Physics Discussion Thread

vina · Post by **vina** » 27 Jun 2011 09:01

Bade wrote:In the context of 1/r potential discussion above, if there are extra dimensions indeed, one can see already that simply assuming 3 spatial dimensions and doing Gauss's theorem in this space will only give an incomplete solution to the true nature of the potential.

Ah, but that is the point isn't it ? If physical reality was actually more than 3 dimensions, the math for 3 spatial dimensions would still exist and be exact in itself ? Because your physical reality was different you just wouldn't apply it !

For instance, using circulation theory, the flow around a cylinder /Lifting line is Exactly described mathematically . Now if you apply a Joukowski transform with a Kutta condition, you describe an airfoil! Now instead of air/water/ fluids described using potential flow , there was something else in say some alternate universe, this particular math and the phenomeno that can be described using this wont work, but that doesn't mean it is "wrong" or inexact in itself. It is just that it doesn't apply.

IMHO, it is something like this. If you solve a quadratic equation in highschool, you are told to ignore "results" that seem "nonsensical" /which are not what we are looking for , given the "problem". Not that the result was wrong, but just that we really dont want it in our physical experience. How about "imaginary" numbers, you cant have anything "imaginary" in the physical world. But you use that in a lot of physics /engg/whatever, because the math describes a lot of it in the physical world pretty well.

GuruPrabhu · Post by **GuruPrabhu** » 27 Jun 2011 09:07

kasthuri wrote: There is whole world of biology out there which physics have no clue about. The phenomenon of transcription and translation is unexplainable in any mathematical term. QM is not an answer for what happens inside a gene. Gene is not a quantum phenomena

I suppose that you have not been reading up on modern biophysics. The fact of the matter is that physics is explaining protein folding to biologists who are slow to catch on

and yes, it is very much quantum. Just google it. Here is a starter:

http://scholar.google.com/scholar?q=bio ... i=scholart

Amber G. · Post by **Amber G.** » 27 Jun 2011 09:24

vina wrote:
Amber G. wrote:Anyway .. here is another problem --

We live in a quiet neighbor-hood but there is a highway not too far from us. In the morning (or day time) we don't hear any noise but in the evening (when we take a walk) we often hear traffic noise from the high-way?
What possible could be the reason? .. (Do others have similar experience? Sound from far away places, much clearer in the evening than in the day or morning..)
Could be multiple reasons. One plausible one could be this. In the morning, there is usually dew on the ground,...]

Vinaji - You may likely to see that just a few posts above, I gave good references and detailed explanation.....

I may like to comment on few of your statements below..

...the air on the ground is usually of lower temperature (the sun needs to burn through multiple layers and reach and warm up everything). So what happens is that the atmosphere is not one homogenous medium, but rather stacked up as different layers of slightly higher density each.

Now when this happens, sound can if conditions are right propagate only in those particular channels and get totally internally reflected at the boundaries and not penetrate the adjacent layers of different density (sort of like optic fiber) and propagate massive distances. The thing is if you are in one of the other channels in which the sound is not propagating (if you are in a higher density channel) , you will not hear it ..

May be a little more sophistication and specifics on details, but essentially "channels" you talk about have been studied in very great detail by many including US military..most of this has been very highly classified (over last 60+ years), some has been unclassified only recently and military has spent billions (literary) on this... may be more of this later, if there is an interest..

But normally this does not happen at the ground level after a few hours after sunrise.. as ground heats up pretty fast. If there is a "channel" near ground, it is almost certain that it is going to be a nasty muggy day.. specially if you are in Mumbai or LA (see "temperature inversion" in wiki )

In fact in underwater warfare/acoustics this is very important. Submarines hide in those kind of thermal layers and if your sonar is not dunked right into it, you would be able to detect it. On the other hand, if you are in that layer, the noise gets propagated hundreds of miles very easily and you can detect from very large distances. In fact , whales can communicate over hundreds of miles using this phemonemon.

Gosh. I cant believe it. I still remember this vibrations and acoustics stuff after all these years from the Madrassa.

[/quote]

Again Navy has literally spent billions .. The Red October (book, not the movie),, described some of the details while it was still classified (though most of the physicists knew)..One very famous physicist had very interesting invention done in second world war (which remained classified until 10 years ago - and I still have not seen too much of it in popular media..) .. may be more of this later...

vina · Post by **vina** » 27 Jun 2011 10:20

Amber G. wrote:Vinaji - You may likely to see that just a few posts above, I gave good references and detailed explanation.....

Thanks. Didn't see that post of yours. So I guess it has to do with refraction of sound due to thermal effects on the atmosphere.

May be a little more sophistication and specifics on details, but essentially "channels" you talk about have been studied in very great detail by many including US military..most of this has been very highly classified (over last 60+ years), some has been unclassified only recently and military has spent billions (literary) on this... may be more of this later, if there is an interest..

Yes. This is a pretty well studied phenomenon ever since WWI and a lot of the details are classified. But then, any Navy which operates submarines and does anti sub warfare will know of it and infact the SDRES are pretty good, in fact top drawer in anti sub warfare and were cutting edge in sonar by mid 80s (lot of work at NPOL Kochi), (infact a current desi prof at Stan Madrassa who does research in MIMO and arrays did exactly that kind of stuff in the Navy and IIT Delhi along with Prof Indarasen and they made their name and fame on that and the signal processing)

Again Navy has literally spent billions .. The Red October (book, not the movie),, described some of the details while it was still classified (though most of the physicists knew)..

Which part ? When I read that book ages ago, I though it was ho-hum "hollywood" sensationalized stuff, though for a lay man, it would have sounded gee-whiz.

vina · Post by **vina** » 27 Jun 2011 11:53

In fact, let me add to this post of mine to Bade Mian. Right now, I am modeling something using the Ornstein-Uhlenbeck process in a context that as a Fyzzicist you would be dumbstruck with horror and with a set of conditions that are hokey at best. Now, I dont expect a "Fyzzicist" like certainty in what I am looking for. I know that the "process" I am working with is like some Paki Abdul on the strongest stuff from Afghanistan and jumps all over the place. During the times when the process is "mean reverting" , I can model it rather accurately using that particular statistical process and the cash registers go Ka-Ching , Ka-Ching. At other times, the Abdul goes soosai and there is a massive Ka-Boom. To cover my Musharraf during such times, I am wrapped in Kevlar Boorqa in multiple layers, so that even if the Abdul goes Kaboom, I am not Shaheedized. I play it on averages. If my model works more number of times than it fails, in expectation , I am not shaheedized! That kind of thing is simply unacceptable in Fyzzics, because you simply REJECT anything that doesn't fit the Physical world you are currently studying.

In my world, I know that the Abdul Paki jumps around. It is "Do I eat tonight or Don't I eat" for me! But all said and done, is the Orenstein-Uhlenbeck process "wrong" , if the Abdul goes Soo-Sai ? How does the statistical process "know" that it fits "Abdul's" pee-havior during some times , and also some physical processes (with absolute boring predictability like clockwork) ? It doesn't. It is math and is complete in itself. We just use it in cases where it fits and discard it otherwise , I would think.

So there you are. I also calculate "Half Life" and "Decay Rates" and all that jazz, but then I take that with huge dollops of salt and a jaundiced eye (if you don't in my business, you are nothing but a sorcerer's apprentice, punching buttons).

I am reading a book currently and in that there is a page right at the beginning, before the preface with this quote which I find quite profound.

"It does take maturity to realize that models are to be used but not to be believed" - Henri Theil

GuruPrabhu · Post by **GuruPrabhu** » 27 Jun 2011 15:35

^^^ ok, I will bite. There *must* be some point to the above in a Physics thread besides letting us all know what model you are working with.

I suppose this is the point:

vina wrote:I play it on averages. If my model works more number of times than it fails, in expectation , I am not shaheedized! That kind of thing is simply unacceptable in Fyzzics, because you simply REJECT anything that doesn't fit the Physical world you are currently studying.

Sir-ji, Yes physics works with reality. That is why we don't make bubbles and burst them.

It is not like Relativity is trading at Rs 400 one day and worth Rs 10 the next and QM suddenly goes crazy and gains Rs 1000 in one day. Think of physics as a simple interest bearing savings account -- society benefits from it. We have nothing in common with bankers.

So, if you have to shoot off on "Fyzzics" why not find a soap-box in the banking dhaga or somewhere similar? -- unless, of course, your goal is to actually discuss Physics like the rest of us here.

Also, do you really think that your Benis language is actually funny? If not, what is the point of using it? Do you use this language in your board-room meetings, or do you make like a good SDRE and say it clearly?

kasthuri · Post by **kasthuri** » 27 Jun 2011 16:29

GuruPrabhu wrote:
I suppose that you have not been reading up on modern biophysics. The fact of the matter is that physics is explaining protein folding to biologists who are slow to catch on

Protein folding is just one aspect of biology and in fact I wouldn't call it as biology proper. I, in fact worked on it during my cs days - applying robot motion planning approach to protein folding (probabilistic road map methods). It is more of a physical phenomena which could be computed to quite an extent using efficient algorithms. What I am taking about is biology proper. In my previous job I worked with a biophysicist and have been to their meetings. I have a clue on what they do. Reducing everything to physics that we know of, is what that concerns me.

GuruPrabhu · Post by **GuruPrabhu** » 27 Jun 2011 16:50

kasthuri wrote: Reducing everything to physics that we know of, is what that concerns me.

I would not put it that way -- one can not reduce reality. Rather, it is more like expanding physics into realms that it was typically shy of.

The problem is best described not by biophysics, but the field of complexity physics. Basically, we all agree that physics explanations work at several length scales but not all complexity scales. For example, from quarks to nucleons to nuclei to atoms to molecules, physics works. Similarly, from dust to planet to sun to galaxy to cosmos, physics works quite well.

It is the range between molecule to very long molecule to DNA, where physics is wanting. The problem is one of complexity. The idea is that there is no new law of physics in DNA dynamics, it is just that the problem is too complex to solve. This is changing with the arrival of large-scale computing. In some ways, it is similar to weather patterns -- we know that there is no new law of physics at play, and yet we can not calculate/predict the weather. The problem is just too complex.

I mentioned protein folding because it is believed that prion diseases (alzheimers, mad cow) are caused by protein mis-folding and aggregation. Physics is taking a stab at this.

Similarly, there is work going on in understanding photosynthesis. There are very sophisticated models of chlorophyll being studied. It turns out that there are current loops within the molecule that enhance photo-conversion. (I am only repeating what I have heard in seminars - I don't fully understand it).

Another area where physics/instrumentation is making inroads is DNA sequencing. My point of saying all this is that biology is the *ultimate* frontier - IMO, it is more important than cosmology/grand unified theory of particle physics.

There is something magical that happens in complex systems - life is created! As living beings, understanding that will give us the ultimate understanding of ourselves, our origins (and our meaninglessness?).

I believe that this endeavor has future - it is not reductionism - it is expansion of the mind and physics to enter the world of complex phenomena.

Here is the Wiki on it: http://en.wikipedia.org/wiki/Complex_systems

[ok, ducking out now. Spent a lot of time here today]

vina · Post by **vina** » 27 Jun 2011 18:17

GuruPrabhu wrote:^^^ ok, I will bite. There *must* be some point to the above in a Physics thread besides letting us all know what model you are working with.

Err. I thought you wanted to be left alone! And thanks, I have no desire to be bitten by anything. Go bite someone/something else . Bye.

I suppose this is the point:
...
Sir-ji, Yes physics works with reality. That is why we don't make bubbles and burst them.

"Complex Systems" .."We have nothing in common with bankers."

. You have a lot more in common than you realize.
And of, if you think, you are working with "reality" and this picture of yours describes anything called "Physics" , what can I say, you want to live in my world!

I dare say that beyond just buzz words, "Game Theory","Collective Behavior", "Pattern Forming", "Evolution and Adaption" , "Networks" etc are literally light years removed from what you as a Physicist do,but if you do want to do this stuff, guess what you want to become.. A banker! Atleast those guys have been doing it for the past 30/40 years now and betting their shirt on it (and sometimes losing it as well , no doubt, but also raking it in most times).

And oh. In case you want to do "Complex Systems", time to junk the Fyzzics talk and get into Pingrezi! That world out there is exactly as I described it I am afraid. Those things deal with Abdul Pakis and not nice particles that behave predictably and stably.

Oh well, lets not be bothered with it. You cannot venture into it. Bye.

GuruPrabhu · Post by **GuruPrabhu** » 27 Jun 2011 19:30

Yup, physicists will shiver in their dhotis while bankers come and lecture us. No problem. I should have left it alone. Bye.

Folks,

I hope I was clear in my post. Complexity is not a new concept. In fact it is older than the 30-40 years claimed by Bankers - they started on modeling after physicists started getting hired on Wall Street. Chaos was first proposed by Poincare in the 1880s.

What makes it interesting NOW, is that there is enough computing available in order to make progress.

Rahul M · Post by **Rahul M** » 27 Jun 2011 19:33

vina ji, what's with the misplaced aggression ?

brihaspati · Post by **brihaspati** » 27 Jun 2011 19:49

kasthuri wrote:Brihaspatiji,

1. "following mathematical logic" or using classical logic to prove theorems will not fetch us too far. One may argue that we have so many wonderful theories in physics due to the standard logic, but it is my humble opinion that unless some sort of axiomatization of physics is explored using other logics (non-standard models, para-consistent etc.) we may not be able to completely reconcile gravity and quantum effects. Hawking's lecture titled "Godel and the End of Physics" rightly points in this direction. Btw, I am aware of Hilbert's failed program for axiomatizing physics.
As far as I have come across, mathematical logic is often taught in philosophy departments than on math. And in fact, CS departments have shown more interest on logic than math folks. In a nutshell, logic matters more now than ever, be it cs, math or physics.
2. I don't see why "meta-mathematics" is not mathematics in the first place.
3 and 4. Math to a large extent is shaped by physics and vice-versa. I simply don't see the reason why they should be separated at all. Almost all legends in either field have contributed to the other. And it is my belief (I don't have any justification) that for any physical phenomena that we see there should be a corresponding mathematical/mental construct and vice-versa. This belief of mine correlates well with the Vedantic viewpoint that physical world is a manifestation of the mind in its complete glory.
5 and 6. I feel that "physics envy" often reduces the reality into the world of atoms and universe. There is whole world of biology out there which physics have no clue about. The phenomenon of transcription and translation is unexplainable in any mathematical term. QM is not an answer for what happens inside a gene. Gene is not a quantum phenomena.

Therefore, the word "physical reality" should really mean "reality as explained using the principles of physics". Biological realities such as gene regulation, cell cycle, signal transductions are macroscopic yet they aren't "covered" by physics so far.

Kasthuri ji,
by condensed logic - I means that the steps of derivation and development used to go from a set of starting statements in maths to another conclusion point - is actually following on a condensation of smaller logical steps. Every mathematical derivation or development can be traced through those steps. Even for the simple quadratic equations being mentioned here, there are assumptions involved. You are assuming a certain "field" of numbers or a ring, on which you have created some constraints by the form of the quadratic equation. What you can do to "solve" it, are logical steps guided and constrained by that field and its properties and operations defined on that field.

Mathematicians are using theorems or results to shorten the representation of that derivation, each of which further condense more such logical steps.

I don't see why there should be confusion about the role of maths in physics. Maths is not the starting point in physics. Every so-called mathematical model of physics is actually an attempt at describing a hypothesized model of what is considered a good model for a particular aspect of physcial phenomenon in mathematical terms.

Combined with this is perhaps a standard urge to apply Occam's razor. Try to minimize the set of axioms which can still however explain/predict successfully a complex phenomenon. This is why some of the physical reality models may seem sparse and oh-so-mathematical in their description, and hence do not carry the sense of physical reality that we psychologically expect.

Moreover, talking about potentials etc, is a bit hazy. Flux/divergence and force-fields are all associated with slightly dated concepts about actual "flows" of "action" etc and connected to "action at a distance" views. There are some serious problems with that view. "Forces" in QM are effects supposed to be generated by "exchange of particles". That is slightly difficult to fit in with the earlier view.

There are various astrophysical "anomalies" that may indicate departures from the "inverse square" law, and it is not just the more accurate GR calculations which do not assume anything about Gaussian divergence, but still reproduce the Newtonian as an approximation for large distances from point masses. It is also about such contradictory things like dark flow and extra energetic phtons. A host of such stuff exist.

kasthuri · Post by **kasthuri** » 27 Jun 2011 19:50

GuruPrabhu wrote:
kasthuri wrote: It is the range between molecule to very long molecule to DNA, where physics is wanting. The problem is one of complexity. The idea is that there is no new law of physics in DNA dynamics, it is just that the problem is too complex to solve. This is changing with the arrival of large-scale computing. In some ways, it is similar to weather patterns -- we know that there is no new law of physics at play, and yet we can not calculate/predict the weather. The problem is just too complex.

I beg to differ. Unlike weather, it is not the question of range in biology. It is about the order which every biological system undergoes and our inability to explain this order. Gene regulation and cycle cycle would serve as examples. This is far from weather prediction in which we have multitude of variables that makes the "curse of dimensionality". In biology it is not just the curse of dimensionality, it is much more. The near-perfect order in which life operates is beyond the scope of morden day physics and its laws. And any extension of physics to explain these laws would radically alter the scope of what we mean by physics - it can no longer be called "physics" in traditional sense. Btw, computing can only reduce the curse of dimensionality but not explain the underlying order.

brihaspati · Post by **brihaspati** » 27 Jun 2011 20:09

There is one fundamental problem in physics trying to explain everything -although it does a pretty good job of it for almost everything. A model of human choice or consciousness is still beyond current physics. Hence Vinaji has a point.

brihaspati · Post by **brihaspati** » 27 Jun 2011 20:12

Kasthuriji,
even the very formation of self-replicating DNA from organic compounds and their enclosure within selective membranes is still problematic as a mere by chance physical phenomenon. Some experimental studies indicate that both impact as well as the early special chemical soup that happened to form on earth might have helped. But this is still far from being a certainty and conclusive indication.

But the consciousness problem is a most difficult one.

brihaspati · Post by **brihaspati** » 27 Jun 2011 20:20

No use blaming the dimensions. That problem arises because physicists are driven to explain as much by as little as possible. The incorporation of higher number of dimensions is simply to bring together the current three-interaction (some will say two) model into a single GUT. They want one single theoretical curvature-energy concept to be used to derive all three interactions, the observed or "required" particles, and hence one approach has been to extend the curvature-energy concept to a higher dimension and then take projections into 4D.

kasthuri · Post by **kasthuri** » 27 Jun 2011 20:24

brihaspati wrote: Kasthuri ji,
by condensed logic - I means that the steps of derivation and development used to go from a set of starting statements in maths to another conclusion point - is actually following on a condensation of smaller logical steps. Every mathematical derivation or development can be traced through those steps. Even for the simple quadratic equations being mentioned here, there are assumptions involved. You are assuming a certain "field" of numbers or a ring, on which you have created some constraints by the form of the quadratic equation. What you can do to "solve" it, are logical steps guided and constrained by that field and its properties and operations defined on that field.

Mathematicians are using theorems or results to shorten the representation of that derivation, each of which further condense more such logical steps.

I don't see why there should be confusion about the role of maths in physics. Maths is not the starting point in physics. Every so-called mathematical model of physics is actually an attempt at describing a hypothesized model of what is considered a good model for a particular aspect of physcial phenomenon in mathematical terms.

Combined with this is perhaps a standard urge to apply Occam's razor. Try to minimize the set of axioms which can still however explain/predict successfully a complex phenomenon. This is why some of the physical reality models may seem sparse and oh-so-mathematical in their description, and hence do not carry the sense of physical reality that we psychologically expect.

Brihaspati ji,

I completely understand what you mean by condensed logic (mathematical proofs), the physical models that *uses* math as an approximation to describe reality and the urge to apply Occam's razor. Being a mathematician before I journeyed through computational physics and now biology, I understand what it means by "proving" a theorem and ingredients that make up theorems aka meta-theorems and what it means to "actually prove". I don't believe that reducing the axioms would serve better purpose. For that matter one can't reduce the axioms to a large extent - the theory will be inconsistent. Math decided to be incomplete than being inconsistent, which seems to be a sane choice. This choice allowed us to answer some questions in physics. But if you ask whether these choices of axioms are sufficient to answer other questions such as gravity vs quantas, I doubt it. It is not the reduction of axioms but the scope of axioms and logic, in general. The reason I see why some physical reality models are not so mathematical is not because of the Occam's razor but "incompleteness" acting in its entirety.

brihaspati · Post by **brihaspati** » 27 Jun 2011 20:34

kasthuri ji,
actually I am with you - in the sense that I don't see why there is any confusion about somehow maths determining "physics". It is physics which limits and determines physics. Maths is just a condensed logical process of derivation of conclusions. To a certain extent people may think that the very constraints of maths is constraining physics - but the real blame then should be put on the physics modeler - who ha sfailed to include or describe that "extra" bit of reality into his/her maths description to start out with.

kasthuri · Post by **kasthuri** » 27 Jun 2011 20:45

brihaspati wrote:kasthuri ji,
but the real blame then should be put on the physics modeler - who ha sfailed to include or describe that "extra" bit of reality into his/her maths description to start out with.

Well said, precisely my point - "extra" bit of reality is what is needed. This may alter the underlying structure of logic (in both rules and axioms).

GuruPrabhu · Post by **GuruPrabhu** » 27 Jun 2011 21:10

kasthuri wrote: I beg to differ. Unlike weather, it is not the question of range in biology. It is about the order which every biological system undergoes and our inability to explain this order. Gene regulation and cycle cycle would serve as examples. This is far from weather prediction in which we have multitude of variables that makes the "curse of dimensionality". In biology it is not just the curse of dimensionality, it is much more. The near-perfect order in which life operates is beyond the scope of morden day physics and its laws.

I don't disagree with this. However, I will not venture to say what is more complex than the other. These problems are *all* beyond the scope of physics - or, any other branch of science for that matter. If you are convinced that one system is more complex than the other, fine - I am just saying that we don't know enough.

And any extension of physics to explain these laws would radically alter the scope of what we mean by physics - it can no longer be called "physics" in traditional sense.

This has been true every time there was a major revolution in physics. Physics of today is not the same as physics of nineteenth century. The only "traditional sense" I know of is simply this: Physics is a science of measurables.

Once we have measurables in DNA dynamics, it will be physics.

Btw, computing can only reduce the curse of dimensionality but not explain the underlying order.

Recall that two pages back, I had asked Bade Saar: "How do we accommodate critical phenomena in his view of mathematics?"

Underlying order is a matter of formulating the order in mathematical terms. Before people knew about strong isospin, they would have laughed at anyone claiming that a proton and neutron were the same particle. Are there any symmetry groups and broken symmetries in biology?

I will ask you this question and leave it for you to ponder:

Why does DNA helix come in only one handedness?

Rahul M · Post by **Rahul M** » 27 Jun 2011 21:30

that's an interesting one.

Bade · Post by **Bade** » 27 Jun 2011 21:39

Dileep Kondepudi (?) from Wayne State in NC once gave a talk on the chirality (handedness) in the context of biology while I was a student. I will just post his link for those interested to look into.

http://users.wfu.edu/dilip/Research.html

GuruPrabhu · Post by **GuruPrabhu** » 27 Jun 2011 23:20

^^^^ Thank for posting that, Bade Saar. It is a nice and compact presentation of several phenomena in chiral symmetry breaking. As you well know, nobody really understands its origin. It is a problem for particle physics in both neutrino sector (parity violation) and strong sector (CP violation/no axion in sight).

At a broader level, why do humans mostly have their heart on their left side of the body? IIRC, one in million doesn't and doesn't live long. However, if the entire body mirror symmetry is flipped, longevity is restored. I haven't read too much about this, but I believe that parity violation occurs early in the embryo development -- around when there are about 32 cells. Some bio guru may comment -- my info is pedestrian.

Amber G. · Post by **Amber G.** » 28 Jun 2011 01:50

I don't know if folks know that quite a lot of original work on DNA / genes by Watson and co had lot of input and actual work by Feynman who applied tools learned as a physicist..

I know, CV Raman in his later years was quite a bit interested (and did work) on biology (mainly Eye and how it perceives color etc) related field..

My own son (fresh PhD --fairly dry physics..) is being told by quite a few that there are more interesting problems to be tackled in bio field ..

(Of course, I know of more than one case where a large group of physics grad students/post-docs left en masse to work on wall street..

Amber G. · Post by **Amber G.** » 28 Jun 2011 01:55

GuruPrabhu wrote:^
At a broader level, why do humans mostly have their heart on their left side of the body? ...

Can't one just travel a full round on a Mobius strip or Klein bottle (or whatever you guys call it) and then, at least the heart will be on their right side...

brihaspati · Post by **brihaspati** » 28 Jun 2011 02:00

One can try to do computational biology from a molecular viewpoint, and optimize the appropriate wave function to predict the handedness. But if one really tries it - both handedness turns up with equal probability.

Rahul M · Post by **Rahul M** » 28 Jun 2011 02:24

no theories for symmetry breaking yet ? and wave fn of what exactly, since I am not too knowledgeable about biophysics.

Amber G. · Post by **Amber G.** » 28 Jun 2011 02:52

vina wrote:
May be a little more sophistication and specifics on details, but essentially "channels" you talk about have been studied in very great detail by many including US military..most of this has been very highly classified (over last 60+ years), some has been unclassified only recently and military has spent billions (literary) on this... may be more of this later, if there is an interest..
Yes. This is a pretty well studied phenomenon ever since WWI and a lot of the details are classified. But then, any Navy which operates submarines and does anti sub warfare will know of it and infact the SDRES are pretty good, in fact top drawer in anti sub warfare and were cutting edge in sonar by mid 80s (lot of work at NPOL Kochi), (infact a current desi prof at Stan Madrassa who does research in MIMO and arrays did exactly that kind of stuff in the Navy and IIT Delhi along with Prof Indarasen and they made their name and fame on that and the signal processing)

Yes, existence of sound channel and lot of this was known around WWI and later.. but as some one (pretty famous expert) rightly said , some specifics (some quite surprising and simple) were among the most successfully kept secrets.. of WWII and later.. (till 80's or even 90's) .. Prof Ewing (who is credited for discovering SOFAR) remained fairly quiet about his later work)

( A few things are still not that well known, outside specialized scientific world)

( Some what related ..Roswell (area 51) UFO.. (1940's) is one of the most discussed CT / mystery etc (If you have not heard about it, check out wiki) .. and I believe, only in 1990's .. US conceded that it lied about the details of the crash of a "weather balloon" ... that was Prof Ewing's work too.. Officially no one talked about it, at all in all these years ... only recently there are some scientific details..)

Again Navy has literally spent billions .. The Red October (book, not the movie),, described some of the details while it was still classified (though most of the physicists knew)..
Which part ? When I read that book ages ago, I though it was ho-hum "hollywood" sensationalized stuff, though for a lay man, it would have sounded gee-whiz.

Movie was ho-hum but the book described some parts and techniques of 'sofar' fairly accurately.. (this was almost 10 years before it got unclassified) .. I remember talking some interesting stuff with an US Navy scientist (Physics PhD and a student ) about that movie..

GuruPrabhu · Post by **GuruPrabhu** » 28 Jun 2011 03:09

Amber G. wrote:
GuruPrabhu wrote:^
At a broader level, why do humans mostly have their heart on their left side of the body? ...
Can't one just travel a full round on a Mobius strip or Klein bottle (or whatever you guys call it) and then, at least the heart will be on their right side...

The problem is quite puzzling if you break it down:

How does an embryo floating in a liquid "know" which way is "up"? The embryo is fairly spherical at that stage. It has to "decide" which end of the sphere is "head" and which end is "legs" -- after it decides that, it has to decide which end is "chest" and which end is "back".

Does it do so randomly? Probably. From what I have read, an individual cell takes on the role of being the "brain" and from then onwards multiplies as per the DNA instructions for becoming a brain.

Ok, so after these random choices, it somehow "knows" which end is "left" and puts the heart there. How does it do that? Apparently, a cell decides that it will be the "aorta". It then somehow develops into a tube which hooks to the left - the end of the hook starts out becoming the "heart".

Bio gurus -- please correct the above. I am recalling from memory something I had read ages ago.

It has always bothered me how the end of a tube knows which way is "left". But then, such questions only bother physicists, perhaps not biologists and certainly not bankers

Vayutuvan · Post by **Vayutuvan** » 28 Jun 2011 03:25

brihaspati wrote:No use blaming the dimensions. That problem arises because physicists are driven to explain as much by as little as possible. The incorporation of higher number of dimensions is simply to bring together the current three-interaction (some will say two) model into a single GUT. They want one single theoretical curvature-energy concept to be used to derive all three interactions, the observed or "required" particles, and hence one approach has been to extend the curvature-energy concept to a higher dimension and then take projections into 4D.

Brihaspati garu

As far as I know the "curse of dimensionality" usually refers to the large dimensionality of the state space. In protein folding, while the spatial dimension is only 3, the number of state variables are exponentially large (as a function of the size of the molecule being modelled).

Kasthuri ji

Computations cannot cure the "curse of dimensionality" and the electrostatics based protein folding in silico would largely be a failure, even though is producing some results for smaller molecules(IM V HO, of course). Another line of research which has a more statistical flavour (one of the exponents of this approach is Peter Wolynos) probably is the ticket to solving this problem.

Amber G. · Post by **Amber G.** » 28 Jun 2011 03:26

It has always bothered me how the end of a tube knows which way is "left". But then, such questions only bother physicists, perhaps not biologists and certainly not bankers

May be I am missing the crux.. but what exactly is the "problem"..I can determine 'right'. (and drive on the right hand side... traffic on the road is not symmetric and parity is not conserved in typical traffic pattern). The gene is not at the elementary particle level .. (so even if I don't worry about weak interactions

) .. there is certainly no left-right symmetry in molecules in general.

Amber G. · Post by **Amber G.** » 28 Jun 2011 03:56

Okay a puzzle...let us see what the gurus think...

It has more to do with down to the earth useful physics..No tensors or higher dimensions are involved..

There was a news paper story about four strong swimmers who drowned. All were young (18-20 years old) and the place where it happened was familiar to them, except at this time their haunt was engrossed with foamy water after a heavy rain. A waterfall close by was the cause of that foam and turbulence. One person slipped on a rock and fell into that water and other friends, one after other, to help, jumped and all died. The expert (police recovered the body) remarked that, that place was known as a "drowning machine"... and even the strongest of the swimmers would not have had any chance..."The laws of physics were against them".. it was remarked...

What laws of physics?

(If you have read the news paper story or heard its analysis .. please give others a chance to guess)

brihaspati · Post by **brihaspati** » 28 Jun 2011 04:29

Haven't read it - but I think it has to do with buoyancy being reduced by air/gas bubbles. It lowers the density.

GuruPrabhu · Post by **GuruPrabhu** » 28 Jun 2011 04:45

Amber G. wrote:May be I am missing the crux.. but what exactly is the "problem"..I can determine 'right'. (and drive on the right hand side... traffic on the road is not symmetric and parity is not conserved in typical traffic pattern). The gene is not at the elementary particle level .. (so even if I don't worry about weak interactions ) .. there is certainly no left-right symmetry in molecules in general.

You did not know right and left when you were a kid -- you were *trained* to know that, weren't you? But, somehow your embryo knew when it has just a handful of cells.

Plus, you have a sense of orientation because you walk upright and you know which way is up. If you are an embryo floating in water, you don't know which way is gravity pointing.

Also, the embryo at that stage is pretty much a sphere. So it *has* no left and right. It *breaks* symmetry by choosing a left.

I am not saying that it is impossible -- I would like to hear suggestions about what algorithm an embryo could *possibly* employ to determine left.

What is astonishing is that all nearly all embryos choose left for the heart -- but *not all*. Some go "right". And for this simple mistake they die, most likely as an infant.

[or, alternately, they were destined to die because of some flaw in their DNA ... choosing "right" may just be a symptom of this flaw]

Rahul M · Post by **Rahul M** » 28 Jun 2011 05:44

Amber ma'm, the point is how do you identify left from right ?

Amber G. · Post by **Amber G.** » 28 Jun 2011 05:56

GuruPrabhu wrote:
You did not know right and left when you were a kid -- you were *trained* to know that, weren't you? But, somehow your embryo knew when it has just a handful of cells.

I certainly did right from left when I was a kid..and the cells /dna certainly "knew" left from right... forget about a handful of cells, a single protein molecule has enough complexity to know the orientation ..

Plus, you have a sense of orientation because you walk upright and you know which way is up. If you are an embryo floating in water, you don't know which way is gravity pointing.

I can still tell my left hand from right hand even if I am floating in water - or even in weightlessness condition in space - An embryo is not a spherical ball - even a big enough molecule is not a symmetric spherical ball.

Also, the embryo at that stage is pretty much a sphere.

Not really .. with right approximation even earth may look like a sphere (just like Jupiter with a naked eye) ..but it has enough structure .. has north pole.. equator etc..

Anyway I am sure I am missing something deep...

Amber G. · Post by **Amber G.** » 28 Jun 2011 06:07

Rahul M wrote:Amber ma'm, the point is how do you identify left from right ?

Same way I identify "up" from "down".....

Or I can say.. look at the Jupiter's moon (or our own gibbons moon).. which ever direction the farthest moon is ..l etc... etc...

Above assumes that I am on earth and we understand that the term Jupiter and its moons are well defined..

Besides parity is not conserved in weak interactions...so I can define/identify left from right even at the most basic levels, by say watching a beta decay.. or something...

(I don't believe cells do this by that method though..)

Rahul M · Post by **Rahul M** » 28 Jun 2011 06:19

up and down can be decided by gravity (isn't that how seeds germinate ?)

I am not sure biological systems have the option of watching a parity violation.

kasthuri · Post by **kasthuri** » 28 Jun 2011 07:35

matrimc wrote: Computations cannot cure the "curse of dimensionality" and the electrostatics based protein folding in silico would largely be a failure, even though is producing some results for smaller molecules(IM V HO, of course). Another line of research which has a more statistical flavour (one of the exponents of this approach is Peter Wolynos) probably is the ticket to solving this problem.

Matrimc ji,

I was careful when writing about "curse of dimensionality (COD)". Computations cannot cure COD, they can only try to reduce. Unless someone comes up proving P=NP, in which case we can hope to have non-deterministic polynomial algorithms have polynomial solutions. That would be one of the greatest break through (almost equivalent to solving Riemann hypothesis), but yet COD will still be an issue. Even the simplest n-body problem which is O(N^2) complexity would take years on a HPC for 10 million bodies!

kasthuri · Post by **kasthuri** » 28 Jun 2011 07:49

Rahul M wrote:Amber ma'm, the point is how do you identify left from right ?

I vaguely remember reading that direction is absolutely determined by the electron spin. I am not sure if it is Feynman lectures or Penrose article.