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    The Relationship Between Physicists and Biologists
    By Michael White | May 7th 2009 04:22 PM | 16 comments | Print | E-mail | Track Comments
    About Michael

    Welcome to Adaptive Complexity, where I write about genomics, systems biology, evolution, and the connection between science and literature,

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    As Feynman told the story in late 1959:

    We have friends in other fields---in biology, for instance. We physicists often look at them and say, "You know the reason you fellows are making so little progress?" (Actually I don't know any field where they are making more rapid progress than they are in biology today.) ``You should use more mathematics, like we do." They could answer us---but they're polite, so I'll answer for them: "What you should do in order
    for us to make more rapid progress is to make the electron microscope 100 times better."

    ...It is very easy to answer many of these fundamental biological questions; you just look at the thing! You will see the order of bases in the chain; you will see the structure of the microsome. Unfortunately, the present microscope sees at a scale which is just a bit too crude. Make the microscope one hundred times more powerful, and many problems of biology would be made very much easier. I exaggerate, of course, but the biologists would surely be very thankful to you---and they would prefer that to the criticism that they should use more mathematics. 

    There's some truth to this: advances in biology have frequently been driven more by technology than ideas about biology. For long time, many (not all, but many) answers to biological questions have been obvious once we have the technology to "just look at the thing."

    As a result, you have generations of biologists with little training in math, who approach their work primarily by intuitive reasoning about their system of interest. And of course you have some very clever, amazing technologies (developed by biologists as well as physicists).

    Many of the fundamental questions that can be solved by just looking at things have been solved; as a result, a lot of biological research isn't about fundamental questions - it's about details, about how something works in a different cell type or a different organism, or at a different stage of embryonic development.

    The result is that there is a growing recognition that there are important, remaining fundamental questions that can be solved by getting quantitative - by having more formal, mathematical ideas about biology. We can generate mountains of data, and we can do unbelievable, nano-scale experimental manipulations that Feynman would have loved, but do we know how to think about biology instead of technology?

    Some of these important questions include how the structure of regulatory networks gives rise to the network dynamics: how do regulatory networks control gene expression in space and time? How do you get irreversible transitions in cell division or development? What types of structural features produce robust biological oscillators? How do regulatory pathways evolve - either adaptively or neutrally? How can we formally describe information transduction or processing inside of a cell in a way that leads to useful insights?


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    Comments

    You know I love Richard Feynman - but what about Theoretical Pop Gen?
    adaptivecomplexity
    but what about Theoretical Pop Gen?
    You're right, and I'd toss in much of biochemistry as well. Genetics and biochemistry are the two biology disciplines with with solid foundations in quantitative theory.  But the vast majority of biomedical scientists never go very deeply into these fields - molecular and cell biology have dominated for years, because they have been so successful. And they've been successful by 'just looking at things' as Feynman put it in an admittedly oversimplified way.
    Mike
    Hank
    I might argue that biology needs to be less about technology, though aspects like physical behavior of cells are interesting.   The Russians did some pretty good theoretical physics at the end of the Soviet Union because they had no money to do applied; likewise 'applied' biology can be one aspect but it ain't where the big leaps will arise.
    adaptivecomplexity
    This is a good point. But I don't mean to suggest that technology development is just about applied research - the questions you can answer are limited by the technology you have. Next-gen DNA sequencing has lots of applied value, but it's also a fantastic tool for answer fundamental questions. My worry is that, our tools for asking questions have made such great progress, but our ability to come up with important new questions has lagged somewhat. Many biologists are swimming in data and aren't quite sure what to do with it.
    Mike
    mossnisse

    Can’t it be that many people only count “general theories” as science and not “specific facts”  where the physicist are really good at come up with the general theories and it’s often damn difficult in biology where the generalisations often are dodgy.<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />

    But I agree that the math knowledge and development are bad in some disciplines that are math heavy like ecology I think ecology scientist should at least now enough math so they can cooperate with mathematicians, statisticians and programmer, m.m. It maybe is a question if money and interest from mathematicians.

    adaptivecomplexity
    Can’t it be that many people only count “general theories” as science and not “specific facts”  where the physicist are really good at come up with the general theories and it’s often damn difficult in biology where the generalisations often are dodgy.

    Many a philosopher of science has run aground in biology because so many have used physics to define what a science should be. 
    Mike
    Math knowledge need not be synonymous with calculation for it to be useful to biologists. The late Robert Rosen, a mathematical biologist, very clearly described ways to use abstract mathematics as a reasoning tool for understanding biological processes. His math can be scary, even to a mathematician. But his method was a means to the end; confirmation was still needed - what Rosen call "realization".

    Perhaps the type of relationship that exists between theoretical and experimental physicists might find a place in biological research and prove just as fruitful.

    adaptivecomplexity
    confirmation was still needed - what Rosen call "realization". 
    That has been the sticking point so far - a variety of people have some up with neat formalisms, but to transform the way biology is practiced, someone has to conclusively demonstrate that it makes a difference in the lab.
    I'm not familiar with Robert Rosen - I'll have to go check him out. Walter Fontana at Harvard has also been doing some interesting mathematical stuff, and he's putting together a wet lab, which will be a great place to test out the utility of new mathematical reasoning tools.
    Mike
    My apologies; I should have included at least one link. Robert Rosen's book (published in 1991!) Life Itself was the starting point for me. Panmere.com is a well-organized source for many other references. Rosen is cited in a couple of Kauffman's books.

    Fontana Lab's work is fascinating but its approach - and I do not mean to sound dismissive - is to understand life's mechanisms through the modeling of biological components. In contrast, Rosen believed that a different type of understanding came from the modeling of the functional organization, not the parts, of the biological system. He further suggested that a mathematical abstraction, a category, could be used. Unfortunately, category theory is so abstract as to be known by some as "abstract nonsense". Nevertheless, category theory is all about how objects interact with each other. One can understand the role of an object only through its relationships with other objects, not from some intrinsic value. A logician, Jean-Yves GIrard, characterized objects in terms of their "social lives" [cited in Fiadeiro, Categories for Software Engineering.

    adaptivecomplexity
    Thanks for the links - I'm eager to start reading.
    In contrast, Rosen believed that a different type of understanding came from the modeling of the functional organization
    I'm on board with this - I just want to see it work in real systems. My father-in-law is an algebraist, and whenever I hear him talk about various problems tackled by modern abstract algebra, I can't help but wonder if somewhere in there is buried something useful for capturing biological organization.
    Whenever this topic comes up, I'm reminded of Einstein - when working on General Relativity, he was fishing around for the math that would do what he needed to do, and he ended up finding tensor analysis incredibly useful. Later in life, his fishing expeditions through various areas of math were less fruitful, but he was motivated by two things - a strong physical intuition of what nature had to be like, and a belief that there was some mathematical formalism out there somewhere that might be just what he needed.

    What's needed is someone with a good intuition for biological problems, who can seriously wade through various areas of math (although not necessarily unaided), and who has enough grant support to be free to explore.
    Mike
    Gerhard Adam
    I personally think that this is one of the problems with the controversies that surround biology (like creationism) is the lack of a mathematical foundation.

    In particular, since life is fundamentally a chemical process, then it follows the laws of physics and chemistry long before it can manifest as a living organism.  As a result, whatever occurs, must be definable within the context of a mathematical principle that gives rise to the various forms and functions we see.

    The failure to arrive at such principles allows an opening whereby challenges arise that lend credence to things like an "intelligent designer" because it appears that biology is attempting to come up with unique answers for every variation that exists.  It should be clear that regardless of the level of variation, there are only a finite number of things that can occur and these are very much subject to the discipline of mathematics.
    Mundus vult decipi
    I personally think that this is one of the problems with the controversies that surround biology (like creationism) is the lack of a mathematical foundation.
    Actually, evolutionary biology has had a rigorous mathematical foundation for close to a century. When people say they don't believe in evolution, mathematics doesn't enter into it.
    adaptivecomplexity
    Don makes a great point. For at least half a century, evolutionary/population genetics  has been one of the more mathematical fields of biology, and it's been extremely successful in that form. 
    Gerhard, I think you touch on a key issue: how do you get from chemistry to life, in terms of a theory? Biochemistry is strongly grounded in the principles of chemistry, but the next step up in organization is difficult to formalize. Stuart Kauffman has been one scientist among many who has said we need a "science of organization" - some way of mathematically dealing with things like energy and entropy beyond the level of individual molecules (or zillions of identical molecules a la statistical mechanics).
    Mike
    Gerhard Adam
    I know getting from chemistry to life has been the point of much speculation here.  I think that we need to assess how chemicals can isolate themselves to maintain a closed environment.  Once they're isolated we have the basis for determining what constitutes a cell from which we need to exam networking strategies and cooperation (in the sense of organization and synchronicity).  All of these processes must work because it is in the nature of the chemistry to produce such results.  

    It carries a certain inevitability so that based on the initial conditions, situations that might otherwise be chaotic can stabilize and form the structures that can be conserved to form the components of life.

    It's a tall order, but ... what the hell ... take the weekend too if you need it. 
    Mundus vult decipi
    adaptivecomplexity
     I think that we need to assess how chemicals can isolate themselves to maintain a closed environment.  Once they're isolated we have the basis for determining what constitutes a cell from which we need to exam networking strategies and cooperation (in the sense of organization and synchronicity).  All of these processes must work because it is in the nature of the chemistry to produce such results.  
    This is why origins-of-life research is the ultimate systems biology problem - origins of life research has the potential to help us better understand modern biological systems.
    Mike
    Binbin Liu
    I work in both experimental biology and theoretical physics world. When I was trained to become a microbiologist  (which I decided not to later ) over a decade ago,  I was taught that biology is  an 'observation science': you draw conclusions and test your hypothesis based on what you 'see' in lab. When the human genome project was vastly progressing, it was shown that the biology world was in need of knowledge from maths, physics and even chemistry to decode the huge mount of information behind ATGCs, and uncover the mysteries of  the complexity of biology systems.  This is an example to show us the necessity on applying what we know well in physical science to study biology.  Another example on the heavily application of physical science technology in biology lies in the field of the structural biology. X-ray, NMR, mass-spectroscopy etc etc all are based on physics.

    The application of technology to biological systems results in the high requirement for biologists to be able to understand the theories of maths, physics and chemistry behind the 'machine' which gives plots/numbers etc.  Thus, I think it requires biologists to take up more studies besides classical bio-science modules. Unfortunately, in the UK, it is even not required that students who apply for bio-science studies in univ to complete maths/physics/chemistry in A-level. It is sad to see some bio-science undergraduates even PhD students not able to convert basic molar to  mass/ml  in the lab.