More on the Naked Mole Rat

I’ve written about the naked mole rat before, about how it seems to be immune to acid.

Well, it turns out it has more tricks up its genetic sleeve.

To compare how the naked mole rat made their proteins, they inserted an engineered gene in the naked mole rat as well as in mice, which allowed them to compare the rate of errors in making proteins. And here’s what they found:

[The naked mole rat] built the engineered protein far more accurately, in other words. Naked mole rats, the scientists found, made anywhere from four to ten times fewer mistakes. Yet the naked mole rats can make their proteins as quickly as the sloppier mice.

This seems to be a fascinating creature the more we study it!

I wonder, though, why other species did not pick up this brilliant piece of evolution. Are there side effects to this that are detrimental, overall, to other species but which don’t affect the naked mole rat? As I said in my earlier post, intriguing.

(Original source, quoted by National Geographic: Jorge Azpurua et al.“Naked mole-rat has increased translational fidelity compared with the mouse, as well as a unique 28S ribosomal RNA cleavage.” PNAS 2013

It looked fine from the outside.’

An old building in Secunderabad collapsed today. The building was used as a hotel, which means that quite a lot of people were inside when it happened. Although some of those people have been rescued, 11 people have already been declared dead, and many more are still trapped inside.

Some points from the report–

  • The hotel was planning to build an oven on the first floor (this is India, which means they’re talking about the ‘second floor’ in American parlance). The building may have collapsed under the weight of bricks being transported for this; the building lacked concrete pillars to support the weight.
  • The building had structural weaknesses, but the hotel was not issued safety notices (recently, along with many other buildings) because “the building looked fine from outside”.
  • In future, all buildings over 60 years old will be given orders for renovation,” says the city planning commissioner.

This is appalling, on a number of counts.

  • Did the hotel seek permission from the city planning commissioner’s office before undertaking their oven-building project? If not, this is gross negligence on the part of the hotel authorities. They are presumably not experts in structural engineering, and should not be in a position to judge the capabilities of a structure.
  • Looked fine from the outside’ is not a structural health monitoring technique. However much the city planning commission tries to blame anyone else, they were grossly negligent too. Laziness in health monitoring of public structures causes lives, and they should know and acknowledge that.

    Health monitoring norms and procedures are in place for a reason, and even the most exhaustive and advanced health monitoring techniques don’t work if ‘looked fine from the outside’ is treated as an adequate criterion.

  • How about, instead of treating every building older than 60 years as needing renovation, the city planning commission does its job of inspecting buildings thoroughly? The problem isn’t that they can’t identify structural flaws—they’ve recently issued notices to 57 other buildings recently. It’s just that this building fell through the cracks, because ‘it looked fine from the outside’.

    The problem with the diktat about 60 year old buildings is that it increases the overall cost of maintaining buildings, and decreases the efficiency of health checks. Even well designed buildings, which are for all intents in great shape, will be forced to undergo renovations, or at least exhaustive checks, when they clearly don’t need them. On the one hand this increases the overall cost of inspection and renovation, because you’re spending resources where they’re not needed. On the other it increases the risk of ‘it looks good from the outside’ assessments. This is because the more the number of buildings tested that turn out to be perfectly healthy, the more the officers are prone to become lax and take shortcuts in making assessments.

    Instead, why not improve the work ethic of the inspection officials? Why not make them actually follow the health monitoring guidelines, and make sure that buildings that actually need detailed renovations are the only ones that get notices?

Can you tell that the line about ‘it looked fine from the outside’ has irked me? It has. Structural health monitoring is extremely important for public safety, and such negligence should have no place here. Compare this with a recent tragic story of a building inspector in Philadelphia, USA, who apparently committed suicide because a building collapsed under his watcheven though he had nothing to do with it:

A city building inspector who examined a demolition project just weeks before a building collapsed at the site and killed six people has been found dead in an apparent suicide […]

This man did nothing wrong,” Mr. Gillison [deputy mayor for public safety and chief of staff] added. “The department did what it was supposed to do under the code at the time.” Officials have said they will make any necessary changes to the city’s building code to prevent such incidents in the future.

Some accidents, like the one in Philadelphia, are unavoidable, and it is indeed tragic when the building inspectors blame themselves. The whole point of health and safety standards, and inspection codes and permissions, is to avoid accidents where possible, and the whole system stands on inspectors and officials with acute eyes and sharp skills.

The collapse in Secunderabad is sad and tragic, but the most important question is and should be—was it avoidable? Apparently it was. Does Secunderabad need a change in safety standards? Only the planning commissioner’s office can determine that—although they’d do well to remove ‘it looked fine from the outside’ from their manuals.

How would you explain to a public audience the importance of interdisciplinary research?

A few years ago, there was a competition of sorts (I don’t remember the details) where the brief was to write 500 words or less on the importance of interdisciplinary research, aimed at a “public audience”. My submission didn’t qualify for final selection, but here it is anyway. :)

Research, development and innovation plays a crucial role in human life. Not only technological and scientific advancements, but the study of the human condition, our societies, our art and culture, and what it is that makes us who we are—it all involves research, and it is all indispensable. From what makes us happy and sad, frustrated or psychotic, to how we can mimic the gecko’s foot, our research is what defines us.

The thing about education and learning is (and this becomes more applicable with more specialized training) that we tend to focus on narrow areas to become experts in. There is no other way—it is quite rare for an individual to be able to master and be experienced in diverse fields. The problem, of course, is that reality is not divided into specializations and ‘majors’, and areas of expertise.

Consider an example: designing an automobile. Does it only involve the aesthetics of how it looks? Certainly not. The designer has to consider the materials that will build the vehicle, and how strong it needs to be. More, there’s also the thought of minimizing air resistance as the vehicle speeds down the road. Even the most elementary consideration leads us in this case to the artist, the structural engineer, and the aerodynamicist. These are diverse areas of expertise, coming together to create a beautiful and functional automobile.

Consider again the psychologist who wants to improve how people manage their life’s problems. She has certain new ideas, and wants to test them out in a variety of conditions, with a variety of individuals. She makes full use of her expertise in psychology, but in addition, she must now extensively use statistics, so see if her results are meaningful! Once again, real life finds a way to bring together two completely different areas of specialization.

The best and the most productive and beneficial research has to be interdisciplinary. This has the benefit of involving individuals who are specialists in their areas, who can bring insight to a problem that no one specialist can contribute. More, the nature of a problem in one area often benefits from knowing how a similar problem is solved in another area. Most importantly, interdisciplinary research means a new body of knowledge in one field can be extended for use in another area—a benefit that wasn’t originally anticipated while doing the research.

Recently, a NASA effort to improve how jet fuels mix inside rockets when burning had an unintended consequence: the technology was used to improve firefighting equipment. Where the old system needed a few men, 220 gallons of water, and 1min 45seconds to control a fire, the new system did it in 17seconds, using 13.6 gallons of water and one fireman.

This is why research must be interdisciplinary—because you never know how the next rocket technology can save lives quicker in a fire, and conserve precious water while doing it.

My scientific writing workflow

I am not fond of MS-Word. Correction: I cannot really tolerate MS-Word, and the only times I really use it are for work, where documents must be shared, modified, commented upon, and tracked for changes between multiple authors, contributors and edit cycles. For those particular circumstances there really isn’t another viable alternative to MS-Word, is there.

But of course, the criteria for my own scientific writing are very different. The only sharing and discussion is with my dissertation adviser, and I can easily handle one other contributor without needing MS-Word. So, of course, I’ve moved as far away from that bloated, cranky piece of software as I can—which is to say, completely away.

Instead, here’s what I use.

My word processor of choice on the Mac is Mellel. It’s beautiful, runs smoothly, and is a joy to use. Its listed feature set is vastly inferior to that of Word, but the features it does carry are executed extremely well. After all, what use are a plethora of features that really make the program bloated and difficult to use? (Please, go read that article; it’s cathartic for frustrated Word-users.) Plus, these features are more than sufficient to meet my needs (and, I think, that of most other scientic writers). I have not felt the need—yet—to incorporate the math rendering excellence of LaTeX, and for all other purposes, Mellel works great.

Mellel in Full-screen mode

Mellel in Full-screen mode.

But here’s the thing. I don’t like writing in word processors. Even in great ones such as Mellel, you’re distracted every once in a while by the formatting, and how the headings are looking, and whether a paragraph should flow on to the next page, and so on. Plus, I’ve developed a universal distaste for proprietary document formats, and this extends as much to Mellel’s proprietary format as to Word’s. I’d like to read and make sense of my documents irrespective of which software I happen to have available for use.

For another thing, I’ve really taken to John Gruber’s simple text document markup format, Markdown, and since discovering it have started using it for almost everything I write—including blog posts like this one. Well, it turns out, there are a number of extensions to Markdown, among which Fletcher Penney’s Multimarkdown must take pride of place. And what do you know—Multimarkdown even has provisions for including references, cross-references and footnotes! How much more perfect can it get!

A related app that has quickly become indispensable for me is Marked. This nifty tool shows a ‘preview’ of what your markdown (or multimarkdown) document looks like, and directly provides output documents in various formats, including PDF, RTF and HTML. This is excellent for quickly creating an RTF document to send to my adviser for review.

Marked preview of this blog post

Marked preview of this blog post.

If you’ve been keeping count, the only piece of software necessary for scientific writing that I haven’t mentioned is a citation/bibliography tool. Endnote is a popular choice for many, and I’m sure it’s pretty good, but there’s a couple other excellent Mac apps for this–Bookends and Sente. Based on online reviews and forums, I ended up selecting Bookends a few years ago, and I haven’t regretted the decision. As a bonus, Bookends integrates perfectly with Mellel, making life very easy indeed. (I noticed while writing this post that Sente’s pricing terms seem to have changed quite a bit since I was researching it, and for all I’d heard, Sente is excellent too.)

There’s another Mac writing tool that’s great for writing long documents, especially where the document is divided into chapters and sections. This is Scrivener. Plus, the basic document format for Scrivener is plain text, which straightaway satisfies my wariness for proprietary formats. Scrivener is also excellent, and would have suited my type of scientific writing perfectly, except for one solitary reason. It doesn’t play well with Bookends. To use Bookends, you have to export your document to an RTF file, and then use Bookends. This means you’re once again left with an extra step of having to include formatting. Not good for me, and Mellel wins. (Scrivener, on the other hand, is the only app in my list that is also available for Windows. If you’re a Windows user, this is an excellent app that you should certainly explore.)

So now that we’ve identified the pieces of software that I use, here’s my workflow.

  • Choose any text-editor (Sublime Text, BBEdit, Text Wrangler, or even the ever worthy, simple TextEdit), and write the actual text in Multimarkdown format. Include citations as required; for the ‘citation’ portion, use any label of your choice, and for the ‘link’ portion, include the identifier string from Bookends that you must use to finally automatically create the bibliography. This way, when I use Marked to export to RTF, my citations are already automatically shown as citations, even though I haven’t done anything with Bookends yet. The bibliography section at the end looks funky, but that’s not a problem with documents in progress.
  • When ready, export the document as RTF, and copy-paste the entire contents into a new Mellel document.
  • For each citation, replace the custom label I had chosen with the Bookends identifier. This is a simple matter of doing a ‘Find-Replace-All’ for each citation.
  • Use Bookends to add the bibliography!

Here are the advantages to this scheme:

  • No use of MS-Word, but you’re able to export to RTF or .doc format, if needed, from Mellel.
  • You’re always able to deal with plain text for all your documents, up until the very last stage where page-setting must come into the picture.
  • Even for a document in progress, it takes only a moment to create a perfectly readable document, via Multimarkdown, that includes inline citations instead of the ugly Bookends identifier.

If you don’t care about using plain text formats, or are simply not comfortable or don’t want to get used to Markdown, just replace MS-Word with Mellel. You can still do all your document writing in a word processor, just like in Word, and you’ll quickly find that it’s way more efficient to use Mellel. You’ll love it—guaranteed.

Chicago Sun-times fired its photographers. How’s that turning out?

A few weeks ago, the Sun-Times fired its entire photography staff, and decided to train their reporters to shoot with their iPhones.

Here’s the result.

(Go visit the link above, and come back to read the rest. I’ll wait.)

Here’s a tip: photography is quite a bit more than knowing how to operate a camera. Anyone can operate a camera; not everyone can be a photographer.

Worse, it’s really, really hard to be on photography assignment and do anything else at the same time. This sometimes gets to the extent of not being able to fully experience the surroundings you’re in, because your mind is constantly thinking of what the best vantage points might be to capture the moments unfolding.

I’m sure it’s the same for journalists and reporters, who are similarly too busy focusing on the news to do the photography job well, even if they are otherwise excellent photographers.

I think we’ll soon find the Chicago Sun-Times reversing their decision and making alternative arrangements. One thing is for certain: the top brass that made the call have no idea about what photography is, and that’s a pity, coming from a group that’s running a newspaper.