Some good bits of advice for writing about science for the public, including this one:
Readers can be very clever, but it is not their job to know all of the words that you and the twelve people you call colleagues made up.
I particularly like the focus on telling a people-centered story. This is so far from the comfort zone for most researchers, but I agree that it’s essential to effectively connecting.
I’ve read more and more in recent years about ‘gamifying’ education, and I have to admit, I never got it. This helps to put it in a little more context:
If what you want is an answer and not an exploration then I don’t recommend pretending you’re looking for an exploration. Students are very attuned to bullshit.
Using gaming to engage students and teach certain skills like exploration and problem-solving makes some sense to me.
It also reminds me of an episode of the Debug podcast I listened to recently, with software developer Mike Lee. His current company made a chemistry game for iOS based on actual chemical reaction modeling. Lee tells the story of creating the game in the interview, and how the lack of access to real chemistry sets for kids these days played a small roll in the idea, but rather than trying to replicate mixing chemicals on the iPad, they approached it from the standpoint of letting the technology do what it’s good at. Taking that approach, it seems like there are so many opportunities to create games that teach, it’d hard to know what to work on next.
You may not realize this, but most fruits and vegetables are still living when you eat them — this is what keeps them from turning mushy and limp. In a new study, researchers from Rice University have shown that these plants are not only living, but their metabolism continues to cycle in response to light/dark periods, influencing their nutritional quality:
“Vegetables and fruits don’t die the moment they are harvested,” said Rice biologist Janet Braam, the lead researcher on a new study this week in Current Biology. “They respond to their environment for days, and we found we could use light to coax them to make more cancer-fighting antioxidants at certain times of day.”
Several weeks ago, the USDA announced it had confirmed the presence of Roundup-Ready wheat in an Oregon field. Roundup-Ready wheat underwent field trials in the late 90’s and early 00’s, but trials were suspended before final approval was granted. The wheat is a match to the exact strain tested by Monsanto. Now it appears somebody may have planted evidence (sorry, couldn’t resist at least one bad pun):
“None of standard farming practices are consistent with, or can explain, a smattering in only one percent of a field or in patches or clumps,” he said. “In our view the finding is suspicious.”
The strain of wheat has never been shown to be harmful, and it carries the same genetic construct as several Roundup-Ready crops that have been approved. But the wheat has not completed the approval process, so the finding caused considerable concern.
The Supreme Court ruled today in the case involving Myriad Genetics’ patent on the BRCA1 and BRCA2 genes. Thankfully, they found that DNA sequences are not patentable because they are a product of nature. The Myriad lawyers had argued that the acts of isolation and sequencing make DNA “inventions” rather than natural discoveries, but the court wasn’t buying that argument.
As I’ve noted previously, not only do I find Myriad’s argument wrong in theory, I also find it misleading in practice. They did not bear any of the costs or risks in actually discovering the sequences in the first place. These two genes were identified in an academic lab at the University of Utah. The original paper describing BRCA1 and BRCA2 acknowledges numerous NIH grants as the source of funding.
Most comments I’ve seen on Twitter seem excited or relieved about the ruling, including one by the NIH Director himself, Francis Collins:
Science writer Carl Zimmer linked to a blog post pointing out some factual errors in the ruling:
Comments on the blog post point out not only factual mistakes, but also an inherent contradiction in the reasoning of the ruling, which is more disturbing still. Details matter, and I’m not impressed by the way the law is (mis)interpreting molecular biology.
It looks like the next version of OS X will improve on AirPlay, turning an AppleTV display into a full-on display for the Mac and overcoming some of the severe limitations I’ve experienced and written about previously.
Here’s what Apple says about the new feature, called AirPlay Display:
With AirPlay and Apple TV, your HDTV works as a fully functional display. So while you’re using your TV to present a slideshow or stream a video lecture, you can take notes on your Mac or chat using Messages.
I’ll revisit this issue when the next version of the OS ships, later this fall.
I’m also reasonably excited about iBooks for Mac, as this will bring the iBooks store into closer feature parity with the Kindle store. As it stands, I can read my Kindle books anywhere, but my iBooks are restricted to the iPad and iPhone/iPod touch. The demo looked good, and the big advantage of interactive, high-quality artwork and feature-rich note-taking could potentially tip the balance in favor of iBooks for me.
I’ve been reading on plant water sensing to get some better background for projects we’re starting in the lab this summer. I came across the photo below in a paper describing the identification of a gene involved in sensing water gradients, called miz1, short for MIZU-KUSSEI1, the words for “water” and “tropism” in Japanese.
The photo shows an elegant experiment the researchers designed to pick out mutants in water sensing. They allowed the roots to grow in a Petri dish along a block of agar (seen in the upper left part of each panel) and into an opening. Normally, an open space in a closed Petri dish would have very high humidity, but they added a solution that soaks up water vapor, so the air was very dry.
The two photos across the top (D1 and D2) show the response of a wild-type root when it grows into the dry chamber — it immediately turns back toward the agar surface, where the water is. The two photos across the bottom (E1 and E2) show the mutant failing to curve back toward the agar. They found this mutant like a needle in a haystack, by looking at 20,000 mutant lines for ones like this, that fail to respond to the water vapor gradient.
The researchers have gone on to study this gene in great detail, and have made a number of exciting discoveries about how plants sense water.
Citation: Kobayashi, A., A. Takahashi, Y. Kakimoto, Y. Miyazawa, N. Fujii, A. Higashitani, and H. Takahashi. 2007. A gene essential for hydrotropism in roots. Proceedings of the National Academy of Sciences of the United States of America 104: 4724–4729.
This summer the lab is using Evernote again as an organizing tool for our work. I upgraded to a premium account on a month-by-month plan to test and see how well it would work, and so far it’s exceeding expectations. We just have a single account for all five research students, with each student maintaining their own notebook within the one account. I like this approach for a community space like a lab because I can keep each computer logged in to the one account and everything’s already there. If they each had their own account, I could imagine students accidentally saving to another user’s account if they sat down at a computer where somebody else had been working.
Each student has a slightly different approach to using it, but they all post their daily activities, experimental plans, timelines, and observations. A couple are collecting primary data in their notebooks. Some attach spreadsheet files with results. Some have uploaded images that they are analyzing. All use it to take notes on the articles they are reading.
Speaking of readings, I also created a notebook for journal articles related to all of the various projects going on. That is the main reason I upgraded, so we could upload and store many PDFs without running into the upload limit. A few of them have found articles on their own and uploaded them, but I’m mostly the one collecting the literature.
Whenever I would come across an important paper in my Papers library, I would hop over the Evernote on the web, create a new note, make an attachment, open the PDF in Finder, and drag it in — a tedious process, to say the least. This would be easier if I logged in to the lab account in the Evernote client on my Mac, but I like to stay logged in to my personal account with that.
As I was looking over the options in Papers, I remembered I could email notes to Evernote through a private address. I created a contact on my Mac called Lab Evernote, pasted in the private email address for the lab Evernote account, and tried it out — BOOM! it worked. I can even specify the ‘papers’ notebook by adding @papers to the subject line. The PDF becomes fully searchable, too, which makes it easier to find later.
I’ve tried lots of different tools for managing lab groups, including blogs, wikis, Dropbox, and network shared folders. I have to say, Evernote is the best tool I’ve found. I can’t think of any way to do it better.
I’m not a huge Twitter user, but it has largely replaced reading RSS feeds in daily use for me. My primary interface for it is my phone or iPad, and I chose Tweetbot as my client a long time ago. I was pleased with it, especially once it could sync my position in my timeline. But over the last few weeks its sync began failing for me, and none of the troubleshooting I tried revived it.
After poking around a bit, Twitterific seemed like the closest competitor in terms of features and polish, so I took the plunge. Sync via Tweet Marker has worked perfectly for me so far, and there are several features that are implemented better in Twitterific than in Tweetbot, in my opinion.
For example, I love how I can set it up to save links to either Instapaper or Pinboard at the same time. It never made sense to me why Tweetbot made me choose between these two services — there isn’t much overlap in the way I use them, yet it lumped these and others into the “Read Later” services. I tend to save lots of links to Pinboard that I think I might want to access later, but Instapaper is only for long articles I know I want to read later, most likely offline. Everything I post to Instapaper I want in my Pinboard account, but I don’t want random links cluttering up my Instapaper reading list. I never found a comfortable configuration in Tweetbot, even resorting to emailing links to my Instapaper account as a workaround.
I also like the implementation of “muffling” better in Twitterific than “muting” in Tweetbot. When I muffle a user in Twitterific, the program displays a single line indicating that the muffled user has posted something, a reminder that I’m still following them and can check back in any time. In Tweetbot, if I “mute” a user, I don’t see anything in my timeline from them.
I just finished chapter 14 of the Objective-C book and realized I haven’t written about it again since my first post. That is partly because I fell out of rhythm during the first week of teaching summer session, and when I returned to it, I had to back up and repeat a few chapters. But I found my groove again over the weekend and am hoping to keep it up as class resumes tomorrow.
It has been exciting learning (again, in some ways) how to do something new. I feel like I learn about new things fairly regularly with my job, but I don’t have that many opportunities to learn a new skill. The doing aspect really started to become apparent around chapters 7 (loops) and 8 (addresses and pointers); in both of these cases, the challenges were surprisingly satisfying to solve. I also spent a good bit of time wrestling with structs and typedefs in chapter 10.
Crossing into the Objective-C part of the book was a welcome change, as I feel more affinity for the syntax and wealth of tools compared to straight C. The challenges feel more like puzzles in part because of this, like all the pieces are there and I just have to learn how to put them together.
The discussion forum for the book is also helpful as a reference and to see how others have solved the challenge problems. I was stuck on how to convert a BOOL type return into the word ‘Yes’ or ‘No’, and someone had posted their syntax for doing so:
BOOL dst = [tz isDaylightSavingTime];
NSLog(@"Is it daylight saving time? %s", dst ? "Yes" : "No");
I continue to appreciate the Kindle version. When I’m working in my office, I can have a browser open to the Kindle Cloud Reader on one side of the screen and Xcode on the other; at home, I can command-tab between them. I’ve read this book on my iPad far less than I anticipated due to the need to practice the exercises while reading. I did find myself doing some review and re-reading on my phone while away from my computer for a few days, which was nice.
Gravitropic 