Appendices to “Guns, Germs and Steel”

A particularly exciting part of scientific writing involves broad views on earth and human history; basically coming to very insightful conclusions starting from sparse and specific experiments. This is especially true when using archaeological data, which is very sparse and incomplete by its very nature. A prominent example of such broad insight on human history is “Guns, Germs and Steel” by prof. Jared Diamond, which represents a successfully attempt on removing racial prejudices regarding the reasons why western countries “succeeded” in conquering other civilizations. The most notable example is of course the south-american empires, but many other examples within African and Oceanian civilizations are presented. The bottom line of the book is relatively simple: the presence of domesticable plants and animals, together with a geographical configuration enabling exchanges boost technological advances. The relative western immunity to some infective agents derived from cattle domestication is also indicated as a decisive factor in the western expansion in America.

The book also features some pretty interesting bits, such as the accurate description of how a handful of Spanish soldiers kidnapped the Inca emperor Atahualpa (surrounded by 7000 soldiers!), and more interestingly how the Chinese empire (whose technological level has always been on par, if not more advanced than western civilizations) decided to abruptly stop naval explorations, therefore possibly changing the world’s history with such single minor decision.

Many critics to this book focus on the lack of clear and specific experiments that could confirm some of the most challenging conclusions of the author: Tom Tomlinson summarizes such critics by saying “it is inevitable that Professor Diamond uses very broad brush-strokes to fill in his argument”. It doesn’t necessarily need to be that way though: in another book by Walter Alvarez, every single experiment that led to the conclusion that the cretaceous mass-extinction was caused by a giant rock falling from the sky is clearly outlined and explained, including other quite convincing alternate theories. (As a side note, the book has the best name ever invented: T-rex and the crater of doom).

Given the use of this “broad brush-strokes”, it is inevitable that new experiments will eventually pop-out and provide details that could change the interpretation given by professor Diamond, maybe not completely, but at least by posing significant challenges, or the need to update parts of the book.

By chance I stumbled upon some very interesting studies that would very well fit as appendices to the book. The first study involves tuberculosis, which is one of the illnesses that badly affected south-american populations after contact with the conquistadores. The first deviation from Diamond’s theory is the fact that Mycobacterium tuberculosis (the bacteria causing the disease) was probably transmitted from humans to domesticated animals and not the contrary; the other more challenging discovery is the presence in Peru of human bones showing clear signs of tuberculosis some 300 years before Colombo set foot in the Americas. Luckily enough the bacterial DNA in those bones was still readable and allowed the authors of this study to conclude that tuberculosis was brought in Peru by… sea lions. This study itself is also another example of a huge insight coming from sparse and incomplete data: much of the conclusion relies on 5 non-synonymous SNPs shared between the Peruvian strain and those that infects modern-day sea lions; there are of course a number of other experiments in the article, making the conclusion pretty robust. It is entirely possible that the distance with the “regular” western tuberculosis was such that native populations had less resistance, but it also shows how new emerging experiments can threaten parts of a convincing theory. The devil is indeed in the details.

The other three studies all came in this week, as I attended a very interesting talk by Eske Willerslev on the analysis of ancient genomes (the oldest so far being a 700’000 years old horse!). The first study somewhat challenges Diamond’s idea that most of the large mammals have gone extinct by human intervention (thus reducing the availability of domesticating cattle for some civilizations), but could instead have been caused by a drastic reduction in the presence of some protein-rich plants after the end of the latest ice age. The other quite amazing couple of studies suggest that there have been contacts (and you know, admixture) between south-americans and Polynesians: this conclusion is based on two specular experiments: genotyping of natives from Rapanui and of two individuals belonging to the Brazilian Botocudos population (which actually seem to show no signs of native american origin). According to the genetic data this encounter has happened no later than about 1400. This exciting conclusion promises to revise the way human migrations in the new continent are currently taught, and it is also very likely that new surprises will pop out sooner or later.

P.s. I’m pretty sure that there will be many other studies out there challenging Diamond’s book details that I completely ignore 🙂

Congo red

This article is going to mix three things that apparently have little to do with each other: art, war, and microbiology.

As in the previous post, it all started with an art exhibition at the Strozzina museum in Florence: as part of the exhibition called “Unstable territories“, a room was all covered in black and featured several screens in the middle. A wild and alien landscape was being screened: it featured hills filled with trees and grass fields, all red. Some of the screens started showing soldiers marching through refugee camps, while tanks and guns were firing in the distance; all the people were looking at the camera in complete silence. A few dead bodies on the side of the roads were shown too, surrounded by fluorescent red grass. The piece is called “The enclave” by Richard Mosse, shoot in Congo using an infrared film used by the army to spot disguised weapons. The objective of the piece is quite straightforward: by showing an environment full of what resembles blood, the impact of the war on the population is exposed for everyone to see. The beautiful and quiet landscapes are transformed into a nightmare.

Image-111

A few months later, an article suggested that, instead of increasing the awareness about the too-often forgotten war in Congo, the art piece caught the interest of many people only because of the peculiar effect obtained through the use of infrared film. I first thought that it was wrong, but I soon realized that I knew close to nothing about that subject; kindly enough, the author pointed out a truly complete book on that war, called “Dancing in the glory of monsters“. The author does a great job in telling the long and intricate story of this war, going from the responsibility of the international community and state corruption down to the dreadful stories of the single civilians.

After reading that book, a few considerations come to mind: first of all, it is true that the work of Richard Mosse cannot be fully appreciated without a minimal knowledge on this horrible conflict. Among other things, the fact that the victims of the many mass killings have been buried in a hurry results in countless nameless graves that have been eaten by the jungle; the symbolism of the red landscape acquires then additional depth, pointing out the long trail of death that the war has brought. But something else quite unusual comes to mind after reading this story, which relates to conflicts in other parts of the world (a prominent example is the conflict in middle-east). We tend to pick a side in many of the traditional conflicts, for cultural reason or even just family tradition; not on this one (at least for me). Being such an unknown story, and given the horrors that have been perpetrated by all sides, the only possible side to pick is the civilian population. In fact, picking sides in the “traditional” conflicts after reading this book feels just wrong.

Now’s the turn of microbiology: in a visit to the Typas lab at EMBL, I’ve joined some experiments measuring biofilm formation on some bacterial strains. In this essay, a red dye is added to the agar plate, which binds to biofilm components: if a bacterial colony makes it, it turns red. Surprisingly, the name of the dye is Congo red, named by the German company Bayer in the heat of the colonization in Africa (perhaps it’s time to use another name in publications?). Looking at the agar plate doesn’t help but think about the work of Richard Mosse, and how strange this connections are.

Abstract “painting” with Fourier transforms

TL;DR: Fast Fourier Transforms can be used to make some pictures look a bit like abstract painting (here some scripts on top of ImageMagick).

One of the most recognized contemporary painters is Gerhard Richter; he basically has two distinct kind of paintings: “copies” of photographs and abstract paintings made in a procedural and somewhat mechanical way (have a look). Some years ago many of his paintings were hosted in the Strozzina museum in Florence; the very good guide challenged the crowd to understand the abstract paintings, whose impact on other artists was also shown in the very well-curated exhibition. I remember thinking that those paintings, by the “mechanical” way they were made, resembled the application of another mathematical procedure, called Fourier transform. For the non-technical crowd, I suggest reading a couple of articles to better understand what this transform is and most importantly how it affects everyday life: by a way of example, the mp3s that we listen to everyday are made through a series of Fourier transforms on the original sound wave, resulting in a much smaller file, which we can even stream on the fly over the internet. Its inverse is also used to interpret x-ray crystallography, which brought us the discovery of the DNA helical structure, above other things. To better understand how it works, you can have a look at this very nice article, or even play with it in your browser with this neat Flash (yuk) page.

After a couple of years I got involved in a discussion about Richter’s paintings and thought that would have been nice to see if it was possible to produce similar paintings using a somewhat automatic and mechanical procedure. Luckily, Fourier transforms are also used to produce JPEGs (the equivalent of mp3s for picture files), so bending this transform could have produced interesting results. The difference would have been that Richter uses is sensibility and experience to direct the process, while this other process would have been totally automatic, but also unpredictable to a certain extent.

After some research I’ve found a nice article that explains how ImageMagick, the popular Unix command-line tool for image manipulations, uses Fourier transforms and its inverse to manipulate pictures, showing for instance some practical examples on how to extract the phase and magnitude component from a picture and combining them back to the original file. What would have happened when thinkering a bit with this commands? I’ve done some experiments, and crafted a few bash scripts to make it a bit easier.

Reverse transform using only the image magnitude

The first experiment results are more similar to Richter paintings (not in terms of actual art of course!). Once the magnitude and phase components are extracted from a picture, much of the outlines of the image are stored in the phase component, while the colors are mainly found in the magnitude part (the fact that there’s no complete separation is a good thing, since it makes x-ray crystallography feasible). What happens when the inverse transformation is made using just the magnitude part? We should obtain a picture whose outlines are mostly gone, sprawled in an abstract way.

Magnitude transform

Magnitude transform (original picture on the left)

The results are even more surprising when a picture with regular patterns is used, demonstrating that part of the outlines are still retained somehow when doing the inverse transform.

Magnitude transform

Magnitude transform (original picture on the left)

Pretty abstract right? As you can see, using an image with a pattern generates more predictable results, which are still interesting. But we can do more…

Reverse transform with phase swap

Once we’ve extracted the magnitude and phase component we can separate them and do something stupid, like doing the reverse transform swapping the phase component of two images. Given the non complete separation of outlines and color, we can expect the resulting images to contain some of the tone and outline of the other. A bit like multiple expositions in photography, but with an abstract touch.

Swap transform (original pictures on top)

Swap transform (original pictures on top)

Again, using pictures with regular patterns results in interesting and slightly predictable results.

Swap transform (original pictures on top)

Swap transform (original pictures on top)

Sometimes, only one of the swaps looks interesting, usually due to the presence of patterns that somehow interact with each other.

Swap transform (original pics on tops)

Swap transform (original pictures on top)

These results look less abstract than the first trick, but look what happens when we use two pictures with clearly outlined patterns.

Swap transform (original pictures on top)

Swap transform (original pictures on top)

 Reverse transform combining two magnitudes

Swapping two images is quite interesting, but as we saw with the third example, sometimes only one of the swaps is worth keeping. What we could do is tampering with the magnitude component prior to the reverse transform, for instance by multiplying together the magnitude components of two different pictures (the original and another one). For this experiment I had no idea what to expect.

Multiply transform (original pictures to the left)

Multiply transform (original pictures on the left)

It’s really nice how the original image is still “there”, but gets contaminated by the other one. Again, using patterns produces predictable but cool results.

Multiply transform (original pictures on the left)

Multiply transform (original pictures on the left)

The fact that the second picture is mostly black produces a weird blurry effect, a bit like tampering with fresh paint on a canvas.

That’s it for now! Any addition or nice abstract result you get using your pictures is more than welcome. Let’s see if we can fool someone in hosting a Fourier transforms exhibition somewhere!

Getting up-to-date in science

Keeping the pace with the current flow of scientific publications is a herculean task; the number of journals to keep track of is growing every year. Moreover, in some fields the number of people doing research might as well be higher than some small nations. Despite this difficulties, finding (and reading, you lazy!) the latest relevant literature is very important for scientific success. For instance, it helps in getting the latest research vibes and avoids proposing the same ideas already pursued by someone else. It also helps a lot in writing the introduction of your next paper…

Every one has his own way of keeping up to date; here’s my personal list of things I do. Any suggestion or addition is very welcome.

  • Pubmed searches: this method is very specific and effective. Just make a pubmed search on one of your research topic while logged in; save it and set up a weekly email with all the new articles that have shown up in the last week. Tip: make the search specific enough to have maximum ~20 results per week; better to have many specific emails than just a really fat one.
  • Pubchase: a very recent service that reads your library (either mendeley or a good ol’ bibtex file) and sends you a weekly email with recent publications that match your profile. Less predictable, but works quite well.
  • A (very) few rss feeds: this option is less frequently used, because is less specific and can grow pretty quickly, depending on the number of journals. On the other side may lead to completely unrelated but inspiring works.
  • A Twitter lists: I keep all the scientists I find interesting in a quite big (and private, sorry) list, which I keep on a tweetdeck column. Some interesting papers came out just through this source, and sometimes even before they got published, as pre-prints. The signal-to-noise ratio is absolutely low, but a casual scrolling with the morning coffee never hurt anyone.

There are other options that I’m not currently using, like the Google scholar updates: I have just my articles in my scholar library, so I get really boring Genome Announcements papers. I’m pretty sure that Google is more than able to set up a recommendation service if given the right library.

That’s it! Now go read something interesting!

Drawings – Cambridge (3)

It seems the best moment to make fun of the royal family now that the queen is in Italy; last week there was a story in a local newspaper about prince William eating in an Italian restaurant while attending a course on agricultural management. The article kindly told us that the prince had a salad and then penne boscaiola (which is odd: salad should have come as the second dish!). Apparently he enjoyed the meal so much that he cleaned the plate.

"Crapa pelata la fa i tortelli" (cit.)