RSS 2.0 Feed

» Welcome Guest Log In :: Register

Pages: (9) < 1 2 3 [4] 5 6 7 8 9 ... >   
  Topic: The Magic of Intelligent Design, A repost from Telic Thoughts< Next Oldest | Next Newest >  
Richardthughes



Posts: 11178
Joined: Jan. 2006

(Permalink) Posted: Sep. 27 2007,12:50   

Quote (Thought Provoker @ Sep. 27 2007,12:39)
Hi K.E.,

You wrote...
 
Quote
It's a quantum god of the gaps unless you are an atheist in which case it’s still a god.

And TP is not an atheist even if he says so.


I agree I am not an atheist since I won't say there is no god.   Of course, Richard Dawkins also concedes there might be a God.

Most people think Richard Dawkins is an atheist.  A lot of religious people think I am an atheist.

Labels aren't important, ideas are.

P.S. I like your signature line about conservatives.

You can be atheist agnostic.
Atheism is a position of faith, like theism. In many ways it has to be, as you can't prove a negative.

Agnosticism answer the epistemological question, honestly.

Believing isn't KNOWING.

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
BWE



Posts: 1902
Joined: Jan. 2006

(Permalink) Posted: Sep. 27 2007,12:54   

But I want to know! Tell me about front loading. Forget group  think and just spell out your argument.

It looks like a kind of vain attempt to put a place for some special God back into the schematic. Maybe it's just me...

--------------
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

The Daily Wingnut

   
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Sep. 27 2007,13:16   

Hi BWE,

   
Quote
Is this an argument for special creation?

I doubt my Third Choice hypothesis is.

Think of lightening.  For lightening to be "created" it needs positive and negative potentials.  Is lightening pushed or pulled or both?

I suggest, like lightening, evolution might result from being both pushed and pulled.

NDE describes the pushing part.  Front loading would be the pulling part.

And, while more important for philosophical discussion, the other similarity to lightening is that the circuit must be complete.  There must be a path from the beginning to the end of time, otherwise it doesn't happen.

P.S. sorry for the delay, but sometimes I have to do real work.   ???

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Sep. 27 2007,13:29   

Quote (Thought Provoker @ Sep. 26 2007,16:01)
What I have been presenting here is what I call the Third Choice.  A choice other than the status quo and an unidentified Intelligent Designer.

Many ID proponents claim ID isn’t about God.  I am giving them the opportunity to stand by their words.  Here is an ID hypothesis with scientific justification.  The reactions to it are informative.

Once again, I disagree that you've provided any scientific justification. To me (and to most working scientists, I suspect), scientific justification means some reasonable level of empirical data that supports the hypothesis. I don't think you've provided that at all.

Instead, you've taken some observations about QM, made a series of assumptions, and shown that life is inevitable ("retrocaused") under those assumptions. The problem with that is one can show virtually anything with the right set of assumptions. I don't consider it scientific justification unless there's some evidence to support the assumptions.

Now, maybe I still don't grasp what your Third Choice really says. So let me try to boil it down, and you can tell me if I've got the gist.

1.  Particles can be quantum entangled. This is demonstrated.
2.  Based on (1), you propose that the universe is interconnected across all of space and time due to quantum effects.
3.  For reasons that aren't clear to me, you further propose that living things (perhaps specifically intelligent living things) are required for the universe to exist.
4.  Thus, life developed because it had to. The requirement for (intelligent?) life at some point in space-time 'retrocaused' life to begin developing at some other point(s) in space-time.

Is that approximately right? If not, feel free to correct my errors. If so, isn't this essentially just the Strong Anthropic principle?

Regardless of the above, I don't consider your ideas to be equivalent to front loading. Here's why.

In 'traditional' front loading, all of the 'information' needed to generate every possible future organism was loaded into the first organism. Proponents generally argue that it was all encoded into the DNA, but most of it was repressed. The key point is that it was all inherent in that first organism.

You're arguing (I think) that the information needed to generate every possible organism was loaded not into the first organism, but into the universe itself. That's fundamentally distinct. You may choose to call that front loading, but it's not compatible with front loading as it's commonly understood.

  
Erasmus, FCD



Posts: 6349
Joined: June 2007

(Permalink) Posted: Sep. 27 2007,14:56   

qetzal if that is true it further entails that either consciousness is not a property of organisms or that it is a property of matter.

Woo-woo-woo-woo!!!



--------------
You're obviously illiterate as hell. Peach, bro.-FtK

Finding something hard to believe based on the evidence, is science.-JoeG

the odds of getting some loathsome taint are low-- Gordon E Mullings Manjack Heights Montserrat

I work on molecular systems with pathway charts and such.-Giggles

  
Erasmus, FCD



Posts: 6349
Joined: June 2007

(Permalink) Posted: Sep. 27 2007,15:01   

Just read upthread, don't be mad TP k?

We all take the piss.  Woo-wear is just something that is easy to piss on.  I will never say that it's wrong.  It's not even wrong.  I mean, have you ever really looked at your hand?  



--------------
You're obviously illiterate as hell. Peach, bro.-FtK

Finding something hard to believe based on the evidence, is science.-JoeG

the odds of getting some loathsome taint are low-- Gordon E Mullings Manjack Heights Montserrat

I work on molecular systems with pathway charts and such.-Giggles

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Sep. 27 2007,15:04   

Hi qetzal,

I will readily admit that the Third Choice is repackaged Anthropic principle.  As to whether it is weak or strong isn't as clear.

Skeptic was right to indicate I am violating NOMA in suggesting a purpose, even if it is extremely modest.  I am not suggesting human life is key to the universe's existance.  For that matter, Earth, and all the life on it, many be a meaningless side effect of the universe being consistent with itself.

Maybe it would help if I bring up Dawkin's..."Life results from the non-random survival of randomly varying replicators."

What happens to this if there is no such thing as randomness?

Life results from the non-random survival of replicators that vary based on interconnected quantum effects that may, or may not, be needed for consistency in the universe.

Science makes the presumption that the universe is consistent.  It is a small step over the NOMA divide to say the universe MUST be consistent (i.e. is its purpose).  Note, saying the universe has no purpose violates NOMA just as much as saying it does.

With that, let me try to focus on the scientific arguments.

Hypothesis - Quantum effects are interconnected in both space and time.

Implication - All quantum effects are fixed.  There is no such thing as randomness, just the illusion of randomness in a highly complex situation.

Hypothesis – Evolution has resulted in life on Earth taking advantage of quantum computing (e.g. DNA and photosynthesis).

Implication – “Random” mutations are influenced by quantum effects interconnected to future quantum effects.

Hypothesis – The appearance of life’s awareness (i.e. consciousness) is a direct artifact of life’s use of quantum effects.

Implication - Microtubules are probably the primary mechanism for consciousness.

I will say more in a follow up comment.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Sep. 27 2007,15:39   

Hi qetzal,

You wrote...
 
Quote
Regardless of the above, I don't consider your ideas to be equivalent to front loading. Here's why.

In 'traditional' front loading, all of the 'information' needed to generate every possible future organism was loaded into the first organism. Proponents generally argue that it was all encoded into the DNA, but most of it was repressed. The key point is that it was all inherent in that first organism.

You're arguing (I think) that the information needed to generate every possible organism was loaded not into the first organism, but into the universe itself. That's fundamentally distinct. You may choose to call that front loading, but it's not compatible with front loading as it's commonly understood.


I understand that MikeGene and Krauze of Telic Thoughts are credited for pushing the Front Loading meme for a long time.  I can't speak for them, but I have noticed they have rejected similar characterizations of "traditional front loading" in past comments.

MikeGene has suggested that the recA gene might be a front-loaded evolution gene.  Here is a link to a paper (essay?) MikeGene wrote in the subject (it was the one MikeGene offered when SteveStory came by on his visit to Telic Thoughts)...

RecA is truly a remarkable protein. Even though it is only about 350 amino acids in length, it carries out the multiple functions of binding multiple DNA strands, coordinating their exchange, binding ATP and hydrolyzing it, and interacting with other proteins. In fact, according to one review, the functional domains responsible for these activities closely map together and may even overlap. How is all this carried out?

I’ve left out one very important part of the story – RecA is not functional as a monomer, it only becomes functional when it forms protein fibers that wrap around the DNA.

In other words, recombination occurs because tubulin-like proteins stretch the DNA by forming a dynamically lengthening tube around it. In this way, the growing protein tube can hold onto the single stranded DNA with one “hand” while using its other “hands” to unravel double stranded DNA such that the single-stranded DNA can be used to probe the unraveled DNA for regions that are complementary.

You might have noticed I said “tubulin-like.” Is this simply because RecA forms a semi-hollow protein tube? No. There are several other features that have led one reviewer, for example, to note:

The dynamic behavior protein under conditions of ATP hydrolysis is thus conceptually similar to that of other NTP-hydrolyzing, self-assembling proteins, such as actin and tubulin.

Like tubulin, RecA formation starts slowing with a nucleation step, where a small number of monomers must form a seed that can then be extended. Once formed, like tubulin, RecA then grows at one end by the incorporation of RecA monomers bound to ATP (tubulin dimers add to one end and must be bound to GTP). Like tubulin, the NTP hydrolysis is not needed for assembly, but instead is needed for disassembly. This means that RecA, like tubulin, assembles at one end and disassembles at the other end, forming something like a treadmill. According to one team of researchers:

We argue that RecA can “proofread” the ssDNA by its own binding fluctuations. These fluctuations are similar to microtubule dynamic instability. The assembly dynamics constitute a kinetic proofreading cascade that is a “hair-trigger” sensor of DNA length. Enhancing biomolecular precision by fluctuations, which may seem somewhat counter-intuitive in a deterministic world, is presented as a natural design principle in the noisy realm of the living cell.

A microtubule-like structure is thus in charge of genetic recombination.

Finally, if RecA is an evolution gene, this would lead to an obvious prediction - removal of RecA should compromise an organism’s ability to evolve.


Could the RecA protein be another example of life taking advantage of the power of quantum computing for a key function?  I haven't found the time or resources to explore that, but MikeGene went out of his way to point out how his and my hypotheses were mutually supportive.

Whether or not the Third Choice is considered part of the rubric called "Front Loading" isn't up to you or me.  It is up to those proposing the Front Loading hypothesis.

Labels aren't important, ideas are.

  
creeky belly



Posts: 205
Joined: June 2006

(Permalink) Posted: Sep. 27 2007,16:22   

Quote
Could the RecA protein be another example of life taking advantage of the power of quantum computing for a key function?

Maybe entanglement, but I doubt that it's an actual quantum computer because, again, decoherence at room temperatures will be a problem. For a quantum computer to be truly effective, it must entangle many lines and keep them coherent with a strong perturbation long enough to perform quantum operations (phase flips, rotations like the Hadamard, controlled NOTs, the Quantum Fourier Transform). The photosynthesis article you provided before talked about timing on the level of tenths of pico-seconds and temperatures of 77K (-223 C for those of you at home). This is well below an acceptable level for claiming that the proteins would be able to exhibit the same behavior. It also used a much simpler quantum process of entangling energy eigenstates, not performing true computation.

 
Quote
Labels aren't important, ideas are.

Except when you use labels incorrectly, such as "quantum computer".

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Sep. 27 2007,16:33   

Hi Erasmus, FCD,

You wrote...
 
Quote
if that is true it further entails that either consciousness is not a property of organisms or that it is a property of matter

This approached a decent argument.

If Dr Hameroff is right, the conscious perception of time is based on the rate of conscious events.  Human have about 40 conscious events a second.  A potato (which has microtubules) would have about one a month.

The quantum effects in general matter isn’t organized to fire (massive decoherence) concurrently like living matter with microtubules are.  But suppose, for argument sake it is.  What is a rock with one conscious event a year going to do about it?

P.S. on the extreme chance you are interested in this, you may want to look up Endogenous Adaptive Mutagenesis.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Sep. 27 2007,16:39   

Quote (Thought Provoker @ Sep. 27 2007,15:39)
I understand that MikeGene and Krauze of Telic Thoughts are credited for pushing the Front Loading meme for a long time.  I can't speak for them, but I have noticed they have rejected similar characterizations of "traditional front loading" in past comments.

Whether or not the Third Choice is considered part of the rubric called "Front Loading" isn't up to you or me.  It is up to those proposing the Front Loading hypothesis.

Labels aren't important, ideas are.


Well, this is what MikeGene posted on 9/24/07:

Quote
For years, I have been trying to flesh out the conceptualization of front-loading evolution at the origin of life. A working hypothesis has been that the first cells (uni-cellular life forms) were front-loaded with information that would facilitate the evolution of multi-cellular life.


link

Isn't that pretty much what I said?

In contrast, your version doesn't postulate front loading of information into the first cells per se. It postulates that the information is part of the overall wavefunction of the universe, right?

I agree that concepts are what matter, but when the same label is used to refer to two different concepts, confusion is inevitable.

Regarding RecA, you're in my sweet spot now! I agree it's an amazing protein. But being multifunctional and forming nucleoprotein filaments is not evidence that it's front-loaded. Not unless you're going to claim that it's "too complex to have evolved naturally."

Whether recA is an "evolution gene" depends on what that means. It's a central player in a lot of DNA repair and recombination processes. Where there's repair/recombination, there's mutation. Where there's mutation, there's potential evolution. If that's all that's required to meet MikeGene's idea of an "evolution gene" then recA fits the bill.

On the other hand, if MikeGene thinks RecA somehow directs evolution in a teleological way, he's wrong.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Sep. 27 2007,16:42   

TP

I forgot to add - even though I think your ideas are mostly BS, props for getting RecA protein versus recA gene right!

;-)

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Sep. 27 2007,16:52   

Hi Creek Belly,

It would have been nice of you to provide the link and quote it in context.  But this isn't about being nice is it?

Here it is in context...

Engel said one of the next steps for the Fleming group in this line of research will be to look at the effects of temperature changes on the photosynthetic energy transfer process. The results for this latest paper in Nature were obtained from FMO complexes kept at 77 Kelvin. The group will also be looking at broader bandwidths of energy using different colors of light pulses to map out everything that is going on, not just energy transfer. Ultimately, the idea is to gain a much better understanding how Nature not only transfers energy from one molecular system to another, but is also able to convert it into useful forms.

“Nature has had about 2.7 billion years to perfect photosynthesis, so there are huge lessons that remain for us to learn,” Engel said. “The results we’re reporting in this latest paper, however, at least give us a new way to think about the design of future artificial photosynthesis systems.”


It also would have been nice to think about what they were saying.  This isn't the first time nature has managed to do something that proves difficult to replicate artificially.  Are you suggesting plants operate at 77 Kelvin?

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Sep. 27 2007,17:22   

Hi qetzal,

Thank you for your comment and thank you for providing the link.  As you pointed out, MikeGene said...

"A working hypothesis has been that the first cells (uni-cellular life forms) were front-loaded with information that would facilitate the evolution of multi-cellular life." (emphasis mine)

I have noticed MikeGene is pretty careful with his words.  The word "facilitate" makes a big difference IMO.  Life's use of quantum mechanics facilitates the evolution of multi-cellular life.

Quote
In contrast, your version doesn't postulate front loading of information into the first cells per se. It postulates that the information is part of the overall wavefunction of the universe, right?

I agree that concepts are what matter, but when the same label is used to refer to two different concepts, confusion is inevitable.


MikeGene is more careful with his words than I.  If I said the Third Choice is a Front Loading hypothesis then I was mistaken.  I have asked, MikeGene has not said one way or the other.  I have my opinion, but it is only my opinion.

BTW, I am of the opinion that this is an ID Hypothesis based on the lose definitions used, but I could be wrong about that.

Quote
Regarding RecA, you're in my sweet spot now! I agree it's an amazing protein. But being multifunctional and forming nucleoprotein filaments is not evidence that it's front-loaded. Not unless you're going to claim that it's "too complex to have evolved naturally."

Whether recA is an "evolution gene" depends on what that means. It's a central player in a lot of DNA repair and recombination processes. Where there's repair/recombination, there's mutation. Where there's mutation, there's potential evolution. If that's all that's required to meet MikeGene's idea of an "evolution gene" then recA fits the bill.


I'm glad to hear from a knowledgable source.

You can read MikeGene's paper for itself.  I won't speak for MikeGene.

I look at the recA gene and, especially, the RecA protein as being in the unique position of having great influence over the evolution process in what MikeGene referred to as "deep time".  Pencils balanced on their tips could fall in any direction. I gentile breeze might not make a difference that is immeadiately noticable.  But if there are a lot of pencils over a lot of time, the pencils might be biased to tip a certain way.

I understand the RecA protein acts very much like a microtubule (I am counting on your expertise to argue this point if applicable).  That is a rather convienent coincidence.

I am not suggesting some human-like intelligence designed it that way.  Think of it as some unknown evolutionary advantage to having a quantum computer in charge of this highly important function.

And thanks for noticing the recA gene and RecA protein.  I feel my efforts weren’t wasted.

  
creeky belly



Posts: 205
Joined: June 2006

(Permalink) Posted: Sep. 27 2007,17:24   

Quote
This isn't the first time nature has managed to do something that proves difficult to replicate artificially.

Quite. Evolutionary algorithms are a good example of this (especially the "Macguyver solutions").

Quote
Are you suggesting plants operate at 77 Kelvin?

No, I'm suggesting that some of the ease of observing quantum effects were from keeping the plants cold (average energy state is lower, allows for longer coherence time), even then they were relegated to coherences of femto-seconds. The fact that plants operate at a higher average temperatures makes it difficult to determine how prevalent this quantum effect is when the temperature is closer to 290-300K (I believe the group is working towards this). In addition, it's a pretty basic quantum effect, in the sense that energy levels constitute well defined quantum state, with incident photons accounting for the measurement process. This is quite another thing from performing complex quantum operations; there's just not much from the data that suggests this is being done.

And just to be fair and balanced: "By demonstrating that the energy transfer process does involve electronic coherence and that this coherence is much stronger than we would ever have expected, we have shown that the process can be much more efficient than the classical view could explain. However, we still don’t know to what degree photosynthesis benefits from these quantum effects." from the link.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Sep. 27 2007,18:40   

TP,

Thanks for the reply (and the previous ones). It's nice to discuss this with someone who responds to the questions that are asked, even if we may disagree on the answers.

 
Quote (Thought Provoker @ Sep. 27 2007,17:22)
Hi qetzal,

Thank you for your comment and thank you for providing the link.  As you pointed out, MikeGene said...

"A working hypothesis has been that the first cells (uni-cellular life forms) were front-loaded with information that would facilitate the evolution of multi-cellular life." (emphasis mine)

I have noticed MikeGene is pretty careful with his words.  The word "facilitate" makes a big difference IMO.  Life's use of quantum mechanics facilitates the evolution of multi-cellular life.


Maybe, but in distinguishing MikeGene's (et al.) version from yours, I'd place the emphasis here: "A working hypothesis has been that the first cells (uni-cellular life forms) were front-loaded...."

 
Quote
MikeGene is more careful with his words than I.  If I said the Third Choice is a Front Loading hypothesis then I was mistaken.  I have asked, MikeGene has not said one way or the other.  I have my opinion, but it is only my opinion.

BTW, I am of the opinion that this is an ID Hypothesis based on the lose definitions used, but I could be wrong about that.


Fair enough.

 
Quote
I'm glad to hear from a knowledgable source.

You can read MikeGene's paper for itself.  I won't speak for MikeGene.


I'll try to look over his post(s) tonight. Can't promise though.

 
Quote
I look at the recA gene and, especially, the RecA protein as being in the unique position of having great influence over the evolution process in what MikeGene referred to as "deep time".  Pencils balanced on their tips could fall in any direction. I gentile breeze might not make a difference that is immeadiately noticable.  But if there are a lot of pencils over a lot of time, the pencils might be biased to tip a certain way.


Sorry, I don't follow that.

 
Quote
I understand the RecA protein acts very much like a microtubule (I am counting on your expertise to argue this point if applicable).  That is a rather convienent coincidence.


I don't really think so. There are similarities, of course. It forms filaments assembled from monomers, but it does so by assembling around DNA. Given its function of catalyzing strand exchange during recombination, and the linear nature of DNA, that's not particularly surprising.

There are other proteins that form filaments in a generally similar way. Coat protein from tabacco mosaic virus is a good example, and that's a case where there's no reason to invoke any quantum computing.

The simple explanation is that assembling monomers into helical filaments is a convenient way to generate long filaments from proteins. That's really the common theme I see. RecA needs to make linear filaments to coat linear DNA and promote strand exchange. TMV coat protein needs to make linear filaments to coat viral RNA. Tubulin needs to make linear filaments to provide structural support to the cell. Other geometries could also work, but they would be less efficient.

 
Quote
I am not suggesting some human-like intelligence designed it that way.  Think of it as some unknown evolutionary advantage to having a quantum computer in charge of this highly important function.


Except that you're pretty much begging the question. You've decided that quantum computers exist in biology, and you're using that to justify the hypothesis that RecA is a quantum computer. I see no evidentiary basis to do that.

 
Quote
And thanks for noticing the recA gene and RecA protein.  I feel my efforts weren’t wasted.


You're welcome! I tend to be a bit anal about that kind of thing, so I'm one to notice.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Sep. 27 2007,19:49   

Hi qetzal,

Did you know this science stuff can be exciting?!?

The internet isn't half bad either.

One of the reasons I like arguing on blogs is it forces me to research my responses.  You wrote...
Quote
Except that you're pretty much begging the question. You've decided that quantum computers exist in biology, and you're using that to justify the hypothesis that RecA is a quantum computer. I see no evidentiary basis to do that.


The RecA protein was a surprise bonus.  It isn't key to the hypothesis.  It is just an intreguing possibility.  Life's general use of quantum mechanics, especially in DNA and microtubules is enough.  And speaking of surprise bonuses when I went looking for the latest and greatest on life using quantum mechanics, I found that a new term is being coined "bio-quantum physics."  But that is not all, those fine folk at Berkeley Labs have an update...

Like the peeling of an onion, the secrets of photosynthesis are being revealed layer by layer. Early in 2007 a team of Berkeley Lab and UC Berkeley researchers identified quantum mechanical effects as the key to the astonishing ability of photosynthesis to utilize nearly all the photons absorbed by the leaves of green plants. Now a different team has found new evidence that points to a closely packed pigment-protein complex of the photosystem as the key to those quantum mechanical effects.

Green plants and certain bacteria are able to transfer solar energy almost instantaneously from light-capturing pigment molecules — for plants, the main photosynthetic pigment is chlorophyll — into reaction centers where solar energy is converted into chemical energy. The energy transfer happens so fast and is so efficient that less than five percent is lost as heat.

How nature manages to pull off this stunt was a long-standing mystery until the spring of 2007, when a study led by Graham Fleming, Deputy Director of Berkeley Lab and a UC Berkeley chemistry professor, found the first direct evidence of what he calls a "remarkably long-lived wavelike electronic quantum coherence." Quantum-mechanical effects enable a plant's photosystem to simultaneously sample all the potential energy pathways from pigment molecules to reaction centers and choose the most efficient one.

However, as is so often the case in science, solving one mystery led to another. What is the source of this remarkably long-lived quantum coherence? A second team, again led by Fleming, believes it has found the answer.

Preserving quantum coherence

"From our investigation, we conclude that the protein environment in the reaction center works collectively to keep the fluctuations of excited electronics states of pigment molecules in phase, and therefore protects quantum coherence," says Hohjai Lee, a member of Fleming's research group and co-author of a recent paper in Science describing their work. "This is a brand-new function of the protein in the reaction center."

link

It's no longer a question of whether life directly utilizes quantum mechanics but how and in how many ways.

I will be providing an update on DNA processing next.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Sep. 27 2007,20:30   

continuing...

From a paper (essay?) titled Bio-quantum computing...

BIO-QUANTUM COMPUTERS
The spitting in Informational and Physical Quantum levels of Space-Time can be imagined as a gateway to a new challenge in Bio-Computing , dropping down to the fundamental quantum existence of virtual information. One of these challenges will be to utilize the above concepts and rules of bio-quantum physics to develop Bio-Quantum Computers (8). In fact, DNA gene-communication can use both: 1) the localised copy of genes and also can have 2) a simultaneous delocalized role in communicating gene information. In fact DNA, as a nano-biotechnology, can utilize two functions to communicate: 1) through transfer of quantitative localized information by near contact with RNAs to generate proteins, and 2) to diffuse qualitative information by means of working as an ANTENNA able to transmit at gene signals at a distance , using a system of quantum-teletransportation. This second method of gene information by means of simultaneous transmission is necessary to activate the co-ordination of various living functions in the cell as well as for developing the complex cellular dynamical reproduction of forms , e.g to controll the functional complex folding of DNA and proteins , and to co-organize the metabolic funtionality utill the programmed apopthosis of the cell. (9) Henceforth, following the above quantized space-time theory it is becoming evident that Bio-Computers could be made from organic materials using DNA.


From a paper (essay?) titled Quantum Algorithms and the Genetic Code...

Replication of DNA and synthesis of proteins are studied from the view-point of quantum database search. Identification of a base-pairing with a quantum query gives a natural (and first ever!) explanation of why living organisms have 4 nucleotide bases and 20 amino acids. It is amazing that these numbers arise as solutions to an optimisation problem. Components of the DNA structure which implement Grover’s algorithm are identified, and a physical scenario is presented for the execution of the quantum algorithm. It is proposed that enzymes play a crucial role in maintaining quantum coherence of the process.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Sep. 27 2007,20:39   

Hi creeky belly,

What were we talking about again?

Oh yea!  How a "fair and balanced" view would suggest that room-temperature quantum effects might not be possible.

Excuse me while I suggest it is a pretty safe presumption that nature figured out a way.

  
creeky belly



Posts: 205
Joined: June 2006

(Permalink) Posted: Sep. 27 2007,21:22   

Quote
With all this information, the quantum search algorithmic requirements from the DNA structure are clear. It is convenient to take the distinct nucleotide bases as the quantum basis states in the Hilbert space. Then (1) The
quantum query transformation Ub must be found in the base-pairing with Hydrogen bonds. (2) The symmetric
transformation Us must be found in the base-independent processes occurring along the sides of the ladder. (3) An
environment with good quantum coherence must exist. Thermal noise is inevitable at T ? 300?K inside the cells, so
the transformations must be stable against such fluctuations.
Figuratively, the best that can be achieved is
Actual evolution = lim decoherence ? 0

[Quantum evolution] . (4)
Thus we need quantum features that smoothly cross over to the classical regime, i.e. features that are reasonably
stable against small decoherent fluctuations. Examples are: (a) geometric and topological phases, and (b) projection/
measurement operators.

He talks about enzymes forming a shield, but these are the same temperature concerns I have. I haven't found any links to experiments carried out since this....but if you know of any that would be very interesting. Sincerely.
From another of Dr. Patel's papers: arxiv:quant-ph/0105001v2:
       
Quote
The optimal quantum search algorithm was found by Lov Grover (Grover 1996), and it relates the number of objects, N, that can be distinguished by a number of yes/no queries, Q, according to

(2Q + 1) sin?1(1/pN) = /2 . (1)

This algorithm does not use the full power of quantum logic; concepts of superposition and interference familiar from the study of classical waves are sufficient to describe it. The algorithm starts with a uniform superposition of all possible states, corresponding to equal probability for every building block to get selected. Then it applies two reflection operations alternately: (a) change the sign of the amplitude of the desired state by the yes/no query, and (b) reflect all amplitudes about their average value. The algorithm stops after Q of these alternating reflections
to yield the desired state with a high probability.

   
Quote
Excuse me while I suggest it is a pretty safe presumption that nature figured out a way.

I'd like think so, too, but there's still no evidence for this yet. We both share the same question about the coherence times at high temperatures. As Dr. Patel says in his most recent paper, arxiv:0705.3895v1:
   
Quote
In principle, this is experimentally testable. Our technology is yet to reach a stage where we can directly observe molecular dynamics in a liquid environment. But indirect tests of optimality are plausible, e.g. constructing artificial genetic texts containing a different number of letters and letting it compete with the supposedly optimal natural language [Patel (2001b)]. ... Explicit formulation of a testable scenario, based on physical properties of the available molecules and capable of avoiding fast decoherence, is an open challenge.

  
k.e



Posts: 1948
Joined: Mar. 2006

(Permalink) Posted: Sep. 27 2007,21:33   

Quote
It's no longer a question of whether life directly utilizes quantum mechanics but how and in how many ways


More post hoc reasoning, it's still gods of the gaps.

--------------
The conservative has but little to fear from the man whose reason is the servant of his passions, but let him beware of him in whom reason has become the greatest and most terrible of the passions.These are the wreckers of outworn empires and civilisations, doubters, disintegrators, deicides.Haldane

   
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Sep. 27 2007,22:44   

Hi Creeky Belly,

Thank you for the head's up on the latest Dr. Patel paper.

Here is a link to it.

Patel is clearly more focused on the algorithm as opposed to the computer running it.  His algorithm requires superposition...

The initial and final states of Grover’s algorithm are classical, but the execution in between is not. In order to be stable, the initial and final states have to be based on a relaxation towards equilibrium process. For the execution of the algorithm in between, the minimal physical requirement is a system that allows superposition of states, in particular a set of coupled wave modes.

...and...

Grover’s algorithm needs certain type of superpositions, and catalytic enzymes can stabilize certain type of superpositions. Do the two match, and if so, what is the nature of this superposition? The specific details of the answer depend on the dynamical mechanism involved. The requisite superposition is of molecules that have a largely common structure while differing from each other by about 5-10 atoms. I have proposed two possibilities [Patel (2001a); Patel (2006b)]:

In 2001, Patel presumed the DNA was a quantum computer.  It was the most obvious choice.  Apparently the likes of Max Tegmark insisted that room-temperature quantum computers weren't possible.  This compelled Patel to come up with a "plan B." which is a contrived superposition look alike using classical processing.

As for showing it experimentally; your Patel quote was taken a little out of context, you left off the question being answered.

Do the living organisms use Grover’s algorithm even today?
In principle, this is experimentally testable. Our technology is yet to reach a stage where we can directly observe molecular dynamics in a liquid environment. But indirect tests of optimality are plausible, e.g. constructing artificial genetic texts containing a different number of letters and letting it compete with the supposedly optimal natural language [Patel (2001b)].


This was talking about Patel's entire hypothesis, not just DNA as a quantum computer.

I suspect once Patel sees the data coming out of Berkeley Lab on photosynthesis, plan B will be quickly discarded and Patel will revert back to his original, more intuitive, presumption that superposition implies a quantum computer.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Sep. 27 2007,22:47   

Quote (Thought Provoker @ Sep. 27 2007,19:49)
It's no longer a question of whether life directly utilizes quantum mechanics but how and in how many ways.

AFAIK, that's been clear for quite a while. After all, life depends on chemistry, and chemistry depends on physics. I believe it's old news that chemical bonds and chemical reactions have quantum mechanical aspects.

The work on quantum coherence in photosynthesis sounds pretty interesting. I readily admit I don't have the physics to evaluate their research. Still, I highly doubt that their work gives us much reason to think that life is capable of quantum computing.

Quote
continuing...

From a paper (essay?) titled Bio-quantum computing...


Sorry, but this guy's a crank. There is NO evidence that DNA works as an antenna to transmit gene signals at a distance. His quantum physics language sounds highly bogus to me, but like I said, I don't have the background to really critique it. I DO have the background to critique his biology, and it's crap.

For instance, his reference (9) in the passage you quoted is to another of his essays. In that, he says things like this:

Quote
We know that from the point of view of bio-electrical behaviour, the closed and stable DNA is
considered a bio-polymer ; hence it does not conduct any electromagnetic field as in a wire. Rather,
when DNA is open via the enzyme (DNA-polymerase) into two anti-parallel half chains and after is
closed again from side to side with the binding protein activities, the DNA chains become polarised
and depolarised. During the opening and closing, the DNA can emit quantum particles ("Gene-
Ons") corresponding to the double helix polarization in “bi-polarons”, interacting with “biophonon”
emission. These last are generated by the breaking of hydrogen bonds of the sequences, of
A-T and C-G couplings. Therefore, such quantum particles generated by the opening of the DNA
helicoidal molecular chains, and by the breaking of the h-bonds, can communicate a quantumspectrum,
based on a series of "Gene-Ons". This spectrum has an exact correspondence with
quantum–pulses to the coding information of the gene because it is emitted at the same time that the
gene is copied by the RNA.


Trust me, that is complete and utter BS. DNA is a biopolymer at all times, not just when it's "closed and stable." DNA polymerase doesn't open the helix; helicases do that. The chains don't get polarised and depolarised, and in fact, there's a better chance of DNA conducting electromagnetic fields when it's closed than when it's opened, because of the base stacking that occurs in the double helix. "Gene-ons" are completely imaginary, and, oh yeah, genes don't get copied by RNA.

Quote
From a paper (essay?) titled Quantum Algorithms and the Genetic Code...


OK, this one seems more legit. Again, most of it is physics-speak that I can't critique. However, there's at least one big red flag in the biology:

Quote
Enzymes are able to create superposed states of chemically distinct molecules. This is an active task. Various nucleotide bases differ from each other only in terms of small chemical groups, containing less than 10 atoms, at their Hydrogen bonding end. To convert one base into another, enzymes have to be repositories of these chemical groups which differentiate between various nucleotide bases. Enzymes are known to do cut-and-paste jobs with such chemical groups (e.g. one of the simplest substitution processes is methylation, replacing ?H by ?CH3, which converts U to T). Given such transition matrix elements, quantum dynamics automatically produces a superposition state as the lowest energy equilibrium state. (Note that the cut-and-paste job in a classical environment would produce a mixture, but in a quantum environment it produces superposition.) It is mandatory that the enzymes do the cut-and-paste job only on the growing strand and not on the intact strand. Perhaps this is ensured by other molecular bonds.


Enzymes do not convert one base into another during replication. It sounds like he thinks enzymes generate a superposition of the 4 possible bases during replication, and that superposition collapses down to the one correct base that pairs with the opposite strand. That's just wrong.

A few other things are problematic:

Quote
It is obvious why DNA replication always takes place in the presence of enzymes. If base-pairing were to occur by chance collisions, it would occur anywhere along the exposed unpaired strand.


No, the reason it requires enzymes is that the phosphodiester bond won't form spontaneously under normal, uncatalyzed conditions. Base pairing can occur by chance collisions, but it doesn't lead to a backbone linkage.

Quote
As long as quantum coherence is maintained, the replication process is reversible. This can easily explain the error-correcting exonuclease action of the polymerase enzymes.


No, because the exonuclease activity is separable from the polymerase activity. It resides in a separate domain of the protein.

Maybe his arguments about quantum search algorithms have merit. I don't know. They're not obviously BS, like the previous links were. But I'm still suspicious, because it's clear that he's making at least some fundamental errors regarding the biology, and I can't judge how those impact his quantum models.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Sep. 27 2007,23:20   

Hi qetzal,

Yea, I only skimmed the first paper.  I will take your word on it.

The second paper is Patel in 2001.

Did he improve his biology in the 2007 paper?

  
BWE



Posts: 1902
Joined: Jan. 2006

(Permalink) Posted: Sep. 27 2007,23:22   

Hmmm. My ignorance of quantum mechanics is pissing me off.

Waves cancel by meeting a reverse phase wave. What happens to particles when they meet an opposite phase?

After an hour of google, I'm just asking for a basic answer.

--------------
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

The Daily Wingnut

   
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Sep. 27 2007,23:46   

Quote (Thought Provoker @ Sep. 27 2007,23:20)
Hi qetzal,

Yea, I only skimmed the first paper.  I will take your word on it.

The second paper is Patel in 2001.

Did he improve his biology in the 2007 paper?

Well, the discussion of how the genetic code may have evolved is provacative. I know that this is an active area of investigation, but I haven't followed it, so I can't say whether his ideas are reasonable. I don't see any glaring errors in that part, for what that's worth.

However, he still seems to be advancing the idea of superposition of all four bases during DNA replication:

   
Quote
Grover’s algorithm needs certain type of superpositions, and catalytic enzymes can stabilize certain type of superpositions. Do the two match, and if so, what is the nature of this superposition? The specific details of the answer depend on the dynamical mechanism involved. The requisite superposition is of molecules that have a largely common structure while differing from each other by about 5-10 atoms. I have proposed two possibilities [Patel (2001a); Patel (2006b)]:

(1) In a quantum scenario, wavefunctions get superposed and the algorithm enhances the probability of finding the desired state. Chemically distinct molecules cannot be directly superposed, but they can be effectively superposed by a rapid cut-and-paste job of chemical groups (enzymes are known to perform such cut-and-paste jobs). Whether this really occurs, faster than the identification time scale [t-sub-b] and with the decoherence time scale significantly longer than [h-bar]/[omega-sub-0], is a question that should be experimentally addressed. It is a tough proposition, and most theoretical estimates are pessimistic.

(2) In a classical wave scenario, all the candidate molecules need to be present simultaneously and coupled together in a specific manner. The algorithm concentrates mechanical energy of the system into the desired molecule by coherent oscillations, helping it cross the energy barrier and complete the chemical reaction. Enzymes are required to couple the components together with specific normal modes of oscillation, and long enough coherence times are achievable. This scenario provides the same speed up in the number of queries Q as the quantum one, but involves extra spatial costs. The extra cost is not insurmountable in the small N solutions relevant to genetic languages, and the extra stability against decoherence makes the classical wave scenario preferable. (Once again note that time optimisation is far more important in biology than space optimisation.)


Unless I grossly misunderstand what he's proposing, option (1) above is completely untenable, and it's disturbing to me that he still offers it for consideration, having had 6 years to learn that basic biochemistry rules it out. It makes me wonder about the validity of everything else he says.

I'm not sure what he's suggesting in option (2), so I can't say if it's compatible with known molecular biology & biochemistry or not.

  
creeky belly



Posts: 205
Joined: June 2006

(Permalink) Posted: Sep. 27 2007,23:48   

Quote
What happens to particles when they meet an opposite phase?

It depends on their kinetic energy, if they collide relativistically, they tend to scatter like billiard balls. The Pauli exclusion principle rules electrons most of the time when they're sent to collide at non-relativistic speeds, which means they're never found at the same spot. That's probably why it was tough to find anything on it. The only way they can be found near each other is by coupling two with opposite spin, which usually happens in atoms. This "pseudo-force" actually keeps white dwarfs from collapsing, the fact that particles don't want to be found near each other causes a pressure, which keeps the dying star from imploding.

  
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Sep. 27 2007,23:57   

Hi BWE,

I can empathize.  I had a week off from work with nothing to do so I decided to figure out this quantum stuff.  I had a headache for the whole week.

Your question is the classic wave/particle problem.  It gave people like Einstein fits.

Some in the Copenhagen school dealt with it by suggesting everything is a wavefunction (there are no particles).  This is what Penrose does.

Others answer the problem by saying the particle ended up in an alternate reality (Many Worlds).

I am almost inclined to believe in a God playing cruel jokes over the Many Worlds interpretation.  They are both metaphysical IMO.

  
k.e



Posts: 1948
Joined: Mar. 2006

(Permalink) Posted: Sep. 28 2007,03:11   

Quote (BWE @ Sep. 28 2007,07:22)
Hmmm. My ignorance of quantum mechanics is pissing me off.

Waves cancel by meeting a reverse phase wave. What happens to particles when they meet an opposite phase?

After an hour of google, I'm just asking for a basic answer.

Don’t worry that doesn't stop the quantum quacks, which outnumber IDists by at least 3 orders of magnitude and...... Speaking of magnets…… quantum mechanics is an even bigger attractor of the weekend feral pseudoscientist than is Dembskian Complexity.

Just google quantum pseudoscience .

The great thing is quantum mechanics has such a vast potential for obscurantism that it is not unknown for Engineers to declare themselves experts in the subject.

And since true experts in the field have little interest in wasting time on crackpots, quantum mechanics makes a perfect target for religion as science.

If quantum mechanics was shown to be intricately involved in the formation of the universe some religious nutcase would say it was:

a) Against god and therefore not true.
b) The direct result of gods work and therefore proof for god’s existence
c) True only when it left a single gap big enough to fit gods and therefore while not agreeing 100% with Genesis could be interpreted as being consistent by reinterpreting Genesis in a subjective manner.

Astrology is better able to explain why this is so....than is quantum mechanics.

It all depends where the observer is.

Have you seen this Interpretation of quantum mechanics

--------------
The conservative has but little to fear from the man whose reason is the servant of his passions, but let him beware of him in whom reason has become the greatest and most terrible of the passions.These are the wreckers of outworn empires and civilisations, doubters, disintegrators, deicides.Haldane

   
Thought Provoker



Posts: 530
Joined: April 2007

(Permalink) Posted: Sep. 28 2007,07:45   

Hi BWE,

The Wikipedia link that K.E. provided is a good one to show you shouldn't be too hard on yourself for being confused on the issue.  It isn't an easy question to answer.

Here is a Wikipedia link discussing Wave/Particle duality.

Wave–particle duality is deeply embedded into the foundations of quantum mechanics, so well that modern practitioners rarely discuss it as such. In the formalism of the theory, all the information about a particle is encoded in its wave function, a complex function roughly analogous to the height of a wave at each point in space. This function evolves according to a differential equation (generically called the Schrödinger equation), and this equation gives rise to wave-like phenomena such as interference and diffraction.

The particle-like behavior is most evident due to phenomena associated with measurement in quantum mechanics. Upon measuring the location of the particle, the wave-function will randomly "collapse" to a sharply peaked function at some location, with the likelihood of any particular location equal to the squared amplitude of the wave-function there. The measurement will return a well-defined position, a property traditionally associated with particles.

Although this picture is somewhat simplified (to the non-relativistic case), it is adequate to capture the essence of current thinking on the phenomena historically called "wave–particle duality". (See also: Mathematical formulation of quantum mechanics.)


Alternative views

Particle-only view
At least one physicist considers the “wave-duality” a misnomer, as L. Ballentine, Quantum Mechanics, A Modern Development, p.4, explains:

When first discovered, particle diffraction was a source of great puzzlement. Are “particles” really “waves? in the early experiments, the diffraction patterns were detected holistically by means of a photographic plate, which could not detect individual particles. As a result, the notion grew that particle and wave properties were mutually incompatible, or complementary, in the sense that different measurement apparatuses would be required to observe them. That idea, however, was only an unfortunate generalization from a technological limitation. Today it is possible to detect the arrival of individual electrons, and to see the diffraction pattern emerge as a statistical pattern made up of many small spots (Tonomura) et al, 1989. Evidently, quantum particles are indeed particles, but whose behaviour is very different from classical physics would have us to expect.”


Wave-only view
At least one scientist proposes that the duality can be replaced by a "wave-only" view. Carver Mead's Collective Electrodynamics: Quantum Foundations of Electromagnetism (2000) analyzes the behavior of electrons and photons purely in terms of electronic wave functions, and attributes the apparent particle-like behavior to quantization effects and eigenstates. According to reviewer David Haddon:[12]

Mead has cut the Gordian knot of quantum complementarity. He claims that atoms, with their neutrons, protons, and electrons, are not particles at all but pure waves of matter. Mead cites as the gross evidence of the exclusively wave nature of both light and matter the discovery between 1933 and 1996 of ten examples of pure wave phenomena, including the ubiquitous laser of CD players, the self-propagating electrical currents of superconductors, and the Bose–Einstein condensate of atoms.


And while K.E. may consider it just more "psuedoscience", here are some interesting experimental results (Ashfer Experiment).

Afshar claims that his experiment invalidates the complementarity principle and has far-reaching implications for the understanding of quantum mechanics, challenging the Copenhagen interpretation. According to John G. Cramer, Afshar's results support Cramer's own transactional interpretation of quantum mechanics and challenges the many-worlds interpretation of quantum mechanics.

So what is this "transactional interpretation"?

More from Wikipedia...
Suppose a particle (such as a photon) emitted from a source could interact with one of two detectors. According to TIQM, the source emits a usual (retarded) wave forward in time, the "offer wave", and when this wave reaches the detectors, each one replies with an advanced wave, the "confirmation wave", that travels backwards in time, back to the source. The phases of offer and confirmation waves are correlated in such a way that these waves interfere positively to form a wave of the full amplitude in the space-time region between emitting and detection events, and they interfere negatively and cancel out elsewhere in space-time (i.e., before the emitting point and after the absorption point). The size of the interaction between the offer wave and a detector's confirmation wave determines the probability with which the particle will strike that detector rather than the other one. In this interpretation, the collapse of the wavefunction does not happen at any specific point in time, but is "atemporal" and occurs along the whole transaction, the region of space-time where offer and confirmation waves interact. The waves are seen as physically real, rather than a mere mathematical device to record the observer's knowledge as in some other interpretations of quantum mechanics.

John Cramer has argued that the transactional interpretation is consistent with the outcome of the Afshar experiment, while the Copenhagen interpretation and the many-worlds interpretation are not.[3]


Sound familiar?  It sounds like a different way of describing Penrose's OR interpretation.

I consider Penrose's OR to be a Copenhagen derivative, but that is just a label.

Labels aren't important, ideas are.

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

Pages: (9) < 1 2 3 [4] 5 6 7 8 9 ... >   


Track this topic Email this topic Print this topic

[ Read the Board Rules ] | [Useful Links] | [Evolving Designs]