Genetic testing for the masses (including myself): 23andme

Two years ago, I learned about 23andme.com, a company that does genetic testing for health, traits and ancestry. The idea is as follows: you send them a sample of your saliva (containing your DNA, I guess from cells in the mouth mucosa), they process it and check for specific genes. Then, they compare your genetic information with the currently known research about health (higher or lower chance of getting some diseases), ancestry (maternal and paternal) and genetic traits (color of the eyes, blood group).

It took me a while to decide and take the test: the idea of giving my DNA information to a private company, with information stored and available on the net, didn’t appeal me at all. Call me paranoid, but I can’t help it. I made some reputation checks with some trusted people I know, learned that the company has close ties with Google (a co-founder is Brin’s wife) and decided for it. The main push, however, was curiosity. In my genetic code it is written how my biological computer works, how it can break, and where it comes from. Too much to resist. After you place your order, they send you a sampling container, which is a test tube with a buffer solution in the cap.

What I found out is appealing: I learned that genetically I am a very healthy person, confirmed some hypotheses about my ancestors, and realized I have superpowers: I am immune to the most common strain of viral gastroenteritis. I left my genetic information in their database and, as long as I keep paying a small fee, they perform additional analyses on my sample for new genes. I keep receiving updates about new findings around once a month.

Do I recommend it? Yes and no. The most important point to keep into account is that, once you open the box of your genetic information, there’s no way back. What you learn may change forever how you see yourself, your past, your future and the future of your children. 23andme keeps you health information hidden to you unless unlocked manually. I didn’t even ponder a second about it, and clicked on all the “show my health information” buttons I could find. I cannot deal with not knowing, regardless how bad it can be. Knowledge may also allow to take action whenever possible, but for some conditions there’s not much to be done.

Posted in genetics, Websites. Tags: . 2 Comments »

Academia StackExchange started

More than a year ago, I decided to propose a Question/Answer site for Academia on the StackExchange platform. The idea was to gather academics to share their expertise in academic career strategies, grant proposals, publication process, visa and immigration for academics, and generally all the troubles of an academic lifestyle.

A few days ago, the site finally reached the threshold commitment, went through private beta, and is now open to the public in beta stage. It is now possible to join in and ask questions or give answers.

Posted in Websites. Tags: , . Comments Off »

Academia StackExchange reaches Commitment level

Some time ago, I proposed the foundation of a Question and Answer site for Academia. Now, the Academia StackExchange has reached commitment phase, meaning that the proposal aggregated a consistent number of people who may have an interest in it, and further aggregation of active participant is sought after. You may report your interest in asking or answering at least 10 question as soon as the site enter beta phase by following the link to the Academia StackExchange Commitment.

I really loved some of the comments from early committers, such as

  • “I hope this site will help beginners to initiate their careers in academia, dispel myths to outsiders, and support fellow academics too!”CesarGon
  • “Should help out those who want to start their scientific research careers, especially for the ones with limited access to quality research education.”Kit
  • “There is a great opportunity for young and idealistic people who want to change the world to receive good doses of reality checks and inspiration.” – so true user30906, so true

and this one which made me laugh

  • “Whatever Stefano Borini is involved in is probably worth looking into :)”Dr_bitz

We will see. The jump start is promising!

Posted in Dissemination, Websites. Tags: . Comments Off »

Fear the crowd. Digg 4 spurs users’ revolt.

The community-powered news site Digg played an occasional role on the development of this blog. Some of the findings I posted here started, in some cases, as a spark from a Digg submission, further developed through my personal research. This is the reason why I am writing here about it. News on Digg were frequent and fresh: reloading the page after some minute was already enough to see new upcoming content, and the time span from release to fruition was short, much shorter than Slashdot (which I also follow with very strong interest since almost the very beginning). Last but not least, in addition to interesting scientific or technological news, Digg was also one of the best sites to waste time on when bored.

This all changed recently. Digg’s new version (Digg 4), introduced a radical change on both interface layout and use. Apart from the huge amount of errors the new site presented to the user (the now infamous Ox cart axle message), the main page content has become so stable that reloading and checking “what’s fresh on the web, now” is no longer possible.

The recent changes triggered a raging reaction from the community, and in a perfect and hilarious example of coordinated mob assault, submissions promoted by the community to the current “Top News” front page now contains only links toward the similar site Reddit. If you are the host for an army of users so large they can bring servers down, having them unsatisfied can promote some issue to be dealt with.

I certainly hope the old Digg style comes back, otherwise I will have to look for alternatives to stay fresh on the internet.

Posted in Opinion, Websites. Comments Off »

New StackExchange proposal: Academia

I just created a new proposal at Area51: Academia. The aim of such Question/Answers site, when opened, is to provide assistance to academics of any level and discipline, with particular focus towards academic life, grants, papers and posters, conferences, career, management, research group directions, and academic services.

You can subscribe to the proposal by following this link and clicking “follow”. You will probably have to login using any OpenID provider (such as Google mail).

Posted in Websites. Comments Off »

StackExchange sites proliferation

I am observing with great interest the development at Area51 for new Question/Answers sites to be opened with the StackExchange system. One thing that makes me cringe a bit is the very strong fragmentation. I think this stems either from the need of personal protagonism of each person (nothing bad with it, progress happens also thanks to personal protagonism), or by lack of notice that a similar proposal has already been done. I could be wrong though, and I accept criticism on this point.

(more…)

Posted in Opinion, Websites. 3 Comments »

A Question/Answers site for Popular Science

The kind folks behind StackOverflow, a free Question/Answers website for programming questions, recently decided to open new Q/A websites for many additional interesting topics, from wine tasting and cooking to mathematics. The fundamental requisite for such new sites to be opened is a rather strict community review and development of a critical mass of contributors and interested people. On area51.stackexchange.com the proposals are collected and evaluated by the community.

I really enjoyed the proposal for a Popular Science Q/A site, and if the site is going to be opened, I will certainly be an active contributor. If you are interested, feel free to click on the link and then click “follow” on the proposal. This will largely increase the chances for such site to be opened. I am also positively interested and enthusiast for Q/A sites for Chemistry, Astronomy, Bioinformatics and, as a very old Dungeons and Dragons player, Role-Playing Games.

Posted in Astronomy, Biology, Chemistry, Dissemination, Websites. Comments Off »

Unscientist awards, a prize for unscientific spokespeople

This is something interesting. What about a prize for unscientific claims: “the Unscientist award”? At the moment, only Patrick Lockerby (the author of the  post linked above) proposes such prize according to the following rules: the potential candidate must either make use of an already debunked argument, a logical fallacy, or (verbatim) “self-aggrandising puerile prosey posturing”, to reach and strongly support an unscientific conclusion going against scientific evidence.

It can be safely assumed that hordes of candidates are available out there.

Posted in Opinion, Websites. Tags: , . Comments Off »

Please donate for the Haiti earthquake

After the recent tragic events in Haiti, it is a priority to help doctors without borders as much as possible. Please donate, even a small amount from a lot of people can make a sizable difference.

Posted in Charity, Websites. Tags: , . Comments Off »

Image self consistency from xkcd

I love xkcd. A comic combining fun and math by definition has to be good and geeky and the author, Randall Munroe, is a real genius on this. The latest comic is pretty interesting

See xkcd for alt text

xkcd, by Randall Munroe

The image is self-descriptive, meaning that each graph represents information about the image itself. For example, the first panel contains a pie chart which says how many pixels are either white or black on the image. Clearly, the relative amount of black pixels in the image depends on the size of the slice of that piechart representing the amount of black pixels, a “chicken-egg” kind of problem. It is apparently difficult to obtain such image, because the plotted data must be consistent with themselves via the graphical representation. This kind of problems, where the solution depends on itself, is quite common in many scientific problems, and it’s solved through self-consistency.

The trick is as follows: we start with a first, approximate solution, called a guess, and we apply a method that gives us a result depending on this guess. Then, we take this newly obtained result, and reapply the method again, to obtain a new result, and then again, and again, until, hopefully, the input and the output of the method are the same. When this occurs, we solved our problem via self-consistency. Of course, this convergence is not guaranteed to occur, but if it occurs, we found a solution (there could be more than one).

Let’s see it in action in a simplified form. I wrote two small python programs. They use matplotlib and the Python Image Library. The first (called piechart.py) creates a pie chart from a given data input

import sys
from matplotlib import pyplot

white = int(sys.argv[1])
black = int(sys.argv[2])

pyplot.pie([white, black], colors=('w', 'k'))
pyplot.savefig(sys.argv[3], format="pdf")

If we call this program specifying two values (the absolute values are not important, as the pie chart shows relative amount), it draws the pie chart accordingly:

python piechart.py 100 400 piechart_100w_400b.pdf
convert -geometry 210x158 piechart_100w_400b.pdf piechart_100w_400b.png
Starting guess

Starting guess

This creates a pie chart where white is 1/5 of the pie chart area and black is 4/5. Please note that due to a setup problem of my matplotlib I can only create pdf, so I convert the pdf into png of defined size, in our case, 210×158, using the convert program. The total size of the image is of course important, having an influence on the total number of pixels. I chose a good value for presentation purposes which guarantees quick convergence.

The second program is called imagedata.py and extracts size and number of white and black pixels from an image.

import sys

from PIL import Image

im = Image.open(sys.argv[1])
white = 0
black = 0
for i in im.getdata():
  if i == (255,255,255):
    white += 1
  else:
    # we assume black everything that is not white:
    black += 1
print im.size[0],im.size[1],white,black

If we run this program on the png image, it will tell us how many pixels are white, and how many are black.

$ python imagedata.py piechart_100w_400b.png
210 158 23988 9192

Of the 33.180 pixels defining the full image above (border included, not only the pie chart circle), 23988 are white (72%), and 9192 are black (28%). Hence the image is not representing itself: the plot represents our initial values of 20 % white and 80 % black.

Now we create a new image, in agreement with the iterative procedure, passing the most recently obtained values

python piechart.py 23988 9192 piechart_23988w_9192b.pdf
convert -geometry 210x158 piechart_23988w_9192b.pdf piechart_23988w_9192b.png

and repeat the process. This becomes tedious very soon, so I wrote a driver (driver.sh) to perform the process for me

# generates the starting guess
python piechart.py 100 400 iter_0.pdf
convert -geometry 210x158 iter_0.pdf iter_0.png 

# iterative process
echo "step w   h  white black"
step=1
while true;
do
 data=`python imagedata.py iter_$(($step-1)).png`
 echo "$step - $data"
 python piechart.py `echo $data|awk '{print $3}'` `echo $data|awk '{print $4}'`  iter_$step.pdf
 convert -geometry 210x158 iter_$step.pdf iter_$step.png
 step=$(($step+1))
done

If we run it, we immediately see a very interesting result:

step w   h  white black
1 - 210 158 23988 9192
2 - 210 158 29075 4105
3 - 210 158 30551 2629
4 - 210 158 30977 2203
5 - 210 158 31108 2072
6 - 210 158 31158 2022
7 - 210 158 31164 2016
8 - 210 158 31169 2011
9 - 210 158 31172 2008
10 - 210 158 31172 2008
11 - 210 158 31172 2008
12 - 210 158 31172 2008

The number of black pixels decreases, and the number of white ones increases. At every step, the image slightly changes, until it reaches a point where it does not change anymore: it achieved self-consistency, and it is representing itself. This is a movie of the various steps until convergence

Piechart convergence

Piechart convergence

What if we started from the other direction, namely, with a guess containing zero as the number of black pixels? The result would have been the same

1 - 210 158 31750 1430
2 - 210 158 31320 1860
3 - 210 158 31221 1959
4 - 210 158 31184 1996
5 - 210 158 31178 2002
6 - 210 158 31174 2006
7 - 210 158 31172 2008
8 - 210 158 31172 2008
9 - 210 158 31172 2008

Again, even with a different starting guess, we obtain the same result, here depicted as a movie

Piechar convergence 2

Piechar convergence 2

I hope this gave a brief explanation on how Randall achieved the self-consistent image. His case was more complex, having three plots. Also, the comic is scribbled, so either he drew it by hand,  approximating the  computed result, or he performed some scribble-like transformation preserving the pixel count. I assume it is the former.

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