Thursday, January 29, 2009

"Good" drivers versus "good drivers"

So I'm driving in to work today, down roads with which I am all too familiar. You come down the hill to the main drag through town, stop and start as people turn in and out of parking lots: Shoney's, Krogers, the mall. Once past the McDonalds, the road opens up a bit, and you're going 50 by the time you reach the double-laned right turn. A "good" driver would slow, take the broad, sweeping corner at maybe 30mph, but not me. I've not let off the accelerator, nor have I moved into the inside right turn lane because it's imperceptibly shorter. I blaze past the entrance to Y-12, crest the ridge still going 50, and take the right turn, more of a ramp than a normal intersection, onto the road that leads into the lab. This right turn should only be driven above 45mph, unless it's pouring rain. Or snowing, which never happens.
After the guard gate, the two lane road opens up to a long, relatively straight stretch, down the middle of the valley in which the lab resides. The speed limit is 55, but it's the perfect road for 80. Without a second thought, I check the left lane, flip my headlights on, and pass cars ahead of me who aren't going at least 65. Sometimes two or three at a time. By mid-morning, no one is on the way out of the lab, so there is hardly any oncoming traffic.

So: speeding, cornering quickly, passing several cars at once. Bad driver? Or good driver?

Americans seem to have lost the art of driving. We've become lax; we chat on our cell phones or twiddle with the radio knob or drink and get behind the wheel, and we crash and injure or kill one another. What if we were all stunt drivers? What if we all had the necessary skill to drive 85mph down twisting country road, make a handbrake turn, or parallel park into a space the size of a schnauzer? No, we (and our insurance system) desire "good" drivers, people who drive like they handle raw chicken, people who won't corner at 50mph because they're afraid to do so. We don't want "good drivers," people who are capable and skilled and can maneuver a car like an extension of their body. Instead of countering the idiocy of today's drivers with a demand for skill, we merely demand idiocy-but-wearing-a-helmet.
Driving is a privilege, not a right. Driving is a skill, not a chore. People should be "good drivers," not "good" drivers.

Friday, January 23, 2009

Good words for today

"There is another concept of perfection also: it exists where things are whole, complete, in order and harmony as their Creator intended them to be. In this case, there might be darkness involved in the pattern, but it would be part of its order, functioning with the other elements in a harmonious way." - J.A. Sanford, Jungian psychologist and ordained Episcopal priest

In the creation account, we find a God who makes the heavens and the earth, the light and the darkness, the land and the waters. Why, then, do we assume that God's eternal kingdom, and us in it, does not also comprise seemingly opposing elements? And why assume that certain elements are better than others? Is the light better than the darkness? It is an easy assumption to make, given our animal background: the darkness is when predators lurk, where we are unsure of ourselves and do not feel at home. But God created both light and darkness, and called it "good." Similarly, God's "strength is perfected in weakness" (2 Cor. 12:9); weakness is seemingly the "bad" element of these two possibilities, but in fact is just as necessary as strength for completion of the whole. God's perfection is not in the removal of some elements and the sparing of others, but a completion - a perfection of all of those elements in harmony. This can also be said of our selves and our souls. We are told to "be perfect, as your heavenly Father is perfect," but this perfection implies completeness and wholeness; not a striving toward some goal which, in truth, would make us less of ourselves than when we began. As we strive to be "saved" (Philippians 2:12), we are slowly made whole through God's grace, and this wholeness, this completeness - this perfection - is where we find the image of God within ourselves.

Tuesday, January 20, 2009

Why the system is broken

"The above manuscript has been reviewed by our referee(s). A critique drawn from the report(s) is enclosed. On this basis, we judge that while the work probably warrants publication in some form, it does not meet the special criteria of importance and broad interest required for Physical Review Letters. In accordance with our standard practice (see enclosed memo), this concludes our review of your manuscript."

So begins the e-mail I received early this afternoon. This is the second time my manuscript was returned to me, saying it did not warrant publication in PRL. Why? Because the referees said so. But let's take a moment, shall we?

  1. Referee A states that, despite the fact I've previously answered all of his questions, he is still unconvinced that our experiment makes any difference to novae and x-ray burst nucleosynthesis. He instead points me to a disgusting, 30-page ApJ Supplement (yes, that's right, the "source" that he argues I haven't considered is a "supplement"), saying that, because the authors don't specifically mention the reaction I studied, it must not be important [it is worthwhile to note that the ApJ had this to say: "Several important remarks have to be made at this stage: First, we have chosen a factor of 10 for the level of uncertainty affecting theoretical reaction rate estimates, in general. Other authors (see Schatz 2006; Amthor et al. 2006) claim, instead, that excitation energies of theoretically calculated levels for XRB conditions may suffer uncertainties of ~100 keV, which translates into an overall uncertainty in some rates that may reach several orders of magnitude" - in other words, they arbitrarily picked a factor of ten, but it may not be correct. Additionally, the ApJ is only pertinent to one type of x-ray burst only, and a multitude of reactions are left out of their "comprehensive" study]. He either ignores or refuses to read my pages of notes or peruse any of the references I included, many of which are by prominent physicists (M. Wiescher, for instance, as well as one of the coauthors on the ApJ) who, on the whole, say exactly the opposite of what he argues. I cite 26 separate articles and proceedings which state that the reaction I studied is important; because I didn't cite the aforementioned ApJ (on which the referee is most likely an author), I don't get to be published in PRL. What kind of person demands that my experimental results be in line with a non-mainstream theory paper in order to be published? What kind of strange science rule is that? Our network calculations show that the result could cause a 60% increase in the reaction rate, and a reduction in the uncertainties of final isotopic abundances by orders of magnitude, both in novae and in x-ray bursts; a multitude of papers mention the importance of the reaction in isotope production and energy generation in explosive astrophysical events; this is the FIRST TIME EVER that this reaction has been measured experimentally, the culmination of over a decade of work; yet the referee states that there is no "hard evidence" to support our claims, and that, because "There is not a single mention in Parikh et al. [yes, that's right, the worthless paper on theory which so obviously trumps actual experimental results] that changes in the... reaction rate have any effect..." he feels that our work is inconsequential.
  2. Referee B acknowledges that "A decision on the special criteria [of PRL publication] is of course a subjective view and it may be that my interpretation is rather harsh compared to others." The referee continues, "In addition, this choice is partly an editorial issue, since it reflects the Journal's position with regard to which research areas are currently fashionable (I note the author's comments on recent selection of papers in this area for publication in PRL). If the other referees or the editor have a contrary view, I would be happy to accept this." Directly subsequent to this gem of insight, however, the referee demands that I explain in such great detail every aspect of my calculation, that there is no conceivable way it could fit into PRL's mandated four-page length. They are "Letters," meant to be an overview, meant to be followed later with a more in-depth, longer paper in one of the other Physical Reviews. Everyone knows this. I understand if excellence is required, but for a PRL to be exhaustive is an unreasonable demand.
  3. Referee C recommends publication in PRL. Has, in fact, for both my original and my revised submissions. But two referee approvals are required, and apparently we have one and a half.

Science has become far too much a forum of politics. We do science in order to discover the mysteries of the universe, and to share our discoveries with others. Too bad that now, your publication history depends more on luck than on work. Despite the experiment being enough for a Ph.D. thesis and taking years of preparation on the part of the scientists involved as well as the facility's technical staff, despite the work prompting invited talks and job offers, despite the hours spent doing tedious calculations with as many models as possible to prove that - as stated in the manuscript - our result has a tremendous potential to affect the state of the field of nuclear astrophysics, despite all this, we can't publish in PRL. I am not merely ranting because I am upset that my manuscript "didn't cut it;" ask any scientist whether or not publication has become a game of chance and politics as much as science. I invite anyone interested to read my manuscript and Referee A's complaints, and still maintain that Referee A is being fair and unbiased. It is not just me.

So, dear editors and referees of the Physical Review Letters:
Why do politics and popularity matter in science? Why does a set of simulations based on some theoretical reaction network outweigh a striking experimental result? Why are referees not screened for conflict of interest?
Your journal is an important voice in the scientific community, an avenue by which the newest and neatest of scientific discoveries are heard. But it has become too mired down in issues which should never pertain to science, and for that, we all suffer.

This is a call to arms! Science must work if non-scientists are to trust us, if we are to achieve anything, if future generations of scientists are to emerge.

Inauguration day

There's coverage on NPR. I've been listening to it since I got out of bed. Congratulations, Mr. Obama.

Friday, January 16, 2009

Good words for today

"Until we have reached the perfect understanding, which must be beyond our grasp so long as this life lasts, the wise man will alternate between these two activities, using his religion as the inspiration and guidance of his life unless he sees real reason for disregarding it, while he is as relentlessly thorough as his mental capacity allows in bringing to bear upon that religion the purging criticism of philosophic inquiry." - William Temple

It is an unhealthy and dangerous thing to assume that we know something absolutely, ultimately, or infallibly. One of the basic tenets of science is the understanding that new and fascinating discoveries might - and hopefully will - force us to revamp our theories, improve our grasp of the underlying principles, and thus learn. There is a strange surety which has become prevalent in certain circles that a single religion (and/or philosophy) must be absolutely right, while no others can be right, nor can the chosen religion be the tiniest bit wrong. This is a terrible fallacy. We've only fallen into that same old trap, the one human beings have fallen into since time immemorial, the belief that "I know better than you." We are called to "test the spirits," to not be sure about anything in religion and philosophy but instead test our beliefs rigorously. At the same time, we need to be living out our beliefs as the best option we have available to us. This is to what Temple refers: we use our religion, our spirituality, as our inspiration and guide in life (in practice), but also question its "rightness" (in theory) every day. This is how we grow spiritually. Doubt is ingrained within the human mind, and even that "blessed assurance" must (and will) at some point come into question, because that is our nature. Human beings must be able to perceive mystery in order to be truly human, for it is that divine and ultimate Mystery of God which sustains our very lives.

Thursday, January 15, 2009

Visualizing human chromosomes
Now this is cool.

A group at RIKEN in Japan have just published a study (subscription required) on visualizing, for the first time in 3D, human chromosomes using coherent x-ray diffraction. Coherent x-ray diffraction (as opposed to your regular old diffraction) utilizes, you guessed it, coherence in the x-ray wavefront. The phase differences of the exiting (scattered) x-rays when they hit a CCD camera behind the object of interest can be used to "map" a three dimensional image of that object's electron density. The setup requires no lenses, and can be used to probe objects as thick as a human chromosome - something electron tomography isn't capable of achieving. Additionally, the method has a resolution of about 120 nm, among the highest in 3D mapping of this general sort.

And here, the neatest part about the whole thing (aside from the fact that physics can be - and is - used toward the betterment of humankind): the picture!

Yoshinori Nishino, Yukio Takahashi, Naoko Imamoto, Tetsuya Ishikawa, Kazuhiro Maeshima (2009). Three-Dimensional Visualization of a Human Chromosome Using Coherent X-Ray Diffraction Physical Review Letters, 102 (1) DOI: 10.1103/PhysRevLett.102.018101

Sunday, January 11, 2009

Astronomy Picture of the Day

Just wanted to share this fantastic and fascinating photo with everyone. Go check out the Astronomy Picture of the Day to see a view of Saturn that no one has seen before.

Monday, January 5, 2009


I have just recently returned from a trip partway across the country to visit home for the holidays. The outbound drive cut north to the tangled mass of interstates that is St. Louis, then followed the tornado-corridor of I-70 westward to Colorado. Coming back, the drive first meandered south along the Colorado front range, chasing the Rockies back and forth until finally catching them again at Raton Pass, then headed east along I-40, following the fabled path of historic Route 66 across uncivilized northern Texas, arid Oklahoma and chilly Arkansas. Though winter is hardly the time to be traipsing around the nation's middle if one is seeking nice views or picturesque landscapes, it was still a boon to be so fully immersed in the Eisenhower Interstate System.
But now I am back at work, preparing for another experiment, waiting for a laptop to be shipped, downloading Fedora Core 10 isos, and generally playing catch-up. Such is life, I suppose. Oddly enough, when I picked up my mail from the Post Office this morning, included in the stack was a brochure for Coastal Vacation Resorts, as if to say, "welcome back from your vacation, want to go on vacation?"

Thursday, January 1, 2009

First Post of 2009

Happy New Year, anyway. :-)