Archives For science

A Musician on Mars

December 11, 2013 — 1 Comment

mars_analog

Welcome to Mars. As one of the first colonists on the fourth planet from the Sun, you endeavor to make it your new home. On Earth, you filled your time in numerous ways, but your real passion was music. Luckily, the Indian Space Research Organisation (ISRO) allowed you to bring your prized possession: a Steinway grand piano. Excited to play for the first time in months, you squeeze into your ISRO-issued space suit and wheel the piano onto the Martian surface. It’s noon near the equator. The temperature is around 25ºC (77ºF). You stretch out your arms, relax, and strike your first key. The sound is… quiet and out of tune. Assuming the piano needs to be retuned, you wheel it back into your pressurized vessel, take off your suit, and tune it yourself. Satisfied, you wheel the piano onto the surface again. The Martian surface is quiet, and you notice the colors of the sky are a lot redder than you had seen in NASA photographs. Again, you begin to play. It again sounds too quiet.

What is happening here? Why might a piano sound different when played on the Martian surface? This is a fairly involved question. Luckily, we are considering an instrument with taut strings rather than something that depends more upon atmospheric conditions than, say, a trombone or pipe organ. Furthermore, the equatorial temperature is Earth-like. Why, then, might a piano sound different on Mars?

When tuning and subsequently playing a piano, the frequency you perceive (or pitch) depends upon the tension, length, and mass of the strings within the piano. Since the temperature is about the same as before, and since you did not physically exchange the strings, these properties remain fairly constant. However, the fluid on the strings does play a role. Like any oscillator, the fluid in which it is immersed provides a load which will subsequently alter the frequency at which the oscillator resonates and by how much. On Mars, the atmosphere is more rarified, with a mean pressure of 600 Pa at the surface. Compare this with a pressure of over 100,000 Pa at sea level on Earth. This reduced loading by air results in a bias to slightly higher frequencies (or a higher pitch). If you retuned the piano in a pressurized cabin and then played the newly tuned piano on the Martian surface once again, it would still sound out of tune. A simple solution is to retune the piano while on the surface.

However, this is not the only problem with playing music on the Martian surface. Remember that Mars has a lower-pressure atmosphere. Sound, as you may recall, propagates as an oscillation of pressure in some medium (like air). If the mean pressure is lower, this presumably changes the ability of sound to propagate over longer distances. Without going into too many details here, what happens is that sound will not propagate very far on Mars, and there is an effect such that high frequencies are heavily attenuated. Before, the pitch was shifted slightly higher. Here, on the other hand, higher frequencies will sound softer than lower frequencies, and all frequencies will sound quieter. This means that not only does the piano sound out of tune, but it also sounds muted. The question of sound propagation is so interesting that an acoustics researcher simulated sound on Earth, Mars, and Titan. She found that a scream which may travel over one kilometer on Earth would only carry 14 meters on Mars!

Your out-of-tune, muted piano, probably wouldn’t be audible to a nearby audience on the Martian surface.

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A Troubling Divorce

March 23, 2013 — Leave a comment

The unhappy marriage between the United States government and science (research, education, outreach) ended this month. We’ve known for years now that the relationship was doomed to fail, with shouting matches in Washington and fingers pointed in all directions. I would more likely describe an end to the relationship between elected officials and human reason, but that would be harsh, and I still have hope for that one. Sadly, this generation of congresspeople signed the paperwork for a divorce with science.

America’s love affair with science dates back to its origins. Later, Samuel Slater’s factory system fueled the Industrial Revolution. Thomas Edison combatted with Nikola Tesla in the War of the Currents. It was a happy marriage, yielding many offspring. The Hygienic Laboratory of 1887 grew into the National Institutes of Health approximately 50 years later. We, the people, invented, explored, and looked to the stars. Combined with a heavy dose of Sputnik-envy, Eisenhower formed the National Aeronautics and Space Administration (NASA) in July 1958. We, the people, then used our inventions to explore the stars.

Since then, generations of both adults and children have benefited from the biomedical studies at the NIH, the basic science and education at the NSF, and the inspiration and outreach from NASA. Since Goddard’s first flight through Curiosity’s landing on Mars, citizens of the United States have not only directly benefited from spin-offsbut also through NASA’s dedication to increasing STEM (science, technology, engineering, mathematics) field participation. Informed readers will know that although the STEM crisis may be exaggerated, these fields create jobs, assuming benefits from manufacturing and related careers. Such job multipliers should be seen as beacons of hope in troubling times.

Focusing on the NIH, it should be obvious to readers that biomedical science begets health benefits. From Crawford Long’s (unpublished and thus uncredited) first use of ether in the 18th century through great projects like the Human Genome Project, Americans have succeeded in this realm. However, as many know, holding a career in academia is challenging. Two issues compound the problem. First, principal investigators must “publish or perish.” Similar to a consulting firm where you must be promoted or be fired (“up or out”), researchers must continue to publish their results on a regular basis, preferably in high-impact journals, or risk lack of tenure. The second problem lies in funding. Scientists must apply for grants and, in the case of biomedical researchers, these typically come from the NIH. With funding cuts occurring throughout the previous years, research grants (R01) have been reduced both in compensation per award and number awarded. Additionally, training grants (F’s) and early career awards (K’s) have been reduced. Money begets money, and reduction in these training and early career grants make it even more difficult to compete with veterans when applying for research grants. Thus, entry into the career pathway becomes ever the more difficult, approaching an era where academia may be an “alternative career” for PhD graduates.

The United States loved science. The government bragged about it. We shared our results with the world. Earthriseone of my favorite images from NASA, showed a world without borders. The astronauts of Apollo 8 returned to a new world after their mission in 1968. This image, the one of the Earth without borders, influenced how we think about this planet. The environmental movement began. As Robert Poole put it, “it is possible to see that Earthrise marked the tipping point, the moment when the sense of the space age flipped from what it meant for space to what it means for Earth.” It is no coincidence that the Environmental Protection Agency was established two years later. A movement that began with human curiosity raged onward.

Recently, however, the marriage between our government and its science and education programs began to sour. Funding was cut across the board through multiple bills. Under our current administration, NASA’s budget was reduced to less than 0.5% of the federal budget, before the cuts I am about to describe. The NIH has been challenged too, providing fewer and fewer grants to researchers, forcing many away from the bench and into new careers. Funding for science education and outreach subsequently fell, too. Luckily, other foundations, such as the Howard Hughes Medical Institute, picked up part of the bill.

I ran into this problem when applying for a grant through the National Institutes of Health and discussing the process with my colleagues. I should note as a disclaimer that I was lucky enough to have received an award, but that luck is independent of the reality we as scientists must face. The process is simple. Each NIH grant application is scored, and a committee determines which grants are funded based upon that score and funds available. With less money coming in, fewer grants are awarded. Thus, with cuts over the past decade, grant success rates plummeted from ~30% to 18% in 2011. When Congress decided to cut its ties with reality in March and allow for the sequester, it was estimated that this number will drop even further. (It should be noted that a drop in success rate could also be due to an increase in the number of applications, and a large part of that decrease in success rate over 10 years was due to the 8% rise in applications received.) This lack of funding creates barriers. Our government preaches that STEM fields are the future of this country, yet everything they have done in recent history has countered this notion. As an applicant for a training grant, I found myself in a position where very few grants may be awarded, and some colleagues went unfunded due to recent funding cuts. This was troubling for all of us, and I am appalled at the contradiction between rhetoric in Washington and their annual budget.

Back to NASA. As we know, President Obama was never a fan of the organization when writing his budget, yet he spoke highly of the agency when NASA succeeded. Cuts proposed by both the White House and Congress to NASA in 2011 for a reduction of $1.2 trillion over 10 years have already been in place. This was enough to shut down many programs, reduced the number employed, and led to the ruin of many of its buildings. However, the sequester, an across-the-board cut, also hit NASA very hard. As of yesterday, all science education and outreach programs were suspended. This was the moment that Congress divorced Science.

All agencies are hit hard by these issues, and it isn’t just fields in science, education, and outreach. Yet, speaking firsthand, I can say that these cuts are directly affecting those of us on the front line, trying to enter the field and attempting to pursue STEM-related careers. Barriers are rising as the result of a dilapidated system. Having had numerous encounters with failed F, K, and R awards amongst friends and colleagues simply due to budget constraints (meaning that their score would have been awarded in a previous year, but the payline was lowered to fund fewer applications) and seeing children around New York who are captivated by science education but are within a system without the funds to fuel them, I can comfortably claim that we are all the forgotten children of a failed marriage.

Whether it be due to issues raised in this post or your own related to the sequester, remember that this is a bipartisan issue. There are no winners in this game, except for those congresspeople whose paychecks went unaffected after the sequester. I urge you to contact your elected official. Perhaps, we can rekindle this relationship.

Every year, I read an article written in 1972 by P.W. Anderson, More is Different. This exercise provides two functions. On one hand, it is a kind of ritualistic experience through which I can reflect on the past year. On the other, it allows me to revisit the paper with an expanded knowledge base. The paper revisits an age-old discussion in science: Are less fundamental fields of research simply applied versions of their counterparts?

In 1965, V.F. Weisskopf, in an essay entitled In Defence of High Energy Physics, delineated two types of fields. One, which he called intensive, sought after fundamental laws. The other, extensive, used these fundamental laws to explain various phenomena. In other words, extensive research is simply applied intensive research. In many ways, various fields are closer in proximity to fundamental laws than others. Most of neuroscience is more fundamental than psychology, in that it is reduced to smaller scales and focuses on simpler parts of a more complex system. This psychology, however, is closer to its fundamental laws than the social sciences. Again, where psychology focuses on the workings of individual and small-group dynamics, social sciences use many of these laws to explain their work. Molecular biology is seen as more fundamental than cell biology. Chemistry is less fundamental than many-body physics, which is less fundamental than particle physics. The argument by Weisskopf seems to be in favor when discussing fields in terms of their size scale.

Changes between size scale, however, leads us to a discussion of symmetry. Anderson begins his discussion with the example of ammonia. This molecule forms a pyramid, with one nitrogen at its ‘peak’ and three hydrogrens forming the base. A problem arises, however. When discussing a nucleus, we see that there is no dipole moment, or no net direction of charge. However, the negative nitrogen and positive hydrogens form a structure that disobeys this law, or so one might think. It actually turns out that symmetry is preserved through tunneling of the nitrogen, flipping the structure and creating a net dipole moment of zero. Simply put, symmetry is preserved. Weisskopf’s argument continues to hold, even with the scale change.

However, when the molecule becomes very large, such as sugars made by living systems, this inversion no longer occurs, and the symmetry is broken. The fundamental laws applied at the level of the nucleus now no longer hold. Additionally, one can ask: Knowing only what we learned about the symmetry of a nucleus, could we then infer the behavior of ammonia, glucose, crystal lattices, or other complex structures? The fundamental laws, while still applied to the system, do not capture the behavior at this new scale. On top of that, very large systems break the symmetry entirely.

Andersen goes on to discuss a number of other possibilities. In addition to structure, he analyses time dependence, conductivity, and the transfer of information. In particular, consider the crystal that carries information in living systems: DNA. Here, we have a structure that need not be symmetric, and new laws of information transfer arise from this structure and its counterparts that would not be predicted from particle physics or many-body physics alone.  Considering the DNA example, we must then ask ourselves: Can questions in social sciences, psychology, and biology be explained by DNA alone? We are often tempted, and rightfully so, to reduce these complex systems to changes in our DNA structure. This much is true. However, can we predictably rebuild the same social psychology from such a simple code? With the addition of epigenetics, we are trying to do so, but I argue that we are not yet there. In fact, I argue that we never will be there.

The message here is that larger, more complex systems, while built upon the fundamental laws of their reduced counterparts, display unique phenomena of their own. We can continue to reduce complex systems to smaller scales. In doing so, complexities and phenomena of the larger systems are lost. Starting only with knowledge from the fundamental laws, can we predict all of the phenomena of the larger scales, without prior knowledge of those phenomena? Probably not. This is another kind of broken symmetry, where traverse fields in an intensive direction will lead one in the formulation of a fundamental laws, but traversing in the extensive direction from those fundamental laws will lead to more and more possibilities that need not be the one from where we started. As scales grow, so too does the probability of broken symmetry.

Thus, when stating that “X is just applied Y,” remember ammonia.

Relevant.

For those not aware, peer review is the process by which members of a field evaluate the work of other members in the same field as a form of regulation. This increases credibility and presumably quality within the field. For example, this can refer to review of manuscripts for publication, review of teaching methods by other educators, or the creation and maintenance of health care standards within the medical profession. In particular, scholarly peer review will be the main focus. The term is thus not very specific. I will focus on methods of peer review in publication and in the clinical setting for the purposes of this post. Issues relating to technical peer review in fields like engineering or standardization within education will not be discussed here. However, remember that “peer review” is a broad term encompassing many fields.

In 1665, Henry Oldenburg created the first scientific journal that underwent peer review, the Philosophical Transactions of the Royal Society. Peer review in this journal differed from the peer review we see today. Whereas professionals in the same field and often in competing labs will review today’s articles for publication, articles in this journal were reviewed by the Council of the Society. This journal created a foundation for the papers we see today, disseminating peer-reviewed work and archiving it for later reference. Peer review later developed in the 18th century as one where other professionals, often experts in the field, would perform the review as opposed to the editorial review of the aforementioned journal. This form of scholarly peer review did not become institutionalized until closer to the 20th century. However, professional peer review, such as that performed by physicians, dated back to the 9th and 10th centuries, where one physician would comment on the ethical decisions or procedures of another.

Since that time, scholarly peer review has become a mainstay of academic publication. It is amazing to think that this regulatory process has only been so strong for less than a century. However, the procedure does not come without significant criticism. (Though what topic in science is not heavily criticized?)

First, though, let us consider the benefits of scholarly peer review. Mentioned above was the improved quality of published work. Simply put, this works by first presenting a barrier that authors must overcome in order to get published, and critiques from reviewers are then addressed by authors to improve the quality of a manuscript. These suggestions may include additional experiments that will further test the work. The process filters out scientific error, thus improving accuracy of published information. Poor-quality work is rejected by the peer-review process. Additionally, work is stratified by journal quality, and this process routes papers to the correct tier. In total, peer review is at the heart of scientific critique.

One of the most common critiques of peer review is that it remains untested, as purported by a 2002 article in JAMA. The Cochrane Collaboration in 2003 (and reconfirmed in 2008) concluded that there existed “little empirical evidence to support the use of editorial peer review as a mechanism to ensure quality of biomedical research, despite its widespread use and costs.” Additionally, a study in BMJ took an article about to be published, purposely added a number of errors, and measured the error detection rate to be about 25%, with no reviewer correcting more than 65% of the errors. Finally, single-blinded peer review is open to bias. This could be bias against nationality, language, specialty, gender, or competition. Additionally, there is a common trend of bias toward positive results. Double-blinded review may help to overcome this critique.

Alternatives to single-blind review include double-blind review, post-publication review, and open review. In double-blind review, neither the authors nor the reviewers know the other party, and this would presumably reduce aforementioned bias. Surveys had shown a preference to double-blind review. Post-publication review would be an excellent supplement to the current review system to improve the rate of error correction in publications. Finally, open peer review, where the reviewer is known, would also possibly reduce the bias. However, one may be less willing to critique work by a senior author in the field, and the pilot by Nature in 2006 was far from successful.

At this stage, the system is the best we have, and problems lie less in the peer review process and more in the access to scholarly work without a costly subscription. Discontent in the field does not translate to a desire for one of the alternative methods described. Nonetheless, we should be critical of our process, much in the same way the process itself is critical.

As promised before, I plan to write on topics related to my experience in medical school, graduate school, and the combination of the two. For those who do not know, I am a student in an MD-PhD program (thus the “MudPhud” in the title of the blog). The classic paradigm is one that follows a 2-4-2 model of training. Our particular program follows the following pattern:

  • 2 years of medical school – These are the preclinical years, where we study biochemistry, histology, pathology, physiology, pharmacology, and related topics. It is mostly lecture-based, though our school utilizes a problem based learning (PBL) model. A few graduate school courses are taken in parallel with medical school. 
  • 3.5-4.5 years of graduate school – We then transition to graduate school, where a few courses are taken in the first year of graduate school (third year in the program). After rotating in multiple labs during the previous years, we settle into a lab and perform research for the following years. This ends with the defense of a doctoral dissertation.
  • 1.5 years of medical school – These are the clinical years, where students practice on the wards in each of the required fields. This portion of training culminates in graduation from the medical school and thus the MD-PhD program.
  • After the program – Students take multiple paths, ranging from medical residency to a postdoctoral fellowship to work in industry. Most will go on to residency.

The challenge in the transition from medical school to graduate school is not an easy one. In medical school, one must acquire large quantities of data and share this knowledge at regular intervals (usually on written exams). One could consider it like a very fast treadmill where you do not have access to the controls. The treadmill will continue to push you, but you may feel challenged to keep up. Or you might not feel this challenge. To be honest, I did not find this to be too fast, but the challenge for me was the lack of control over my schedule, from an emotional standpoint. During this time, you build a rapport with a large group of classmates who will later become colleagues. The shared experience of medical school creates solidarity among this group.

In graduate school, things change. You are now on your own, in a place where you are now at the bottom rung once again. It is exciting on one hand, because you can now choose what to study and how to direct your education. On the other hand, you may feel lost. As opposed to a treadmill, this is more like jogging through a forest, where vision is limited. You can take breaks to reorient yourself, and you can move at your own pace. However, it is difficult to know whether you are making progress, how fast you should be moving, or whether you are completely lost. Your friends in medical school are now moving on, and you no longer share the rapport you previously had with them. This creates a distance, and it is often emotionally trying.

For as challenging as the graduate school transition might be, the benefits outweigh the drawbacks. You are now able to study what truly fascinates you. You have control over your schedule, and you determine your own pace. You have access to a vast array of resources, and you can take on additional projects outside of your program. For example, I found myself volunteering with mentorship programs, science fairs, and even with a community clinic. The challenges you face in graduate school make each success far more rewarding than if they were easy. A simple rotation or a year-long research project cannot create the same level of suspense, mostly due to their limited timelines and more structured projects. Failure begets learning. Success begets inspiration.