Does improving microscopy mean improving biology?

In my last article I began exploring the relationship between optics and biology to better determine to what extent optics is capable of solving problems in biology, particularly molecular and microbiology. I posed a set of questions, one of them asking whether "...the current trends in improving microscopies [will] lead to answers of the fundamental questions of molecular and microbiology."

Let me start this brief essay by stating my own current opinion, which is based primarily on speaking with biologists and perusing the internet. I believe that the fundamental problems in biology lay at the molecular level and at the systems level. The molecular-level problems include how certain proteins fold and are transported through organelles like the Golgi bodies [1].  The systems-level problems deal with the coherent interaction of the many elements within an organism. To illustrate this, consider how the coordinated actions of various cells (such as Schwann cells, astrocytes, and neurons) lead to an effective functionality of the nervous system.

Microscopy unfortunately is ill-suited to exploring either of these two levels. It is true that fluorescence microscopy has allowed us to specifically target some structures of interest inside a cell and that superresolving microscopies for beating the diffraction limit exist, like PALM and STORM. However, fluorescent markers--which are also used in PALM and STORM--are known to adversely affect the behaviors of live cells. PALM and STORM are furthermore very complex to implement and limited to some degree by their data acquisition times [2].

One popular line of microscopy research is label-free microscopy, whereby images are acquired without introducing any artificial contrast-generating mechanism into the sample. One example is based on stimulated Raman spectroscopy (SRS). This approach usually is a spectroscopic technique that involves inferring what collection of known substances contributed to a measured spectrum from an image. Achieving a good resolution with SRS or any other label-free technique usually means allowing for a severe increase in the measurement time. At the time of this writing, I see neither the spatial nor temporal resolution of label-free microscopies as good enough for addressing the current open-ended biological problems.

At the systems level, microscopy is simply not the tool to use. I think that computer modeling and experiments on live animals are the norm here, though I am not saying that optics cannot play any role.

Overall, I think that we optical scientists are placing too much emphasis on improving light microscopy [3]. It seems to me that the information that biologists require is not found in images but rather in some other form. This is not to say that optics is of no use to biology. Take the technique known as dual polarization interferometry, for example, which uses light to probe protein crystal and lipid bilayer growth on waveguides. As another example, consider that optical tweezers have been influential in measuring the mechanics of biopolymers like DNA.

So what should we focus our attention on? I think label-free sensing mechanisms are in the right direction because they risk minimal alteration to cell and biomolecule functionality. I also think that techniques for sensing dynamic phenomena will trump anything that looks at the structure of fixed (dead) cells. Structure at this point seems well-known to biologists, but how structure evolves in time is not. Finally, controlling biological systems with light seems incredibly promising (e.g. optogenetics), though I think it is too early to tell whether it'll be valuable in deepening our knowledge.

I will hopefully address whether optics is the best tool for fulfilling these characteristics in the future.

Some references
The Wikipedia articles on Molecular biology, the Central dogma of molecular biology, and Biophysics are worth reading.

Stanford Encyclopedia of Philosophy entry on Molecular Biology

Seven fundamental, unsolved questions in molecular biology: Cooperative storage and bi-directional transfer of biological information by nucleic acids and proteins: an alternative to “central dogma”

Notes
[1] I have personally been exposed to a problem of the mechanics of certain biopolymers in regulating the structure of mitochondria. Biopolymers may arguably lie outside the realm of molecular biology since they are made of many, many molecules and not just a few, but I believe that my experience with this problem gave me some good insight.

[2] I have heard that Nikon microscopes are now offering STORM capabilities.

[3] I should point out that I think that the work in improving microscopies IS worth doing, I'm just not so certain that so much attention should be given to it.