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Thread: Quantum Biology?!

  1. #1 Quantum Biology?! 
    Forum Masters Degree SuperNatendo's Avatar
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    Saw an interesting article on photosynthesis the other day and it said something along the lines that when electrons displaced from PSII enter the electron transport chain, the most efficient path is always "chosen", displaying attributes of being in a quantum state. In the process of plant photosynthesis, the cells use a property of quantum mechanics wherein the electron is in a state of particle-wave plurality in order to find the best path through the "electron chain" before they actually travel through it in order to more efficiently carry out their process.

    Basically the article went on to say that as we study these processes at a smaller scale and with deeper understanding, it appears that all life processes are reliant on Quantum Physics, which on the outset doesn't seem all that relevant, but I am hoping it could help us to understand a few of the things that I was simply taught by my science teachers as "this is how it happens and it happens just because."


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  3. #2 Re: Quantum Biology?! 
    Forum Cosmic Wizard paralith's Avatar
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    Quote Originally Posted by SuperNatendo
    ... but I am hoping it could help us to understand a few of the things that I was simply taught by my science teachers as "this is how it happens and it happens just because."
    I don't know much about quantum physics, but I do know I hate teachers who teach that way. And sadly a lot of high school science teachers do that - phrase everything as though it's solid fact and we can't argue with it even if we're not sure where it came from.

    Getting off my soapbox now. Sorry.


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  4. #3  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    it appears that all life processes are reliant on Quantum Physics, which on the outset doesn't seem all that relevant
    It isn't relevant. So I share your feelings towards this matter..
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  5. #4  
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    Quantum Mechanics certainly plays a role in photosynthesis and for good reason. You have a process where energy from light excites electrons. Photons and electrons are quantum particles.

    One way this process exhibits itself is in what happens to an electron the moment it is excited.

    It is not a guaranteed thing that the electron excited by the photon will then enter the electron transport chain. There are actually four possible fates for the excited electron.

    1) The energy is released as heat.
    2) Fluorescence, in which the energy is released as another photon.
    3) Energy transfer, in which the energy is handed off to another molecule.
    4) Photochemistry, , in which the electron is now involved with a chemical reaction.

    The photochemical reactions that occur during photosynthesis are some of the fastest reactions you can find, which is absolutely necessary in order for these reactions to actually compete with the other three fates.

    Since you are talking about a quantum particle here (electrons and photons) The fate of the excited electron is a quantum mechanical process. This, in part, explains the efficiencies of photosynthesis.
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  6. #5  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    Chemistry also plays a role in photosynthesis. So does geology. So does whatever.

    That doesn't make it automatically relevant for the biological importance.
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  7. #6  
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    spuriousmonkey
    Chemistry also plays a role in photosynthesis. So does geology. So does whatever.

    That doesn't make it automatically relevant for the biological importance.
    Both chemistry and geology are very relevant, so the point that you are trying to make more or less fails.

    Now I know the relevancy of this is probably lost on non-plant biologists, but quantum mechanics is relevant in photosynthesis.

    Did you miss the part where I explained the various fates of an excited electron and my statement about how quantum mechanics "in part explains the efficiencies of photosynthesis."

    Maybe it was the fact that I use the wording "in part" that confused you as to whether or not there was a real relevance. That was a poor choice of words. Quantum Mechanics does explain the efficiencies of photosynthesis.

    ~5% of the energy absorbed by an electron is lost as heat in photosynthesis. That is incredibly low, and the reason why so little is simply lost is because the chemical reactions of photochemistry are incredibly fast.....some of the fasted reactions known. For years, how this all worked was a complete mystery, until Quantum Mechanics was applied to the problem, which was published in Science in 2007:

    Hohjai Lee, Yuan-Chung Cheng, Graham R. Fleming (2007) Coherence Dynamics in Photosynthesis: Protein Protection of Excitonic Coherence Science 316 1462 - 1465

    http://www.sciencemag.org/cgi/conten...urcetype=HWCIT

    But nope, obviously quantum mechanics is completely irrelevant to us biologists. [/b]
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  8. #7  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    both chemistry and geology are completely irrelevant for most biological questions regarding photosynthesis.
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  9. #8  
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    Are you serious?

    First, you can't really talk about photosynthesis without talking about chemistry. To say that its irrelevant in most biological questions regarding the process only shows your ignorance on the matter.

    Over my years of training I have been in six classes that cover photosynthesis and countless seminars.

    There hasn't been one that hasn't covered the chemistry. In fact, everyone of them has STRESSED the chemistry, because that is what photosynthesis is.....chemistry.

    The entire process from the absorption of light to final reactions of the Calvin Cycle are chemical reactions.

    Think about metabolism for a moment. Can you honestly sit there and tell me that chemistry is not central to most, if not all, studies of metabolism? How can you have any sensible discussion of the Krebs Cycle without discussing the chemical reactions taking place?

    This is why that field we call Biochemistry carries the word "chemistry" in its name.

    Chemistry is the most important aspect of photosynthesis.

    As for geology, it does matter whenever you look at photosynthesis outside of the confines of growth chambers and greenhouses.

    I can't tell you how many times the geological and meteorological factors have been discussed in classes and seminars and their impact on photosynthesis. Its a common topic, and its particularly hot amongst those who study photosynthesis because one of the key interests of photosynthesis research today is on how to improve the efficiency of it, particularly in crop plants and even more so in changing environments.

    So don't sit there and give me this bull shit about what is or is not relevant. You are speaking from ignorance here of the field, not surprising given that most non-plant biologist don't bother to even consider the plant related literature (whereas we do read the literature from other organisms).
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  10. #9  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    I can certainly talk about photosynthesis without ever mentioning chemistry.

    Biology isn't reductionism. Biology is a set of specific questions. Some of them relate to chemistry, but most don't. Same for photosynthesis.

    It's better to get this into your head as soon as possible, because without it insight into science is impossible.

    You will be stuck on the wikipedia level.
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  11. #10  
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    Still waiting to se what geology has t do with discussion of photosynthesis. That's a reach - unless it is the intent is to tie the two together.
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  12. #11  
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    I see a progression here:

    Quote Originally Posted by spuriousmonkey
    It isn't relevant.
    Quote Originally Posted by spuriousmonkey
    doesn't make it automatically relevant
    Quote Originally Posted by spuriousmonkey
    irrelevant for most biological questions
    Quote Originally Posted by spuriousmonkey
    I can certainly talk about photosynthesis without ever mentioning chemistry.
    Shall we kill the chase music and conclude that some biologists find chemistry less relevant?


    I dunno, I'm no quantum mechanics fan boy but why pass up an additional lens? We can use many lenses.
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  13. #12  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    It has nothing to do with opinion, but with the nature of scientific practice.

    To do biology on a scientific level you ask yourself small questions of a particular nature.

    Although you may come up with a dataset regarding questions related to photosynthesis that require a chemical approach, most of the questions lie outside this dataset.

    This is true for all topics.

    You may state that the essence of teeth is that they masticate food.

    Now pull up all scientific articles concerning teeth and you will find that the vast majority doesn't refer to mastication, or contains the word mastication.

    Why is that? Because you can approach any biological topic from a multitude of angles.

    To state that chemistry is important for photosynthesis is chasing a dead dodo. You can study photosynthesis for your entire life without doing chemistry or referring to it.

    I feel at a loss for my plant colleague who cannot help the temptation to read up on other organisms, but fails to see the essence of the nature of scientific research.
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  14. #13  
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    spuriousmonkey
    I can certainly talk about photosynthesis without ever mentioning chemistry.
    Sure, if the only understanding of it that you hope to achieve is that of a 9th grader.

    But even that doesn't work, because I remember that even in 9th grade, photosynthesis was primarily explained through chemical reactions:

    Biology isn't reductionism. Biology is a set of specific questions. Some of them relate to chemistry, but most don't. Same for photosynthesis.
    So far all you have done is say "nuh-uh" and assert with out evidence that things like chemistry are largely irrelevant to photosynthesis.

    Please, at this rate all you could only dream of achieving a Wikipedia level knowledge.

    I challenge you to support your statements. Demonstrate that chemistry is only a minor topic in the field of photosynthetic research and that "most" relevant questions are not related to the chemistry.

    Support your assertions or retract.

    Furthermore, I never said that Biology is "reductionism." However, only Biologists who have had their heads in the sand, or those who are not scientists would be so ignorant to dismiss the contributions of the reductionist approach (Molecular Biology and Biochemistry) to our understanding of Biology.

    There is a reason why Molecular Biology is a far larger and higher funded field than those in non-reductionist areas.....it produces more results. Its contribution to fields like evolution are such that now a days many evolutionary biologists are also correctly identified as molecular biologists or even biochemists.

    Pick up any review on the subject of photosynthesis, it will be almost exclusively about the biochemistry.

    It's better to get this into your head as soon as possible, because without it insight into science is impossible.
    Kettle, meet Pot.

    I'm not the one advocating a limited world view here. You have boldly (and in complete ignorance) claimed that such "lenses" (to borrow from Pong) as Quantum Mechanics and even Chemistry are largely irrelevant to Biology....nay...you have been even more specific than that and claimed they are largely irrelevant to photosynthesis, something only someone completely ignorant of the subject would claim.

    The application of Chemistry (and yes geology) to Biology has contributed greatly to our understanding. It is through the application of chemical techniques to life that we get the field called BioCHEMISTRY.

    How do we know what the structure of DNA is?

    .......Chemistry

    How did we sequence the human genome?

    .......Chemistry

    How do we study enzyme function?

    .......Chemistry

    How do we study protein structure?

    ........Chemistry

    etc....etc....etc

    The application of chemistry to Biology encompasses its own department at most Universities....its called Biochemistry.

    To say that it is largely irrelevant.......have you had your head in the sand these last 50 years?

    You will be stuck on the wikipedia level.
    And until you realize the contributions of reductionist approaches, you will never hope to gain any sort of functional knowledge of Biology.

    I assure you, on matters of plant molecular biology, genetics, development, and biochemistry I am far above the wikipedia level and given your demonstration on issues related to this, I would not hesitate in the slightest to match my knowledge against yours. We'll see then who has the wikipedia level knowledge.
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  15. #14  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    How did we sequence the human genome?

    .......Chemistry
    We order a sequencer from one of these prominent company. Feed it DNA. And wait for the printout.

    I guess maybe you are too young to have actually done any sequencing manually, but sequencing isn't actually chemistry. It was the art of pooring a perfect gel. The rest was easy.



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    Clever.

    However, if it hadn't been for Sanger who worked out the chemistry in the first place, that sequencing technology would not be so easy for you.

    And then there are the Next-Gen sequencers, which have been worked out largely by chemists and engineers to enable even better and faster sequencing.

    And then there is protein sequencing, which is even more intensive in the chemistry realm. And for those of us who do any work with proteomics, handling and analyzing mass spec data (definitely chemistry) is a core part of the work you do.

    My research, which started out in classical genetic approaches, has now moved to the point where proteomics and transcriptomics are the two primary components. So I have all that nice mass spec data to analyze and a lot of gene expression data to analyze.

    Gee, guess what, I end up using a lot of bioinformatics to handle my data. I also write programs to help automate and streamline my work. There are entire fields devoted to the application of computer science to Biology which has enabled us to answer all kinds of significant questions......but I suppose that just as you dismiss the importance of chemistry and any other field you deem irrelevant, the same probably applies to Computer Science.

    I'm not the one limited in scope or view here.....that criticism applies to you who casually dismisses any other field as largely irrelevant despite their contributions.

    I'm curious and I have already challenged you in part on this.....

    What do "most" biological questions look like and why are all these other fields largely irrelevant?

    Its time you step up to the plate and actually support some of your assertions.

    Take this as an opportunity to enlightened a poor little ignorant plant biologist who obviously limited in his view of biology (even though he extends it to include nearly everything that may shed some insight) and who is in dire need of guidance from somebody so experienced that they can casually claim what is or is not relevant, even regarding fields they do not work in (i.e. photosynthesis).
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  17. #16  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    What do "most" biological questions look like and why are all these other fields largely irrelevant?

    I already explained it. Maybe you should try reading a post instead of denying something like that happened.
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  18. #17  
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    Chadn, the reason why reductionism is not essential is because it makes answering certain questions much more difficult. Most of the time, in-depth chemistry is not relevant to biology. I study immune responses. For me to dwell on the specifics of exactly how a particular aspect of the response works on a chemical level isn't relevant to the questions I'm trying to answer, which are all in terms of cellular behaviour. Understanding the chemistry of biology is a worthy pursuit of course, but biochemists can deal with that. They can give me the answers in terms I can understand. I can explain cellular behaviour to them in similar terms. We can collaborate in some manner if we feel the need. This is how science works across the board. Frames of reference that allow more meaningful investigation. If a biologist is going to reduce to chemistry, then why not go the whole hog and become a string theorist? Then nobody will be studying biology on the cellular or whole-organism level any more.

    However, if it hadn't been for Sanger who worked out the chemistry in the first place, that sequencing technology would not be so easy for you.

    And then there are the Next-Gen sequencers, which have been worked out largely by chemists and engineers to enable even better and faster sequencing.
    Yes indeed, worked out by chemists and engineers with consultation from biologists. Not worked out and designed by biologists alone. That would be a massive deviation away from what biologists are trying to do. Some biologists do provide tools for sciences in other frames of reference though. What spurious is (I think) trying to impress on you is the need for those frames of reference. The need for focus on the relevant questions.

    You can study the quantum theory implications of biology, but that doesn't make it a relevant consideration for all biologists.
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  19. #18  
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    spuriousmonkey
    I already explained it. Maybe you should try reading a post instead of denying something like that happened.
    You haven't explained shit, nor can you when all you write are one liners with no substance.

    I wonder if you make similarly pathetic arguments with your research.


    Chadn, the reason why reductionism is not essential is because it makes answering certain questions much more difficult. Most of the time, in-depth chemistry is not relevant to biology. I study immune responses. For me to dwell on the specifics of exactly how a particular aspect of the response works on a chemical level isn't relevant to the questions I'm trying to answer, which are all in terms of cellular behaviour. Understanding the chemistry of biology is a worthy pursuit of course, but biochemists can deal with that. They can give me the answers in terms I can understand. I can explain cellular behaviour to them in similar terms. We can collaborate in some manner if we feel the need. This is how science works across the board. Frames of reference that allow more meaningful investigation. If a biologist is going to reduce to chemistry, then why not go the whole hog and become a string theorist? Then nobody will be studying biology on the cellular or whole-organism level any more.

    Quote:
    However, if it hadn't been for Sanger who worked out the chemistry in the first place, that sequencing technology would not be so easy for you.

    And then there are the Next-Gen sequencers, which have been worked out largely by chemists and engineers to enable even better and faster sequencing.


    Yes indeed, worked out by chemists and engineers with consultation from biologists. Not worked out and designed by biologists alone. That would be a massive deviation away from what biologists are trying to do. Some biologists do provide tools for sciences in other frames of reference though. What spurious is (I think) trying to impress on you is the need for those frames of reference. The need for focus on the relevant questions.

    You can study the quantum theory implications of biology, but that doesn't make it a relevant consideration for all biologists.
    I have to disagree.

    If you do Molecular Biology, then you are taking a reductionist approach to Biology.

    Molecular Biology (the predominant field of Biology today) examines organisms and cells in a very limited scope, breaking them down to constituents, studying single (or a handful of) genes and proteins.

    That is reductionism.

    And as this approach has come to dominate the Biological Sciences, then its quite easy to assert that it is relevant in the vast majority of cases.

    Furthermore, its slightly ridiculous to view biochemistry as being uniquely distinct from biology, as if it is somehow on the fringes. It is not, it is a central part to the modern understanding of Biology and as such makes a chemical understanding all the more relevant.

    And just because most Biologists do not study the Quantum effects that go on during photosynthesis, does not mean that it is irrelevant and that really is the issue at hand.

    spuriousmonkey dismissed from the outright, the idea of Quantum Mechanics as irrelevant, but obviously that is not the case because there is a very nice Science paper out on just how relevant it is.

    I don't care if you never utilize Quantum Mechanics, I likely never will either. I don't care if you are an Ecologist who will never bother to isolate DNA once in your life.....just don't be so foolish and dumb to dismiss everything that you have not used in your own research as irrelevant to the field as a whole, and especially don't be so dumb as to make such generalizations about a field that is not your own and which you clearly do not have much knowledge about.
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  20. #19  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    Apparently someone else got my point. That makes me feel warm inside.

    If you do Molecular Biology, then you are taking a reductionist approach to Biology.
    Absolutely not. Currently I am working on an extremely general question, which I am trying to answer with a molecular approach. Several approaches actually.

    What any good biologist should do is to define a problem. Ask what kind of experiment could give insight into the problem, or solve it. And design the experiments to the best of their ability.

    Sometimes that involves molecular biology. Sometimes it involves making a cladogram. Sometimes it involves a statistical analysis.

    I think you should open your mind. You are missing out on the essence of scientific research: understanding life.

    Scientific Research isn't putting yourself in strictly defined box, in the correct place, between the other chocolates, according to the labeling on the back of the box.

    That's just being a molecular biologist.

    Doing a job.

    Linear thinking.

    You use the tools you need to solve problems. You don't use a tool out of personal conviction this is THE tool.

    Chemistry is a tool. Molecular biology is a tool. PCR is a tool. Attending a conference is a tool.

    Science is finetuning questions and answering them with any means (tools) possible.
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  21. #20  
    Forum Cosmic Wizard spuriousmonkey's Avatar
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    spuriousmonkey dismissed from the outright, the idea of Quantum Mechanics as irrelevant, but obviously that is not the case because there is a very nice Science paper out on just how relevant it is.
    I'd rather have a Cell paper. You actually have to prove your point there. I just checked the latest issue of Cell.

    There wasn't a single paper on Quantum Mechanics in it. That's weird. Because according to your black&white logic I allegedly claim that it is irrelevant, so that means that you claim it is relevant.

    Which would mean that a journal with a higher citation impact and reputation such as Cell must contain nothing but papers with this kind of approach.

    Maybe it is time to come down the black&white tree and admit it is a marginal topic. It could very well be the last paper on this topic.

    You do know that most papers in Science actually are never, or hardly cited don't you? The just put them in because they look good on press releases, or they are friends of the system. I predict this will be one of them.
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  22. #21  
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    Quote Originally Posted by chadn737
    You haven't explained shit, nor can you when all you write are one liners with no substance. I wonder if you make similarly pathetic arguments with your research.
    Calm down, that's not the way to go on this.

    Quote Originally Posted by chadn737
    I have to disagree.

    If you do Molecular Biology, then you are taking a reductionist approach to Biology.
    I do molecular biology as a part of my cellular work. I don't often concern myself with chemistry and when I do, I talk to a biochemist.

    Quote Originally Posted by chadn737
    Molecular Biology (the predominant field of Biology today) examines organisms and cells in a very limited scope, breaking them down to constituents, studying single (or a handful of) genes and proteins.

    That is reductionism.
    But you're not going to reduce that further to chemistry or physics for "insight" because it won't help you answer the questions you're investigating. Within a given scope, we always reduce a little bit. I do some molecular biology along with my cellular work. But I don't delve into biochemistry. A researcher with a focus on molecular biology may do some biochemistry, but he probably won't go the whole hog into organic chemistry. Of course there are exceptions, but as a general rule a biologist works within 1-2 frames of reference, and more than that will tend to cause a loss of focus. Collaborations are a better strategy when one moves outside of ones normal focus.

    Quote Originally Posted by chadn737
    And as this approach has come to dominate the Biological Sciences, then its quite easy to assert that it is relevant in the vast majority of cases.
    I think we're talking at cross purposes. I'm not denying that reductionism can be useful- but the extent you're suggesting is not.

    Quote Originally Posted by chadn737
    Furthermore, its slightly ridiculous to view biochemistry as being uniquely distinct from biology, as if it is somehow on the fringes. It is not, it is a central part to the modern understanding of Biology and as such makes a chemical understanding all the more relevant.
    I didn't make such a distinction. I distinguished between me (a cellular biologist) and biochemists, both kinds of biologists. I never suggested it to be on the fringes of biology, but it is on this fringes of my own research focus.

    Quote Originally Posted by chadn737
    And just because most Biologists do not study the Quantum effects that go on during photosynthesis, does not mean that it is irrelevant and that really is the issue at hand.
    It's relevant to those who wish to study it. And they can explain to us how it is relevant to us. But having a research focus from physiology down to the quantum level is something that very few scientists could usefully handle. As the biochemists help me, so can the quantum biologists help the biochemists. But we all need our own focus within a given research project, and it can't cover 5-6 frames of reference.

    Quote Originally Posted by chadn737
    spuriousmonkey dismissed from the outright, the idea of Quantum Mechanics as irrelevant, but obviously that is not the case because there is a very nice Science paper out on just how relevant it is.
    I'm sure it is relevant to the field as a whole, but that doesn't make it relevant to every biologist. Computational biology, systems biology and bioninformatics are massively relevant to biology as whole. They've changed the face of the field. But I never use them. I don't need to use them to answer the questions I am trying to investigate.

    I suspect that spurious would question the relevance of quantum anything to to his own work and to that of many molecular biologists and biochemists. It's not automatically relevant to any of them. We'll certainly not ignore such research, but we won't be delving into it ourselves any time soon. Well, unless it's easy and there are pots of money in it.
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