Our office view

We are enjoying Day 1 of my research group’s semi-annual writing retreat, this year at the visually inspiring Wildflower house at the Sundance Resort.  Besides finally getting all the papers done we have been meaning to do all year, the retreat also gives us an opportunity to do some group professional development with an outside expert.

This evening, that expert was my spouse and science journalist Genevive Bjorn, who led us through a discussion of the Nature article “Initial sequencing and analysis of the human genome” (Lander et al., 2001, Nature, 409, 860-921).  This is the famous “first human genome” paper produced as part of the Human Genome Project.  As a group of astronomers dissecting the 62-page foundational article of the field of genomics, we experienced the frequent perspective of scientists outside our field trying to understand our work.

Genevive led us through a few key sections of the paper (thankfully not the whole thing), directing us to circle verbs, underline clauses, and comment on the flow of the text and our own attention spans.  Our discussions touched on style issues, grammatical “dos and don’ts”, and the still unanswered question of who actually wrote the article (it has roughly 100 primary authors). Several key revelations emerged from these discussions, points that will hopefully enrich our writing in the future:

Jargon: It is well known that jargon can be confusing to a non-expert, yet is rampant in scientific writing as a sort of “shorthand” for complex concepts, methods and equipment. Yet in addition to reader confusion, jargon can also be a sign of unclear thinking on the part of the writer.  Rewriting heavily jargoned sentences into normal terms can result in a more readable text.  If you can’t do this, you may not actually understand what you are writing about.

Short and long sentences: This is a personal issue for me, as I tend to rewrite some labyrinthine and unparsable phrases in my papers.  My graduate student Jackie Faherty made the point that you should be able to read a sentence out loud in one breath.  Sometimes long sentences are unavoidable, however; listing a series of steps or a detailed train of logic can become lengthy.  These long sentences will almost always be skimmed, so its useful to inset short sentences around them to snap the reader back to focus.  Are you back in focus?  In general, variance in sentence length and rhythm makes for more readable writing.

Subjective and objective clauses: Some long sentences are a combination of a subjective clause (incomplete sentence) followed by an objective clause (complete sentence), sometimes married with a conjunction like “however”.  This combination has the effect of making the subject of the subjective clause less important.  Such a tactic is generally not useful, and it is best to just convey two points on equal footing.  An example of this in the human genome article was the following (subjective clause in red, objective clause in blue):

Because the genome sequence has been released on a daily basis over the past four years, however, we can already cite many direct applications.

Both of these points may be important, but the first clause seems less so and is quickly forgotten  (in addition, the combination of “because” and “however” is a bit odd).  A reworking of this sentence, without change of meaning, might be:

The genome sequence has been released on a daily basis over the past four years, so we can already cite many direct applications.

Now both points are clear and come across as equally relevant.

Active verbs: Genevive commented that scientific papers are frequently written almost entirely in a passive tense.  We scientists think this reflects impartiality in our writing, but it really makes for boring reading.  The human genome article had plenty of good active verb forms: “The genomic landscape shows marked variation”, “Five lines of evidence point to an increase”, etc.  They don’t all have to be in present tense, but they should be about nouns doing something, not nouns having something done to them.

To be or not to be: Definitely not “to be”. The verbs “is”, “are”, “was”, “were”, “will be”, “can be”, etc.  are extremely weak, and should be replaced with more specific and engaging verbs.   In one particularly compelling paragraph there were 11 verbs – “arose”, “emerged”, “take”, “accelerate”, “allowing”, “attack”, “creation”, “require”, “attempted”, “helped”, and “crystallize” – and not a single example of “to be”.  Choose interesting, clear and appropriate verbs whenever possible.

However…: Do you use “however” at the beginning, middle or end of the sentence?   Genevive explained that using “however” at the beginning of a sentence sends a strong message of distinction, useful when one wants to turn the flow of an argument.  The middle “however” is softer, and plays down differences that may not be as relevant to the discussion, or are necessary only for completeness.  Never use “however” at the end of the sentence, however. (oops!)

The “speculative” tense: In the section “Applications to medicine and biology”, the human genome article takes on a very different tone, with phrases such as

…a researcher wishing to perform positional cloning had to generate genetic markers…perform chromosonal walking to obtain genomic DNA…

The use of infinitive verbs creates a sense of detachment by the author from the actions s/he describes.  In this case it works well, as the section describes work that has been done by others as a result of the Human Genome Project.  It can also be used to when speculating about a possible consequence of one’s research, or suggesting future directions (“to boldly go…”).

For me, the take home message from this mini-workshop was to pay attention to verbs, clauses and rhythm. An active voice, with simple sentence construction that varies in tone and length makes more compelling writing – and hopefully more citations to our research!

As our pule to Anuhea, my wife and I composed the following “name chant”, or mele inoa.  It was modeled from the mele inoa written for Barack Obama, “Hiki Maila Ke Ali‘i Ho‘oulu” by (Kumu Hula) Manu Ikaika.  The child’s first name, Anuhea, means cool, gentle rain, so part of our mele refers to her as the gentle rain that nourishes our hearts and outlasts even the strongest storms.  Her second name, Po‘maika‘i, means wisdom, good fortune and prosperity, which we of course wish for her in her life ahead.

If anyone could help translate this completely (and properly!) into Hawai‘ian, we’d be very grateful!

Kaikamahine o Maui (Daughter of Maui)

Look at our daughter, gentle and soothing
A child who brings joy to all around her

A gentle rain that nourishes the land
And helps the seed of love spread in our hearts

Her voice is a sweet melody that lifts the spirit
Her strength is her gentle way

Oh child of the land
Allow the goodness in your heart to flourish

Take courage even as the tempests come
Knowing they too return to the gentle rain

May you grow to be a wise, joyful and creative woman
Infused with the love of your ‘ohana

E ola mai
Ka pono o ke ao
E aloha e
He inoa no Anuhea Po‘maika‘i Fortune

Early results have been spectacular.  A few of the image frames from the first week are shown below.  The high quantum efficiency and low readnoise of the Teledyne Hawaii 2RG detectors, and the excellent image quality of the Baade Telescope, has resulted in higher sensitivity than originally planned.   In the echelle mode, Rob has estimated roughly 20-25% efficiency, including telescope and slit losses, and a nearly-flat zero point of 16-17 AB magnitudes (1 count/sec/pixel) across the 0.85-2.4 micron range.  In plain language, this means we can observe very faint sources – such as a the coldest brown dwarfs and highest redshift quasars – with the echelle mode’s moderate resolution (λ/Δλ ≈ 6000).  The prism-dispersed mode has also proven very sensitive, and we’ve been able to follow-up several J ≈ 19-20 cold brown dwarf candidates from WISE with relative ease.  Look for first science results in the literature soon!

An A0 V "telluric standard" observed with FIRE's echelle mode. The 21 orders span a wavelength range of 0.85 to 2.4 micron from bottom to top. This image is a pairwise subtraction of two 10 s exposures, hence the postive and negative traces.

An unprocessed, 600-second exposure of the late T-type brown dwarf 2MASS 1217-0311 (J = 16) in FIRE's echelle mode. The star's light appears as occasional horizontal streaks in the various orders; the short vertical streaks are emission lines from OH in the Earth's atmosphere. The bright region at top is thermal emission (mostly from Magellan's "warm" mirrors) in the 2-2.5 micron region.

A high-redshift (z=6), J = 20 quasar observed with FIRE's echelle mode. FIRE is sufficiently sensitive to pick up continuum light from this ancient source, enabling studies of the gas along its line of sight. This is a pairwise subtraction of 2 900-second exposures.

Prism-dispersed mode of FIRE of the J = 16.7 T dwarf Ross 458C. This mode gives a lower resolution of 250, but high throughput. This image is a pairwise subtraction of two 150-second exposures, and the wavelengths go from 0.8 micon at the bottom to 2.5 micron at the top.

Acquisition image from FIRE's slit-viewing camera, which has a Mauna Kea J-band filter. The target (left of center) is in the slit, so appears to be split in half. This is a pairwise subtraction of two 5-second exposures.

Fully processed spectra of three cold brown dwarfs, obtained with FIRE's prism-dispersed mode, ranging from J=17 to 18. These data will be published in Burgasser et al. (2010, in preparation)

The roughly twice-daily ocean tides ebb and flow on different timescales and to different heights depending on the relative orientations of the Sun and Moon.  It is the gravitational pull of these the two bodies that are responsible for our tides, a fact first explained by Isaac Newton.  When the Moon is full (and again when it is new), it, the Earth and the Sun are nearly aligned – a situation know as syzygy (one of my favorite words). In this orientation, the tidals forces combine to amplify the tidal surge; we have a spring tide.  Throw in some big surf and an unusually close Moon, and you’ve got quite a shorebreak.

This was the case this morning at about 9am near my home in Solana Beach, when a 7.4 foot high tide came in just a few hours after the full Moon had set (note the lag between the Moon/Sun location and the peak tide – this has to do with how long it takes the ocean water to respond to the tidal force).  This particular full Moon was a special one because the Moon is currently at perigee in its orbit – the closet it comes to the Earth.  This makes the tidal force that much stronger, and results in what is known as a perigean spring tide.

What’s more, we had big swells in the NOAA forecast:

CAZ043-302200-
 SAN DIEGO COUNTY COASTAL AREAS-
 200 AM PST SAT JAN 30 2010

 ...HIGH SURF ADVISORY SATURDAY THROUGH SUNDAY...

 ...HIGH RIP CURRENT RISK...

 .THIS AFTERNOON THROUGH SATURDAY...
 SURF HEIGHT.............5 TO 8 FEET.
 RIP CURRENT POTENTIAL...HIGH. VERY STRONG CURRENTS AND DANGEROUS
                         SWIMMING CONDITIONS ARE EXPECTED.
 WATER TEMPERATURE.......58 TO 60 DEGREES.

 REMARKS...BIGGEST SETS LATE IN THE DAY.

 OUTLOOK FOR SUNDAY...6 TO 8 FEET. MAX SETS 9 FEET.

All this combined to make for some pretty strong waves pounding the cliffsides of Solana Beach.

I snapped some photos of the shorebreak and also brought my audio recorder down to try to capture some of the action in sound (see below).  Most of what you hear is the swish of the waves crashing on shore, followed by the roll of water over the shingle beach rocks as it pours back out.  Occasionally you hear a loud rattle, like someone shaking stones in a tin can.  These are indeed stones – up to 6 inches across – being thrown around the bottom platform of the stairs by the bigger waves.  There are also some low booms when the waves crash against the cliffside, wind blown off the cliffs when large breakers come in, and even a plane overhead!

It’s a beautiful, dynamic ocean to watch.  Be sure to keep safe.

Audio

The following is a 10-minute recording of the waves from the staircase shown in the photos below.  The original mp3 file (9.2 Mb) can be found here.

Images

Shorebreak coming onto shore during a perigean spring tide

Waves crashing on the cliffside in Solana Beach

Explosive surf at the bottom of the stairwell

Pre- and post-surge at the stairwell

A hungry little breaker

Mark's presentation on creating educational podcasts

I’ve just finished watching a video presentation by Mark Pentleton of Coffee Break French and Radiolingua fame (see my prior post on Online French Language Resources), describing how he creates enhanced audio podcasts for language learning. This is an excellent roadmap for all kinds of educational podcasts (with a Mac), such as the Mechanics Minilessons I’m trying (slowly) to produce for my Physics 1A class.

A few good tips Mark gives for making an effective educational podcast:

• Start with a lesson plan created with slides in Keynote or Powerpoint.  You can copy those slides into the podcast track in Garageband for the enhanced podcast.
• Focus on just one or two learning points.
• Engage the listener; for example, by giving them time to repeat or respond.
• Speak in a lively, enjoyable voice.
• Keep the podcast to a ~5 minute review, hitting just the main points.
• Include a jingle at the beginning and/or end of the podcast.
• Be sure to save and/or publish your podcast in multiple formats so it can be accessed in multiple ways.

You can watch the presentation on Mark’s personal blog or at blip.tv

This was part of three workshops ran by Mark at the Apple Leadership Conference parallel with the 2010 BETT conference. (my guess is BETT stands for Better Education Through Technology?)

Mechanics Minilesson #1!

I’m trying a (yet another) new thing for teaching, putting together “minilessons” for my Physics 1a class at UCSD covering specific topics that I don’t get to in lecture, or are worth a little focused attention.  This was a somewhat intensive project as time is short (the quarter has already started!) and I’ve never made a “video enhanced podcast” before, but I think I’ve got must of the bugs worked out.  You’ll nevertheless clearly notice some audio edits.

The audio was recorded on my laptop (built-in mic) into Garage Band; the slides were made in Powerpoint and saved off as individual images, and then individually dragged into the podcast track in Garage Band.  The whole thing was saved off as a AAC encoded .m4a file that Youtube seems to be able to handle.

Have a look, let me know what you think and if you learned anything!  The lectures themselves are also being audio and video podcast from UCSD.

Boy or Girl...or both?

I’m currently reading “The Polynesian Family System in Ka’u, Hawai’i” by ES Craighill Handy and Mary Kawena Pukui.  Kawena (her full name is Mary Abigail Kawenaʻulaokalaniahiʻiakaikapoliopelekawahineʻaihonua Wiggin Pukui) was a very notable and respected author on Hawaiian culture, having written over 50 scholarly works including “the” Hawaiian-English dictionary and “‘Olelo No’eau“, a collection of 3000 Hawaiian proverbs.  If you have any interest in Hawaiian culture or history, pick up anything and everything written by Kawena.

“The Polynesian Family System in Ka’u, Hawai’i” goes into detail on the family structure, practices and environment in Ka’u (the southwestern part of Hawai’i encompassing south point and the active volcanic regions) from early ancient culture until the arrival of the missionaries (who failed to understand the fundamental importance of ‘ohana among the islanders).  One of the interesting sections in the book describes the life cycle of Hawaiians within the context of the traditional family structure, and herein is relayed advice on how to determine if an unborn child will be a boy or a girl (page 77):

“An expert in delivery (kahuna pele keiki) could detect the sex of the expected child by various means: by clairvoyance, by dreaming; or more simply at times asking the mother to extend one hand: if she held out the right it would be a boy; if the left, a girl.”

I’m curious to try this with my pregnant friends to see how accurate the last bit is, and I encourage any readers to try the same.  If nothing else, it is always nice for friends to hold the hand of an expectant mother now and then.

Pe'ahi

Nature laid a huge Christmas present under Maui’s collective trees on December 25th: a 23-foot NW swell that was just big enough to power the local break Pe’ahi, commonly known as Jaws.  While “small” compared to the up to 70-foot waves Pe’ahi is famous for, the swell was still big enough to tap the deep reef offshore and produce some massive, fast-moving breakers, and the off-shore/cross-shore winds stood the waves up just a bit more and provided a nice rainbow breeze. Because of the speed of the wave (up to 30 mph), generally only tow-in surfers tackle Pe’ahi (see why on this video).

Thanks to an off-roading lift from our friends Carl and Ivy, we got down to the lookout above Pe’ahi and took some video footage that you can see in the YouTube clip below.  I strongly recommend watching this while looping “Merry Christmas (I Don’t Want to Fight Tonight)” by the Ramones.

BTW, this is the second time Pe’ahi has broken this month, the last being December 7-8.

I'm good enough, I'm smart enough, and I need to put my Nigerian fortune in your bank account

My blog has (barely) garnered enough hits to get seriously targeted by comment-spam; comments that almost sound like someone is interested but clearly is meant to sell something.  While WordPress is very good about catching these spams, and I generally ditch them without a thought, the most recent one caught my eye as it seemed to provide just about every possible permutation of comment-spam I’ve ever seen.  Reading through them, I realized that while they are hideously repetitive, abysmal in their spelling and grammatical structure, and offensive in their obvious lack of context, they are nevertheless subtly appealing in their effusive compliments and positive reinforcement.  Indeed, I would love if one of my blogs forced someone “to try and do therefore” (whatever that means), and only spam would thank me not once, but three times in a single comment.   If we were to shed the buy-me links, are we left with context-free ramblings or psychologically therapeutic mantras ala Stuart Smalley?  Is this mechanized gibberish or literary art for the 21st century?

I’ve trimmed the massive spam to the 10 “themes” that seem to repeat themselves.  Read for yourself and decide if Deepak Chopra should be worried for his career.

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Demographic breakdown of our survey sample

We have finally finished writing up the results for our survey on perceptions of appropriate behavior between students and advisors for the 2009 Women in Astronomy and Space Science Meeting.  It was quite an effort – 10 scenarios, 579 respondents and over 2000 comments have been merged into a poster (presented at the conference) and a four-page write-up for the conference proceedings.  All the details can be found at:

http://www.browndwarfs.org/wia2009

A short summary of our results:

1. Perceptions of appropriateness vary considerably in the astronomical community at all levels, even for situations that might be deemed “obvious”.
2. Perceptions of appropriateness vary with age and professional status, with younger astronomers and those at earlier stages in their careers (students, postdocs) typically viewing behaviors as more appropriate.  In particular, there were frequently differences in perceptions of appropriateness between students and advisors.
3. On average, scenarios were seen as more inappropriate for student/advisor pairs with different genders than pairs with the same genders. Given that female students are less likely to have a same-gender advisor than male students (see my last blog post on this), this trend may have a negative affect on young women’s student/advisor relationships.
4. Our survey attracted a small fraction (8%) of highly negative and fearful criticism, overwhelmingly from men.  There unfortunately appears to be continued resistance to open discussion of appropriate behaviors between students and advisors.

Comments are welcome!