Sep 03 2010
Sep 03 2010
I like my car like I like my lightcycles
Aug 29 2010
Beliefs Deserve Better Science
When religious beliefs are placed into the sphere of scientific test, scientific criticism of those beliefs is fair game. All questions put under the framework of the scientific method enjoy the same scrutiny, and it is imperative to approach the question with the same critical toolkit as one would approach any other question. When my issue of The Economist showed up on my Kindle on Friday, I was at first intrigued to see an article suggesting that prayer makes couples more faithful to one another (as opposed, for instance, to just thinking positive thoughts). As I realized that the reporting on this study was done with some carelessness, however, my interest turned to anger at both the incomplete reporting of The Economist and the questionable conclusions of the study’s authors.
The study in question was recently published in The Journal of Personality and Social Psychology [1]. The Economist [2] reported that the study, of 83 undergraduates from Florida State University, showed that praying for your partner reduced the rate of infidelity by a “significant” amount over the 4 weeks of the study. The group of 83 was initially tested to determine their level of infidelity, scored on a scale of 9 points; the average of the entire group was 3.5, with ” . . . [considerable variation] between the four groups.” (as reported by the Economist). A higher score indicates higher infidelity. The students were then broken into four groups randomly, and each was tasked with a different mental exercise. One of the groups was tasked with prayer for their partner. At the end of four weeks, as the Economist reports, “People who had prayed for their partners averaged 2.4, significantly lower than their initial scores, whereas those who thought positively about their partners or considered their day both showed ratings of 3.9—significantly higher” [2].
What does the paper actually say? As a scientist, my first question is: “What does ‘significantly’ mean – that is, what is the variation in each group around these reported means?”
To answer that, I looked at the paper. The results from this study were reported as follows in the paper [1]:
“Infidelity. . . . participants in the prayer for partner condition reported significantly lower infidelity scores (M = 2.44, SD = 1.04) than did those in the neutral condition (M = 3.91, SD = 2.16), F(1, 78) = 7.61, p < .01, eta_p^2 = .87, and the positive thoughts about partner condition (M = 3.90, SD = 2.37), F(1,78) = 6.70, p < .01, \eta_p^2 = .80, but not those in the undirected prayer condition (M = 3.19, SD = 2.11), F(1, 78) = 2.02, p < .16, \eta_p^2 .45. However, those in the undirected prayer condition did not significantly differ from the other two conditions ( ps > .05, ns). All the means reported in this and subsequent analyses were adjusted for the covariates (see Table 2).”
The notation of the statistical analysis used here, ANCOVA, is described elsewhere [3]. The F-value and p-value above are as determined from the standard Fisher Test. However, the key here is that the means have uncertainties – standard deviations, or “SD” – which result from the small statistics of the samples (four groups made from 83 students means roughly 21 students per group, which is not a lot of people per group). If I took four random samples of 21 students from a single group of 83 total students, whose total average scores were 3.5 and whose SD for those scores were about 1-2 overall, I could easy generate four samples with this trend. The reality is that there is no statistically significant difference between these four groups.
To review the science here, 83 undergrads were broken into 4 groups. One group had to pray for their romantic partner each day (using a prescribed prayer), 2 had to conduct undirected prayer, and the last simply had to reflect on the day. All groups performed their assigned activity for the same time, once per day. At the end of the study, the mean infidelity score for the directed prayer group was 2.44 +/- 1.04. For the two undirected prayer groups, it was 3.19 +/- 2.11 and 3.90 +/- 2.37. For the neutral group (daily reflection) it was 3.91 +/- 2.16. Nothing can be concluded from this limited data set – these numbers are, within the rules of statistics, all the same. In order to shed any meaningful light on this question, a sample size at least 3-5 times bigger is needed.
The worst criticism I have of this study is that in its present form it CANNOT be conducted blind. The participants were quizzed on their fidelity before being broken into groups. One of those groups was asked to pray for their partner. Those people could easily be consciously or unconsciously influenced to act more faithful over the 4 weeks of the study, since there is likely some sense that their fidelity is being directly tested. There is no way to control for that in this study, and by construction it is potentially biased. At the very least, that bias would need to be quantified.
It’s my opinion that it was irresponsible for The Economist to fail to report the standard deviations in this study and to simply regurgitate the conclusions of the study without thinking about the results. The Economist is a major, international news analysis of serious record. Regarding the study authors, the fact that the study uses a small sample and doesn’t include any attempt at blinding or bias correction suggests this area of research needs more maturity. Until then, nobody should take it seriously.
When people want aspects of religious belief to enter the realm of scientific scrutiny, two things need to happen. First, those conducting the test owe those of religious faith the best possible scientific practice; this study, in my opinion, falls woefully short of that responsibility. Second, those whose faith is, literally, being put to the test should demand better methods but be prepared to expect results at odds with their belief system. After all, nature does as nature does, no matter what you or I believe. At the very least, inadequate studies like this only serve the confirmation bias, rather than real scientific discovery.
[1] “Faith and unfaithfulness: Can praying for your partner reduce infidelity?” http://www.apa.org/pubs/journals/psp/
[2] http://www.economist.com/node/16886238
[3] ANCOVA: http://udel.edu/~mcdonald/statancova.html
Aug 27 2010
Second year
The first month of being a faculty member was one of the most difficult months of my life. Changing jobs is always hard, but going from post-doc to faculty is a promotion without a well-defined manual. The federal government made things extra special by creating a new DOE young investigator award program, but placed the deadline on September 1, 2009. A number of us thought it a little odd, if not downright frustrating, that new faculty were expected to hand in a proposal for a lot of money (over many years) in such a short period of time. That first year, you’re trying to establish your research program and get ready to teach. The first month is all prep, in unfamiliar territory, for a journey that at first has no clear path.
After my summer of work at CERN (and a subsequent two-week coma), Jodi and I stepped back into a normal work day. We’re both teaching now, just one course each (since we have research to do as our primary effort). We buried ourselves in prep work during the week before classes. This year, classes started on the Monday after the students moved in, so the semester came fast and furious. We’ve been busy working on proposals, big and small, and getting up earlier to commute in for our morning teaching. Meetings are interspersed with office hours, and research is taking a small back seat this week until we get settled in classes. It’s the typical beginning of a semester.
The start of the second year has been much better than the start of the first. We know a lot more people than we did last year. We feel a lot more like part of a community, both in our department and at the University. We have footing, something we didn’t have a year ago. We have ambitions and goals. The DOE early career award program has shifted to a proposal due date in November. And most important of all, we better understand just what the real lives of faculty are like and are taking advantage of the benefits while managing the surprises.
I’m very happy to be teaching again. That said, I am also eager to stabilize my schedule so that I can turn a lot of attention back to my research. I can’t leave it for too long. I crave the classroom, but I have a deep hunger that rages inside when it comes to tearing at the mysteries of the cosmos.
Aug 14 2010
Back from Vacation
Well . . . sort of. I took a long vacation from personal things this summer to work in Geneva, Switzerland, at the CERN laboratory. I posted lots of things in the SMU CERN blog [1] and mirrored those posts in my own professional blog [2]. If you missed those adventures, have a look.
When I returned from CERN in late July, I got to see Jodi for just one day before she flew to Canada for a meeting of the SuperCDMS Collaboration. I spent the week at home, working on small projects and recovering from my summer of ATLAS work. I needed to get my brain back into something resembling a shape, and time away from work was the best way to do this. This effort culminated, upon Jodi’s return to Texas, in our first vacation since last year (I don’t count Christmas. I draw a distinction between a “holiday,” forced and mandatory institution-sanctioned time off, and a “vacation,” the use of unpaid leave to remember why life is worth living).
We took off for Door County, WI, where mobile phone reception is almost nil and wifi is spotty, at best. We did this on purpose. My e-mail has been going into an electronic DMZ from which I will extract the actionable items when I return. I have avoided work, and instead focused on life. Of course, this is not devoid of physics. I make a distinction between obligations and passions. On vacation, my only obligation is to myself and to my passions. Jodi and I discussed course structure philosophies, the nature of large collaborations, and other bits and pieces. These took minutes over coffee. We spent hours biking and hiking and swimming, or napping, or reading.
Photos from our adventures in Door County are available in our photo album online [3]. We’re not back to Texas yet, but our time in Door County is drawing to a close and we have some last stops to make on our way back to Dallas.
[1] https://blog.smu.edu/smucern/
[2] http://steve.cooleysekula.net/goingupalleys/category/event/cern-summer-2010/
Jul 15 2010
The Carbon Bowl
Apparently, each year the SMU Provost hands out a book for the faculty to read. Last year, that book was Timothy Egan’s “The Worst Hard Time,” a collection of stories (including diary entries) about surviving the worst environmental disaster in American history: the dust bowl. The dust bowl was an event in the 1930s which devastated much of the Southern Great Plains, a consequence of poor farming practices coupled with government and private incentivizing of conversion of grasslands into farmlands. Winds which normally whipped across the plains and caused little damage, owing to the protection offered by Buffalo Grass, suddenly found top soil loosened by plows on unplanted land. These winds kicked up clouds of dust 2000 feet high and 200 miles across, killing men, women, and children and destroying countless communities.
I’m reading this book now, and wondering if the oil spill in the Gulf of Mexico represents America’s “Carbon Bowl,” an environmental disaster that is the face of global warming. Just as greed and poor homesteading policy fueled the farming boom leading up to the dust bowl, an unslakeable thirst for energy coupled with bad public and private policies for energy diversification have led us to desperate measures to drill for oil. Just as the natural forces that move energy across the plains – wind and heat – were then unchecked by the natural ecology that had long developed in and protected the plains, unleashing the dust bowl, the natural forces that move material around the Gulf are sending the fruits of energy labor – crude oil – into bays and marshes. Countless plant, animal, and human life was destroyed during the dust bowl; we probably can’t know the extent of the oil’s damage on sea life for quite some time. Dust pneumonia was the disease of the dust bowl, the delicate tissue of the lung severed by fine silicates; who knows what the long-term health effects of all that oil and oil cleanup will be on Gulf coast residents.
Just as FDR had a chance to do something great to save the land and save the people, this President has a chance to do something great to create good energy policy while bringing relief to the Gulf and its people. With so many other comparisons to FDR under President Obama’s belt, will he rise to the challenge and meet this historical cycle head-on?
Jun 19 2010
Take TV Anywhere
I’ve commented on how much I love my MythTV box, “Stevo.” I’ve found another reason to love it more: streaming recordings from my home in Texas to my laptop in France.
Fundamentally, all MythTV does is take output from a TV tuner card and convert it to MPEG, writing it to disk. MythTV makes the videos available through a “TiVo-like” interface. But in addition to TV, it collects your music and photos, RSS news feeds, web content (Hulu), and podcasts and makes them available through your computer or TV.
Marry MythTV, SSH, and VLC, and you have a personal streaming empire. Let me tell you how I get my videos from Texas to France.
It begins by opening an SSH tunnel, with port-forwarding, from my laptop to the Stevo machine. Since Stevo lives behind a firewalled server, I need to do a “two-hop SSH tunnel”. From one terminal, I type:
ssh -l <USERNAME> -L 8080:<INTERNAL STEVO IP ADDRESS>:8080 -2 <EXTERNAL SERVER IP ADDRESS>
and from another I type:
ssh -l <USERNAME> -L 8081:<INTERNAL STEVO IP ADDRESS>:8081 -2 <EXTERNAL SERVER IP ADDRESS>
The reason for two tunnels with two ports – 8080 and 8081 – will become apparent in a moment.
Using one of the two SSH sessions, I then log into the internal Stevo machine. I navigate to the directory containing my TV recordings and choose the one I want to stream. I then execute VLC, launching both its web server (to control the stream) and its streaming capability:
cvlc -I http –http-host :8080 <FILENAME> –sout \
‘#transcode{fps=25.0,height=320,width=240,vcodec=mp4v,vb=768,acodec=mpga,ab=128,channels=2}\
:std{access=http,mux=asf,dst=:8081}’
You’ll have to tune your bitrate (video and audio) settings to suit the quality of your connection. I find that with my home server upload speeds and the download speeds of my local internet connection, 768kbps for video and 128kbps work very well. We also see why two port tunnels are needed. One is for the HTTP interface that lets you control VLC (8080) and the other is where the stream goes (8081).
Now, one important thing. You may need to tweak the .hosts files provided by VLC for its HTTP interface. By default, it’s locked down and you can’t access the webserver, even with the SSH tunnel, from anyplace other than 127.0.0.1. I edited the /usr/share/vlc/http/.hosts file and made the server allow people from outside localhost to access the VLC interface.
Now, from my laptop’s web browser I go to http://localhost:8080 and I can control where in the stream I am located. I can launch VLC from a terminal on my laptop using
vlc http://localhost:8081
and I can watch the stream.
By the way, here’s a fun tip based on something I learned from Lifehacker [1]: if you are watching a certain GLOBALLY POPULAR sporting event using this method, and you cannot STAND Vuvuzelas, you can open VLC’s audio mixer, enable two-pass mode, and drag down the following sliders to zero: 600Hz, 1kz, 3kHz, and 6kHz. This removes the higher range of frequencies occupied by the Vuvuzela, leaving voices and cheering intact.
[1] http://www.npr.org/blogs/showmeyourcleats/2010/06/18/127928951/vuvuzela-tricks
May 25 2010
Summer vacation is either a lie or a memory
When I was a kid, I got used to the idea that summers were my own. That’s thanks to the way the U.S. school system works, starting in August and ending in June of the next year. Summers were a time for play in my youth, yard work and play in my teens, a job and music in early college, physics research and music in late college, and then physics research in graduate school. The progression from play to steady employment was slow enough that I didn’t notice. By the time I became a post-doc, summers were the crunch time, all prep-work for conferences and no play. Of course, the lack of play led to stress-related health issues that I am still learning to tackle. The lesson: play is important.
As a faculty member, I am first struck by the perception that many students have about what a faculty member does during the summer. Their first instinct is to assume that you have the summer off. The second instinct is to recognize that you’re doing research (or teaching, depending on your track), but to fail to understand how draining that is. For instance, many students don’t seem to realize that to work on the LHC you have to spend time at CERN . . . away from your spouse . . . and home. It’s stressful, but necessary, and certainly not different from what hundreds of other physicists are doing at CERN this summer.
I’ve realized how non-existent my summer is, to the point where I can’t even plan for a summer side project this year. As soon as classes ended, I had a week to recover before the SMU Society of Physics Students trip to California, which I chaperoned (c.f. [1]). That drained me. It was fun – a LOT of fun, actually – but the irregular sleep schedule, plus constant driving and walking and planning . . . it took its toll. I had a few days with family, and one day with Jodi, before my latest travel: to Brookhaven National Lab for the Brookhaven Forum 2010 [2]. I’m speaking here, and while writing a talk for an invited parallel session presentation is a piece of cake at my age, it’s still time away from Jodi and home.
All of this is in the context of the next few months. In mid-June, I’ll be relocating to CERN until Aug. 1. Thanks to the generosity of my friends at CERN, I have a few places to call home for the summer (so as not to burden any one person). In addition, I’ll be starting my own effort on ATLAS with a post-doctoral researcher, also moving to CERN in June, and with a summer graduate student who will accompany me to CERN for the summer.
August will bring a few weeks of down time, including a MUCH NEEDED vacation (I haven’t even started the major summer work and yet I already know in my heart that I desperately need a vacation). It will also bring the need to prep for teaching next semester, which will be MUCH different than teaching was this past semester (pre-med students instead of engineers and physics majors/minors). I’ll be sneaking class prep work into the summer, so as to relieve the burden in August. But it’s a lot to think about.
Nobody said being faculty was easy, and it’s not. But it’s a metric shit-ton of fun, even if it’s exhausting. I just hope I survive to my vacation in August, and I hope I can get my batteries back to where they need to be in preparation for my 50 pre-meds, my post-doc, and my research students.
[1] http://steve.cooleysekula.net/goingupalleys/category/event/smu-sps-trip-to-slacsilicon-valley/
May 25 2010
Seen and Unseen
The oil leak in the Gulf of Mexico is an immediate crisis, getting immediate attention. It poses long-term effects for sea life, coastal life, and human economics (fishing, tourism, etc.). That oil leak represents a major release of carbon into the Gulf; oil in its crude form is a thick and viscous material, rich in carbon and hydrogen. That oil was on its way to a surface platform. Before it exploded, that platform was to raise the oil from the deep and pump it into oil tankers for shipping to coastal refineries. Hydrocarbon, in liquid form, was on its way to being burned in cars and households across the United States. That burning releases the carbon, primarily in the form of carbon dioxide. A potent greenhouse gas, that CO2 is then free to become part of the growing blanket of CO2 covering the entire earth. That blanket continues to affect changes in the global climate.
While the research demonstrating a causal link between human fossil fuel activity and global climate change (e.g. global temperature) is clear beyond any doubt, the United States has been slow in responding to the challenge of addressing the problem: the burning of fossil fuels. Part of that failure is simply due to the politics of fossil fuels, and the challenge of transforming a carbon-based economy to something more diverse. Another part is in American science education, wherein we have failed to educate the general public in the scientific method. This leaves America vulnerable to the false dichotomy of “both sides get equal time” and the belief that science is a democratic process, rather than one of elimination of bad hypotheses. The final problem, I opine, is the invisibility of CO2.
CO2 is colorless and odorless, and while necessary for the functioning of plant life it is lethal to humans in large enough quantities (e.g. in an enclosed space). However, when it’s not directly affecting human respiration it might as well not exist; it’s unseen. A blanket of CO2 surrounds the earth. In partnership with water vapor, it helps keep the earth’s surface at a comfortable temperature. But the size of that CO2 blanket has increased by 50% since the industrial revolution. We know that this extra CO2 is due to the burning of fossil fuels because oil and coal, long sequestered in the earth (millions of years), are free of the radioisotope Carbon-14 [1]. Historical studies of C-14/C-12 ratios in the atmosphere, as through tree ring research, shows that the declining C-14 content in the atmosphere tracks exactly with the increase in CO2, all since the industrial revolution.
The problem is that we cannot see it. CO2 is not like smog; it doesn’t hang on our cities, induce asthma attacks in our children, lead to “spare the air” days, etc. Rather, it rises into the atmosphere, thickening the blanket and affecting average temperatures world-wide. We are fooled by seasonal variations in weather – witness the snow in Dallas this past winter – into thinking climate change is a joke, but meanwhile the CO2 blanket thickens as we warm (or cool) our houses and ignore the problem. In contrast, the Gulf of Mexico oil leak – no less a carbon-based disaster – will coat wildlife in crude, starve sea life of oxygen and sunlight, ruin beaches and choke fisheries. It will stir anger from Congress and from the American people that too little is being done too late to save us. Pictures of the slicks, of tarballs, of sick and dying wildlife, of fisherman and children affected by contaminated food or water, will dance across our TV screens. We will react. There will be no debate about whether the oil spill is real, or whether the devastation of wildlife will have a causal connection to oil. There will be nothing but the intent to act, and a frustration when action doesn’t lead to immediate relief. Anger will rule policy, lawsuits will fly, and no doubt coastal communities will be affected for years, if not decades.
Imagine this level of emotion and dedication was brought to the CO2 problem. Imagine if CO2 could make you sick, hurt your kids, lead to widespread death of wildlife. Imagine if all the false skeptics were silenced by images of CO2 wreaking widespread devastation.
Of course, this is not too realistic. CO2 takes a long time to have its impacts, as we have seen. Those changes are gradual, spreading over generations so that no one generation feels compelled to act. CO2 is truly invisible, and in being so has become conveniently ignorable. The dichotomy in our world is between how we act against things seen (the oil spill) and unseen (the incredible thickening of the CO2 blanket). Ironically, both of these problems have the same cause – our insatiable need for energy combined with a hesitation to change the fundamentals of our energy economy.
Humans are ignorant creatures, by evolution. We are sensitive to only a tiny portion of the electromagnetic spectrum, making us long blind to radio and UV light. It is science that lights a candle in the dark, and makes us aware of the unseen and its daily impacts on those things seen. We know that UV is bad for us, because each of us can get sunburn; as a result, we accept the benefits of sunscreen against an invisible enemy. We know that viruses (polio, measles, smallpox) cannot be seen, but are devastating to us in less than a generation; we accept that vaccination can save us from crippling diseases. We fight the unseen, in the hopes of preventing the seen.
The challenge of CO2 is a cross-generational problem, one which has not been addressed. The oil spill in the Gulf is real opportunity, much as the recognition that viruses (unseen) are connected to disease (seen). The oil spill is the seen, the disease; the energy demand, the need to separate hydrogen from carbon by burning the product is the cause. We have an opportunity to tackle the disease and develop a cure, by diversifying our energy portfolio and minimizing our dependence on old carbon-based fuels. Let the devastation in the Gulf be the face of the invisible CO2 blanket in the atmosphere, and let the devastation wrought by this disaster be a proxy for all the devastation to come from climate change. Maybe, if we recognize THIS as the face of our enemy, we will be compelled to act.
Apr 17 2010
Aerosols
I’m nursing a cold. Laying about on the couch has given me some time to think, and I’ve been thinking about aerosols. The recent eruption of an Icelandic volcano has brought air traffic over Europe to a grinding halt. When this same thing happened after the 9/11 attacks in the U.S., local climate was slightly altered as jet contrails disappeared from the atmosphere. Albedo, the reflectivity of the atmosphere, kicks sunlight back into space and reduced energy input to our global greenhouse. The water vapor in contrails also serves to trap heat once it’s in the atmosphere. As a result, the range of high and low temperatures INCREASED markedly in the U.S. during the days after the attacks [1]. Whether a long term lack of contrails causes more warming (by allowing more sunlight into the atmosphere) or cooling (by preventing the trapping of radiation in the atmosphere) is unclear.
Volcanoes, on the other hand, seem to have a more clear impact on climate. The fine particulates in volcanic ash increase the albedo of the earth’s atmosphere and cause more sunlight to be reflected back into space. Less sunlight then gets trapped as heat in the atmosphere, and cooling results [2]. In fact, perhaps not coincidentally, “Ben Franklin noted that volcanic aerosols reflect sunlight to space, and therefore argued that the eruption of a large volcano on Iceland may have been responsible for unusual cold in 1783-4.” [2]. Franklin was even in Paris in 1783 [3], working on a peace treaty, so again the prevailing westerly winds brought the ash over Europe.
So I make a prediction, as a very amateur climate science armchair guy. I predict that Europe will experience unusually cold temperatures in the next year. In the next days, this will likely be a combination of the lack of contrails and the ash, but once air travel is restored I’ll wager that local temperatures in the European continent will still go unusually cold this coming year due to the ash. As a result, global warming detractors will seize on this as “more evidence” that global warming is a myth, making the same mistake they make when arguing that “global cooling” happened in the 1970s – neglecting aerosols.
[1] Travis, D.J.; A. Carleton and R.G. Lauritsen (8 2002). “Contrails reduce daily temperature range.”. Nature 418: 601. doi:10.1038/418601a
[2] JE Hansen, AA Lacis – Nature, 1990 http://hokulea.soest.hawaii.edu/ocn435/papers/1990_Hansen_Lacis.pdf
