Vote for your favorite science blog (this one!)

3quarksdaily.com, a website whose editors “present interesting items from around the web on a daily basis, in the areas of science, design, literature, current affairs, art, and anything else [they] deem inherently fascinating”, has launched its first of four annual best blog prizes. This maiden edition of the award, The 3QD Prize in Science 2009, purports in fact to elect the best entry in a science blog.

Nominations will remain open until June 1st. If you wish to nominate a blog entry, all you have to do is go to the bottom of this page and post a comment containing (in the body of the comment) the URL of your favourite blog entry, with or without some brief accompanying remarks about what motivated your choice.

After the end of the nomination period, everyone will have the opportunity to vote on their favorite.

Timeline:
- June 1st, 2009: The nominating process will end at midnight (NYC time) of this date (so there are very few days left to participate in this phase of the process!). At some point on this day, the public voting will be opened.
- June 8th, 2009: Public voting ends at midnight (NYC time).
- June 21st, 2009: The winners are announced.

Other practical infos, gleaned from the 3QD website:
- Anything written between May 24th 2008 and now is eligible for nomination.
- Between June 8th and June 21st, Stephen Pinker will select the winning entry from six finalists.

And now the most important part: if you like this blog, YOU can nominate one my posts....

Here's the post I personally recommend

Passage to Brazil

I've always been told, by my mother’s side of the family, that before going to Argentina, her father had emigrated as a child from Russia to Brazil, right at the beginning of the twentieth century, where his own father had “founded” the city of Nova Odessa, in the state of São Paulo. And also that afterwards, due to problems my great-grand-father had had with other immigrants there (the place was then known as the Colonial Nucleus of Nova Odessa), the family had quickly decided to leave Brazil and gone to Argentina, where they finally settled in the village of Basavilbaso, north of Buenos Aires, in the Argentinean province of Entre Rios.

Well, it looks as if that story is actually true, or at least almost true! I just found out, in a book published in 2008 under the title Judeus no Brasil: Estudos e Notas (“Jews of Brazil: Studies and Notes”), by Nachman Falbel, professor at the University of São Paulo, a passage about my great-grand-father himself! I must say I was flabbergasted - and couldn’t help laughing out loud thinking that after all, my family’s oral tradition, which I had never fully beleived (the idea of one of my ancestor being a “founder” of cities in the New World had always seemed a little too much) wasn’t that far from reality.

I don’t know if my great-grand-father was or not “thrown out” of the place by other colons – who, according to the family’s version of events were furious with him because he had promised them idyllic life conditions in Brazil which obviously didn’t come true. But the thing is that the historical account, as told by Nachman Falbel in his book, while clearly more realistic, isn’t that different from the one I was told in my youth.

For one thing, as Nachman Falbel remarks, the first Jewish colons to arrive from Russia to Santos, Brazil, starting in 1905 – and among them seven members of my family – weren’t all farmers: that’s what they had stated as their profession before embarking on the voyage, simply because they wanted to flee their native country and its pogroms.

But they didn’t like being farmers, they knew little about farming – and the hot and damp Brazilian climate didn’t help. Maybe my great-grand-father had actually convinced others to leave Russia with him, telling them they would be able to work at what they knew best – they were typographers, tailors, etc. –, and maybe they really became infuriated, and were preparing to ride him out of town with tar and feathers. I don’t know.

Nachman Falbel describes, in page 218 of his book, the very serious complaint my great-grand-father, Shaia Hassik, presented to the local authorities concerning the fact that his baggage was taking too long to be delivered to him. And the footnote on that same page adds some more salt and pepper to clearly show my great-grand-father’s negative state-of-mind at the time with regard to his new life in Brazil.

Based on information provided by the book about passenger lists of the ships arriving from Southampton, in 1905, I was also able to find online (through findmypast.com), the original embarkation document of the vessel Magdalena – and the exact date of their departure from England: April 21st.

This confirms that my family was in fact part of the very first group of Russian Jewish immigrants to arrive, at the beginning of May, at the Nova Odessa colony, which had officially just been founded by the Brazilian authorities – precisely on that month of April. So, even though my great-grand-father wasn’t “the founder” of Nova Odessa, he was after all one of its true founders…

Image credit: The National Archives, UK

Spittle

Today, for the first time in more than two weeks, I have some time to spend on this page. These last few days, I’ve dedicated myself full-time to writing and publishing news stories in PÚBLICO about other genes – namely, those the new flu virus.

It’s amazing how such a tiny genome as that, made of just a few genes, can be so hard to dissect and comprehend. But in fact, it’s fairly easy to understand why: the virus changes from one person to another – and to find out, for instance, where it came from, you have to construct its genetic evolution tree taking into account an ever-growing number of infected people. It’s is a different kind of “personal genomics” - but one which becomes extremely important in pre-pandemic circumstances such as those we are experiencing right now.

Let’s go back to my genes. The Spittoon, 23andme’s blog, which I have already mentioned, includes in its SNPWatch section very up-to-date reports on studies involving (reduced or increased) genetic risks links to disease as they are published in the major scientific journals around the world. Here is some of the more momentous “spittle” of the last weeks – which I have of course been comparing to the raw data from my own DNA.

These potential relationships between a given point mutation (or SNP) and a given disease haven’t been confirmed – and for the most part, they only represent slight deviations from the normal risk level for the general population. Nevertheless, they can give you an idea of the feeling you get when it’s not just some anonymous person’s SNPs you’re looking at – but your very own. Some excerpts from SNPWatch:

1 – New England Journal of Medicine (April 15)
Combined analysis of data from Caucasian study participants from the United States and the Netherlands revealed that the A version of [the SNP bearing the code name] rs12425791 is associated with a 1.29 times increased risk of ischemic stroke.

At the end of the article there’s a direct link to the pair of DNA “letters”, or bases (one inherited from my mother and the other from my father) that make up my own rs12425791 SNP. I click on the link, and go directly to my data at that position. They turn out to be: AG.

2– Nature (SNPWatch, April 28)
[The team] found several SNPs associated with autism. All were located in a region of DNA between two genes, CDH9 and CDH10, which encode proteins called cadherins. “These molecules are expressed on the cell surfaces of neurons, and they are involved with shaping both the physical structure of the developing brain and the functional connections among different brain regions. Although a particular gene variant may contribute a small risk for an ASD [Autism Spectrum Disorders] in a particular individual, we estimate that the variants we discovered may contribute to as many as 15 percent of ASD cases in a population,” said [one of the team members] in a statement. The strongest signal came from rs4307059 — compared to two copies of a C, each copy of the more common T version increased the odds of autism by 1.19 times.

My own rs4307059: CT. (For those who are wondering what I might conclude from this: I decided that any “autistic spectrum” personality traits I might have in real life I will only share with my image in the mirror.)

3 – Archives of Ophthalmology (April 14)
The researchers found that one SNP in the TGF-β1 gene in particular was associated with high myopia [-8.00 diopters or worse]. Each A at rs4803455 decreased the odds of developing the condition by 0.67 times.

My own rs4803455: AA (Doubly reduced risk? You don’t say! It seems that I don’t qualify for what they consider “high myopia” in the study, since I don’t quite make it to minus 8 diopters, but I’m pretty close to it. So I don’t give much credence to this result.)


4 – Journal of the American Society of Nephrology (May 1)Researchers studied 260 people who had had bypass surgery and found that those who carried an A at both copies of rs4680 went into shock more often compared to those with other genotypes (69% vs. 57% in AG people and 46.6% in GG people). (...) Prolonged shock, lasting more than 48 hours, was also more frequent in people with two As (25% vs. 13% for AG and 6.8% for GG). (...) people with two As at rs4680 also had greater frequency of acute kidney injury. The median hospital stay after bypass surgery was longer for people with two As at rs4680: nine days vs. eight days for AG and seven days for GG.

My own rs4680: AG (Right in the mid-range; could spell trouble, I suppose.)


(Main image credit: net_efekt/Flickr)

Surname

“Ça c’est un nom bien de chez nous!” – That’s a typical Alsatian name! This was the answer given to me some years ago by an Alsatian gentleman, to whom I was speaking on the phone, when I offered to spell “Gerschenfeld”. I was stupefied: for the first time in my life, someone was telling me my surname sounded typical to him.

On the contrary, I’d gotten used – then in France and now also in Portugal – to remarks such as “ouch, what a complicated name!”, or “that’s a foreign name, isn’t it?”. Or even worse, to phonetic deformations of my patronym that go beyond what one might reasonably expect (“Mme Chantapel? I’m calling you about…” – that was the beginning of another unforgettable phone call, also in French).

For those who have always known their surnames were “typical” of some place, wherever that might be, my reaction may seem strange. But believe me: I was utterly surprised and delighted by that (immediately) nice Alsatian man’s reaction. My name, I realized, might be from somewhere after all…

Five years after his death in Paris, my father’s memoirs have just been published by Libros del Zorzal Editions, under the title Autobombo (which means something like “showing off”), in Argentina, where he had emigrated from Poland with his family when he was only six months old. And as I reread the book, I discovered a historical explanation for the spontaneous familiarity that gentleman from Alsatia had expressed with regard to surnames like mine.

My paternal and maternal surnames [Gerschenfeld and Rosenblatt], my father writes, make me think that my family came from Alsatia or Rhenany, were Jews had settled in the fourteenth century, after their exclusion from France and England. A further series of expulsions forced them to move eastward, to other regions of Germany, and in the fifteenth and sixteenth centuries, they finally settled in what was then the Kingdom of Poland (which also included parts of Ukraine).
At that time, Jews were not allowed to reside in the Empire of the Tsars, but after several partitions of the Kingdom of Poland, between 1772 and 1795, more than 70 percent of that kingdom’s territories had been annexed by the Russian Empire. In this way, and since Catherine the Great imposed on them to remain in the so-called “reserved zone” (in Russian, Cherta Osedlosti), those Jews automatically became the discriminated subjects of that empire, which spanned territories that are today part of Poland, Lithuania, Ukraine, Romania, and Belarus.
Pages of the book, written in Spanish, containing this excerpt

So this explains that… And it also explains why, when I looked more closely at the genetic similarity map 23andme had constructed based on the results of my DNA test (which I have already written about in this blog), I realized that, although the “Ukrainians” are, as I already mentioned, the population whose genetic makeup is closest to mine, that map places me, in fact, at the confluence of people from all over Europe – and in particular of Northern Europe, which includes the French and the Germans.

On the other hand, I’m also very close to the Austrians – and, from Southern Europe, to the Italians –, which suggests that my ancestor’s trail, maybe before the end of the Middle Ages, may have been even more tortuous.

Credit for the photograph appearing on the book's cover: Mario Muchnik

Uncertainties

Is knowing the genetic mutations that lurk at certain locations of our DNA really useful in terms of assessing our risks with respect to diseases like diabetes or stroke?

Some specialists have lately voiced their doubts about this, countering the idea – which has been dogma these last years – that each common disease is the product of a few common genetic variants. This assumption has motivated dozens of so-called “genome-wide studies”, where geneticists set out to hunt down disease-causing genes through the detection of sets of point mutations – the famous SNPs – that would be frequently present in sick people but not in healthy people.

The problem with this approach is that such a simple situation is actually the exception, says David Goldstein, a geneticist at Duke University, who a few days ago commented on the subject in the New England Journal of Medicine. On the contrary, according to him, the most likely is that in their great majority, common diseases are caused by a myriad of rare mutations that, in a given person combine, as in a genetic lottery, to produce a specific disease.

If that is correct, getting a personal genetic test done by firms such as 23andme – which I did myself – or others is practically useless in terms of finding out our disease risks. The tests those businesses offer are merely a reading of half a million (sometimes a bit more) locations in the DNA molecule near which it has been inferred, from genome-wide studies, that one of those common disease-causing mutations may lie. This means that, in most cases, the results will never let us see the big picture. Better, then, to trust our family history of disease to tell us what to expect – the good, old “clinical history”, so dear to physicians a century ago.

According to Steve Jones, a well-known geneticist at University College London, writing today in the Daily Telegraph, those who order commercial genetic tests are simply throwing their money out the window. Goldstein, for his part, also argues that, if we really want to dig out the true and complex roots of human disease, rather than decoding many little bits of DNA from many people it might be better, from the point of view of medical research, to read the whole DNA sequences – the whole two times three billion letters – of a smaller number of individuals.

But not all the news is bad: up to now, nobody has questioned commercial personal genetic tests from the perspective of genealogy – and by the way, Goldstein is a big experts in that field. In fact, as I see it, that part is much more fun and exciting; I never doubted it and I intend to keep digging.

Allergies

I clearly belong, on my father’s side, to a family of allergic people. Happily for me, I haven’t suffered much from it (I’m allergic to drugs such as penicillin and little else, as far as I’m aware, notwithstanding the occasional itchy skin for reasons unknown). But the men in my family tell a whole different story. I remember, as a child, seeing my father’s hands full of eczema plaques (atopic dermatitis) between his fingers, which he was often scratching. This was due, he explained to us, to the fact that the reagents he used in his lab (he was a biologist), triggered allergic reactions. My brother and his sons have had more serious cases of it all through their lives. The most famous victim of this ailment appears to have been the French painter Paul Gauguin.
This morning, I received confirmation that this disposition for eczema is in fact in our genes. The Spittoon, 23andme’s blog, refers to an article published earlier this month in Nature Genetics which suggests that, although having a clear environmental component, eczema is also genetic. The study concludes that 13 percent of Europeans have a letter T at position 75978964 of their DNA sequence of both their 11th chromosomes (each inherited from one of their parents) – and that this multiplies by 1.46 their odds of getting eczema compared to the general population. I looked up my DNA bases at that precise location and found out I’m… TT. Bingo!
This may not be a very big risk – and maybe that’s why I didn’t get it myself. But another article mentioned in that same Spittoon post mentions that the very same configuration, at the same position in the same chromosome, also raises the risk for contracting Crohn’s disease, an chronic auto-immune inflammation of the bowel. For which I discovered, when I had my genes tested, that my risks are three times higher than average. It seems as though the pieces of the puzzle are starting to click into place.

Sharing

One of the most thrilling things you can do with your genetic test results from 23andme is sharing the information with others, in search of unknown relatives. This is how it’s done: when we find someone, for example through a website forum, that we are curious about comparing our genes with, we simply send that person an invitation and wait for an answer.

Almost everybody is willing to share at the “basic” level, that is, as long as no specific DNA details are revealed, namely in terms of disease risks. Even so, it took some effort on my part to start sharing with people I don’t know, but once I understood that my privacy was not at stake, I quickly became addicted. Currently, I already have 17 “friends” in this genetic social network, each and every one of them an absolute stranger, that I invited or who invited me to share.

Once the sharing principle is accepted by both parts, it becomes possible to compare genomes through a functionality called “family inheritance”, that allows both persons to see if there are coinciding pieces of DNA in their respective chromosomes.

In fact, this option is supposed to be used to compare genes among family members, who know from the start that they share big chunks of DNA. And, from what I’ve read, it’s pretty unlikely to find this type of genetic coincidence, by chance, in people we’ve never heard of before.

So imagine my amazement when I found out that 4 out of my 17 “friends” are probably distant relatives, distant “cousins” of mine! It’s hard to believe, but that’s how it is: when I compared my genome-wide genetic data with the data from those 4 people, I discovered that whole segments of certain chromosomes suddenly turned blue on the diagram. In one case, the coincidence spans a sequence of 20 million DNA “letters”, or bases, on chromosome 5. In another, as the image shows, the coincidence involves a 10 million-base sequence on chromosome 4 (I’ve hidden the person’s name for obvious privacy reasons).


What does this mean? It means that, according to the partial genetic results we both received, we both inherited, from one of our parents (either our mother or our father), an identical chunk of some chromosome. In other words, we our DNA present a so-called “half-identical” match (i.e., contributed by only one of our parents). Which, in turn, means that our mother and the other person’s father (or whichever combination is responsible for the coincidence) shared (still share) half-identical chunks of their own DNA too. That is, they also were (are) distant (though slightly less distant) “cousins”. And so on, right back to a common ancestor who probably lived a few centuries ago.

Here is the answer I got from another one of my “cousins”, with whom I share a half-identical DNA sequence 10 million-bases-long on chromosome 9, when I voiced my doubts about such a conclusion: “Yes, it means that we definitely share a common ancestor. The precise point in time may be 300-400 years ago, depending on the rate of recombination in that region. It is unlikely that the common ancestor would be further back than 300-400 years, because recombination would have eliminated it from our common ancestry.” Seems reasonable enough to me.

I also asked a scientist I know who specializes in genetic ancestry and she confirmed.

Apparently, such a state of affairs is not that uncommon in those human communities, namely religious, where people didn’t marry much outside of their group – and which, at some point, became part of a Diaspora, spreading worldwide because of political and religious contingencies that arose in their home-countries.