Talking to Prof. Church about machine learning applied to genomic research

During my flight to Boston I read “Regenesis”, the interesting genomic science book by Professor George Church, which was a gift from my friend Dr. Raminderpal Singh.

George, Raminder and Jorge 2016 Boston

On Wednesday evening I had a very interesting conversation in Boston with both of them. Neither of them needs an introduction in the genomics world, but for those of you outside the field:

  • Raminder is Vice-president at Eagle Genomics and Advisor at Kanteron Systems. He was previously Genomic Medicine Strategy Lead at IBM, where he was responsible for the Watson Genomics project.
  • George is a bestselling author, Professor of Genetics at Harvard Medical School and Professor of Health Sciences and Technology at Harvard and MIT. His PhD led to the first genome sequence and contributed to nearly all “next generation” DNA sequencing methods.

Since George’s lab work revolves around chip-DNA-synthesis, gene editing, stem cell engineering, super-resolution, molecular computing, dark matter and similar subjects, and since he has PhD students from Harvard, MIT, Boston U., and Cambridge, during the conversation I could not resist the opportunity and I asked him about de novo computational discovery of motifs.

It is an idea I had a few weeks ago while sailing from Saint Petersburg to Helsinki: what if we apply machine learning/intelligence (whether Random Forests or Hierarchical Temporal Memory) algorithms, or even better quantum computing, to look for sequence motifs (nucleotide or amino-acid sequence pattern) to help us predict and engineer structural motifs (chain-like biological molecules)? We could begin with those related to binding and folding, which could lead to an exponential advance in the field of information storage and synthetic biology. But that would be only the beginning. The possibilities and implications could be really far fetching. It would overflow the SFLD 😉

In a nutshell (graphical silly example), it would make it much easier to go from this:
to this:

And not only describe it, but also understand it and facilitate its application in de-novo engineering.

There are already over 100 software programs which try to do this programmatically (MEME, EXTREME, AlignAce, Amadeus, CisModule, FIRE, Gibbs Motif Sampler, PhyloGibbs, SeSiMCMC, ChIPMunk, Weeder, SCOPE, MotifVoter, MProfiler…). Weirauch et al. evaluated many in a 2013 benchmark. But what I am proposing is a lot more powerful, versatile, and quick than anything done before (as far as I know).

He mentioned some of the research work his wife (Harvard Professor Ting Wu, whom I also met in Boston) is currently involved in around Super-resolution imaging for chromatin folding, and evolutionary conservation, and told me “your idea is really interesting”.

Honestly, I usually can care less about what others think of my ideas (I’m a scientist, I value evidence and data, not “beliefs” or “judgements”) but I personally admire and respect his work, and agree with his views, specially on sharing knowledge and human genome editing, so his comment made my day and encouraged me to further pursue that hypothesis… someday. Right now in my spare time I am redesigning a multi-sensors data stream interface for NASA (pro-bono, unrequested… but that’s my idea of fun!).

Let’s pretend none of this ever happened

Walking towards my London Shoreditch office
to meet the Swiss investor and his impeccable suit,
leaving the City bankers’s coffee-holding fast pace behind,
I notice the absence nobody seems to
Where did he go?
His sleeping sack and pillow still on the sidewalk
as annoyingly positioned in the corner as always
But he’s gone
I wonder and I worry
his failing body, almost as absent as his lost gaze
with nobody to return it,
had been a constant and silent companion of my daily walk
We never spoke, but we connected
He needed help that I did not offer
but he was also longing for a contact that I did accept
with my eyes and my smile
He fed on that with desperate hunger
but I fear that could not keep his body alive
I look for him
Did he finally manage to gather enough crumbs in the form of coins
to enter the new temple of exclusive abundance
and be able to reach for an edible item that might keep him going for one more day?
Or did he perish, vanish, and was removed out of our sight and our path?
In that case they did not remove him from my life, from my heart,
where you all live, far away from me
As my gaze, still in the lookout, turns the corner
in the hopes that he’s defacing the wall with his urine,
I see the ultimate social irony:
inside the Bloomberg Space
a neon sign
someone most definitely put up for me today
“Let’s pretend none of this ever happened”

The romantic poet in me stops there
no more words, no more thoughts,
the insulting irony has spoken, in obvious terms, to nobody
But I can not
let it go
and enraged with fury and disbelief
I go on
determined as I always was
to subvert the system
to penetrate it, hack it, and milk it
for then I will have the dirty tools the system uses to turn our alienation against us
And then the day will come when we will see each other as one, and the world will be full of “us”,
as there will no more “them”,
and then I will be gone
for my job will be done
I see you
open your eyes
35000 decisions a day
this is the one
I’m not hiding
Hello Mr. Banker
here’s my soul
give me the tools
to obliterate your world
and free you all

“Big Bang Data” and “Tintin” exhibitions at Somerset House, London

Yesterday we went to see a couple exhibitions at Somerset House, in London.

The first exhibition we saw was “TINTIN: Hergé’s Masterpiece”. Basic but obviously appealing, it was too crowded to be enjoyable.

The second one was “Big Bang Data”.

While undoubtedly interesting, especially for someone who works in, teaches, and loves bid data and technology like myself, to me the most interesting aspect of this exhibition is that everyone who was there had already experienced the subject. Even more, we are all part of it. We generate that “big data”, we process it, we benefit from it, and we are abused through it. Furthermore, most of the works exhibited had been featured in mass media outlets. Such as the outdated but nonetheless striking Debtris

So, what’s the role of such a very well curated and exhibited collection of works in today’s world?

Art exhibitions can have many functions and serve many purposes. I won’t talk about it here now, for there are already countless books and debates revolving around such a complex subject. But it is obvious that as digital communications break the physicality barrier, any objectual gathering of non-physical content can be deemed irrelevant.

Romantics, demagogues, luddites, and even some anthropologist will persistently demand a return to material in the age of the digital. Yet, as an evolving organism, shouldn’t we embrace digital in digital form? shouldn’t we adapt our experiential expectations to the possibilities that digital content allows? I completely support Bret Victor’s point of view on the matter.

Food for thought as I look forward to #Utopia2016: celebrating the 500th anniversary of Thomas More’s inspirational text. A year of artists, designers, provocateurs and thinkers experimenting with ways we might live, make, work and play.

I stood up against a terrorist in a German train

Yesterday, after spending the day at a tradeshow in Düsseldorf, on my way by train to the hotel in Mülheim, I stopped in the town of Duisburg, which was on my way, because I heard they were setting up a Christmas market. The market was indeed being set up, but it was still closed, so I decided to go back to the station. To avoid the sprinkling rain I took the 901 tram at König-Heinrich Platz.

From the window I saw three kids (around 12-13 year old, I guess) wearing some team sports uniform, laughing and rushing onto the tram. They were not particularly disrespectful or anything, but one man standing in the platform (tall pale and bolding German, around 40 years old) apparently didn’t think so, because they did not let a woman board the tram before them. Some of us appreciate old-fashioned manners more than others, but it is hardly a crime, anywhere in the world, to not let a woman board a train ahead of you… specially when you are a pre-teen or teenager, so commonly unaware of your surroundings.

So this man started screaming at the kids. I saw that out of the three kids (two white and blonde, the other one middle-eastern looking), he was only screaming at the foreign-looking one. My German is not too good, but I picked up words like “schwein” (cerdo), “mohr” (moorish, used pejoratively for “muslim”), “Paris”, “terrorist”… You did not need a PhD in Germanic Languages to understand what was going on there: an obviously mentally unstable person, directing xenophobic fury at the wrong “target”.

Had my German been better, I would have told this person that while I defend his freedom of speech, that is no way to address a kid. Or anyone for that matter. Since I could not communicate in his language, I did not say anything, but remained alert, fearing things could get worse. And they did.

This man held the automatic tram door, preventing the departure on time, while his screams got louder, his tone more aggressive, and his body language more menacing.

I was at the other end of the tram-car, but I looked around and nobody did anything. The car was full of people, most of them German looking. But they all acted as if that was not happening. Some looked around the platform, as if looking for the police, or some “authority”.

I have found, excuse my gross generalization, that while the English are to a large degree “conformist”, the Germans are to a large degree “obedient”. Had the police, or any other form of formal authority been there, things would have gone completely different. But upon lack of authority, brutality and submissiveness took over. Sorry to sound so obvious, but let’s keep in mind the dangerous results that mixing the “wrong” circumstances, xenophobia, ignorance, and mindless acceptance can produce.

At this point, seeing that nobody else was doing anything at all to stop this violent escalation, I got up from my seat, walked across the car, and positioned myself between that kid and the aggressor. The man kept holding the door and shouting at the kid as if I was not there. Everybody else remained still.

Then, a good four minutes into this non-sense, and after having gestured several menacing signs (“cut throat”, “fist smashing”, etc), the man, who was still in the platform, reached into the car, holding the kid’s uniform and pulling towards him trying to get him out of the car and onto the platform.

This is what I call a “terrorist”. Someone with the intent to instill terror in others, particularly to prove a point or avance a particular ideology. If you find the use of this word not appropriate, ask yourself about state-sponsored terrorism, or about the constant mis-use of the term “terrorism” by the media (western or eastern) or politicians.

That was the line, that was it. I grabbed the man’s hand, twisted it (I think my Aikido sensei, years ago, used to call this “sankyo”), kicked him in the chest, and knocked him onto the platform.

Free from the man’s hold, the doors automatically closed and the tram moved on. Nobody did or said anything. Nobody even looked at me. Not even the kid.

I have witnessed and suffered my share of violence throughout the years, but what struck me the most was not a demented criminal, a “terrorist” attacking a “victim”. What struck me the most was the appalling passivity of everyone in that train.
What’s happened to us? When did we become “lambs”? Have we always been “lambs” (whether “God’s”, “the crusade’s”, or “Bush’s”)?

What happened to idealism, utopia, values and beliefs? How can an agnostic like me have more “beliefs” (or at least be more willing to act on them) than the church-going and flag-rallied crowd? What do we think we have to loose, that makes us fear helping others? How can we be so blind in not seeing that inaction will cause us more harm than putting ourselves in harm’s way to defend our values and ethics (not “morals”)?

We are so full of ourselves. We talk non-stop about modern western civilization’s grandeur. I consider myself a liberal free-thinking humanist and peacifist. We are so proud of our humanism, our liberalism, or democracy, our liberty, our rights… but all those are little more than nice sounding ideals, tergiversated and manipulated by politicians, corporations and mass media.

Is John Gray right when he talks about “The Human Animal”, the “Homo rapiens”? When I look around me, that is what I see.
But a Zen monk once told me while sipping some green tea in Japan: “we are what we choose; not so much what we do, or even why we think we chose it”. Some contemporary information technology theories, behavioral neuroscientists, as well as some metaphysical philosophers, would agree with that to a surprising large extent.

So I chose. I chose to stand up.

Learning quantum computer programming

Yesterday I started learning and experimenting with quantum computing programming. It’s not easy to express the fun and excitement that experience brought me, but I’ll try:

quantum computing simulator

Programming a quantum computer is different than programming a binary (0 and 1) “digital” computer. To program a quantum system, you have to map a problem into a search for the “lowest point” in a very large pool of options, which corresponds to the best possible outcome. The processor considers all the possibilities simultaneously to determine the lowest energy required to form those relationships. A quantum computer is probabilistic rather than deterministic, so the computer returns the best answers in a short amount of time. This results not only in the optimal solution or a single answer, but also other alternatives to choose from.

Of course, I don’t have access to a quantum computer (yet), so I used a GPU-accelerated quantum computer simulator with a simple IDE interface, its own scripting language with debugging, and 3D quantum state visualization which can efficiently simulate quantum registers up to 22 qubits, run Grover’s and Shor’s algorithms, and has a variety of quantum gates built in.

To use the quantum computer you map the problem to an equation whose objective is to return the minimal values (optimal solutions). There are two values that must be provided – the “weights” of the qubits (which can exist in any superposition of states 0 and 1, and are represented by a complex number) and the “strengths” of the interaction between them. When N qubits are in superposition, a combination of 2^N states is created.

Quantum gates are similar to the logical gates used in binary digital computers. With quantum gates (which define the most basic operations performed on qubits)  you can build complex algorithms, that usually end in a measurement operation obtaining a classical value of qubits (either 0 or 1, but not a superposition).

A set of qubits called quantum register, can be visualized in a number of ways, typically as a 2D or 3D graph, on which points or bars represent the “weight” superpositions of qubits, while their color or bar height represent the “strength” (amplitude and phase) of a given superposition.

An interesting property of quantum gates is their reversibility, allowing for program execution both forward and in reverse without any side-effects.

The problem is no longer getting an answer, but asking the right question.

Natural Language Processing, Cognitive Computing, Quantum Computing… if you don’t want to fear your rapidly approaching new overlords, better start learning and programming them NOW.

AI is coming


Barack and Michelle Obama congratulate us on our wedding

A couple days ago, when we returned home from the SVA Theatre at the School of Visual Arts, where we were invited to attend the screening of selected videos by winners and finalists from the 2013 Los Angeles Music Video Festival (and an interesting panel discussion with Bob Giraldi, Christopher Walters, Steven Gottlieb, Scott Reich, August Schram, and others), we found this in our mailbox:

White House card

Corporate cowardice, political hypocrisy

On July 25 I was asked by someone at IBM to write an article about the use of the cloud in healthcare:

I’d like to offer you the opportunity to author an article which we would look to promote across all of our social properties, other external communications as well as our paid media sponsorships, i.e. blogs.

I was given suggestions on article length, topic, and keywords, but freedom to write whatever I wanted. So I did (you can find it here) on July 31.

On August 7, I received the following feedback (and two more points about sources and brands):

Thanks for the submission. I shared this with my team and they have requested some edits.

We need to avoid calling attention to controversial news, i.e., National Security Agency 

I replied the same day:

On the contrary, we need to address it.
The market, customers, are talking about it.
When you mention “cloud”, the first thing they say now is “fear” (even more than ever before). Particularly in Healthcare.
Many of those customers are from other countries, or working in international networks, so it is of particular concern to them that a government may breach their laws and make them liable.

I believe I have addressed it in a “non-controversial”, “non-partisan”, “non-beligerant” manner. My own personal opinion is much much stronger. But since this is a professional article, I have kept it professional. For that very same reason, I believe this issue must be addressed.

To which I received this reply:

Jorge,  I understand your view regarding the point below, but unfortunately I have been advised by our comms team that we can not publish an article with this content. 

And this is what I had to say to that:

With all my respects to your comms team:

“Recent revelations about the extent to which the NSA obtains electronic data from third-parties will likely have an immediate and lasting impact on the competitiveness of the U.S. cloud computing industry if foreign customers decide the risks of storing data with a U.S. company outweigh the benefits. Unless the White House or Congress acts soon, the U.S. cloud computing industry stands to lose $22 to $35 billion over the next three years.”
Source: The Information Technology & Innovation Foundation

You are seeing a $35 BILLION train coming at you and you want to look somewhere else? If you don’t address the issue, your customers will be the ones looking somewhere else. And the way to address the issue is through transparency.

Sorry, my personal convictions and ethics are stronger than my ego or the need for publicity of my company. Without that aspect on my article, I can not publish it.
I am willing to work on the wording, but any article on the cloud today needs to address the issue.

The next day, the final word came:

I appreciate all your efforts, but it might be best if you don’t continue with this article. 

And here is what I have to say about that decision:

Corporate cowardice makes me sick, and it is toxic. Such meekness betrays not only a lack of ethical courage, but also a poor sense of where their real interest lie. Sure, it is easy to understand that individuals are afraid to loose their job (from the advertising exec being fired by the VP of Marketing to the CEO being ousted by the C-Board, who is afraid of stockholders, who are afraid of media, who are afraid of government, who is afraid of lobbies and the military-industrial complex…). But its also easy to understand that soldiers have to follow orders, even when those orders mean committing crimes. And then its all about punishing the whistle blower.

As a society, we owe to ourselves to be clear, transparent, and honest. Corporations are not different than that. Only those who sell “concepts” have to hide behind the “appearance”. And that is the problem. We are constantly sold things we don’t need, or worse, things that are bad for us. From junk food to addictive pharmaceuticals that alleviate symptoms but do not cure the cause of disease, to airport body scanners that are dangerous to our health, to operating systems designed to spy on you. Everybody has come to believe that “we” are consumers, tax-payers, statistics, and “they” are profit-maximizing machines. But that is not true. Corporations are made of people. People who can and should make decisions and be responsible for them. People who have or should have ethics.

Why is everybody hiding behind a title, a badge, a desk, a uniform?

The more aggressive the behavior, whether it be through censorship, or through forceful compliance, the more it shows weakness and fear.

Take the Government of the U.S.A. Hiding behind a “sounds-so-good-I-want-to-believe-it” “humanitarian” excuse, planning the bombing of another country. Use of chemicals on civilians regardless of the 1925 convention you say? How about the U.S.A. using millions of gallons of Napalm and Agent Orange in Vietnam in the sixties? That caused over 4 million dioxin victims. Or take the Gulf War syndrome: depleted uranium, sarin gas, pyridostigmine, organophosphate pesticides… The US Government and military again using chemicals weapons against an enemy and exposing his own troops! That was 1991.

Don’t get me wrong: what Assad is doing with his own people is a crime. A crime Western countries knew about for decades (and now, thanks to Manning, we know that and the NY Times writes about it, but Manning continues in jail for giving us proof of the big hypocrisy). But so was the US using the army against striking coal miners in the 1920-21 West Virginia coal wars. And nobody paid for it. Or the Kent State student massacre by the Ohio National Guard in 1970. Or Abu Ghraib. Or Guantanamo. Or… you get the point.

So the political hypocrisy is colossal. Why does the US Government need it? If you are the biggest and mightiest, you don’t need excuses to bully your weight around a region you want to control for oil (or rare earth minerals, or whatever the resource happens to be at any point in history). A region that was messed up largely by the USA and the UK even before “the victors” threw it into forced conflict by drawing artificial borders after WWII. 

But here comes fear: it was fear of the communist, then fear of losing control of military bases, then fear of losing key resources, then fear of terrorists… it’s a weak and paranoid state afraid of its own shadow. This is not even a great and mighty empire. It will never be respected. And with such hypocrisy, it will never even be feared. Other countries have sustained millions of lost lives pursuing principles or defending themselves. No excuses, no fear. And after their ordeals, they have gone back to living their peaceful and cooperative lives. Why can’t the USA do the same?

The USA “sells itself” as the defender of international law and order. But then it should start with its own actions. And look everywhere. Somalia, Sudan, Congo, Kenya, Yemen, Chad, Afghanistan… Or is it that only those with strategic interest (military, resources) “deserve” help? Perhaps it is shameful that most of those crises have been directly or indirectly been caused by US intervention in other countries’ affairs? 

“A matter of resources”, you say. “We can not be everywhere and help everyone” (if by help you mean bombing, and financing assassins and terrorist, supporting military coups, etc).

Another fallacy. There are resources. Lots of resources. Discretionary budget to be assigned to whatever government chooses. There was money to bail out unsupervised greedy private banks. Why aren’t those nationalized? Why aren’t all their executives in jail? 

And that happens everywhere. The Spanish Government says there is no money for public schools, public healthcare, or research. They are taking the dangerous and failed austerity approach as prescribed by Germany (Greece and Portugal should have been examples enough). But when it comes to politicians’ salaries, Olympic Games bids, or bailing out failed private banks with proven ties to corrupt politicians, there is money, lots of money.

FEAR. That is the reason. Fear to lose the next election. Fear to lose the private jet, or not to be able to pay the mortgage. Eventually just fear to lose power and riches. But we are born naked. We leave this world alone. Like Samurais, Buddhism, Søren Kierkegaard, or bad sci-fi movies say “Danger is real. But fear is a choice.” And sometimes we create danger by being afraid.

Our life begins to end the day we  become silent about things that matter

I Have a dream speech. Martin Luther King Jr.

Speak up. Take a stand. Don’t hide behind a desk, a title, a badge, a uniform. 

“What can I do?” you ask. That’s another post. Coming up. Stay tuned. But in the meantime: gather information, facts, data, think, debate, and take a stand. And above all, don’t be afraid.

I am requested to take a link down and… Streisand effect!

Today I received this email (it was in Spanish, I have translated it into English because that is the main language of this blog, and in order to give this issue the international coverage that it deserves – sorry for any translation mistake since I am not a lawyer and he writes like an old-fashioned one trying to sound intimidating; here is the original):

Mr. Cortell:

Currently I am suing Greg Prévôt in the Courts of Barcelona, author of a defamatory site which infringes upon my honor, whose link appears in which you administer, at the following address: 

I presuppose your good faith and understand that the comment with the link to the defamatory web has so far escaped your supervision as editor and moderator. However, given the blatantly criminal content of the linked web, as soon as you gain knowledge of its existence, you are bound to not spread it, since otherwise you would breach the duty of minimum care required of every Internet service provider and would be criminally imputable as necessary collaborator to Greg Prévôt.

The content of the page object of the complaint, temporarily suspended by the author to prevent criminality, is available still using the “cached” function by Google:

http://webcache.googleusercontent. com/search? 

I also have in my power a public deed also proving this point.

I hereby request that within five days you remove the link in your page to “Cyberspace trolls“, and notify me about it.

While I hope and wish for your immediate cooperation in order to solve this unpleasant matter amicably, I beg you not to underestimate my firm resolution to take all legal actions the law allows me in the legitimate defense of my interests.


Daniel Vincent


And this is what I answered:

Mr. Daniel Vincent, if that is your name,

Let me reply to your message.

I find it disgusting that Spanish law (or any other country’s) try to find web/blog administrators responsible for the comments of third parties, especially when these are non-profit and the administrator has not participated in the speech or debate.

While neither I nor my blog reside in Spain, and therefore your legal threat does not worry me in the least, your tone and attitude do bother me.

The referred link is inoperative. It does not lead to any website, so it not only can not be defamatory, but it can not be verified by me either.

Additionally, the link you provide as reference does not lead to any website, leaving me, again, unable to check anything.

You state in your message that you “also have in my power a public deed also proving this point” without even describing or giving proof, which is of no use to me.

You understand that under these circumstances, and since you are unable to prove your allegations, I flatly refuse to censor anyone.

Moreover, since you seem to show preference for threats (“you are bound to not spread it, since otherwise you would breach the duty of minimum care required of every Internet service provider and would be criminally chargeable as necessary collaborator”), belligerence (“given the blatantly criminal content”), ultimatums and poor grammar [in Spanish, corrected in English] (“I hereby request that within five days you remove the link in your page”), in your own words,” I beg you not to underestimate my firm resolution.”

In my case, my firm resolve to defend the presumption of innocence, to avoid censorship, to fight against unfair laws and those who abuse with them, and not to get intimidated by strangers, as you do not give any proof of your identity, especially writing from an email like

Despite our profound differences of personal opinion, let me give you some advice from someone who has gone through slander and cyber disputes with ruthless mafias: let it be. Otherwise, do you know the “Streisand Effect?”, well, there you have it.

One last comment: I do not wish to receive further communications from you. I hope that as a connoisseur of telecommunications laws, you understand what this means.


Jorge Cortell

And this is how the movie industry chokes itself

On May 13th, on my way to a friend’s apartment, we stumbled upon the set of Ben Stiller’s new movie right outside the 125th St. subway exit. They were filming in the middle of the street. What struck me the most was that one of the façades of the building had been completely redone (cast, cement, wood, paint… it looked absolutely real and solid) for the film.

Really? No building façade will do? They had to build a complete new one?

That is exactly what is wrong with the film industry. It’s an industry. Mr. Stiller is a star, and he does not have time to move around. Efficiency over cost. It doesn’t matter how much it costs, it must be done this way, on this day. The contract. The producers. Promotion. Deadlines…

Of course movies end up costing millions of dollars. And they could cost billions if there was such a return.

It’s a formula. An industry. Predictable (or so they like to think and try) returns. Which needs predictable environments. No unions. No imagination. No technology innovations. No criticism. No tendencies. No art. No nothing but block buster after block buster. 

Have you noticed how some “friends” make movie after movie together? Do you think it is because they have “chemistry”?

Then these people meet and splurge and demand that they be “defended” because they “create jobs”. Just like any criminal organization, or political party, or  any other group involved in monetary exchange.

We have to suffer copyright and DRM restrictions on our rights and access to culture so they can create mostly trash and force illegal distribution budling deals. We have to suffer fallacious ads in the subway saying “Film production generates $400 million in tax revenues for NY, with equals to the salary of thousands of firefighters” while they hide the fact that the film industry received $420 million tax “incentives” in New York.

And that is how the industry chokes (itself). Concentrating on money, revenue and return, and demanding “protection”, instead of offering innovation, access and quality.