This Revolution needs a Revolution

Yesterday I went with my wife and son to visit the Victoria & Albert’s Museum exhibition You Say You Want a Revolution? Records and Rebels 1966-1970. The aim of the exhibition was quite clear:

How have the finished and unfinished revolutions of the late 1960s changed the way we live today and think about the future?

I was very much looking forward to visiting the exhibition. It is SO timely, and SO needed, I thought.

After visiting it, I left enraged. Why? After all, it was very well “put together”, full of artifacts and information, with a fancy sound system, and beautifully arranged and orchestrated.

ORGANIZED

More importantly, it was not a nostalgic attempt at regurgitating old revolutionary slogans.

What enraged me is how co-opted the whole collection felt. How all those efforts and sacrifices, how all that energy and suffering from past revolutionaries, has been assimilated by the system.

From the ® Registered slogans to the “no photographs” signs at the entrance (to which I, OF COURSE, paid no attention to whatsoever):

® slogan!

To the texts denouncing powerful corporations and states controlling Western media making it difficult to broadcast alternative opinions. You don’t say??!! How about adding “even museums”?

You don't say??!!

Of course, the whole thing had a watered down flavor, “ready for the masses to consume it” (at over£17 or over $20 per ticket). Not just because of the large dedicated-store (“Exit through the gift store” as Banksy brilliantly highlighted), where many appealing objects were for sale for nostalgics and revolutionary wannabes.

Interesting mash up poster

But also for the paternalistic tone of the whole exhibition, surgically isolating issues (identity, sexuality, peace, music, fashion…), even (correctly) including the new contemporary totemic theological substitute: technology.

Origins of Personal Computers

I was very happy and proud to tell my son that his grandmother was in Paris throwing cobblestones to the police in the student revolts of 1969; that his grandfather took me, when I was a little kid, to see a forbidden theater play during Spain’s democratic transition, fearing the secret police repression; that I participated as a kid in discussions with adults about anarchism and communism, when both were outlawed in Spain; and that I have participated in some of the revolutions and protests that came in the decades after that.

I’m not angry because they took “my” revolutions and repackaged them for easy digestion by accommodating masses. That was foreseeable, and an obvious result of the reigning empire of consumerist capitalism.

I’m not even nostalgically refusing to accept that times have changed.

What really annoyed me and made me angry was the lack of reference to a combative present, to the continuation of the struggle.

The fact that they showed, at the end of the exhibition “How have the finished and unfinished revolutions of the late 1960s changed the way we live today” but completely left out “and think about the future” is what enraged me. Particularly as Trump is president in the USA, May PM in GB, the PP rule Spain, the far right advances in France…

We need to remember that the fight is not over, that fascism is not only back, but stronger and more powerful than ever. We, all of us, and the institutions that serve us, including museums, have a duty to promote thoughtful debate around ethics and values, and fiercely protest and fight through self-organisation, unity, and collaboration. We owe it to ourselves, we owe it to those who fought for us in the past, we owe it to those who will come after us.

If the urban bourgeoisie wants to be the first to fall under the boot of the oppressors again, so be it. If proto and pseudo-intellectuals endlessly self-delude themselves into thinking that our democracies and institutions will save us from authoritarian demagogues, fascist megalomaniacs, and our own blind pursuit of endless consumerism, so be it. In the meantime, I will be teaching my children about the struggle and participating in the smartest and most effective way I can.

My EU policy recommendation published: “Hacking Policy. Exploring Innovative Ways to Advance Policy Reform”

Under the title “Hacking Policy. Exploring Innovative Ways to Advance Policy ReformStartupEurope has published a report listing the Policy Recommendations that came out of the Policy Hackathon in San Francisco, where my team won the competition.

Download it here.

Spare time fun: protein structure analysis of mutations causing inheritable diseases

Most people I know would not consider protein structure analysis of mutations causing inheritable diseases “spare time fun”. Then again, most people I know don’t think I am like most people they know.

This week I’m a “single-dad”, since my wife is traveling. So my spare time right now is almost non existent. Nevertheless, the thought of mutating a Proline into a Glycine at position 22 intrigued me, so I spent a few minutes simulating it. Here is what I found out:

Method

The 3D-structure of my protein of interest was obtained from the UniProt database using Reprof. The structural information was obtained from the analysis of PDB: 3NIR. Annotations were obtained from UniProt entry CRAM_CRAAB.

Amino Acids

I was interested in the mutation of a Proline into a Glycine at position 22.

The figure below shows the schematic structures of the original (left) and the mutant (right) amino acid. The backbone, which is the same for each amino acid, is colored red. The side chain, unique for each amino acid, is colored black.

 mutates into 

Each amino acid has its own specific size, charge, and hydrophobicity-value. The original wild-type residue and newly introduced mutant residue differ in these properties: the mutant residue is smaller than the wild-type residue, while the wild-type residue is more hydrophobic than the mutant residue.

Variants

A mutation to “S” was found at this position, which differs from the mutation I was simulating. The effect of this variant is annotated as: In isoform SI.

Conservation

The wild-type residue is not conserved at this position. Another residue type was observed more often at this position in other homologous sequences. This means that other homologous proteins exist with that other residue type than with the wild-type residue in my protein sequence, but the other residue type is not similar to my mutant residue. Therefore, the mutation is possibly damaging.

Domains

This residue is part of an interpro domain named: Thionin IPR001010

The mutated residue is located on the surface of a domain with unknown function. The residue was not found to be in contact with other domains of which the function is known within the used structure. However, contact with other molecules or domains is still possible and might be affected by this mutation.

Amino Acid Properties

The wild-type and mutant amino acids differ in size. The mutant residue is smaller than the wild-type residue. This will cause a possible loss of external interactions.

The hydrophobicity of the wild-type and mutant residue differs. The mutation might cause loss of hydrophobic interactions with other molecules on the surface of the protein.

Images

Overview of the protein in ribbon-presentation. The protein is coloured by element; α-helix=blue, β-strand = red, turn=green, and random coil=cyan.

Overview of the protein in ribbon-presentation. The protein is coloured grey, the side chain of the mutated residue is coloured magenta and shown as small balls.

Close-up of the mutation. The protein is coloured grey, the side chains of both the wild-type and the mutant residue are shown and coloured green and red respectively.

Close-up of the mutation (seen from a slightly different angle). The protein is coloured grey, the side chains of both the wild-type and the mutant residue are shown and coloured green and red (not show from this angle) respectively.

Close-up of the mutation (seen from a slightly different angle). The protein is coloured grey, the side chains of both the wild-type and the mutant residue are shown and coloured green and red respectively.

Movies

Close-up of the mutation. Both the wild-type and mutant side chain are shown in green and red respectively. The rest of the protein is show in grey.

Close-up of the mutation, same colours as animation 1. The animation shows alternating the wild-type side chain and the mutant side chain.

Citation

Protein structure analysis of mutations causing inheritable diseases. DOI: 10.1186/1471-2105-11-548. PubMed: 21059217.

Exponential Medicine Conference San Diego day 4

Tuesday, October 11th, was day four, and last, at the Exponential Medicine Conference in San Diego.

Some of the talks I enjoyed the most:

Exponential Thinking & Future Predictions: Ray Kurzweil Co-founder & Chancellor, Singularity University

Exponential Entrepreneurship:

  • Zayna Khayat, PhD Lead, MaRS Health and Director, MaRS EXCITE
  • Stephanie Marrus, MBA Entrepreneurship Center Director, UCSF

Investing In The Future: Vinod Khosla Founder, Khosla Ventures

Visualizing the Future of Medical Education, from VR to the OR:

  • Stefano Bini, MD Professor of Orthopedics, UCSF
  • Stephen Swensen Medical Director- Leadership and Organization Development, Mayo Clinic

Synthesis- From Imagination to Innovation to Impact
Kevin Wildenhaus, PhD Behavioral Science Lead: Janssen Disease Interception Accelerator, Johnson & Johnson

And right after that, I left for the airport.

Here you can see more photos from the event.

Exponential Medicine Conference San Diego day 3

Monday, October 10th was day 3 at the Exponential Medicine Conference San Diego.

For me the highlights were:

Bold Innovation: Peter Diamandis, MD Co-Founder, Singularity University and Founder & Chair, XPRIZE

Redesigning Care: Tony Young, PhD FRCS National Clinical Director for Innovation, NHS England

Bakul Patel, MBA Associate Director of Digital Health, Food and Drug Administration/Center for Devices and Radiological Health

Getting the xMED Scrubs Photo on the Beach, with an awesome drone:

The Brain and Beyond

  • Divya Chander, MD PhD Anesthesiologist/Neuroscientist, Stanford University
  • Arshya Vahabzadeh, MD Psychiatrist, Harvard Medical School
  • Anthony Bossis, PhD Clinical Assistant Professor- Department of Psychiatry, NYU School of Medicine

Off the Planet, Remote Medicine: Scott Parazynski, MD Managing Director, Apogee Interests & 5 Time NASA Astronaut (Retired)

Security & Privacy Threats in Healthcare (And What to Do About It): Marc Goodman, Resident futurologist at the FBI, Policy Law and Ethics Faculty Chair, Singularity University and Founder, FutureCrimes

The day ended with dinner on the beach, and a beach party, with bonfire and drum circle.

Award and Exponential Medicine Conference San Diego day 2

Sunday, October 9th, was day two at Exponential Medicine Conference in San Diego.

Some of the highlights were:

From ‘Omics to Action

  • Moira Gunn, PhD Host, NPR’s Biotech Nation
  • Larry Smarr, PhD Professor, UCSD and Director, Calit2
  • George Poste, DVM PhD FRS Chief Scientist, Complex Adaptive Systems Initiative- Arizona State University

Mobile, Connected, Digital Health

  • David Albert, MD Founder, AliveCor
  • Stanley Shaw, MD PhD Co-Director, MGH Center for Assessment Technology & Continuous Health
  • Bakul Patel, MBA Associate Director of Digital Health, Food and Drug Administration/Center for Devices and Radiological Health
  • Ulrik Wisløff Professor: Faculty of Medicine, Norwegian University of Science and Technology

Innovating at Scale: John Mattison, MD CMIO and Assistant Medical Director, Kaiser Permanente

Connecting the Dots: Mark Hyman, MD Chairman, Institute for Functional Medicine

Future of Intervention

  • Catherine Mohr, MD Vice President of Strategy, Intuitive Surgical
  • Tippi MacKenzie, MD Professor of Pediatric Surgery, UCSF
  • Amir Szold, MD Chairman, Technology Committee: European Society for Endoscopic Surgery
  • Olivia Hallisey Grand Prize Winner, 2015 Google Science Fair

Disrupting Clinical Practice: Todd Huffman Founder & CEO, 3Scan

Future of Cancer

  • Marty Tenenbaum, PhD Founder, Cancer Commons and Chairman & Founder/Chairman, CommerceNet
  • Sangeeta Bhatia, MD PhD, Director of Laboratory for Multiscale Regenerative Technologies, MIT
  • David Roberts, MBA, Former Special Agent, Business and Technology Disruption Expert

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The other cool thing that happened on day 2 is that I received an award: the Precision Medicine Impact Challenge Award launched by the White House Initiative on Precision Medicine and awarded by the State of California, presented by Elizabeth Baca, MD MPA, from the California Governor’s Office.
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Exponential Medicine Conference San Diego day 1

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Saturday, October 8th, I attended day 1 of the Singularity University Exponential Medicine Conference in San Diego at the amazing Hotel Del Coronado.

The event was organized mainly by Will Weisman and the incomparable Daniel Kraft, MD (whom I met last year at the London Stock Exchange), both from Singularity University.

The Conference was fully packed with activities. Morning activities started at 7am and included Yoga, Meditation, Art, and Beach Run. Evening activities changed every day, and included things like Team Collaboration & Innovation Games, Gadget & S’mores Bar, Music & Magic at the Bar, UnConference, or Silent Disco.

There was also an expo area called The Innovation Lab, where innovative companies showcased their latest and greatest.

But, without a doubt, the most important part of the conference was the extremely interesting and thought-provoking speakers and subjects. Day 1 included, amongst many others:

  • Blockchain: Rajeev Ronanki – Principal, Deloitte Consulting; and Mariya Filipova – Healthcare Transformation, Deloitte Consulting

  • From Big Data to Actionable Information: Leroy Hood, PhD – President & Co-Founder, Institute for Systems Biology; Senior Vice President & Chief Science Officer, Providence Health & Services

We ended up the day with a beachside dinner under the stars.

 

Last day in San Francisco: ART

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Saturday, September 17, was my last day in San Francisco, and the only one I had with some spare time.

After breakfast, I went to but some gifts from Japan Town and then headed to Union Square, for the Korean Day (Chuseok) culture festival.

Then I went to the Yerba Buena Center for the Arts to check out Tom Sachs’ Space Program: Europa. As I feared, after the failure of Sony Outsider, Tom Sachs’ obsession with demonstrating his hand-made “bricolage style” continues. Further more, it feels like yet another bourgeois manboy “fun” exhibition. It is as if the art world is taking a more and more polarized position as if an artist and her work can only fit one of these buckets: escapist detachment from the hardships of everyday life, snobbish detachment from popular accessibility, or rejection of any institution or establishment.

My suspicion that Space Program: Europa was all about the first option was enhanced by the fact that I did not see any African-American person there, although I was there for quite a while. So I decided to test my thesis.

I wanted to go to the Museum of the African Diaspora, but someone told me it was closed today for a private event (later I found out it closed early, but I could have gotten in), so I went to the nearby San Francisco Museum of Modern Art instead.

The lack of diversity was beyond appalling. It was mesmerizing. In the SF MoMA store everyone was white, many blonde, tall, with perfect teeth… are you kidding me? After reading everywhere about it, and visiting so many tech companies, I knew this city has a diversity and divide problem, but this was ridiculous.

I walked into the museum, and the lack of diversity remained apparent, although diminished by the presence of a healthy number of tourists. Very sad, but it was time to focus my attention on the art.

What a collection! Of course, I enjoyed the usual suspects (Rothko, Calder, Judd, Warhol, Serra, Picasso, Mondrian, Kelly, Martin, Twombly, Sherman, Murata, Duchamp, etc) but I also got to experience some works from Roy Lichtenstein and Gerhard Richter that were not their best known (most certainly I did not know about those pieces), which gave me a completely new appreciation for them, and reminded me that you can’t judge an artist by one piece, just like you can’t judge a book by its cover.

I also enjoyed very much the exhibition “Typeface to Interface”, which had it been exhibited in NY it would have been packed with hipsters, but here it was full of techies (interface designers perhaps?). Special mention: the mesmerizing Sagmeister & Walsh video “Now is better”:

So with one delightful overdose of art, I headed to the airport to fly back to London.

I won the Anti-Patents Policy Hackathon


On September 13, Mind the Bridge hosted a policy hackathon sponsored by Dell at the MTB Innovation Center in San Francisco. The Dell PolicyHack™ brought together entrepreneurs and U.S./EU policy experts to solve policy challenges. The goal is to productively brainstorm and to provide top-line thinking that can inspire and serve as basis to develop and implement full policies.

My team was formed by:

  • Sara R. Klucking (Section Chief, Innovation & Programs, Office of Science and Technology Cooperation, US Department of State)
  • Bogdan Ceobanu (Policy Officer, Startups & Innovation, European Commission)
  • David Hodgson (CEO, Hummingbird Labs)
  • me

The five teams had 75 minutes to come up with a policy solution to issue areas that impact entrepreneurs. Each team was then be given five minutes to pitch their solution to the panel of judges formed by:

  • Pēteris Zilgalvis (Head of Unit, Startups and Innovation, European Commission)
  • John Zysman (Professor Emeritus, Political Science, UC Berkeley)
  • Burton Lee (European Entrepreneurship, Stanford University)
  • Richard Boly (Principal, Beaurichly Llp)
  • Alberto Onetti (Chairman, Mind the Bridge and Startup Europe Partnership).

Master of ceremony was Kristen Mattern (Senior Government Affairs Manager, Dell). The issue areas were: funding, trade, migration, patents, and privacy. Obviously, I chose patents.

When I started telling my team my ideas about patents (basically, how to effectively end the system, since it is so broken and dysfunctional, and what would happen), they thought I was out of my mind. But I ended up convincing them with evidence. So finally my proposals were the ones I presented . We were supposed to present as a group, but Sara and David fled right before we were up for the presentation, and Bogdan “let me do the talking” and the answering of questions.

Although the other teams did a great job, my team won!

The award: to have my ideas written in a paper that will be presented to the European Commission as “expert policy advice”.

It’s ironic: over a decade after I was lobbying against software patents in the European Commission in Brussels, having Microsoft’s lobbyist as my main adversaries, now the European Commission takes my anti-patents ideas as expert advice, and Microsoft is my free-software company’s main partner. I guess time puts everything in its place.

That’s how you hack the system from inside.

Although I never believed that was the way to real and meaningful change, at least now I can say “been there, done that”.

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!).