science in Latin America

Ten years ago, when I set out as a full-time freelancer, I was hoping to make science in Latin America a geographic focus of my work. I set up a web portal called "ciencia sin fronteras" (the domain name is now used by somebody else for a different project), and I did cover some science stories over the years, but it didn't really take off.

I'm now hoping to revitalise this side of my work a little bit (although on a modest scale) by introducing a new tag for this blog, indicating all science news that is related to Latin America, i.e. both research performed there environmental issues that affect Latin America, like rainforest conservation. The tag is LA_ciencia (though blog entries will also be tagged by country).

To start things off, I I'm compiling here a list of some of the relevant pieces I have published over the last 6 years, sorted by country (will add items to the list as and when I remember them!):


Bolivia

--2008--


1. Gross M:
   Chemistry World 11.08. (online only)
   Hot chillis evolved to kill fungi
   [free access]

Brazil

--2009--


1. Gross M:
   Current Biology 19, No 11 (09.06.), R427-28
   Embryonic development
   As the UK updates its pioneering Human Fertilisation and Embryology Act, legal boundaries for research in the life sciences are redrawn in other countries as well.
   [restricted access]
   

Colombia

--2006--


1. Groß M:
   Biologie in unserer Zeit 36, Nr 4, 17
   Humanevolution: Kolumbien nach Kolumbus
   An English version of this piece appears in The birds,the bees and the platypuses, page 154: Colombia after Columbus
   

Costa Rica

--2009--


1. Gross M:
   Current Biology 19, No 21 (17.11.), R965
   Coffee growers feel the heat
   Coffee and tea farmers already appear to be suffering from the effects of climate change.
   [environment]
   
   [abstract and restricted access to PDF]

Cuba

--2004--


1. Groß M:
   Nachrichten aus der Chemie 52, Nr 7/8, 812-814
   Die zweite Revolution: Biotechnologie in Kuba
   
   [@][@]
   
   

2. Gross M:
   Current Biology 14, No 11, R401-R402
   Fighting isolation
   





3. Gross M:
   Darwin No 2, 22-26
   Biotecnologie -- l'altra rivolucione cubana
   





4. Gross M:
   Chemistry World 1, No 9, 19
   Cuba synthesises blockbuster vaccine





5. Groß M:
   Spektrum der Wissenschaft Nr 10, 23
   Kommentar: Der Fall Kuba. Der Inselstaat konnte sich mit Biotechnologie aus der Isolation befreien.





6. Groß M:
   Chemie in unserer Zeit 38, Nr 5, 306-307
   Biotechnologie in Kuba: Mangomittel gegen Altern und Aids





7. Gross M:
   Chemistry World 1, No 11, 38Biotechnology: the second Cuban revolution
   



--2005--



8. Groß M:
   Biologie in unserer Zeit 35, Nr 4, 227
   Arzneimittelforschung: Impfstoffe aus Kuba





9. Gross M:
   Chemistry & Industry No. 15 (01.08.), 16-17
   Fortress of success: Biotech companies in Cuba are making the best of what they have



--2006--



10. Gross M:
    Chemistry World 3 No. 1, 7
    Chemists queue up for Cuban collaboration





11. Groß M:
    
    Chemie
    in unserer Zeit 40, Nr 1, 68-71
    Kuba -- Improvisationstalent gefragt





12. Gross M:
    Current Biology 16, No 3 (7.2.), R66-R67
    Cuban efforts bolstered





13. Gross M:
    Oxford Today 18, No 3 (Trinity 2006),
    Chemistry in Cuba





14. Gross M:
    Chemistry World No 10, 23 (online: 4.9.)
    Antibodies in the greenhouse
    [@@]

numerically confused

I'm getting the impression that the English language is getting increasingly mixed up at its interface with maths, i.e. the use of numbers, singular, plural, etc.

Examples:

* Nobody agrees what speciation means (quote from a news feature highlighted in a read box, Nature last week, page 867). "Nobody" means: Not a single person, mathematically: 0 Surely, to disagree, you need at least two people, so every single person on his or her own would be in agreement with the rest of the set, i.e. him or herself. So the smallest possible level of agreement, if you have as many opinions as people, would be: No two people agree ...

* often heard in speech and also seen in print: She's one of those people who ... If you deconvolute that, it means: "She's one people out of the number of people who ..." As there is no singular to the word people as used here (as opposed to people meaning population), I find this usage completely unacceptable.

* One thing that is common usage and seems to be insisted upon by editors, though I find it highly illogical, and it is not found in other languages I know: "He's one of the writers who doesn't ..." The verb in the relative clause is, of course, attached to the "who", and who refers to "writers," and is thus plural. I have no idea how this got into the rule books, but it's just stupid and wrong.

* Why does the media hate me? asks Martin Amis in the Guardian. I would argue that media is the plural of medium, so it should be used as a plural. Although I can see what Amis is trying to do - he wants to present "the media" as a sinister power that has decided to ruin his career by writing bad things about him. The alternative view, which I find factually and grammatically more satisfying, is that "the media" are many different institutions and people who have separately come to the conclusion that he is a ...

* Often heard and read: "The amount of items ... " When I learned English many years ago, I believe I was told that countable items should be referred to as "number of items", while bulk materials that aren't countable may be referred to as e.g. "the amount of water". There is of course a further complication in that we tend to speak of amounts when talking about money, which is countable, but if a specific unit is used, we could still say the number of dollars, or the amount (as measured) in dollars.

searching for a second genesis

One of the new(ish) things I learned at the Royal Society discussion meeting in January is that the "search for a second genesis" is now a unifying theme that covers SETI, extrasolar planets, solar systems exploration, and even the study of extreme environments on Earth. I've explained this philosphy of astrobiology in a shortish news feature, which is out in Current Biology today:

High life
Current Biology, Volume 20, Issue 4, R129, 23 February 2010
doi:10.1016/j.cub.2010.02.005
abstract and restricted access to pdf file


PS: for the same issue, I also wrote a short piece on UK feed-in tariffs, which was merged into the climate change piece:

Climate change attack
Nigel Williams
Current Biology, Volume 20, Issue 4, R125-R127, 23 February 2010
abstract and restricted access to pdf file

recognise that cover star ?

Went to WHSmith this afternoon for no reason whatsoever (except that I had bought something else on the other side of the road and had five mins to spare), stood next to a shelf with magazines and had a funny feeling that somebody was watching me. Investigating the origin of that funny feeling I found this:



It turns out that this is the first ever issue of a new socially aware lifestyle magazine, and who better to put on the cover ... The photos aren't new, the interview is ok (the founding date of PiesDescalzos is wrong, people!), but it is of course a very nice specimen for the collection, and I might even buy the magazine more often.

You can flick through selected pages of the magazine here, or check their blog or follow @RECOGNISEmag on twitter.

making Mona Lisa smile

Analytical techniques used for characterising materials have progressed to the point where it is now possible to investigate the composition and internal structure of valuable pieces of art and cultural artefacts with only microscopically small sample removal or without even touching the object.

Key techniques that have revolutionised the analysis of art in recent years include Surface-Enhanced Resonance Raman Scattering (SERRS), where a spectacular signal enhancement is produced by nanoparticles, and the NMR-MOUSE (for MObile Universal Surface Explorer), a portable NMR device pioneered by Bernhard Blümich and colleagues.

I have summed up developments in this exciting field (am very jealous, in fact, of the scientists who get to play not just with fascinating instruments, but also with art objects!) in a feature article that should be out in Chemistry & Industry today, and should be showing up on their website soon (appears to be open access!).

I've also covered the SERRS work by Marco Leona at the Metropolitan Museum in New York in a recent Spektrum piece:

Spektrum der Wissenschaft 2009 Nr 11, 16-17
Madonna mit Schildlauslack

the oddest vote

At last, the shortlist for the most important of all literary prizes has been reveiled. In the running for the Diagram Prize, which honours the oddest book title of the past year, are:

The Changing World of Inflammatory Bowel Disease

Collectible Spoons of the 3rd Reich

Crocheting Adventures with Hyperbolic Planes

Governing Lethal Behavior in Autonomous Robots

What Kind of Bean is this Chihuahua?

Afterthoughts of a Worm Hunter

More details about these titles are here, and you can vote for your favourite at http://www.thebookseller.com/. Once you've voted, you'll be shown the current percentages of votes. I was very surprised to see that my favourite title was in the lead, though my second favourite was only in 5th place.

Sadly, I had no luck with the titles I proposed this time round, but will keep trying ...

A book collecting timeless jewels from the first 30 years of the prize has been published in 2008, it's called "How to avoid huge ships".

more dubious cancer genomes

Update 15.6.2010:
A paper studying a lung cancer genome the way it should be done, using fresh samples from a live patient with known smoking record has appeared in Nature on 27.5., page 473. Of course, as the papers using cell lines got the scoop, this one wasn't hyped or reported in the press, so I managed to miss it and only discovered it when going back to the issue to look up something else. Goes to show that cutting corners pays off nicely in science. Still, lots more studies like this one are needed before one can arrive at definitive conclusions.

The current issue of Nature includes a news piece relating criticism of "cancer genome" sequences based on cell lines, which I have also voiced here. After some ifs and buts, the piece fails to come to a clear conclusion.

Personally, I wouldn't mind people sequencing the old cell lines if they think it helps them understand all the research that has been done on them in the past decades. What annoys me is the claim that this is "the cancer genome" and tells us something important about how cancer works. If the papers appeared in some middling journal for the record, that would be fine. But as articles in Nature, they are automatically overhyped in the press.

I think to find out something meaningful about real cancers, one would need to advance a bit more carefully and study proper cancer cells (the argument that in real tumours cancer cells are mixed with healthy cells doesn't stand up, as 1) it is now possible to sequence DNA on single molecule basis, thus from single cells, and 2) if they want lots of cancer cells, they just have to sort them out).

And of course, after all that huffing and puffing, the journal goes ahead and publishes another big "article" by the same people, also based on cell lines. I still think this is just cutting corners to be quicker than the people who do the research properly, and to get all the rewards that come with a "first" being published in Nature or Science. (And I am speaking as someone who has also been a co-author of an "article" in Nature in my time, and I'd also be happy to tell you what was wrong with that paper!)

who's who in Ancient Egypt's New Kingdom

very excited to hear that for the first time DNA sequences have been analysed to sort out the family relations between various mummies of Egyptian pharaohs. According to this report in National Geographic, Egyptian researchers using DNA from Tutankhamun and ten other members of his family have been able to establish a detailed family tree of Tutankhamun, demonstrate that the sun-worshipping inventor of monotheism, Akhenaten, was his father, and identify Akhenaten's mummy, previously known only as KV55. King Tut's mother appears to be one of Akhenaten's sisters, but her identity remains unclear. This rules out the previously popular hypothesis that his mother might have been Akhenaten's most famous wife, Nefertiti. Oh, and they also found evidence of various health problems, including malaria, allowing them to speculate on the likely causes of Tut's premature death at age 19.

Haven't read the paper yet, which is out today in the Journal of the American Medical Association:

Zahi Hawass et al., JAMA. 2010;303(7):638-647:
Ancestry and Pathology in King Tutankhamun's Family

a different view

This may look like the steppes of Central Asia (not sure, have never been there), but it is in fact central Oxford. Turning to the right, one would see the Radcliffe Camera and various dreaming spires. The building is the University's Islamic Studies Centre, which has been sitting there in an almost finished state for something like two years now but hasn't opened yet. Not sure what's holding it up, maybe some politicking going on behind the scenes.

another old bloke with a genome sequence

I was intrigued to find out from the article featured on the cover of Nature this week that the ninth man to have his complete genome sequence published (we’re still waiting for the first woman) has been dead for some 4,000 years. A lock of hair conserved in permafrost in a Greenland location inhabited by the Saqqaq culture had kept the DNA well enough to do a proper sequencing (20fold coverage) of most of his genome.

To be fair to the researchers, they didn’t know they were looking at a male genome until they read out the results, so it isn’t their fault if we get another old bloke. What’s also interesting is that this work appears to have been inspired by the sequencing of the woolly mammoth genome a couple of years ago, which demonstrated that frozen hairs are a good source of relatively pure DNA for sequencing. By contrast, Egyption tombs would yield more samples, but the DNA would be less well preserved and more likely to be contaminated with DNA of other species and indeed of modern humans.

Studying the SNPs (one-letter variations) of the individual in comparison with the spread of SNPs today, the researchers found he was most closely related to people living in Siberia today, pointing to an additional migration event that hadn’t been on record before. They also obtained genetic clues to his looks, from his hair and skin through to the shape of his teeth, hence the fairly detailed portrait that graces the cover.

As genome sequencing is likely to become a lot cheaper and faster still, we can look forward to other ancient genomes from frozen or indeed museum specimens (eg the genome of Tycho Brahe might cast an interesting light on Danish history and the rotten affairs that possibly inspired Shakespeare to write Hamlet). The ethical side of sequencing long-dead people will be tricky though, especially if there may be an impact on our understanding of their biographies.


Reference:
Morten Rasmussen et al.
Ancient human genome sequence of an extinct Palaeo-Eskimo
Nature 463, 757-762 (11 February 2010) | doi:10.1038/nature08835;
full text (appears to be open access)

physical mystery

Here comes a physics question. I constructed the kinetic toy shown below from "GeoMag" magnets and steel balls, it's suspended from the ceiling and has two joints that move freely, i.e. the places where two steel balls touch directly. So there are three parts that are independent of each other. If I spin the bottom part quite fast, the middle part will rotate too (but not as fast, I think), will then stop, rotate for a while again, etc.



Any clues ?

I'm thinking the magnetic field of the dumbbell in the middle should be symmetrical with respect to the rotation axis, so I can't think of a magnetic reason for this "behaviour". Maybe it's just random small differences in the friction depending on how the balls touch. But in any case it's fascinating to watch and procrastinate over ...

twitter 101

How to use twitter

… without wasting your time!

After a bit over six months on twitter, I’m still enjoying this enormously, but I have heard from a few tweeps who have struggled with addiction-like problems or have had to pull the plug because they found the medium too distracting. (Someone commented: “other online stuff is containable, but twitter plants apps in your brain!” and then seems to have deleted her account!) Not to mention those people who never really tried it for longer than 2 minutes and believe that it’s all full of rubbish. For me, however, although it sometimes feels like time-wasting, I believe that twitter works quite efficiently. So here’s a brief round-up of how I use it and how it helps me with my work.

I distinguish between two types of activity I do on twitter, namely 1) network-building/exploring beyond my existing contacts, and 2) reading from and broadcasting to the existing network. I do both things in turns, of course, but as 1) is what new users need to do first, I begin with that.

1) Exploring beyond my contact network is where I am most at risk of addiction, as there are so many interesting people out there, and each new site comes with another 100+ links to other interesting sites, so one could really spend all day clicking around the world just following the following links (or the lists people make). After the initial burst phase, I have restricted my explorations to specific topics and set maximum times for these explorations. For instance, I have spent an hour checking up on people and businesses tweeting from my city (Oxford), and then created a list from that. Once the list was there, it grew autonomously, as other people from Oxford found it and followed me because I had that list. I did the same for people tweeting in Spanish (there’s amazingly few of those), and more recently for French contacts. On other occasions, I build specific network extensions based on who uses hash tags I’m interested in, such as #astrobiology, or on who writes for specific publications, e.g. Guardian journos. It’s also worth checking whether the papers, magazines, scientific journals you’re interested in already have a tweet feed.

2) Hoping that one has done step 1) sensibly and hasn’t followed too many celebrities or lunatics with chronic logorrhoea, the reading and broadcasting part is quite straightforward. Most of the stuff that ends up in my timeline (NB: I never, ever look at the public timeline!) is actually interesting to me, and even with 400+ followees I can still read faster than people post, so it’s not overwhelming. My timeline has actually provided me with topics to write about, and with background info for certain stories. It’s essentially like a newspaper, except that I get to see the articles one day earlier than they appear in the printed papers, and that there is a higher concentration of things I am interested in than there would be in any newspaper or magazine. And if the headline (i.e. the tweet) isn’t all that interesting, I just skip to the next one, as I would in a paper. Oh, and there is of course the very handy option to unfollow people who clog your timeline with stuff you don’t want to read. I rarely use it, but if I see the same avatar five or more times in a row, I consider it.

In terms of my own broadcasting, I post links to my blog entries and other activities, just the occasional random thought, and RTs of things that I either consider worthy of wider attention, or want to be able to access again (if I RT it, it will be in my profile, so easy to find). Certain topics, e.g. at the moment anything to do with astrobiology, I RT systematically and add the hash tag if it isn’t there already. So I can later pull out all #astrobiology tweets and put them in a word doc and have all the links handy.

What I find tremendously useful is the link shortening at http://bit.ly – the site gives me instantaneous reports re. how many people clicked the link I shortened and posted on twitter. Typically there are around 7 hits within the first minute, but this can go up significantly if others retweet the link.

I sometimes use twitter from my phone, but find it a bit frustrating that I can’t retweet there, and have to retype people’s user names if I want to reply to them, so I only use it if I’m cut off from computer access for a day or longer.

One problem with getting heard is that twitter is sensitive to time zones, as everybody uses it in real time and doesn’t go back to old stuff. To address that I sometimes tweet links to my stories or blog entries in the morning (when Asia and Australia are still awake) and then again in a slightly different version in the late afternoon, when the Americas have joined the discussion. Assuming that nobody will be sitting on twitter and reading every tweet for eight hours, I think it’s OK to send out the same info twice, with a 5-8 hours interval. (Even though twitter does notice and complain if one posts the same thing unaltered!)

Easy, isn’t it?

@michaelgrr


PS just discovered: a useful site to see all the people you're following but who aren't following back is http://friendorfollow.com/username/following/ -- replace "username" with your username.

under the sea

Desertec is an extremely ambitious plan to harness solar energy in North Africa and the Middle East and export it to the more energy-hungry European countries via a direct current (DC) high voltage grid.

A similar project on a smaller scale has now been drawn up for a grid around the North Sea instead of the Mediterranean. The idea is that the various countries around the North Sea will feed renewable energy from different sources (e.g. solar from Germany, hydroelectric from Norway, wind, at some point, from the UK), so any gaps in the supply of one kind could be filled by the others.

Read my story in today's issue of Current Biology:

Chain effects
Current Biology, Volume 20, Issue 3, R80-R81, 9 February 2010
doi:10.1016/j.cub.2010.01.029


PS: About the Desertec project I had a story in CB last August:

New grids on the block
Current Biology, Volume 19, Issue 15, R626-R627, 11 August 2009
doi:10.1016/j.cub.2009.07.043

german pieces in Feb

This month we have induced pluripotent stem cells, cancer genomes, single molecules genome sequencing, polyoxometallate capsules, and a dose of cognitive enhancers to cope with all this intellectual excitement:

Nachrichten aus der Chemie p 111
Ausgeforscht: Chemisch aktiviertes Superhirn

Nachrichten aus der Chemie p 137
Blickpunkt Biowissenschaften:
Einzelmolekülmethoden zur Genomsequenzierung

Chemie in unserer Zeit p 6
Nanokapseln: Eingekapseltes Fett-Tröpfchen
abstract and link to PDF

Chemie in unserer Zeit p 8
Krebsforschung: Genomanalyse von Tumoren
abstract and link to PDF

Spektrum der Wissenschaft p22
Ethisch unbedenkliche Stammzellen in Reichweite?
extract & link to PDF

radio revolt

I read in the Guardian this week that the UK broadcasting authorities aim to switch off analogue radio signals by 2015, and to speed up the switchover they want to introduce a scrappage scheme (like the one for old cars last year) to entice people to trade in their old radios for digital ones.

Now I understand that the people who sell the digital radios want to make loads of money, but why would radio users give up something that is absolutely indestructible and works a lifetime, only to buy new, probably less reliable gear that does the same for a lot more money? Considering my experience with CD and DVD players, these digital devices last about three years if you're lucky.

Our (analogue) radios, by contrast, are all doing fine, and the oldest is over 30. There is at least one in almost every room in the house (come to think of it, some rooms have more than one), so I'm supposed to be throwing them all away to buy something that will be horribly expensive and probably broken in three years time? I don't think so.

I hear the switchover date depends on how many DAB radios get sold. So there is a simple way of stopping it. If people don't buy digital radios, we can keep the technology that costs virtually nothing and actually works.

noughties book

The first copies of my self-published collection of book reviews, "The noughties brought to book" have arrived and are looking fine, so I have now set up web pages for the book in the same style as for my other titles.

Next I will figure out how to make the book available via amazon. So far you can only order it from Lulu.com. They appear to ship it from the US, so for the rest of the world shipping charges can be quite expensive.

what's bugging the bees?

I have on various occasions reported on CCD (colony collapse disorder) and other disasters affecting honey bees around the world in recent years, mainly for Current Biology.

Now I've done a major round-up of the bees problems as a full length feature which is out in the Feb issue of Chemistry World. Essentially, I've been looking at the more serious possibilities, including pesticides, stress, environment (i.e.monoculture), and parasites. The emerging picture is that a combination of several factors is causing the problems. I also talked to Mike Edwards, an expert on wild bee species who maintains that their contribution to pollination is underappreciated, and the main problem of honey bees is domestication. He is featured in this month's CW podcast.

What's bugging the bees? (restricted access)

feliz diaaaaa!

a very happy birthday to the little girl shown third from left in this picture:



The twitter hashtag for the event is #HappyBDayShakira, and as I write this, it is already trending in Brazil (where it must be 5 am or something).

february

As it's february now, I've put up a new title picture for the blog (new year's resolution: new picture for every month, like a good old-fashioned wall calendar!). What looks like the road to nowhere there, is actually the much appreciated (and normally much busier) cycle path towards Oxford city centre.

It also means that Valentine's Day is coming up. If you're looking for a present for your scientifically minded love interest, I recommend:

Lust and love: is it more than chemistry?

... which I translated and edited. The book is still available in the original German edition, and has also been translated into Korean and Spanish.