunction that is our universe.

Think of a Mandelbrot Set.  All of the Mandelbrot Set's features are interconnected.  However, the interconnection of some features are more obvious than others.

Here is a link to a Mandelbrot Set claimed to be the size of the known universe.  Note, this is a very simple function with only ONE complex dimension.  Our universe has at least four.

Queue the DEPAK CHOPRA EXPRESS.

 
Quote
You can have a pure quantum state that is not entangled, and will therefore not be interconnected.  Look at the state |001> + |011>. A pure state? Yes. Entangled? No. The effect of measuring one of the bits will not affect the measurement of the others (in the same basis) which is the whole reason the GHZ game works.

At best you only mathematically described the observation and without offering an explanation.  On the other hand, you might have provided support for what I have been saying.  Quantum effects are interconnected pure states of the wavefunction existing in Minkowskian space-time.  Some are entangled, some are not.

BTW, are you still holding on to a dogmatic belief that matter has substance and there is such a thing as randomness?

It is hard to see past your own philosophical presumptions.

  
creeky belly



Posts: 205
Joined: June 2006

(Permalink) Posted: Oct. 16 2007,21:08   

Quote
Quantum effects are interconnected because quantum effects are patterns in the single space-time wavefunction that is our universe.

You mean connected by the same wave function? Yeah, ok write out the formula, what potentials are you assuming? What happens when this wavefunction is measured, does it collapse into an energy eigenstate? What is the time evolution like? When you get to the gravitational potentials, let me know, there are some Nobel people waiting for you. Try googling quantum field theory.

     
Quote
At best you only mathematically described the observation and without offering an explanation.  On the other hand, you provided support for what I have been saying.

Ok, here's the setup, which has already been done with quantum computers:
Couple three qubits, could be quantum dots, whatever.
Initialize them to the ground state in whatever basis (x,y,z-momentum etc): |000>
Perform the Hadamard transformation on the second qubit: |000> -> |000>+|010>
Measure each qubit. You will get the following:
qubit1: always 0
qubit2: 50% 0, 50% 1
qubit3: always 0

Let's run this again, but with a twist:
Initialize to |000>
Perform Hadamard on first qubit: |000> -> |000>+|100>
Perform controlled NOT on both the second and third qubit, with the first as control: |000> + |100> -> |000> + |111>
Measure each bit:
If you measure 0 on qubit 1: then 2 and 3 will also be 0 (entangled)
If you measure 1 on qubit 1: then 2 and 3 will also be 1 (entangled)

That's exactly how it's been done experimentally; they even did something slightly more complicated, Shor's algorithm.

     
Quote
BTW, are you still holding on to a dogmatic belief that matter has substance and there is such a thing as randomness?

It is hard to see past your own philosophical presumptions.

WTF is substance? The word isn't random, it's stochastic, and it's not dogmatism, it's an empirical and mathematical result (from Hilbert space). If quantum mechanics isn't stochastic, then I believe you can collect some money from Magiq when you break their quantum number generator.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Oct. 23 2007,20:59   

TP,

If you're still around, you might appreciate this.

I don't have an immediate opinion on the paper in question, but it has this much going for it:

 
Quote
This theory naturally explains recently observed marked increase in dominance duration in binocular rivalry upon periodic interruption of stimulus and yields testable predictions for the distribution of perceptual alteration in time.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Oct. 25 2007,15:25   

Hi qetzal,

Thanks for pointing out the paper.

I am still around, but Real Life is demanding a lot of my focused attention.

A lot of things have been happening recently that suggest things are coming together of the idea of quantum consciousness.  The "warm, wet brain" dismissal is losing traction.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Jan. 20 2008,12:43   

Bumped for Doc Bill

  
  268 replies since Sep. 25 2007,09:43 < Next Oldest | Next Newest >  

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