Writing a Scientific Software Package: Motivation and Background

Posted by admin on April 1, 2018
Posted in: Data Science. Tagged: , , .

Ancient software developers meticulously punched holes in paper cards to write programs.

In the eons before my graduate career, scientists rarely, if ever, publicly distributed their codes, with authors zealously guarding their coding projects.

But just as I was finishing my PhD, it was becoming common for scientists to make the code they developed as part of a published project readily available on the internet. However, the methods to post code online (at least those I knew about) were pretty clunky.

Nowadays, the infrastructure for posting and sharing code online is robust, mature, and relatively easy to use. Consequently, scientists are creating beautiful code repositories, along with accessible documentation.

Open-sourcing code is becoming ever more important: as codes become more complex and capable, readily available codes with good documentation are critical to support reproducibility, a cornerstone of the scientific process. Moreover, federal funding agencies are starting to require investigators to make their code and data products public.

Unfortunately, since I was one of the last generation of grad students before these repositories were common, I never really learned how to distribute and document code properly.

So as part of an ongoing effort to improve my science output (and as an aide to my future students), I’m going to begin a series of semi-regular blog posts describing my process of learning how to write, document, and post scientific code.

A few caveats upfront:

  • I intend to mostly (probably exclusively) write the code in python, which has become (at least in astronomy) the language of choice, so not all of what I write will be generally relevant.
  • I was ushered into the Cult of Mac many years ago, so not all of what I write will be relevant for other OS’s. Here again, though, I’ve found anecdotally that most astronomers use Mac.
  • This blog series is in no way intended to be comprehensive or rigorous. I’m just planning to describe what I learn as I go along, and what time I can devote will almost definitely not suffice to explain all the details, nuances, or technical aspects that intersect the project.

As to the actual science code I intend to write, several years ago my colleagues and I wrote a paper about ellipsoidal variations induced by massive exoplanets orbiting very close to their host stars. The accompanying code, EVIL-MC was written in IDL, an older language still widely used in astronomy but proprietary and requiring the purchase of an expensive site license.

My plan is to convert that IDL code into a Python package over the next several weeks.

EVIL-MC – Ellipsoidal Variations Induced by a Low-Mass Companion


Tidal distortion (exaggerated) of a star (orange-yellow disk) orbited by planet (white/black disk). The plot below shows the brightness variation of the star due to the tidal distortion.

LPSC Meeting – 2018 Mar 18-23

Posted by admin on March 23, 2018
Posted in: Meetings. Tagged: , , , .

I’m sitting in the hotel lobby at the Woodlands Marriott, waiting for my supershuttle to IAH and recouperating from my second Lunar and Planetary Sciences Conference, LPSC. Before I’m whisked away back to Boise, I thought to write about a few of the fascinating and mind-blowing things I saw this week.

First of all, LPSC is an annual conference that focuses on the geology, geochemistry, and geophysics of planetary science. There’s a lot of focus on solar system bodies with solid surfaces, as opposed to the annual DPS meeting, which has a bit broader focus.

I arrived on Sunday evening and dove immediately in, helping with the First-Timers’ presentation review, an opportunity for new-comers to the meeting to have more senior folks provide feedback on their posters or oral presentations.

Monday dawned cloudy, and I sat through several talks about our sister planet Mars. One that stuck out for me was one about field experiments to explain the perennially mysterious gully formations found on martian slopes with sleds of dry ice.

Tuesday saw me in a session on Saturn’s moon Titan, a cornucopia of geology and atmospheric physics. One particularly impressive talk discussed work to understand how methane deluges on Titan modified the surface.

Tuesday evening, I presented our group’s work flying drones through active dust devils.

Wednesday was packed with talks on sediment transport experiments and analyses, attempting to decipher the martian aeolian cycle, including a neat study of time-lapse imagery of martian dunes.

Thursday was packed with Pluto and results from New Horizons. One talk that stuck in my mind was an analysis of landslides on Pluto’s moon Charon, which, frankly, was a little bit of a tear-jerker. Hard to believe that not one hundred years ago, we didn’t even know Pluto existed. Now we’re trying to understand the system’s geology.

Friday morning wrapped up the meeting with a series of talks about glacial geology on Mars, including a fabulous presentation on mysterious geomorphic features on Mars. Even though these features look for all the world like glacial flow, they appear on totally flat ground, where flow shouldn’t be possible.

And now to catch the shuttle.

The Solar System Turns Out To Be A Little Weird (Again)

Posted by admin on March 10, 2018
Posted in: Journal Club. Tagged: , .

Figure 1: The number of planets per star as a function of the planet-star mass ratio as discovered by Kepler. Dark and light blue curves are for stars less massive than the Sun, while the pink curve is for more massive stars. From Pascucci et al. (2018).

Among the mind-blowing discoveries of the Kepler Mission is that the most common type of planet in the galaxy is the super-Earth/sub-Neptune. This unexpected type of planet straddles the boundary between Earth and Neptune in size and mass, and so they may be super-sized rocky planets or anemic gas-rich planets. We just can’t tell.

Stranger still is that this bizarre chimera orbits one out of every four stars in the Milky Way, but we don’t seem to have one in our solar system (unless the Planet Nine hypothesis pans out).

If that wasn’t enough to make you feel like a planetary outsider, a recent study suggests most planet systems have very different architectures from our own.

In their paper, Prof. Ilaria Pascucci of the University of Arizona and her colleagues studied the distribution of masses for planets discovered by the Kepler Mission. Unlike other recent work, though, they considered not just the planet masses but how they compare to the masses of their parent stars.

Naively, we might expect that more massive stars grow more massive planets, and there is good evidence that more massive stars host more massive dust disks. So as long as the processes that make planets are happy to operate around most any kind of star, then we can use the distribution of planet-star mass ratios to disentangle the influence of stellar mass from other effects.

And Pascucci et al. found exactly what we expected – big stars, small stars, they are all more likely to host planets more massive than Earth — but only up to a point. As shown in Figure 1, the number of planets per star increases with the planet-star mass ratio until it reaches about 0.00003 (or 10 Earth masses for one solar mass) — somewhere between the Earth and Neptune. Above that ratio, the occurrence rate drops, meaning more massive planets are less and less common.

But something even more interesting emerged when Pascucci et al. compared their results based on the Kepler Mission to other surveys. Because Kepler is good at finding planets close to their host stars and not at finding planets farther away, Pascucci’s results don’t tell us much about planets in orbits like Jupiter’s. But microlensing surveys, which use a totally different planet-finding technique, *are* good at finding these more distant planets.

Figure 2: The number of planets around each star with a given planet-star mass ratio for planets close to their host star (as found by Kepler) and planets farther away (as found by microlensing surveys). From Pascucci et al. (2018).

Comparing mass ratios from the two kinds of surveys, Pascucci et al. showed more distant planets found by microlensing also show a preference, but for a ratio several times larger than what’s preferred by closer-in planets — somewhere between Neptune and Jupiter in mass, as shown by the figure above.

What does this all mean? Apparently, the universe seems to like make planets about ten thousand times less massive than their host stars, whether the stars are tiny red dwarfs or massive F-stars. And the farther away the planet is from its star, the more likely it is to be more massive.

Standard planet formation theory predicts this trend: protoplanetary disks (from which planets form) have more solid, icy material farther from the host star, and more solids means more planet.

But these results also make our solar system look even stranger than before. In most solar systems, orbits like Earth’s (and closer) are occupied by planets somewhere between Earth and Neptune in mass, and more distant orbits like Jupiter’s are occupied by planets between Neptune and Jupiter.

It’s tempting to speculate that things that make the solar system unique in one way (in this case, the type of planets we have) are related to other unique things (like, the fact that there’s life here). We don’t know much about super-Earths, but if they turn out to be more Neptune- than Earth-like, it’s not hard to imagine they wouldn’t be good places for life to get started.

Life as we know it needs a planet with a solid surface and lots of liquid water, and so maybe it’s not surprising we haven’t found life elsewhere in the galaxy yet: most of the planets are lifeless, gas balls.

Hot Jupiters and Zeno’s Tortoise

Posted by admin on February 23, 2018
Posted in: Journal Club. Tagged: , , , .

With the very first discovery of an exoplanet around a Sun-like star (51 Peg b), astronomers were introduced to hot Jupiters. These totally unexpected planets resemble Jupiter in mass, composition, and size, but they have orbits that nearly skim the surfaces of their host stars. Some of them are even losing their atmospheres under the apocalyptic glare of their host stars.

How their lives began remains a mystery, but we have a pretty good idea of how their lives will end – they will be engulfed or torn apart by their host stars. That’s because hot Jupiters are big and close enough that they can actually raise a tidal bulge on the stars (and we can actually see the bulge in a handful of cases).

This tidal interaction can cause the planets to spiral downward toward the stars, and at the same time, it causes the spins to spin faster until the planet is destroyed by the star. The same tidal effect, just in reverse, is driving the Moon away from the Earth, while slowing down the Earth’s spin. But here’s the key: we don’t know how quickly the planets are spiraling in.

Tidal decay of planetary orbital period over billions of years (Gyrs). From Penev et al. (2018 – https://arxiv.org/abs/1802.05269).

Enter Prof. Kaloyan Penev of UT Dallas Physics Dept. On Valentine’s Day last week, he and his colleagues published an academic love note exploring planetary tidal decay. To do this, they modeled the evolution of planetary orbits and stellar spins under the influence of tides. The tracks in the figure at left show how a planet’s orbital period (or distance from its star) might shrink over billions of years, thanks to tides. The clump of spaghetti noodles in the figure shows that evolution for a range of assumptions about the rate of decay.

By comparing the stellar spin rate and planetary orbit predicted by their model to those we actually observe for each system, Penev and colleagues showed that the tidal decay rates might actually slow down as the planets approach their stars. So perhaps instead of an reckless death dive into the star over a few million years, the planets make like Zeno’s tortoise and tiptoe closer and closer without plunging in.

Upcoming surveys such as the TESS mission and the Large Synoptic Survey Telescope may soon allow us to test whether planets do or do not plunge into their stars. Theoretically, we expect stars that eat their planetary children dramatically brighten up by a factor of 10,000 over a few days – faster than a supernova brightens but nowhere near as bright. These surveys might able to see stars engaged in this act of cosmic infanticide.

Observing the Atmospheres of TRAPPIST-1 Planets

Posted by admin on February 16, 2018
Posted in: Journal Club. Tagged: , , , .

Comparing the TRAPPIST-1 system to the solar system. From http://www.spitzer.caltech.edu/images/6294-ssc2017-01h-The-TRAPPIST-1-Habitable-Zone.

In astronomy, when you look for evidence supporting a hypothesis and don’t find it, that’s called a “null result“. The null result is usually not all that exciting, but last week, an attempt to detect the atmospheres of potentially habitable exoplanets came up null, and that, as it turns out, may mean the planets are habitable.

In a recent study published last week in Nature Astronomy, Dr. Julien de Wit of MIT and colleagues observed the transits of four of the planets in the TRAPPIST-1 system. The discovery of this system was announced last year and generated a lot of interest — it comprises seven Earth-sized planets orbiting a red-dwarf star, and at least four of the planets orbit in the star’s habitable zone. So astronomers are scrambling to determine the climatic conditions on these planets and find out whether they host life.

Key to those conditions is the composition of the planets’ atmospheres, and the best way to probe atmospheres lightyears distant is to detect the colors of the planets’ shadows as they pass in front of their host stars, i.e. as they transit. When light from the star passes through a planet’s atmosphere, the cool gases can imprint spectral signatures, which we can then detect using a very sensitive telescope — de Wit used the Hubble Space Telescope.

Now, even though the TRAPPIST planets are Earth-sized, that doesn’t mean their atmospheres are Earth-like — astronomers have founds lots of weird planets in the last several years. The atmospheres could be hydrogen-rich like Jupiter, hydrocarbon-rich like Neptune, or rich in nitrogen and oxygen like Earth.

In principal, each kind of atmosphere would give a distinct spectrum, but in practice, atmospheres rich in hydrocarbons or nitrogen, potentially good atmospheres for life, are difficult to detect because they are weighty and drape over the planet like a heavy blanket. By contrast, a hydrogen-rich atmosphere, although probably not great for life, can be light and fluffy, relatively easy to detect.

When de Wit and colleagues analyzed transit data they collected from Hubble showing transits for planets TRAPPIST-1 d, e and f, they found no atmospheric signals down to their detection limits. The spectra below show this lack of atmospheric coloration and what they would have detected if the atmosphere was hydrogen-rich.

Now, of course, this non-detection does NOT mean the planets are habitable or even Earth-like. As the figure shows, their atmospheres could still be radically different from the Earth’s (drenched in water vapor or carbon dioxide-rich like Venus), but it rules out the possibility that they are Jupiter-like — potentially good news for life there.

Very likely, when the James Webb Space Telescope finally launches next year, the TRAPPIST-1 system will be one of its first targets. JWST’s vastly improved sensitivity will help reveal not just a potent null result for the TRAPPIST-1 system but may also reveal the glimmer of distant Earth-like worlds.

Spectra for TRAPPIST-1 d, e, f, and g. From de Wit et al. (2018) – https://www.nature.com/articles/s41550-017-0374-z.

Inclusive Teaching – 2018 Feb 9

Posted by admin on February 13, 2018
Posted in: Brian's Presentations. Tagged: .

I’m a participant this academic year in the Boise State Teaching Scholars, a program to promote the scholarship of teaching and learning. As part of that program, participants are asked to give presentations on various topics, and I led a discussion last Friday on inclusive teaching. In case the presentation and the links provided are useful to anyone else, I’ve posted it below.

Wednesday’s Super Blue Blood Moon

Posted by admin on January 29, 2018
Posted in: Public Outreach. Tagged: .

Total lunar eclipse on 2015 Sep 27. From wikipedia.

As a follow-on to our spectacular total solar eclipse last August, North America will be treated to a total lunar eclipse early on Wednesday (Jan 31) morning. The eclipse will start about 5:51am MST and will end just after 7a. No special equipment needed to observe the eclipse. If you can see the Moon, you’ll be able to see the eclipse.

A lunar eclipse occurs when the Moon passes through the Earth’s shadow (as opposed to a solar eclipse, when the Earth passes through the Moon’s shadow). Because red light from the Sun is refracted around the Earth by the atmosphere, during eclipse the Moon can appear murky red (similar to why sunsets appear red).

In fact, Wednesday’s eclipse is triply special — not only will the Moon pass through Earth’s shadow. It will also pass near perigee (the closest point in its orbit to the Earth), making the Moon appear especially large and bright in the sky (about 14% larger and 30% brighter). It will also be the second full moon in the month of January, making it an unofficial blue moon.

These three celestial events aren’t all that rare individually — lunar eclipses happen roughly every six months, supermoons happen every few months, and blue moons happen every two to three years. The confluence of all three is also not all that rare — the last time was in Dec 1982. So while Wednesday’s sky show may be impressive, it will not be the harbinger of doom claimed by some false prophets.

For Boise, though, another more mundane event may spell doom — we’re slated for clouds that morning, and no sky = no eclipse.