Cells = Organisms?

I just finished reading this brief article about the history and (somewhat) current state of cell culture engineering. My academic background has been almost entirely focused in the physical sciences, so I am continuously amazed by the body of common knowledge that exists in the life sciences.

The article states that the methods used to maintain cell cultures are very consistent and reproducible. However, one of the main limitations to maintaining cell cultures over a long period of time is that the individual cells adapt to their artificial environment and begin to take on traits that are different from the primary cultures. I was not expecting this; normally, I am used to the idea that organisms adapt to external stimuli. Of course, an adaption by an organism could be argued as being caused by changes at the (sub)cellular level, but still I am amazed that the individual and basic units of life behave much like the larger organisms they conspire to form, despite their much smaller degree of complexity.

I also found it interesting that massive vats of cultures are used to produce many therapeutic drugs and biochemicals. This too could be considered common sense, but for a humble physicist who remains naive on the subject of biology and medicine it is very much different than the common image of drugs being harvested by dutiful lab technicians from individual Petri dishes.

I wished to live deliberately

An article in the New York Times about a seven day rafting and hiking trip taken by a few neuroscientists has been making its way around my circle of friends lately. This article in part inspired my previous post and takes a scientific (as opposed to philosophical) look at the relaxing effects of a vacation and time spent away from distractions, namely those caused by technology.

Interesting excerpts from the article and my thoughts:

The study indicates that learning centers in the brain become
taxed when asked to process information, even during the
relatively passive experience of taking in an urban setting. By
extension, some scientists believe heavy multitasking fatigues
the brain, draining it of the ability to focus...

Behavioral studies have shown that performance suffers when
people multitask. These researchers are wondering whether
attention and focus can take a hit when people merely anticipate the arrival of more digital stimulation.

This suggests that some neuroscientists believe that the total amount of mental processing power available during a given time is limited and quantifiable. I interpret the second paragraph as meaning that the brain is capable of performing a limited number of tasks at a time, and when a person is anticipating inputs, the act of anticipation takes away from the available processing power.

The comparison of the brain to a PC might be a dangerous one. Our ideas and preconceptions with how a PC works might cloud our understanding of the actual working principles of the brain.

“To the extent you have less working memory, you have less space for storing and integrating ideas and therefore less to do the reasoning you need to do.”

Neuroscientists quantify this processing power in terms of something called working memory. This could be analogous to RAM in a PC.

Mr. Kramer says he wants to look at whether the benefits to the brain — the clearer thoughts, for example — come from the experience of being in nature, the exertion of hiking and rafting, or a combination.

It is not clear what specific aspects of a vacation can lead to more attentive thought. A parent who has to herd three children through Disney World is not likely to experience the same benefits of a vacation as someone who went hiking for a few days with one or two other adults.

Even without knowing exactly how the trip affected their brains, the scientists are prepared to recommend a little downtime as a path to uncluttered thinking. As Mr. Kramer puts it: “How many years did we prescribe aspirin without knowing the exact mechanism?"

There's really nothing new in terms of the perceived benefits of such a vacation. The real challenge is correlating changes in the brain---electrical activity, blood flow, etc.---to feelings of relief and increased attentiveness.

I also often wondered about one particular point while reading the article. The author speaks about performing better or to our "cognitive potential." In what sense is our thinking made better by removing an abundance of digital stimuli? While the quality of any one particular project may suffer if a person is inundated with digital information, could not the increase in the work output make up for it (if such an increase actually exists)?

Kauai

I'm back from my trip to Hawaii (specifically, Kauai). It  was an amazing trip, the first half of which consisted of a hike along the Kalalau Trail to the Na Pali Coast. Before I set out, I established a rule for myself such that I would allow my brain to wander and think on any topic freely and without effort; in this way I hoped to allow my thoughts to constantly cycle in both my conscious and unconscious and eventually settle into some logical structure. Immediately prior to the hike I had been focusing entirely upon my candidacy exam for the better part of two months and had been having difficulties in processing any new information. Vacations are a great time to let things settle in one's brain and make room for more knowledge.

So why talk about any of this? I did at least come to one philosophical realization that I think is worth mentioning. I have for a long time felt that the feeling of complete and total relaxation that accompanies camping after a long day of backpacking is made possible by the extreme effort that a backpacker puts into a hike. In other words, to truly relax one must really work hard. On this particular hike, I realized that there is a reciprocal relationship here: to do quality work, one must really relax. Like I said above, if one's thoughts aren't allowed to settle, then one can't really make the best of his or her time spent working.

You spin me right round

Ben Goldacre always has interesting things to say about the science behind health care and the pharmaceutical industry. In one of his recent posts he writes about a research project that examined 72 trials with negative results, i.e. an investigated drug or treatment did not cause a desired effect. Out of all of these trials, he quotes that only 9 gave any figures in the trials' abstracts and that 28 gave no numerical results at all.

What was in the reports was "spin," or the authors' attempts to project the results in a positive light. In order to prevent this, he says, trials are supposed to be registered before they are performed so that their intended purpose can not be changed. Additionally, there are guidelines that dictate what must be included in a report. These rules, however, are more akin to suggestions since there is no enforcement of them.

Can such a system be implemented in the physical sciences? I don't think so. Often, we're actually learning about the topic as we proceed through the research. No amount of preparation can allow us to establish a hypothesis sufficient for inclusion in a detailed report before we undertake the experiment. Hypotheses, I feel, are best constructed concurrent with an experiment. And as for report guidelines? Well, anyone who has had to deal with reviewers' critiques of their papers will tell you that there is rarely any consensus about what makes a good report.

I suppose that one could argue that a grant proposal tries to satisfy this purpose, but I can't say that I'm experienced enough to comment one way or another on it.

On science and faith

Here is an interesting article from Talking Philosophy Magazine. The author discusses the similarity and difference between religions faith and scientific faith. I believe it is often taken for granted that much of what we know about the natural world does not exist in the strict sense; all that we truly know is the outcome of an experiment. Theoretical models, such as the concept of protons and electrons or the theory of gravity, create entities or concepts that don't actually exist in the same way that a ball or dog exists. They are simply mental constructs that are used to explain repeated experimental outcomes and predict future behavior.

Of course, one can always argue that these constructs are "true" in the sense that they are predictive and can be tested as opposed to religious concepts. But I'm not so certain that their predictive powers and testability prove that they exist. "Truth" and "existence" seem to be two separate ideas here. So, in some sense, all of us, whether religious or not, believe in things that don't exist.

Fun with thermodynamics

Admittedly, the thought experiment I'm about to tell you about is simply explained by thermodynamics. Despite this, I puzzled over it for a while since it is very counter-intuitive, at least to me.

Suspend a weight from an elastic band so it is stretched (only slightly) beyond its equilibrium point. Now, heat the band with a hair dryer. Does the weight move up or down?

Give up? It moves upward. Do you know why?

I plan to verify this experimentally at some point.

If you swim after eating, your stomach will cramp

As a student of the physical sciences, the importance of experimentation for determining the true principles behind many natural phenomena is impressed upon me on a near daily basis. However, I am becoming increasingly convinced that carefully designed experiments are even more important for the social sciences.

Within the the social sciences, there are (to my untrained eye at least) few theories to predict the behavior of individuals or groups. Furthermore, their behavior is often influenced greatly by the interests of other groups. For example, McDougall's Born to Run contains a chapter about the drastic increase in foot and knee injuries that occurred following the development of the athletic shoe in the 1970's. Despite an enormous amount of evidence that running shoes are the cause of many running-related injuries, companies such as Nike create a "false truth" for the public: the more cushioned a running shoe is (and the more expensive), the better it is for your feet and knees. Though this is a misconception perpetrated by a company in the field of sports medicine, the idea can be carried over quite easily to the social sciences (see Levitt's Freakanomics). Thus, common wisdom in the social sciences can be attributed to a lack of predictive power and conflicting interests.

The importance of these fields to society is enormous when compared to the physical sciences. After all, if the common wisdom is wrong in the physical sciences, the general public is likely to be affected by not having a new iPod or smart phone until the misconception is discovered and the science is applied to new technologies. However, if misconceptions exist in the social sciences, large groups of people could go without health care, school curricula could be poorly engineered by state governments (New Math, anyone?), and governments could be buried by incredible deficits.

Thus, carefully designed and controlled experiments in the social sciences, and really any science, are important for everyone. Without them, the truth might remain buried in speculation and deception.