I'm the author of Airpocalypse, a medical thriller


Welcome to the digital era of biology (and to this modest blog I started in early 2005).

To cure many diseases, like cancer or cystic fibrosis, we will need to target genes (mutations, for ex.), not organs! I am convinced that the future of replacement medicine (organ transplant) is genomics (the science of the human genome). In 10 years we will be replacing (modifying) genes; not organs!


Anticipating the $100 genome era and the P4™ medicine revolution. P4 Medicine (Predictive, Personalized, Preventive, & Participatory): Catalyzing a Revolution from Reactive to Proactive Medicine.


I am an early adopter of scientific MOOCs. I've earned myself four MIT digital diplomas: 7.00x, 7.28x1, 7.28.x2 and 7QBWx. Instructor of 7.00x: Eric Lander PhD.

Upcoming books: Airpocalypse, a medical thriller (action taking place in Beijing) 2017; Jesus CRISPR Superstar, a sci-fi -- French title: La Passion du CRISPR (2018).

I love Genomics. Would you rather donate your data, or... your vital organs? Imagine all the people sharing their data...

Audio files on this blog are Windows files ; if you have a Mac, you might want to use VLC (http://www.videolan.org) to read them.

Concernant les fichiers son ou audio (audio files) sur ce blog : ce sont des fichiers Windows ; pour les lire sur Mac, il faut les ouvrir avec VLC (http://www.videolan.org).


Why you need to have a purpose in life: "Having a purpose reduces your defenses to change."


Photo : Marie Berry

"Having a purpose can even repair damaged chromosomes!"

http://www.dungbeetle.org

Grant Lichtman's upcoming book "The Road Ahead: Leading Learning in a Time of Change": "Change in schools is not hard; it is uncomfortable." Big difference

"Nonsurgical Fix Could Replace Open-Heart Surgery, Study Suggests"

"Medtronic Inc.’s CoreValve is photographed at an American College of Cardiology Conference in Washington, on Saturday. A new study gives a big boost to fixing a bad aortic valve, the heart's main gate, without open-heart surgery."
"A new study gives a big boost to fixing a bad aortic valve, the heart's main gate, without open-heart surgery. Survival rates were better one year later for people who had a new valve placed through a tube into an artery instead.
The results were reported Saturday at an American College of Cardiology conference in Washington and prompted some doctors to predict that in the near future, far fewer people will be having the traditional operation.
'It's going to be very hard to tell a patient that if they need an aortic valve, surgery is going to be their best option,' said one of the conference leaders, Dr. Prediman K. Shah of Cedars Sinai Heart Institute in Los Angeles.
Several hundred thousand Americans have a bad aortic valve, which can stiffen and narrow with age, keeping blood from passing through as it should. Until a few years ago, the only solution was a major operation to open the chest, cut out the bad valve and sew in a new one.

Earlier this year, (...) Medtronic Inc.'s CoreValve was approved for treating people at too high risk to have surgery. The new study tested it in nearly 800 people less sick — eligible for the operation but still with elevated risks.
One year after treatment, 19 percent of the surgery patients but only 14 percent of those given a CoreValve had died.
'It's a great leap forward' for fixing valves through blood vessels, said Dr. David Kandzari of Piedmont Heart Institute in Atlanta.
The study was paid for by Medtronic, and many study leaders consult for Medtronic, Edwards or other heart device makers. Results also were published online by the New England Journal of Medicine."


Cloudera Launches Data Scientist Certification

http://www.datacenterknowledge.com/archives/2014/03/28/cloudera-launches-data-scientist-certification
"Concurrent’s application platform for big data is certified with the Intel Data Platform, Datameer 4.0 introduces 'flip side' view for big data analytics workflow, and Cloudera addresses the industry need for big data skills with a certification program and big data challenge for data scientists."

Cloudera launches certified data scientist program. Cloudera announced the industry’s first hands-on data science certification, called Cloudera Certified Professional: Data Scientist (CCP:DS). Consisting of an essentials exam and data science challenge, the new program helps developers, analysts, statisticians, and engineers get experience with relevant big data tools and techniques and validate their abilities while helping prospective employers identify elite, highly skilled data scientists. The demand for data scientists is at an all-time high, and they possess a rare combination of engineering capabilities, statistical skills, and subject matter expertise that is difficult to find. Once candidates have passed the Data Science Essentials exam, they must then successfully complete a Cloudera Data Science Challenge, offered twice annually. Cloudera’s second Data Science Challenge opens on March 31 and is about detecting anomalies in Medicare claims.

"IBM’s Watson Tackles Genetics-Driven Brain Cancer Treatments"


"IBM’s Watson supercomputer is again expanding its reach into medicine, this time through a partnership between IBM and the New York Genome Center. The new project will analyze genetic mutations present in tumor genomes, with hopes of then discovering treatments that could target those specific mutations.
This new genome-focused approach to cancer treatment is not entirely science fiction. Researchers have been studying tumor genomes and the mutation within them for years. Throughout that research, the focus has been first on identifying mutations, and then on discovering whether those mutations are harmful. Pharmaceutical companies are piggy backing on that early work to begin creating new treatment options that can target and neutralize the harmful mutations.
At this point, there is a significant amount of data available on harmful genome mutations. The problem with applying these findings in the clinical setting is that there is no central database of genome information. As each mutation was studied, a research paper was published with the details of what was discovered about it. The data has not been consolidated into a searchable database to date, leaving oncologists with no way of sequencing a patients tumor, and then reviewing the individual mutations, their positive or negative affect, and any potential therapies that have been identified thus far for combating those negative mutations.
Enter Watson. With 23 million medical research studies within its database, researchers are hoping that it can power a new application that will analyze a patients genetic mutations and then present oncologists with recommended treatment plans that will target the most damaging of those mutations with medications that have been shown to work in other trials. Each patients overall treatment plan would likely be different, but would be optimized for their tutors genetic makeup.
To start the project will focus on a brain cancer known as glioblastoma. Robert B. Darnell, an oncologist and president of the New York Genome Center explains, 'It’s as close to a death sentence as you can get.' Patients typically survive a year after diagnosis, and surgery, radiation and chemotherapy have only been able to extend like by an average of two months.
For the project, 20 patients will be selected, their tumors will be genetically sequenced, and then Watson will have the opportunity to search its database of medical literature to create a treatment plan that will address the tumors harmful mutations. Watson will be free to recommend any treatments, including drugs that may have been studied in conjunction with other cancers, but never glioblastoma.  Oncologists and pharmacists will review the recommendations and move forward with the treatment plan based on the their clinical judgment.
A major drawback with Watson is that the supercomputer has only been loaded with the abstracts from the 23 million studies it has access too, rather than the full text papers. Some oncologists question whether Watson will be able to generate clinically viable treatment plans given the limited amount of detail within its data set. Heidi L. Rehm, a molecular geneticist at Brigham and Women’s Hospital, commented, 'It’s only as good as the data going in.'
Because this particular cancer is so devastating, researchers are hopeful that they will know whether Watson’s recommendations are helping in a relatively shot period of time."

Source: http://histalkmobile.com/ibms-watson-tackles-genetics-driven-brain-cancer-treatments

"About A Boy: 3D Printed Heart Model Saves Young Life"

http://www.forbes.com/sites/tjmccue/2014/02/26/about-a-boy-3d-printed-heart-model-saves-young-life
"'If a picture is worth 1,000 words, then a model is worth 1,000 pictures,' said Gornet, whose center had already done models of spinal defects and tumors.
Using data from thousands of cross-sections of hospital X-rays, Gornet chose a flexible polymer known as ‘Ninja Flex’ to create a 3-D model. In about 20 hours on a $2,500 printer, he created a replica of the heart at a cost of about $600.
The world of bioprinting is rapidly changing how we think about healthcare and healing. In this young boy’s case, his heart was modeled with 3D software, and that helped surgeons see the problems and create solutions before the critical moments of surgery. Stanford researchers have been reporting progress on modeling the heart and other organs.
Scientists and doctors are teaming up all around the world to print organs, layer by layer, with 3D printing technologies. From 3d printed livers at San Diego-based bio-printing company Organovo to 3d printing skin cells at Wake Forest University, all from your own cells.
The story of this 14 month-old baby is inspiring and amazing, if you pause to think about it. By thinking about other options, surgeon Erle Austin found a way, via a savvy engineering team with a MakerBot 3d printer, to save the child before he started the critical surgery.

Correction: I originally put Erie for Dr. Austin’s first name. His full name is Erle H. Austin III." (Source)

"How To Decode A Genome In Just A Single Day"

http://www.fastcompany.com/3028107/healthware/how-to-decode-a-genome-in-just-a-single-day
"Other Intel partners in the genomics sphere include London's Francis Crick Institute and the Beijing Genomics Institute. Dishman added that '(We work) on the technical challenges. We need to make the computer as fast as possible and then there's the storage. This is some of the biggest of big data, if you generate a file every time a patient goes to the clinic, someday that will be a huge problem.' The end goal? To make the Broad's genomics programs 'hum like a well-tuned engine.'"

Eric Dishman, TED: "Healthcare should be a team sport"

"DIY Chromosomes"


http://www.economist.com/news/science-and-technology/21599754-first-synthetic-chromosome-creature-complex-cells-designed?fsrc=scn/tw_ec/diy_chromosomes

Fabrication de la vie artificielle : des applications qui vont concerner les médicaments rares, vaccins et biocarburants

http://www.generation-nt.com/vie-artificielle-chercheurs-synthetisent-chromosome-levure-actualite-1870422.html
"Grâce à ce succès et à une technique éprouvée, les chercheurs vont désormais pouvoir manipuler le génome de la levure dans le but de lui offrir de nouvelles propriétés. L'idée étant d'arriver à produire des levures capables de fabriquer des médicaments rares, des vaccins, ou certaines substances difficiles ou impossibles à synthétiser directement.
Mais l'application pourrait également déborder dans d'autres domaines que le milieu médical. On pourrait ainsi concevoir des levures capables de produire des biocarburants plus efficaces. Enfin, ce premier pas dans la création de vie artificielle pourrait également amener à la création d'une nouvelle forme de vie, c'est alors qu'interviennent les questions d'éthiques et l'encadrement d'éventuelles dérives expérimentales. L'institut Pasteur a déjà déclaré 'Même si la levure n'est pas considérée comme un organisme risqué, une charte de bonne conduite a été conçue pour encadrer ces travaux et signée par tous les participants.'" (Source)

"First comprehensive atlas of human gene activity released"


http://tinyurl.com/q4cw4ug

http://tinyurl.com/q4cw4ug

Kurzweil: Simulated human liver achieved in 'benchtop human' project

"3-D imaging and electron microscopy to see high res cellular structures"

Eric Topol MD's review on genomic medicine: "the human panor-omic info"

"That each of us is truly biologically unique, extending to even monozygotic, 'identical' twins, is not fully appreciated. Now that it is possible to perform a comprehensive 'omic' assessment of an individual, including one’s DNA and RNA sequence and at least some characterization of one’s proteome, metabolome, microbiome, autoantibodies, and epigenome, it has become abundantly clear that each of us has truly one-of-a-kind biological content. Well beyond the allure of the matchless fingerprint or snowflake concept, these singular, individual data and information set up a remarkable and unprecedented opportunity to improve medical treatment and develop preventive strategies to preserve health." (Source)

"Artificial Genetic Sequencing may create new life forms"

"Families Would Welcome Alzheimer’s Screening, But Task Force Says It’s Too Early"

Breast Cancer: BRCA1&2 15%, other known genetic factors 35%, unexplained 50%

http://www.sciencemag.org/content/343/6178/1466.abstract

Healthcare oriented sensor tech on the rise with Basis-Intel. The rest is just wellbeing oriented cuz that's what the market is ready for


23 & Microsoft


"Dozens of global Digital Health accelerators & incubators listed" By Paul Sonnier

I ❤ (Genomic) Microsoft


Microsoft and 23&Me working together? Welcome to the era of digital biology


"Watch A Woman Get A 3D Printed Skull"

http://www.cnet.com/news/woman-gets-a-3d-printed-skull-and-you-can-watch

"First Day Of Tomorrow" in Paris -- April 18-19/2014. Book now!




https://www.eventbrite.fr/e/the-first-day-of-tomorrow-tickets-10710217549

Xavier DuportetPhD Student in Synthetic Biology, an "Hyperactive scientist and creative entrepreneur", (twitter handle: @duportet), is the event organizer.

"Biohackers, you should get your earlybird tickets asap!"

 

"For the first time in Paris, we're gathering all these biotech & DIY/DIYBIO superstars!
Founder of the Arduino, Founder of Genspace, VP Research of SynBio leader Amyris, Inventor of the lab grown hamburger, HAXLR8R mentor, inventor of the iKnife, the medical 3D printing guru, European Inventor of the Year 2013, founder of SynBioAxlr8r, Andrew Hessel from Singularity University, IndieGogo executive, CEO Global BioEnergies, CEO IntelClinic, CEO QuantuMDx, CSO BreakoutLabs and many more!!"

Genomic analysis to "switch from 80% research in 2013 to 80% clinical in 3-5 years"

"Whole-Genome Sequencing in Newborns: Good points on 'proceed with caution'"


http://stm.sciencemag.org/content/6/229/229cm2

"I Take Risks. I Am A Scientist."

"Tell us why you think personal genetics matters to medicine"

Genomic Confidence


Cancer Signalling

SCIENCE ON GOOGLE+

Self-powered, biodegradable (heart) implants?

A game to map the brain

I ❤ Genomic NY



"Men occasionally stumble over the truth..."

"The only way to do great work..."

Former Yale President Richard Levin to head Coursera

http://www.buzzfeed.com/mollyhensleyclancy/former-yale-president-will-become-new-ceo-of-online-educatio

"IBM Watson is using big data analytics to address healthcare's hierarchy of four needs"


http://www.techrepublic.com/article/ibm-watsons-impressive-healthcare-analytics-capabilities-continue-to-evolve

Cognitive Computing To Be The Standard For Big Data Analytics

http://ww2.saffrontech.com



"Instead of bringing data to computation as we do today, we can now bring computation to data."

"From 140 base pairs a year to 65 million a second."

"Engineers design new hybrid materials that combine bacterial cells with nonliving elements"

MIT neuroscientists classify retinal neurons into 15 types, ncluding some previously unknown

"The researchers believe there may be still more types of neurons that did not appear in their data set and remain to be identified. In future work, they hope to examine larger sets of neurons in hopes of finding some of these other neuron types. They also hope to use their technique to study parts of the brain that have many layers of neurons — especially the neocortex, where most cognitive functions take place." (Source)

Small molecule makes glioblastoma cells explode

2B2I: "Too Busy To Improve"


"Linguists are like vacuum cleaners..."

https://www.coursera.org/course/logic1
Barbara Partee works at the intersection of linguistics and logic. She brought linguistics and formal logic together. Recently, she wrote: "Reflections of a Formal Semanticist as of February 2005". Link to PDF version here.

Great course on logic, now live on MOOC plateform Coursera!

https://www.coursera.org/course/logic1
Very busy studying right now...

"How next-generation sequencing and families are altering the way rare diseases are discovered, studied, and treated"

http://www.nature.com/gim/journal/vaop/ncurrent/full/gim201423a.html

To cure cancer, we'll need to target gene mutations; not the organ

"Want Watson To Meet Prof Lander Too!"

https://www.facebook.com/700xIntroToBiology
"Anyone interested in taking more MITx biology courses on edX? More information to come regarding a third release of 7.00x and a new course in June 2014. Registration is not open yet."

The hierarchy in your brain: Ray Kurzweil at TED 2014

"Kurzweil predicts that in 20 years nano-bots will enter the brain through capillaries to connect us to a synthetic neocortex in the cloud. So if someone walks past you whom you want to impress, but your 300 million modules aren’t enough to come up with something clever to say, all you need to do is tap into the neocortex in the cloud and another billion modules will become available. The future human, says Kurzweil, will be a biological and nonbiological hybrid.
Two million years ago when we developed large foreheads, it was a quantitative increase that led to a vast qualitative explosion – of art, culture and technology. In the next few decades, Kurzweil predicts, we’re going to do it again: And this time, 'We won’t be limited by the fixed architecture of the enclosure. We will expand without limits.'"

http://blog.ted.com/2014/03/20/the-hierarchy-in-your-brain-ray-kurzweil-at-ted2014/

How the invention of the alphabet usurped female power in society sparked the rise of patriarchy

http://www.brainpickings.org

Any "IBM Watson" Brain Cancer Patients at the NY Genome Center Interested In #TheWalkingGallery Project?

"IBM's Watson Attempts To Tackle The Genetics Of Brain Cancer: IBM and the New York Genome Center announced a partnership to test whether Watson, the computer that won on Jeopardy, can sift through the genomes of cancer patients and help doctors pick drugs. This effort could hold the key to making DNA sequencing for cancer affordable, but there is a vast amount of work to do that will take years at a minimum.
The effort is starting small, looking at 25 patients with glioblastoma multiforme, a rare brain cancer that is almost always fatal. Without treatment median survival is only a few months; surgery, drugs, and radiation extend that to about a year." (Source).
 



Find out about project on Twitter!


Google invites geneticists to upload DNA data to cloud for research

Which countries read this blog?


The Jacket of A Wounded Healer Is Not A Doctor's White Coat

I'm a big fan of #TheWalkingGallery, by American paintress Regina Holliday. Great ideas, great art, talented people... Engaged art at its best, and we need it! -> #CDoM

What does "Creative Destruction of Medicine" (#CDoM on Twitter) mean? Read here.

Breakthrough of 3D Printing DNA in Cancer Prescription

Understanding living things, legos & cancer-killing viruses

The virtual autopsy table

"Robot surgeons, BART trains, 3D printers and drones, oh my!"

Toys and games company @MakieLab makes 3D printed toys that are game enabled

A pinprick of blood may be all that is needed in the future to gather enough material to grow replacement organs

"We Got a Mystery to Solve."

Harvard Research Reveals EarlySense Monitoring System Reduces Length of Stay in the Hospital and ICU

IBM et son Watson en France, une interview de Jean-Michel Billaut

http://billautshow.tv/Pascal-Sempe-Ibm
Merci beaucoup à Jean-Michel Billaut et à Pascal Sempé pour cette interview passionnante !

Livre dédié à Jean-Michel Billaut : "Cliffhanger, le monde en 3013"

CLIFFHANGER PDF French Version
Auteurs : Isabelle Provost, enseignante en Histoire & Géographie, globe-trotteuse, spécialiste de l'Inde, du Pakistan et Bangladesh. Catherine Coste, diplômée du MIT en génomique.

Version anglaise en cours, avec l'aide de deux de mes profs du MIT. Cette version sera différente de celle française. Enrichie, augmentée, revue.  

"Citizen Science Project Markets Test for Damaged DNA "

http://www.scientificamerican.com/article/citizen-science-project-markets-test-for-damaged-dna/

"Physicians often share their patients’ sorrow, but rarely their joys -- A Wedding in Intensive Care"


http://opinionator.blogs.nytimes.com/2014/03/19/a-wedding-in-intensive-care/?ref=opinion

"In today’s outcome-driven, efficiency-obsessed medical world, it’s easy to forget that healing patients isn’t just about treating diseases and relieving symptoms. There are things doctors and nurses can do, meaningful interventions — like helping patients fulfill final goals or spend quality time with their families — that cannot be documented in a discharge summary or be converted into a blip on a screen."


Larry Page: "Making our medical records open for sharing will save 100,000 lives a year"

http://mhealthinsight.com/2014/03/20/larry-page-making-our-medical-records-open-for-sharing-will-save-100000-lives-a-year/

IBM Watson Helps Fight Cancer At New York Genome Center



Gene sequencing? Yeah, Watson can help with that too -- IBM Watson Welcomes You To The Digital Era Of Biology

New York Genome Center Announcing A Partnership With IBM -- Bringing Watson To Genomics

http://www.xconomy.com/new-york/2014/03/19/ny-genome-center-ibm-to-bring-watson-to-genomics/
"The deal is essentially a test run. The NYGC will use Watson to try to help oncologists tailor specific drug regimens to individual patients with glioblastoma—an aggressive form of brain cancer that typically kills people 12 to 14 months after they’re diagnosed—based on the specific genetic mutations in each patient’s tumor. The goal is to use this process to improve the standard of care for glioblastoma patients, and then expand the NYGC/Watson effort into other types of cancer. Bloom says nine hospitals and 20 neurologists, all in New York, are on board so far, but that the NYGC isn’t limiting the effort to any particular hospitals.
Here’s how the process is expected to work. Once a patient is diagnosed with glioblastoma, the NYGC will get a tumor sample. Researchers there will sequence the tumor’s genome, and analyze it to come up with a set of mutations that look like the 'drivers' for that specific patient’s tumor, Bloom says. Researchers will then feed that list of mutations into Watson, which will do all of the computational dirty work to find a list of drugs that would target them specifically.
Watson’s job will be 'to do the literature search, the drug database search, and find all the relationships between those specific mutations and drugs that are available or maybe in clinical trials that they can find, or even drugs that are related to the pathways that those mutations are associated with,' Bloom says.
From there, a team of neurologists and pharmacologists will look over the list of drugs that Watson generates, pick a set of them that they think would best work together, and recommend those to the patient’s doctor. Should the patient decide to follow the recommended regimen, the NYGC will track his condition, the rate at which the tumors spread, etc.—and then start feeding that information back into Watson.
'So we’ll be giving Watson back information about combinations of mutations, combinations of drugs, and the outcomes of using those drugs on those mutations,' Bloom says. 'That’s a very complex set of associations, and we’re hoping that Watson, and Watson’s learning model, can then find information in that that we can not see so fast.'
The study hasn’t started as of yet, but the hope is that as more patients start undergoing treatment, and more data is fed to Watson, the computer will find things researchers wouldn’t, and 'we can iterate more quickly and improve care more quickly,' Bloom says. Assuming the lists Watson produces leads to treatment regimens that helps patients keep tumors in check longer, and live longer—which has yet to be seen—the project would then expand. Presumably, Watson would also be used by other genome centers as well (the NYGC does not have an exclusive license).
'There are 1,700 glioblastoma patients in NY every year,' Bloom says. 'So there’s a lot to be done in New York.'" (Source).


Understanding the biology of the disease:
http://www.nygenome.org/events/revolutionizing-genomics-personalized-medicine-ibm-watson/

IBM Watson coming to London!

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Find Kindle version of this book on Amazon
http://www.kurzweilai.net/smart-machines-ibms-watson-and-the-era-of-cognitive-computing
Catherine Coste, author of this blog. I come from France, native german speaker. Previously, I earned a certificate in a genomic course, "7.00x the secret of life" MITx (edX). I love languages, genomics. Post-graduate in German litterature and language (La Sorbonne, Paris). Fascinated in IBM Watson. Currently a MOOC student: "Logic: Language and Information 1", University of Melbourne, Coursera -- study of Watson analytics included in this MOOC!


Translating the potential of genomic medicine into routine healthcare is what I am most enthusiastic about. Working on a genetically coded computer, with switches that are in DNA code (A-T-C-G); not in bit code (1-0), designing life, the business and the ethics of synthetic biology, targeting gene mutations to cure cancer; not the organs: I want to be part of it! Interoperability is what Watson is about.

Interoperability? Does this mean that Google Glass and Watson (as an app for iPhone & Google phone) and iBlue Button (with Microsoft Health Vault) and Human Longevity Inc.
and AliveCor Heart Monitor and Scanadu (a handheld medical "tricorder") and the cloud will interact?! I am not a techy person, however I am at my best when working with them.

Since the digital age of biology is a revolution that is happening right now under our feet, we all need to anticipate the $100 genome era and the P4™ medicine revolution -- P4 Medicine (Predictive, Personalized, Preventive, & Participatory), which is catalyzing a Revolution from Reactive to Proactive Medicine.  




Valérie Cabaret-Bourgoin, French paintress. "Not So Blind", 100x80 cm, 2014.

An expat wannabe, I realize that nothing much is going on in France (my country), where it is forbidden by law to have your genome sequenced.

Genomics and Watson is the equation at hand. Eric Lander PhD says we will need one or two decades before we can turn cancer into some kind of chronic disease... Hope Watson helps us speed up the process a little bit...