30 November 2009

Data set reproducibility

Data are messy, and all data have problems.  There's no two ways about that.  Any time you set about working seriously with data (as opposed to knocking off some fairly trivial blog comment), you have to sit down to wrestle with that fact.  I've been reminded of that from several different directions recently.  Most recent is Steve Easterbrook's note on Open Climate Science.  I will cannibalize some of my comment from there, and add things more for the local audience.

One of the concerns in Steve's note is 'openness'.  It's an important concern and related to what I'll take up here, but I'll actually shift emphasis a little.  Namely, suppose you are a scientist trying to do good work with the data you have.  I'll use data for sea ice concentration analysis for illustration because I do so at work, and am very familiar with its pitfalls.

There are very well-known methods for turning a certain type of observation (passive microwaves) in to a sea ice concentration.  So we're done, right?  All you have to do is specify what method you used?  Er, no.  And thence comes the difficulties, issues, and concerns about reproducing results.  The important thing here, and my shift of emphasis, is that it's about scientists trying to reproduce their own results (or me trying to reproduce my own).  That's an important point in its own right -- how much confidence can you have if you can't reproduce your own results, using your own data, and your own scripts+program, on your own computer?  Clearly a good starting point for doing reliable, reproducible, science.

29 November 2009

Last call for submissions

The deadline for submissions to the Openlab 2009 is midnight EST, 1 December.  This is aimed at being a collection of the best blogging from 1 December 2008 through 30 November 2009.  Use this submission form to submit your favorites (from here and elsewhere). The current summary of submitted articles is at Blog Around the Clock. Two of mine, Science Jabberwocky, and Results on Deciding Trends, are already submitted. If there's something else you like as well or better, time to submit them. If those are your favorites from here, no need to do anything.

Though it would probably help my odds if you didn't submit others' articles, I see there are several quite good articles from other blogs that haven't been submitted. I'll be doing some of that submission myself, and I encourage you to do so as well. I'd just like to make coturnix's (the editor) job as hard as reasonably possible :-) -- give him a lot of excellent articles to consider.

28 November 2009

Science Anniversaries

150 and 400 years ago, two major events in the history of science occurred.

400 years ago, the telescope was invented and started to be used for astronomy.  For $100-$150 you can now get a telescope far superior to what Galileo used to carry out a major revolution in our understanding of the universe.  More in a moment.

150 years ago yesterday (November 27th), Charles Darwin's On the Origin of Species by Means of Natural Selection was published. Different major revolution in our understanding of the universe.  You can read this for yourself.  I don't actually recommend reading it unless you are really interested in history of science, and like Victorian-era writing.  (If you like my style, you're a couple steps in that direction.  My wife noted that I write something like Trollope, a prolific Victorian whom she likes.)  We've learned an awful lot in the 150 years since then, and many things that were mysteries to Darwin, such as how inheritance occurs, are well-known to us now.  Instead I'll suggest you read the evolution sections of modern biology texts.  Two such texts recommended by my biologist friends are Futuyma's, and Campbell and Reece.

24 November 2009

PhD Thesis Defended

I've been the (name of employer)-side mentor for a student working on her PhD.  Yesterday, she successfully defended her PhD thesis.  Not sure she wants to be named, so I won't for now.  But it's a lot of work to get to where she is, and I'll congratulate her.  She knows who she is :-)  Good job!

Jamese Sims successfully defended her thesis at Howard University on Monday.  She'll be writing up something about her experiences for the blog one of these days. 

16 November 2009

Where is the surface?

I just commented on my facebook status that I'm at a meeting about sea surface temperature.  That part was safe.  Rest of the comment was to observe that I'm now back to wondering whether the sea has a surface, where it is if it does, and if it does, whether it has a temperature.  That prompted a friend to comment 'Great ... this is going to bug me now.'  So for him, here's a longer version.

This sort of question is very common to science.  Of course my musing for facebook is overstated.  But there is usually a real question about what exactly it is you've observed when you take an observation.  When you have very different observing methods, they may well observe things that are different from each other.  There are, let's say 4, different ways of observing the sea surface's temperature.  For a diagram, see the wikipedia article on sea surface temperature

The standard method, and reference for others, is calibrated buoys that carry a thermometer at a known depth, typically 1 meter.  A major drawback to this method (all methods of observing have drawbacks!) is that you need a buoy.  They're not cheap, and it would take several million of them to give us a high resolution data set for global sea surface temperature (acronymed SST).

11 November 2009

Veteran's Day

Veteran's Day or, in some other parts of the world, Remembrance Day today. 

My thanks to those who have served.  My daughter and son-in-law are among you.

09 November 2009

Racing again

Saturday I got to meet a barn owl and a red shouldered hawk.  Both were amazingly calm for all the runners who were milling around.  The owl was looking around at all the dogs, deciding whether they were snack sized or not.  (Concluded 'not', though I think a couple of dogs caused some serious calculation.) Fun to watch an owl look around.  They were out as part of the parks and planning commission entertainment for the Jug Bay 10k (and 5k, and 3k walk). 

I and a fellow club member were out for the 10k, with our plan being to run 1 minute, walk 1 minute.  This being a much flatter course than last week's cross-country, I was able to follow the plan pretty well.  Passed the mile 5 marker in 49:45, vs. last week's 8k (a touch shorter) in 54:25.  My rule of thumb for the cross country course worked out pretty well -- about 10% slower than a flat course.  Finished the 10k in 61:23, which also satisfied my check list for the conservative goal at my February 10 miler.  Needed 72 minutes to be in line with the 2:00 goal; this time also meets the more aggressive notion of a 1:45 10 mile, having needed 63 minutes for that.

Bad news, good news being that my calf/achilles acted up again.  Bad news being that it did so.  The good news being that I've now got a better line on what, exactly, is the problem child.  The major muscle in the calf area is the gastrocnemius.  That is the one I had been focusing on when doing my stretching and Alfredson exercises.  Day after the race with the calf complaining as I started to walk, I stretched (as my doctor had advised) the calf -- the gastroc.  Didn't feel any response, no complaint, no difficulty.  So finally I stretched the other muscle down there -- the soleus.  That is where the problem is (now).    I may well have just rehabilitated the gastroc earlier.  Either way, the soleus is what needs the work now.  It's a little harder to stretch, and a little harder to do the Alfredson exercise for.  Not a lot, but enough that I'd been slack about doing it.

To go back to the more typical theme of this blog, I'll observe that probably a fair number of the people running with me were scientists.  In particular, in earth sciences (lumping geology, oceanography, meteorology, glaciology, paleontology, ...) it seems very much the norm that scientists are physically active in one way or another.  Running is not the only sport.  We also have tennis players, swimmers, basketball players, bikers, ....  Team sports are harder to manage later in life, so most people are doing individual sports, even where we like team sports.  But, whatever it is, we get out and do something.  And this is true whether the person does field work (which would require a degree of physical fitness, just to carry out the job) or sits in an office (as I and my coworkers do).  It might be that scientists in other fields don't do as much sport as earth science types do.  I don't know of any research on it.  But we folks interested in the earth also seem to like to run/walk/bike/swim/... around it.

To turn back for a minute to the running ....  In terms of final race times, this 10k was very slow for me.  When walking, I averaged 16-17 minutes/mile (10-11 minutes per km), which is normal for my walking.  In running, I was around 7 minutes/mile (4.5 minutes per km).  If I were in good shape, which is the goal, I'd have run the whole 10k at about that pace.  For my current training level, with the current goal (that 10 miler, 16.1 km) run/walk is the way to get to the finish of a workout or race in best health.  Best health then means I can get out for the next workout, and the ones after that.  It's getting out consistently that is the key for training.  Given the achilles/calf issues, the next workout is tonight -- swimming.  Rest the calf and work the lungs.  The lungs (cardiovascular system) have a long way to go as well. 

Plus, one of these years I'll be doing a sprint triathlon.  My plan being: don't drown in the swim, don't fall off the bike, and then pass a lot of people in the 5k.

05 November 2009

Experimental reading

I've been reading more general audience science books lately, which is part of the reason for relative quiet here.  But it makes for ideas later.

The first book in the experimental line is geared for middle school to junior high students.  It's perfectly useful for older folks as well.  And it will probably be a good idea to have one at hand for some of the experiments if performed by the younger.  101 Incredible Experiments for the Weekend Scientist by Rob Beattie.  The experiments cover a range of things, from making slime to making a cloud.  Some weather and climate examples, but not especially aimed to that.  The experiment descriptions do also contain a 'how it works' section, which I take to be very important.

The second is geared to an older audience, college age, but I think most experiments and observations can be done by middle school to jr. high students.  They just might want someone else to do the translation to more familiar language.  That's Clouds in a Glass of Beer: Simple Experiments in Atmospheric Physics by Craig F. Bohren.  This is the book (chapter 10) that prompted my Tuesday note.  Its 22 chapters include much more by way of explanation of the science behind what you're observing in doing the experiments, and how this ties in to the atmosphere. 

In both cases, the authors mention some things that the experimenter can use for proceeding to further experiments.  They usually aren't laying it out exactly this way, so keep your eye open for comments like 'best results are for doing X' (using a small tube, for instance, to see surface tension).  That's a sign that you can get different results if you use a larger tube, and it can be informative to see just how much the result depends on the size of the tube.

03 November 2009

How CO2 matters

It turns out that the argument that there isn't a lot of CO2 (true, compared to total mass of the atmosphere) and therefore it can't matter much for climate (false) has been around longer than I had thought.  I was just reading Craig Bohren's book Clouds in a Glass of Beer: Simple Experiments in Atmospheric Physics and he's got reference to it (chapter 10, on the Greenhouse Effect),   The collection of experiments was published originally in 1987, and had evolved over some period before that.  So at least 22 years that the argument has been around.

From page 82 in my Dover edition:There seems to be little dispute that carbon dioxide concentrations in the atmosphere have been increasing because of increased burning of carbonaceous fuels such as coal and oil.  At present, for every one million molecules in the atmosphere, about 340 of them ar carbon dioxide (this is written 340 ppm, parts per million).  To those who snort that 340 ppm of anything must surely be of no consequence, I recommend 340 ppm of arsenic in their coffee.  I don't second the recommendation as the lethal dose is somewhere around 1 ppm.  Craig was being sarcastic, and blunt, two common words for describing him.   The 340 ppm was about the Mauna Loa station's reading for 1981, and the last year that would round to that (nearest 10 ppm rounding) is 1984, so it's probably 3-6 years before book publication that Craig was writing.  It's now past 385 ppm.

For climate purposes, we'll consider two different things.  First is, how can a rare thing (CO2) be important to the system?  Second is, is CO2 really all that rare?

02 November 2009


Yesterday I ran a good, challenging, and distinctly muddy 8k cross-country race.  It's one of my favorite races.  My training, which I've been sparing you, has not been going well, so injury rehabilitation notes are at the bottom.  September was good.  The last Saturday I walked/ran the 5k according to plan, and finished in 28:25.  Not a great time compared to if I were in reasonable training, but a lot better than a few months earlier.  The following Monday, I forgot about a certain gravel path being irritating to my calves, and the fact that I've been on the edge or over it for calf problems (maybe it's Achilles), and went running on the path.  That did seriously annoy the calf/Achilles, which the race hadn't, and October was mostly given over to non-running (and, unfortunately, non-exercising). 

I had, of course, signed up for the cross-country race right before nailing the calf.  On the other hand, even when I was in very good shape (for me), I walked some of the cross-country course.  In years of moderate training, the walk fraction goes up.  This year, it was going to be even more walking, I decided.  It was.  I flew on the downhills (though I can't run for very long at the moment, when I do, I can carry a good pace), took it easy on the uphills (walking more slowly than I would if the cardio system were in condition), and mixed on the flats.  Not a lot of flat to this course.

The plan worked out pretty much.  I did not injure the calf/Achilles, and I did finish the race.  I feel invigorated for getting out and doing more exercise, and, in one of those ironies of peoples' psychologies, am more willing to do 'just' swimming/biking/rowing/....  Final time of 54:37 (my watch -- I didn't start at the front of the pack!)  Which I mention more for establishing it so that when I talk next year of my improvement, you'll know the base.  It would not be unreasonable to improve by 10 minutes in the next year.