Some notes on colloids, surfactants, and the Debeye length

In the lab I frequently handle and create colloids--suspensions of one type of material in another, such as solid particles in water. A good reference site I just found for understanding and working with colloids is at SubsTech's website.

Things I also learned today:

1. The Debeye length may be conceptualized as the characteristic size of a fluctuation of the electrostatic potential inside a solution of charged particles. Longer Debeye lengths mean longer distances for which the potential remains roughly the same.
2. Surfactants may be used to stabilize a colloidal dispersion. This is different from electrostatic stabilization, whereby some charge is permanently located on/inside the particles to cause them to repel one another.

Unfortunately, I do not yet have a good concept for why surfactants may stabilize a colloid. I suspect that the concept is related to polymeric stabilization.

The debate between data-centric science and hypothesis testing in soil microbiology

I've recently explored the topic of data-centric science, i.e. the art of answering scientific questions using data mining instead of generating hypotheses and testing them. I was therefore very interested by an article in this week's issue of Nature entitled "Microbiology: The life beneath our feet." The article was written by two scientists who study the relation between the microbial content of soil and its encompassing environment. One of them, Janet K. Jansson, promotes the use of data-mining from "omic" studies while the other, James I. Prosser, argues more in favor of hypothesis-driven experiments. Omic studies is jargon for the practice of identifying microbial species through detection of DNA (genomics), RNA (transciptomics), proteins (proteomics), and metaboloites (metabolomics).

Dr. Jansson argues that data-mining reveals new species of microbes and provides a sufficient base from which to carry out further experiments and tests of hypotheses. She claims that the primary critique of omic studies (which is that it provides only descriptive data) is weak since we simply don't know enough about the different species of microbes to begin with. Data mining from omics fills those gaps in our knowledge. Finally, she provides several examples where omic data mining has led to new discoveries and understanding around the world.

Dr. Prosser, on the other hand, claims that better value is obtained from hypothesis-driven research since it provides new concepts and logical frameworks for understanding the microbe-environment relationship. One quote from him that I particularly liked was the following:

Hypotheses lack value, however, if they are based solely on observations, or if they are relevant only to the data used to construct them. They are worthwhile if they incorporate novel ideas and flashes of inspiration; they can propose (ideally universal) explanations and mechanisms; and they generate predictions that can be tested by experimentation. It is this process, and not the initial observations, that truly increases understanding. Hypothesis-driven research can thus provide counter-observational, non-intuitive predictions and conceptual frameworks, and can indicate which techniques are, and are not, needed to test them.

He furthermore argues that the information obtained from data mining can generate new hypotheses but cannot be used to test these hypotheses, an argument that I have never before considered but believe to be true.

One final sentiment worth noting is delivered by his statement "In practice, purely descriptive studies of microbial communities are rare." I believe that he is arguing that, while one would argue there is value in using both approaches, the payoff from hypothesis testing is much greater and should therefore receive more resources.

I am quite pleased to see someone arguing against the use of data mining for no other reason than to balance out the arguments, but since I believe that scientific man power is growing faster than the number of hypotheses that can be generated, I see no reason to abandon data-mining as tool in this regard.

What do biologists want? It's probably best to ask them.

Just a thought: more than likely, if a biologist wants to learn something, they'll need a tool that is specialized for measuring exactly the quantity that they're interested in. A general measurement tool will almost always be less-than-ideal for measuring some specific quantity. Therefore, we optical scientists should spend less effort in optimizing a mature imaging technology and instead work routinely with biologists to help solve their problems.

The relevance of multiphoton microscopy to physicists and biologists

There is a comprehensive review article in this month's Nature Photonics concerning many of the technological capabilities and recent advancements of multiphoton microscopy (MPM). The article details many recent advances in MPM engineering for achieving faster image acquistion, increased signal-to-noise ratios, and deeper imaging capabilities.

These advances are impressive and lead me to believe that MPM has become a rather mature technology. I'm curious to know to what extent biologists have used MPM to solve problems in their research since the review article is somewhat lacking in references that come from journals outside of physics and optics.

This is the same problem I encounter again and again in optics. It's very difficult to identify worthwhile work in a research field that primarily develops tools for researchers from other fields to use. I do not blame the optical scientists for this difficulty, though, and here's why. An optical sensing technique is usually not suited for publication in pure biology journals, so they must publish in optics and applied science journals. In this arena, they must argue for their technique relative to other related techniques, not to the suitability of their work for solving biological problems. A sentence in the introduction and conclusion of an article is usually sufficient for reviewers to acknowledge the technique's worth towards a biological problem of interest.

Horse Pens 40: My favorite bouldering location

I returned Monday morning from a three day trip up to Chattanooga, Tennessee for a bouldering trip to LRC, a.k.a. Stonefort. Unfortunately, we got only one good day in before a large amount of snow fell on the site and made travel up and down the mountain a bit dangerous. So, we packed up and drove to Horse Pens 40, a natural boulder field atop Chandler Mountain in northeast Alabama.

I love HP40, and not just for the climbing. It has a rich human and natural history. HP40 has been inhabited by humans for about 15,000 years. The sandstone rock formations have served  as natural horse corrals and Native American burial sites, among other things. This rock is full of huecos (climber lingo for holes or pockets) and many large slopers (more climber lingo for big, rounded features). Much of the rock has been shaped by water grooves, where water running off the top of a boulder has etched shallow grooves into it. This rock is tough and harsh on the hands. I found it rougher than LRC's boulders.

The setting of HP40 is also very scenic, being located in the woods atop the mountain. I'm not sure what the dominant tree here is, but I did notice many shells that looked similar to the hickory nuts we have back home in Ohio. I also noticed many seed-bearing structures that were spherical in shape with a diameter roughly larger than a quarter. These structures had already released their seeds (the date was early February), which I presume covered the surface of this sphere.

The outstanding science question of this trip is: why is rock "stickier" when it's cold? By sticky, I mean that a climber's hands and shoes are less likely to slip.

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.

An optical scientist considers the question: what do biologists want from a microscope?

Optics and biology have been intertwined for hundreds of years. Robert Hooke and Antonie van Leeuwenhoek both contributed greatly to the fields of microscopy and microbiology in their infancy, advancing each field by establishing a greater understanding in the other. As optics evolved and technologies derived from it became more refined, the number of discoveries in the realm of microbiology witnessed a concomitant increase. This fact was perhaps recognized in part with the award of the Nobel Prize in Physics in 1953 to Fritz Zernike for the phase contrast microscope, a tool which rendered otherwise invisible cells visible with relatively modest modifications to an existing microscope. Much work in microbiology followed as a result of this along with other developments in optics.

The relationship seemed to change, though, starting in the mid-twentieth century with the advent of molecular biology. During this time, molecular biological technologies evolved and matured to the point where discoveries were facilitated primarily by non-optical means, with microscopes serving as more of a tool for routine lab work than as significant drivers for learning something new. After all, a traditional light microscope is limited to observing structures no smaller than about one wavelength of light across, or about half a micron (one millionth of a meter). DNA, proteins, and all the other biomolecules are just too small to see, even for the most powerful microscope objectives.

Of course one could argue that the development of the targeted fluorescent proteins that reveal the location of a molecule's existence within a cell helped to advance the field of optics, but in this case the role of enabler switched sides; molecular biology led to an increase in the number of optical technologies for imaging fluorescent markers, such as fluorescence correlation spectroscopy. From the viewpoint of a scientist, this reversal is a bit distasteful. We would like for technology to enable new discoveries about the fundamentals of life, not for new discoveries to lead to technology that tells us what we already know.

Now we are well into the twenty first century and are rooted firmly within the scientific age of molecular biology and biotechnology. (The age of physics is now past and now concerns itself primarily with the ultimate limits of space: the infinitesimal quark and the awesomely large cosmos.) Given the history between optics and biology and the recent change in their relationship, I think it's necessary to make an assessment, so to speak, of this relationship.

In the near future I will write posts that explore this topic. I hope to answer questions like

1. What do biologists want out of a measurement technique?
2. Will the current trends in improving microscopies lead to answers of the fundamental questions of molecular and microbiology, or are we moving in the wrong direction?
3. Are optical scientists misguided in the search for improved images? Are there other forms of information carried by light that are more useful than images?
4. Will it be possible to better control biological processes using light?