'Quantum smell' idea gains ground

Originally posted by OccamsRazor04

Heavy water is not toxic. Some animals can survive with near 100% heavy water intake. Humans would need to consume extremely large quantities for it to be toxic.

A paramecium can tolerate 100% D2O, you cannot. If the bond angles and lengths are different, and they are, and I can toss probably 100 cites at you, then the shapes are altered, if only slightly. If the difference between smell/not-smell is also slight, Bob's your uncle.

Originally posted by Bedlam

Originally posted by OccamsRazor04

Heavy water is not toxic. Some animals can survive with near 100% heavy water intake. Humans would need to consume extremely large quantities for it to be toxic.

A paramecium can tolerate 100% D2O, you cannot. If the bond angles and lengths are different, and they are, and I can toss probably 100 cites at you, then the shapes are altered, if only slightly. If the difference between smell/not-smell is also slight, Bob's your uncle.

Wrong. Smell is determined by the receptor. As long as both of them still fit the same receptor then the point is moot. Do you think you know more than the premier expers in olfactory science? They say the shape is fine. Why are you creating an issue EVERY expert says is not an issue?

Originally posted by OccamsRazor04

Wrong. Smell is determined by the receptor. As long as both of them still fit the same receptor then the point is moot. Do you think you know more than the premier expers in olfactory science? They say the shape is fine. Why are you creating an issue EVERY expert says is not an issue?

The receptor's mate to the stimulant molecule depends TOTALLY on the molecular shape. You can't debate that, and I can toss a hundred scholarly cites at you about THAT as well. You can't really debate it. The closer the mate, the more likely the receptor will fire.

Change the shape, reduce the likelihood of the receptor triggering.

Van Hook (9) has shown that when a deuteron is involved in a chemical re- action, consideration oust be given to a slight change in the inductive effect, as deuterium is more electronegative than hydrogen. Hyperconjugative effects are also involved since CD3, for example, is less delocalized than CH3, and, more important, the effective size of a C-D bond is smaller than the effective size of a C-U bond. Thus steric effects have a part to play, reinforcing our conten- tion that any highly stereospecific enzyme molecule containing a deuteron in an important position has a potential for participating in an error reaction.

(...)

This thinking may also be extended to include the process of synthesizing enzymes. Naturally occurring deuterons participating in this process can bring about the formation of mis-constructed enzymes which will subsequently partici- pate in forming error proteins, or if their function is to repair proteins, they
may not be able to perform their normal task, thereby permitting errors to accumulate.
The definition of a defective enzyme under these circumstances is difficult. A molecule containing a deuteron naturally would not normally be regarded as a defective molecule. However, the special properties of deuterons can cause a molecule with precise stereospecific properties to react differently from its protonated analogue.

warning - link to a VERY big pdf

Griffiths - one of many cites on enzyme/protein shape distortion caused by deuterons.

All of this to say - steric distortion caused by deuterons is more noticeable the larger and more complex the molecule. And the receptor's triggering or not depends on shape. Thus the study's observation that small molecules cannot be distinguished whereas larger ones can makes perfect sense given the physics.

reply to post by Bedlam


Show me where them changing hydrogen to deuterium will prevent the olfactory receptor from firing. Tell me EXACTLY how much their molecules shape was changed.

The traditional camp is the one who began using deuterium. If they thought it would change the shape and change the smell they never would have used it.

The participants smelled the molecule, clearly the receptors fired.

Originally posted by OccamsRazor04

Show me where them changing hydrogen to deuterium will prevent the olfactory receptor from firing.

Do you agree that the receptor depends on molecular shape to fire? And that degree of fit determines the odds of any particular receptor firing? Or do we have to bang heads on that one?

Originally posted by Bedlam

Originally posted by OccamsRazor04

Show me where them changing hydrogen to deuterium will prevent the olfactory receptor from firing.

Do you agree that the receptor depends on molecular shape to fire?

Yes

And that degree of fit determines the odds of any particular receptor firing?

Yes

Or do we have to bang heads on that one?

No. We have to bang heads on your creating an issue where there isnt one. As long as the SAME RECEPTORS are being fired the smell should be the SAME. Whether the original molecule has a 99% chance to fire and the new one has a 95% chance to fire doesn't matter. It only matters when the shape is changed to the point where the SAME receptor is not firing. There is ZERO evidence this is the case.

reply to post by OccamsRazor04


Ok, so you agree that the odds of a receptor firing depends on the degree of conformation to the shape it's designed to detect. Great.

Now, the next point. Do you agree that the bond length, angle and energy level are different for deuteron bonds than for protium bonds? And that by something like 1-4% per bond, depending on what the other element is that you're bonding to?

edit to add - I'm not trying to browbeat you here, I'm trying to lay out the reason why I read this study and yawn. And yes, I've seen published refereed studies that just suck experimentally. This may be one. I'm a science professional, I do this stuff for a living. Part of that is reading other peoples' papers and looking for the holes.

Originally posted by Bedlam
reply to post by OccamsRazor04

 

Ok, so you agree that the odds of a receptor firing depends on the degree of conformation to the shape it's designed to detect. Great.

Now, the next point. Do you agree that the bond length, angle and energy level are different for deuteron bonds than for protium bonds? And that by something like 1-4% per bond, depending on what the other element is that you're bonding to?

edit to add - I'm not trying to browbeat you here, I'm trying to lay out the reason why I read this study and yawn. And yes, I've seen published refereed studies that just suck experimentally. This may be one. I'm a science professional, I do this stuff for a living. Part of that is reading other peoples' papers and looking for the holes.

edit on 27-1-2013 by Bedlam because: (no reason given)

No I do not agree on any percentages. Why would I agree? How can you claim you are a 'science professional' (whatever that means) and then ask me to agree to percentages for no reason at all. You tell ME. How different are the two shapes. Tell me to what degree that will prevent the firing of the receptors, and then exactly how that affects smell and by how much.

reply to post by Bedlam


Write a rebuttal and get it published. Then link it to me.

Originally posted by OccamsRazor04

No I do not agree on any percentages. Why would I agree?

Well, let's start with Soper and Benmore:

First, the scientists found that H2O has a longer intramolecular OH bond than D2O’s corresponding OD bond length. Specifically, the OH bond is longer by about 0.03 angstroms, or 3%. Second, the intermolecular hydrogen bond (which connects two separate molecules) is shorter in H2O than in D2O. Here, the difference is about 0.07 angstroms, or 4%. Neither of these differences in bond length had been predicted in previous studies. Further, because the OH/OD bond length difference and the hydrogen bond length difference are not equivalent (3% and 4%), there also exist geometrical differences between the structures of light and heavy water. While previous research had predicted an overall broadening of the H2O structure compared to the D2O structure, Soper and Benmore have pinpointed three specific differences, some of which are in opposition to earlier predictions. For one thing, the intermolecular OH peak is more asymmetric in H2O than D2O. Also, the distance between the hydrogen atoms on neighboring molecules is about 2% larger for H2O than in D2O. Finally, the number of hydrogen bonds per water molecule is less in H2O than in D2O (3.62 vs. 3.76).

There's you one. Need lots more? hint - look up "primary isotope effect" + deuterium.

Originally posted by OccamsRazor04
reply to post by Bedlam

 

Write a rebuttal and get it published. Then link it to me.

Try reasoning for yourself...I'll drop all the pieces here for you.

Don't put your metaphoric fingers in your ears and go la la la. Whether or not you respond, I'm still going to spell it out in small pieces. It's not like I'm getting this stuff from Alex Jones, Educate Yourself or bibliotecalyapades.

reply to post by Bedlam


That's what I thought. Big ego, very self important, but can't answer questions. Go puff your ego up somewhere else. I suppose research from MIT professors, that is peer reviewed and published equates bibliotecalyapades. Stop being so self important and sticking your fingers in your ears. You can answer my simple questions or you can copy and paste from a text book something that doesn't address my question whatsoever. I wouldn't want to bruise your ego though, you know, since you think you know better than EVERY expert on the subject.

Ok. So, the shapes of deuterated molecules are, in fact, different from non-deuterated molecules. Not a huge amount, but somewhat. And that's per bond - if you've got a molecule that's got hydrogen bond after hydrogen bond in a chain or circle, then the amount of shape difference adds up on a per-bond basis. It's like trying to put together something with Tinkertoys and someone's slipped in a few sticks of different size than standard.

It's also a given that the shapes of the molecules determine which and how many scent receptors fire for a given compound. So, how do you actually perceive an odor? It seems to be a spectrum of perception, like your perception of colors.

Originally, some people theorized that in order to perceive the rainbow of colors that we can see, you would have to have specific retinal receptors for each and every possible color. That doesn't make sense in one regard, because you've only got so much space on your fovea for cells, yet you can see a broad spectrum of discrete colors in high detail. How would you cram so many color receptors there, if you had to have one for every distinguishable shade?

Nature solved it by giving you four (unless you're a mutant) different receptors in the retina - one for intensity, and three moderately broad color receptors, nominally for red, green and blue. Red doesn't just respond to one color of red light. It will respond to a wide range of generally red colored light, the same with the blue and green receptors. By taking info from the intensity, red, green and blue receptors, your brain perceives all the inbetween colors by doing some mathematical wizardry on the fly. You see any color as a percentage of brightness, red, green and blue. Your brain interprets that to match a specific color.

For smell, it is commonly believed that you perceive the same way - you have olfactory receptors that are not as specific as, say, an estrogen receptor. Instead of requiring an exact fit, they look for features of the molecule being detected. This results in a broad triggering of receptors for any particular scent, but your brain perceives the thing as being a specific odor based on the percentages of different triggers, the way your eye detects color as percentages of triggering red, green or blue receptors. So buttered toast might be 3% receptor A, 15% receptor B, 2% receptor C, and 80% receptor D and so on, whereas rotten eggs might be 99.8% receptor A and 0.2% receptor C, in the same way the perception of purple might be 35% red, 1% green and 64% blue.

Thus, your perception of a particular odorant depends ENTIRELY on the percentage triggering of various odotopic receptors. And that triggering is dependent on the molecular shape. And the shapes of molecules are altered by incorporating deuterons - the more deuterons they incorporate instead of protons, and the larger and more complex the molecule is, the more distortion of shape. The simpler the molecule, the less distortion.

Since your perception of smell is determined by the response rate of various odotopic receptors, any molecular distortion of an odorant will alter the percentage of triggered receptors. And the more the distortion, the more the perceptual drift should be. After all, your perception of ANY scent is dependent on that - it's how your sense of smell works.

Thus, it's not a matter of 'the receptor didn't fire at all', it's more like a tiny change in hue caused by a slightly different dye. The percentage of receptors that will fire for the distorted molecule is different than the one that's not distorted. And that will be a larger change for larger molecules, since the isotopic shape distortion is additive for each bond in the chain.

Originally posted by OccamsRazor04
reply to post by Bedlam

 

That's what I thought. Big ego, very self important, but can't answer questions.

I am answering them. You don't want to listen - that's ok.

BTW, while you seem to have a big emotional investment in Turin, as your op said, it's unicorns to most of the field, apparently.

I don't have a dog in the hunt, here. But it seems odd, as I say, to try to say that deuteration does not cause steric distortion of molecules - it does.

Here's you a nice link

Edit to add: as a trivia point, you actually DO have olfactory receptors that are very specific as to shape, sort of like an estrogen receptor, you also have olfactory receptors that will fire but not elicit a perception of scent. These are often tied to other brain areas and elicit memory or emotion. It's not sure exactly what they're for, although it may be some pheromonal system. The Army spent a wad of your tax dollars on it - can we exploit this effect to produce a very specifically shaped molecule that will trigger these 'neutral scent' receptors and induce terror, panic, hallucination, false memories, perception of time distortion and the like. Very interesting research, which is why I know anything much about olfaction. My interest in the field was rather narrowly focused.

Originally posted by Bedlam

Originally posted by OccamsRazor04
reply to post by Bedlam

 

That's what I thought. Big ego, very self important, but can't answer questions.

I am answering them. You don't want to listen - that's ok.

No, you aren't. You are acting self important giving me information that has nothing to do with my questions.

BTW, while you seem to have a big emotional investment in Turin, as your op said, it's unicorns to most of the field, apparently.

Now who is emotional? I had never heard of Turin before today. Zero emotional investment. One person said unicorns, I guess due to your emotional investment that becomes the rest of the field. Here is what others have to say.

Tim Jacob, a smell researcher at the University of Cardiff, said the work was "supportive but not conclusive".

"But the fact is that nobody has been able to unequivocally contradict [Dr Turin]," he told BBC News.

"There are many, many problems with the shape theory of smell - many things it doesn't explain that the vibrational theory does."

One person who thinks the research is valid.

Columbia University's Richard Axel, whose work on mapping the genes and receptors of our sense of smell garnered the 2004 Nobel prize for physiology, said the kinds of experiments revealed this week would not resolve the debate - only a microscopic look at the receptors in the nose would finally show what is at work.

"Until somebody really sits down and seriously addresses the mechanism and not inferences from the mechanism... it doesn't seem a useful endeavour to use behavioural responses as an argument," he told BBC News.

"Don't get me wrong, I'm not writing off this theory, but I need data and it hasn't been presented."

Another who sees no problem with the research, but doesn't think any behavioral response is enough to say either way.

But, you know better than the experts, including a Nobel prize for physiology winner, who find no flaw with the study.

I don't have a dog in the hunt, here. But it seems odd, as I say, to try to say that deuteration does not cause steric distortion of molecules - it does.

Apparently you do since you liken the research that has been peer reviewed and has interested serious people who are well known in the field to a fringe non-scientific website. Either you do have a dog you are invested in, or you are just being a complete tool.

An interesting detail, the just published PLoS paper - the citation number 10 for a 2 months old quantum model, the last author

Gregg Roman, was funded by DARPA(grant N66001-11-1-4119)

jcp.aip.org/resource/1/jcpsa6/v137/i22/p22A551_s1

J. Chem. Phys. 137, 22A551 (2012); dx.doi.org... (6 pages)
Quantum origins of molecular recognition and olfaction in drosophila

Eric R. Bittner 1, Adrian Madalan 2, Arkadiusz Czader 3, and Gregg Roman 2

1 Departments of Chemistry and Physics, University of Houston, Houston, Texas 77204, USA
2 Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
3 Department of Chemistry, University of Houston, Houston, Texas 77204, USA

The standard model for molecular recognition of an odorant is that receptor sites discriminate by molecular geometry as evidenced that two chiral molecules may smell very differently. However, recent studies of isotopically labeled olfactants indicate that there may be a molecular vibration-sensing component to olfactory reception, specifically in the spectral region around 2300 cm−1. Here, we present a donor-bridge-acceptor model for olfaction which attempts to explain this effect. Our model, based upon accurate quantum chemical calculations of the olfactant (bridge) in its neutral and ionized states, posits that internal modes of the olfactant are excited impulsively during hole transfer from a donor to acceptor site on the receptor, specifically those modes that are resonant with the tunneling gap. By projecting the impulsive force onto the internal modes, we can determine which modes are excited at a given value of the donor-acceptor tunneling gap. Only those modes resonant with the tunneling gap and are impulsively excited will give a significant contribution to the inelastic transfer rate. Using acetophenone as a test case, our model and experiments on D. melanogaster suggest that isotopomers of a given olfactant give rise to different odorant qualities. These results support the notion that inelastic scattering effects may play a role in discriminating between isotopomers but that this is not a general spectroscopic effect.

EDIT : the free arXiv paper pdf from here arxiv.org/abs/1207.2796

reply to post by wujotvowujotvowujotvo


Thank you for the information!

Originally posted by OccamsRazor04
No, you aren't. You are acting self important giving me information that has nothing to do with my questions.

Giving you information you don't want to hear, because it contradicts what you want to be true, more likely.

Now who is emotional? I had never heard of Turin before today. Zero emotional investment. One person said unicorns, I guess due to your emotional investment that becomes the rest of the field. Here is what others have to say.

In addition to the repeated "I'm rubber and you're glue" arguments, you become very heated when any evidence to the contrary is presented.

Tim Jacob, a smell researcher at the University of Cardiff, said the work was "supportive but not conclusive".

"But the fact is that nobody has been able to unequivocally contradict [Dr Turin]," he told BBC News.

And according to Keller and Vosshall, "Whether because of skepticism or 'scientific conspiracy' (as alleged in the book and echoed in most reviews) his predictions have failed to generate empirical tests by other researchers", meaning, not many people have been interested in it enough to try contradicting him.

Columbia University's Richard Axel, whose work on mapping the genes and receptors of our sense of smell garnered the 2004 Nobel prize for physiology, said the kinds of experiments revealed this week would not resolve the debate - only a microscopic look at the receptors in the nose would finally show what is at work.

"Until somebody really sits down and seriously addresses the mechanism and not inferences from the mechanism... it doesn't seem a useful endeavour to use behavioural responses as an argument," he told BBC News.

"Don't get me wrong, I'm not writing off this theory, but I need data and it hasn't been presented."

Another who sees no problem with the research, but doesn't think any behavioral response is enough to say either way.

And I agree with him. What I don't agree with is that deuterating substances does not cause steric changes - it does.

But, you know better than the experts, including a Nobel prize for physiology winner, who find no flaw with the study.

That's not what he's saying at all. He's saying it's equivocal, and doesn't properly determine anything, which again, I do agree with.

Apparently you do since you liken the research that has been peer reviewed and has interested serious people who are well known in the field to a fringe non-scientific website. Either you do have a dog you are invested in, or you are just being a complete tool.

You are revealing your inability to read for understanding. Here, let me help you:

"It's not like I'm getting this stuff from Alex Jones, Educate Yourself or bibliotecalyapades."

You may note that I did not say "your cite is the equivalent of Alex Jones", when you disagreed with the differences in hydrogen bond lengths and angles in deuterated substances, I said that I am not getting my data from Educate Yourself or bibliotecalyapades. And I'm not. I understand on ATS that those are considered legitimate sources, but I am citing peer reviewed information.

I do not agree that deuterating a molecule does not change its shape - it does. I especially do not agree that it doesn't change the shape of a complex organic molecule with a lot of hydrogen bonds - it does there too, and to greater degree. Thus I find the original post's contention that since deuterated molecules have a different smell than protic molecules if they're relatively complex, it automatically infers that the sensation of smell is solely due to QM effects - to be questionable. The steric shape change is a confounder. And the people you quote in this reply agree with me.

edit to add: So does the arxiv paper. Reread the part about chiral molecules having different odors - they do. But they have EXACTLY the same QM behavior, although their shapes are mirror images.

There is a very insightful and entertaining read about the history of this claim:

The Emperor of Scent: A True Story of Perfume and Obsession, by Chandler Burr.

Very well written and entertaining. Most likely a bit biased, very insightfull in any event.

What is fascinating about the story is how much scientific communities can behave like a religion towards alternative paradigms, instead of critically evaluating the data.

This is especially true if your reputation and employment is built on the encumber paradigm.

Originally posted by OccamsRazor04

Originally posted by darkbake
In science, unicorns often turn out to be real. Like pretty much every time.

I wouldn't go that far. In fact, I would say that's not very true. I would love some instances though. In this case, there is no unicorn. We have verifiable, repeatable, scientific experiments. One of two things must be done. The science must be shown to be faulty (which has not been done), or an explanation must be given. The traditional view has no explanation for this. This isn't a unicorn, just a new breed of horse that answers a lot of questions we had about horses.

That is very true, in this case we are dealing with verifiable, repeatable scientific experiments - so that demands an answer eventually.