Weekend shorts (including Japan earthquake links)

By Grant Jacobs 12/03/2011

A collection of links and comments on articles and discussions elsewhere that might interest my readers. I hope there is something here for everyone.

This post has been overtaken by the massive earthquake in Japan last evening, hitting with over 1000 times the force of the Feb. 22nd Christchurch earthquake. An early collection of images can be seen on the LA Time website (who also brought an excellent photo collection for the Feb. 22nd Christchurch earthquake); another can be found at the Boston Globe. The tsunami is clearly a major disaster, and has breached whatever tsunami walls were present. Japanese rescue workers assisting at Christchurch are travelling back to Japan to assist.

For New Zealand, Civil Defence statements on television are that the tsunami will hopefully only have an impact in upper Northland and mainly on boaties (e.g. strong currents). Advice is to stay away from beaches and rivers near coastlines, not to go swimming (etc.) and not to go sightseeing. The full advisory is available at the Civil Defence website.

ScienceInsider explains that the event was larger than was expected to occur. (‘And Japan’s latest national seismic risk map gave a 99% chance of a magnitude-7.5 or greater quake occurring in that area in the next 30 years, Geller says.’) John Horgan writing at Scientific American offers a few words on earthquake prediction and warning.

My thoughts and best wishes for all those in Japan.

The remainder of this post was written prior to the Japan earthquake.

Drawing the map of life - cover

The Human Genome Project celebrated it’s tenth anniversary a little while ago. Michael Morgan’s review of the Victor McElheny’s book, Drawing the Map of Life, has itself a potted history of the early stages of the project, one well worth reading. (I admit to a slight vested interest: I was a student at the institute that John Sulston worked at, at the time.)

Still on the subject of genomes, Emily Willingham writes about her and her partner’s experience of personal genomics.

Discussions You could try an interactive involvement and encourage those uncertain about Ken Ring’s earthquake ‘predictions’ to look more closely at his claims on his Facebook page. (Be warned, though, that this Facebook group has an element of a ‘fan’ scene with a few individuals thinking it their job to muscle out those who offer constructive criticism or point to sources of information.)

While we’re on the subject of earthquake predictions, the US Geological Survey has a page of articles about earthquake predictions, including a ‘web’ copy of the Geller and colleagues letter to Science and a seven-week long debate through the letter column of Nature.

I previously posted a few photos of stunning places to read. This series shows more libraries, with more of a focus on architecture. The first in the series has similarities to the interior of the University of Otago main library. Columbia’s Biblioteca España (photo 3) looks like, well, a geometric rock. (But where are all the windows??) The interior of Brazil’s Real Gabinete Português de Leitura with it’s four story room (below, photo 13) looks like a set for Harry Potter.

brazil library

Apple Mac-owning readers might want to read Martin Fenner’s review of the reference manager / bibliography software Papers 2. I’ll be looking into this application myself. I don’t want to get ahead myself–I haven’t looked at the program first-hand–but in addition to PDFs, you can apparently manage all your other documents too – on-line articles and emails as well as your off-line word processor files, graphs, etc. There is an accompanying iOS application.

A virus that gets viruses with transposon-like genes ArsTechnica has alerted me to an interesting finding via their brief account of research reporting a virophage that infects the CroV virus. The Cro virus is a large marine virus with a more than 700,000 base pair genome. That’s more DNA than in some bacteria, a whopper of a genome for a virus. The new study reports that this virus itself is apparently infected by a virus, a virophage, that’s been named Mavirus (’Maverick virus’). What’s interesting is that the virophage genes more closely resemble those of a transposon, the classic mobile genetic element, than those of a virus. (There’s more to this than meets the eye, I think. I’d write this research up in more detail myself if I had time (and motivation!), in the meantime these pointers will have to suffice; unfortunately for readers the original paper is paid access only.)

Regular readers will know that I have previously (two links!) touched on career issues for science graduates. There has been on-going discussion on-line about post-doc careers for some time, with recent contributions from Jennifer Rohn, writing at Nature–with extensive commentary that follows–Steve Caplan and ‘Mike’.

Bora Zivkovic has recommended that all those interested in science read Polanyi’s The Republic of Science (1962) once a year. I have to confess I haven’t read this through myself yet–it’s long piece, but thus far while a little abstract it looks one worthy of a quiet day in the weekend.

(Edited to remove some blank lines the WP editor has somehow entered. It’s like that sometimes…)

Other articles on Code for Life:

On alternatives to academic careers and ’letting go’

Deleting a gene can turn an ovary into a testis in adult mammals

Map shows New Zealand with lowest death rate on earth in 1856, over 11 in 1000 dying

Bibliographies-why can’t research papers self-document what they are?

0 Responses to “Weekend shorts (including Japan earthquake links)”

  • I’m just going to add a few more links to the Japan earthquake here for those that have come to this post for that reason:

    Video footage of tsunami (note automatic earthquake warning system laid over screen):


    The Guardian has an FAQ-styled article:


    This via twitter (@sciam is Scientific American magazine):

    @sciam: Scientists on CNN now is saying entire island of #Honshu #Japan moved eastward by 8 feet (2.3 m)

    There are several articles explaining how Japan’s high building standards, etc., will have limited the impact, but I feel reluctant to post these at present.

    Civil Defence alerts in New Zealand continue. Stay off beaches, away from rivers near the coast and out of the water.

  • More links; I’d shift these to a separate post, but it’s the weekend and I’m being lazy…

    The Science Media Centre has a “backgrounder” page:


    IEEE Spectrum have an article about tracking tsunami across the Pacific Ocean:


    This Washington Post article writes about earthquake prediction in the context of M=8.8 in Japan (mentioning Christchurch in passing):


  • eviltwit,

    Did you check out the ones I showed last year? They’re Baroque, wildly ornate things. Personally, I prefer ones with good places to read rather than just look at, but they are stunning.

  • Hey Grant: No. i just found Sciblogs during the whole Ken Ring thing. Wow. I’ve been to the Austrian National Library. They’re just gorgeous. I’ve been to Lisbon (when I was 10), but not to Coimbra (my dad was Portuguese) it does seem like a place he would have taken us if we’d gone there on that trip. However, I, also prefer places you can read in:) I really love the one in Melbourne. I would totally go there all the time!

    Thank you for that link on the Japan earthquake not being related to the CC earthquake. I was pretty sure they weren’t, but it was good to read why.

  • I lived in the UK for 4+ years (Ph.D. and all that). I didn’t explore the libraries or museums enough—a bit of a shame. (I spent more of my time away from work outdoors anyway.) I did get to read in some of the small old college libraries in Cambridge, though, which was great. Leather-bound books, ancient astronomers globes, a bay end to yourself looking out on a garden, etc. Sounds like you’ve travelled a fair bit. Wish I had time and money to travel more. It’s why I leave my computational biology consultancy work open to offers from interesting locations…!

  • I’ve been to the UK several times, but have never been to Cambridge – it kind of holds a certain scholarly romance for me. – all the things you mention sound fantastic! Also, I watched every single episode of Inspector Morse, so I have to go someday!

    Speaking of traveling, we were in Tokyo a month ago. We stayed on the 44th floor of a hotel, and in the middle of the night, we had an earthquake (unsurprisingly). I tell you, I think those buildings have to be built well. I think it was a 5.5 or something. We super-swayed, and it was a bit jarring, but wow, when I think of an 8.8 – and they felt it all that distance…

  • Cambridge is an excellent place to wander around, esp. if you have access to the colleges as (grad) students do.

    Another Morse fan, eh? 🙂 Lewis is on tonight, as it happens, but I prefer Morse. I doubt I’ve watched every show, I’d need a DVD collection to do that!

    I’ve read a couple accounts of buildings in Japan moving side-to-side strongly in the earthquake and there is video of it on YouTube somewhere (from outside showing the high-rise buildings moving). One account claimed his building shook for 30 minutes. (DailyTelegraph, Australia; I’d want to confirm that, but there you go.)

  • Super Morse fan:) I’ve watched every single one. I totally bawled my eyes out when he died. I like Lewis also – it does have the same feel, but slightly different. I love that they still have the same doctor on. Ooh is it on tonight? (I’ve seen them all already, but I need my Oxford fix!) You need access? Hmm. I’ll just have to go back to grad school then. Good thing I still look like one!

    30 minutes. Yikes. I think I saw that video. I’ve been watching the Japanese news livestream on TBStv . http://www.ustream.tv/channel/tbstv#utm_campaign=twitter.com&utm_source=4939766&utm_medium=social The footage has just been unreal.

  • Another source of science-related articles/blog posts on the Japan M=8.8 earthquake is the ‘All-geo’ site that collates geology blogging: http://all-geo.org/

    As one example from that site, is this from Highly Allochthonous looking at what caused the earthquake:


    (In the links at the end is a dismantling on the notion that a ‘super moon’ is a cause or major contributing factor; shades of Ken Ring, for New Zealanders, etc. Oh, heck, here.)

    The BBC website has a rolling update (as do other news sources): http://www.bbc.co.uk/news/world-middle-east-12307698

  • You need access?

    You can walk into the main areas, but there are private gardens and libraries, etc., you can’t just walk into. At least not “officially”.

    Some of the footage is remarkable, if awful.

    The Japanese have a warning system that I wrote about it some time ago & forgot to link to it in case people were interested (this was written in lighter times and so may appear slightly flippant in today’s atmosphere, it wasn’t written with an unfolding disaster in mind):


    One of the things that struck me was the presenter is warning—ahead of time—that one is to strike.

  • CNN rolling news snippets:


    Video of high-rise buildings swaying during earthquake, YouTube:


    Another (long) article on warning systems from Scientific American (by Richard Allen):


    Peter Griffin has also added a post on the same theme:


    There’s even a short article explaining in surfing terms why trying to surf a tsunami is daft:


    I think with that I may sign off from the Japan earthquake. As much as I feel for the Japanese, I need a break from disasters. (And astrologers exploiting them, as much as I object to Ken Ring trying to claim after the fact that this earthquake was consistent with his tables and writing.) Plenty else has happened over the past few days, after all. Among this is a study comparing the outcome of those who vaccinate and those who don’t, a topic I’ve written about before. There’s an entertaining “for the masses” short video on neuroscience that I’ll put up shortly. And a few thoughts on TED lectures I hope to write about. And I have a whole collection of science articles that lie in notes or a half-written state. (But then, as I’ve previously blogged, these take time.) You get the drift…


    There are reports of an explosion that has caused the “outer structure of building that houses reactor at Fukushima plant appears to have blown off.” (Quote from Reuters, see source below.)

    Suggestions are that it may be hydrogen used to cool the plant.

    This is unconfirmed at this stage, but no doubt this will draw a lot of attention. There are conflicting accounts of what this may mean, but they seem to err on the side of that things will work out fine. Let’s hope that’s that story.

    MSN is currently carrying this article on the subject:


    (via Reuters; H/T @kubke. OK, Fabiana, how do you stay so on-the-ball?!)

  • Excuse the melodramatic ‘developing news’ in my previous comment. I try to verify what I write and I just wanted to make clear the details were still emerging.

    Slate has a video of the explosion (also hosted at Reuters and elsewhere): http://www.slate.com/id/2288171/

    Scientific American have a number of articles covering the nuclear plant and the earthquake itself, with an emphasis on ‘earthquake’ as opposed to tsunami but I guess that reflects American interests.

    I’ve tried finding MMI values (a measure of ground shaking experienced) for the both the Honshu and Christchurch/Lyttelton earthquakes so that I might compare them, but I’m currently finding wildly conflicting numbers, sometimes even within the same source.

    RMS reports indicate that that Honshu experienced shaking of approx. the general scale (VII) as central Christchurch/Lyttelton (VIII), perhaps slightly less. The area of strong shaking is much greater in Japan: 100s of km vs. a few. But as I say, I’m seeing conflicting values out there.

    The RMS reports are here:

    RMS Christchurch/Lyttelton:

    RMS Honshu:

    This large PDF from iris.edu has pulled together a lot of geological/geographical information (it’s well worth browsing):


    Their account of the Christchurch/Lyttelton earthquake is here (including CCC liquefaction hazard map):


  • wooo! thank you for all the links – i ended up directly to this post from my blog:)

    it’s gotten kind of out of control for me, too, posting stuff, but i can’t help it

    Really interesting MMI stuff – i was wondering, actually because i’d just read that the general scale of shaky was less in Japan

    i’ve already seen so much panicking on the nuclear plant developments already. one of my friends on facebook practically had a meltdown (excuse the expression) on her wall, which was actually good for me, because it sent me scurrying for facts (which usually have the effect of making me feel better, even if the news isn’t great) – that link you cited, i’ll post right on my blog – thank you

  • Hello eviltwit 🙂

    There are a number of articles explaining the issues of the nuclear plant around now. One is on Boing Boing, of all places, from memory.

    I use bit.ly as it’s 5 characters shorter than tinyurl.com. Just sayin’…

  • oh yeah. i saw that article on Boing Boing. i noticed most of the MSM US-based reported was so totally over-the-top – i stopped reading them – i mean, i’m glad to know the WorstCaseScenario, but i really don’t need my friends to be scared to death by super hyped reporting of it!

    they get smaller still? I’m so behind when it comes to tinyurls! can one ever keep totally up-to-date with this stuff? it’s like a never ending battle! i mean, i have to tear myself away from my laptop sometimes! lol!

  • This amateur video gives a startling first-hand on-the-ground view of the tsunami. What impresses me is how modest the water movement is at first, and how long it goes on. The notion of a “wave” doesn’t describe this. It starts with what looks like a water main burst, with—minutes later—whole houses being lifted off their foundations and carried off.


    [Corrected mis-edit.]

  • That’s startling all right, Grant.
    Closer to home, there has been a project in Island Bay to paint lines on the roads indicating a tsunami safe zone.
    Some of the comments below the story are predictably hostile to this initiative (e.g. Pete says “Oh this is some kind of make work scheme isn’t it ? from the Wellywood sign crowd no doubt. They are going to have a hell of a job painting all of Miramar to Haitaitai, after their tokenism in Island Bay. And if it doesn’t go ahead EVERYWHERE, they can remove their tagging from Island Bay thanks very much.”)

    It would be nice to think that the Petes of Island Bay, and elsewhere, have some pause for thought upon watching footage of the tsunami in Japan.

  • Hi Carol,

    Saw the ‘painted line’ on TV when it was first done. Mixed reactions at the time, eh? One of my early tweets in response to the Honshu earthquake was to the effect “Anyone complaining about the tsunami lines in Wellington now?”

  • Well, exactly, Grant.
    It was also quite unfair of Pete to describe the Island Bay project as ‘tokenism’. It was a pilot project, and was the result of quite extensive consultations between GNS, the WEMO office and the Island Bay community. The plan is to roll out the zones acros the neighbouring south coast suburbs – but the point is that the groundwork needs to be done first.

  • While I’m here, I’ve a post collecting a few videos and articles about tsunami and earthquake warning systems going up later this afternoon sometime.

  • Hey. I don’t know if this is where this link belongs, but it is related. Been seeing a lot of hysteria about the nuclear plants. Ran into a solid post entitled, “Why I am not worried about Japan’s nuclear reactors” by a research scientist (mechanical engineer) at MIT and further maintained/edited by the scientists at MIT’s Dept. of Nuclear Science and Engineering. You probably all already ran into it, but I thought it was worth mentioning. http://bit.ly/mitjnr

  • Thanks, eviltwit.

    I’ve run into a few myself, e.g (in terrible gray-on-black; why do some people do this?!*) –


    One catch for me is that I can’t easily assess which ones are on the money, as it were, as I don’t have a background in nuclear physics or nuclear power plants. It’s frustrating to see the mainstream media reports. A pattern I see with MSM is of reporting as they see, then correcting later, partly because of their mad rush to get things out first. I could warble on, but it’d end up being a rant that would be better placed in it’s own blog post.

    * Fortunately Safari’s Reader option presents things in black-on-white!

  • thank you, Grant – another one to add to the links – here’s yet another one (by an Aussie), who basically explains the MIT article in a way that people can more clearly understand it – i know i appreciate that! – http://bit.ly/mitjnrst

    well, not being any kind of scientist, so i’m doing the best i can to stay informed by trying to pick people/scientists who i think would be informed (like you all) to find accurate information

    yeah – the MSM, especially CNN, which i have NOT watched, is doing a great job of spreading the hysteria *cue more inane conversations with my friends who’d rather go with their gut feeling on things*

    gray-on-black – awesome for photo blogs, not so great for text blogs!

  • Nature’s The Great Beyond blog has a few more details and figures for the nuclear power plant issues in Japan (note link to PDF with details for each plant):


    If you look under ‘Recent posts’ to the left of this article, you will see earlier posts they have put out on this topic. My subjective (and naïve) impression is that these articles take a harder view than others presented elsewhere. My impression is that events at BWR4 may have altered the situation for at least in the immediate environment of the nuclear plant. You will note in the PDF they link to, that the ‘Containment Integrity’ is listed as ‘Damage suspected’.


    This biologist would now like more details… hopefully these will come without over-dramatising the situation, although I suspect that is not something to hold my breath over.

  • Rats, just to be clear: I don’t mean any slight on eviltwit in my previous post. The thing is, are we to believe ‘Genius Now’ or ‘The MIT guy’?

    Personally, what I’d prefer to first see is hard data from Japan, then work back to the background to place that data in it’s context.

  • Very interesting Grant, thanks for the head’s up. See, this is why I run things by other people. (I did check out the Josef guy on the LAI website before hand, and his CV.) However, I have noticed that there is actually a link to the WP site from MIT:NSE’s official website (and also noticed that the WP site says it’s now run by students at MIT). That article you cited is the only one I can find that is like it, but I am continuing to investigate (and holding off posting it). So, the crux of it is that article is that Josef’s article is basically nuclear power propaganda in the vein of making us think this whole thing isn’t bad at all? Because of who’s involved with LAI – including Siemens. That’s not really what I got from the article, but okay. I found out more about the workings of the containment stuff, but as for the danger issues, that definitely remains to be seen. All this noise about Chernobyl (I have been reading, that even at the worst case scenario it is impossible to be as bad as that – although it won’t be good) was making me cringe.

    What are the thoughts on nuclear energy anyways?

  • p.s. i did learn something, though. i don’t know if you know who Bill Nye the Science guy is in the US. apparently, CNN had him on as an expert, which is pretty hysterical (i know which network NOT to watch). he said that there was Cesium in the control rods used to stop the chain reaction in the core. but, after reading the article at http://bit.ly/mitjnrst and his subsequent updates (and checking with other articles), i already know that this Bill Nye was misinforming the entire country as Cesium is a common product of nuclear fission, and not a material used to control it. This is why I’m trying to stay informed. How do you know who’s doing the misinforming when you don’t even know what the heck people are talking about. My brain is fried!

  • You’re right, Bill Nye stuffed up: Caesium 137 — with an ‘a’! — is radioactive with a half-life of about 30 years.

    I don’t “know” Bill Nye, but I’ve heard the name with “mixed” opinions from others in science communication circles.

  • Ha! Well, I still have to get my Britishy spellings all down. So,, I read that Caesium *lol* 137 decays into Barium 137, Is that they same Barium isotope they made me drink when I had to go get a Barium stomach test several years ago. (I have IBS) They made me drink this white, thick, pepperminty liquid with the Barium in it and then turned me upside down on this table thing and then i had to walk around for 20 minutes while the radioactive particles made their way down my digestive tract. If so, it’s certainly a small world of elements. Lol!

    p.s. perhaps i didn’t go quite as far as i should have, checking out the sources of that article. no worries. it still holds some validity to me in that it got me reading. a lot. i did try to check out Genius Now. but, there’s not much to go on, except for this http://geniusnow.com/category/featured/ – which is…interesting, to say the least.

  • It did miss saying that he did actually did study mechanical engineering (although didn’t major in it). here’s the blurb on LAI

    they didn’t actually debunk him, as much as say he’s a Risk Management person and was probably wrong on his conclusion was “no danger part” (which, frankly, the degree of which was going to remain to be seen anyways) – my thing is if the rest of the explanation of what happened correct, than i did learn something – and i ended up linking to the other guy’s blog on Great Beyond instead – for the info. and reading other stuff also

    I think i’ve seen far worse misinformation on many of the MSM outlets

    (Genius Now turns up in the comments, btw)

    it’s a wait and see situation now, but at least i know what the science behind it was

  • hey:) thanks for the links to the pics – i’ve shared them on FB – the before/after ones are particularly heartening to see after such a catastrophe

  • eviltwit,

    They’re amazing photos, just the scale of the thing and the little and not so little touches. That tourist boat resting on top of a two-storey tourist building is startling.

    I see from your blog that you’re in Europe – lucky sod. I travelled there a little as a Ph.D. student (I was based in England). Still fancy a job overseas in many ways, but perhaps what I really want is a gazillion dollars and I’d live here and travel whenever I wanted 🙂