Scientific MOOCs follower. Author of Airpocalypse, a techno-medical thriller (Out Summer 2017)


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).


Affichage des articles dont le libellé est GENOMICS. Afficher tous les articles
Affichage des articles dont le libellé est GENOMICS. Afficher tous les articles

The Envelope Pushers



We've all heard about these books. How the future of medicine is in the patients' hands. Great. But this medicine of the future seems to suffer from a transition or procrastination problem.

Yesterday Sir John Burn MD, Professor of Clinical Genetics, Newcastle University (UK), wrote to me:

"There are still many people throughout healthcare who consider genomics as ‘nothing to do with them’. This is an attitude we need to change as the technology's ability to change people’s lives develops. There will come a time when genomics is no longer niche, but will be absorbed into medicine. It will apply to every aspect of pathology and be an integral part of care. Therefore, it is vital for everyone to know and understand its terminology and implications."

 How do we get there? Patients worldwide are starting to realize they can be in charge of their own health, especially in cases where no diagnostic could be achieved, no treatment could be offered.

Australian physician Leah Kaminsky (Melbourne) calls them the envelope pushers. For ex., Angelina Jolie in medical bestseller "The Patient Will See You Now" by Eric Topol MD (San Diego, CA, USA), but equally interesting:







1) Mission Massimo in Australia
Leah told me she is working on the sequel to this book: "Fixing the Code". I absolutely loved "Cracking the Code", this is my favorite book for 2015.
2) Mission Matéo in France
Two major differences here: Massimo's story was written by a Doctor, Leah Kaminsky. As she saw Massimo's disease (her patient, she is a pediatrician) was beyond the realm of her competence, she decided to write about the father's story. Massimo's father is actually at the center of the book: he is the envelope pusher, the pioneer. He got a diagnostic for his son where nobody else could. Leah tells about the diagnostic odyssey and reflects on some of the ways that conventional medicine and genomic medicine could find common ground.

I will meet with Leah, Massimo and his parents in Melbourne in a few days. How can we build synergies to take advantage of what pioneer patients have achieved and democratize genomic medicine? Surgeons and doctors should attend congresses about genomics; not only geneticists. And geneticists should attend medical congresses to show what can be done. Robert Darnell PhD at the NY Genome center showed his work about genomic precision medicine at the Academy of Medicine in NY.  See the Genomics and Health Care Conference, two months ago (link to videos). Doctors at the Academy of Medicine had a lot of questions for Darnell, they showed real interest.

The French case is different. Matéo did get a diagnostic, acute leukemia, but there was nothing doctors could do that was helpful. If he does not get a new treatment (CAR-T cells) he will die in a couple of months. French biotech Cellectis was not helpful. It turns out they do have a trial for the new treatment but due to regulation matters, things are being slowed down to such an extent that by the time the new drug trial starts, Matéo will be dead. So the parents looked for solutions, found this innovative treatment in the US and started a crowdfunding action (treatments are 10 times more expensive in the US than in France) to speed things up and save their son's life as no doctors seem to be in charge. The contrast between the media uproar (Matéo is now a star on French TV) and the extreme apathy of French medical establishment is mind boggling. 

While doctors are burying their heads in the sand
Matéo is taking the Future of Medicine in his hands.


Finishing my exams at MIT (genomics). Can't wait to meet with Leah, Massimo and his parents...

Jennifer Doudna: We can now edit our DNA. But let's do it wisely

NY Genome Center's Darnell Wants to Build A Consortium To Change Health Care




The Eternal Jewdi



 (by Catherine Coste)

I am the Eternal Jew
Wandering in Doctors’ Death Valley
Waiting rooms in hospitals
Waiting to see my local Doctor
I am Ahasver 
I know Wounded Valley
Like the palm of my soul.

Keep looking for the disease
Do not treat the pain
As it is the pain that will lead to the disease
Find the disease first,
Then take care of the pain.

I am the Eternal Jew
Of Chronic Pain
Bouncing and drifting
Silently pacing
From exam to exam
Useless, expensive
Invasive
Pacing and waiting
I am the Eternal Jew
I chose Death over
Careless love
But...

Death ridiculed me:
“Don’t look askance.
Find the pathway
Of your chronic pain
Or disease,
You can.

Death Valley is
Not in your genes.
Find the mutation
Crack the code
Fix it.

Do it,
You must.
Judas,
You are not.
The Eternal
Jewdi,
You are.”

Pic

Midsummer Night's Science (live from the Broad Institute, Boston MA, USA)

https://youtu.be/jQvi60EzGcU





http://www.frontlinegenomics.com/1408/front-line-genomics-magazine-issue-four

RNA (mRNA, RNAi etc.) seems to be all the rage! Can't wait to enroll for MITx EdX MOOC 7.28.2x Transcription. 7.28.1x was about DNA replication and repair. Third part -- 7.28.3x will be about translation (from RNA to proteins). Both DNA and proteins seem to be working for RNA...

"The Monster High Genome Project": Genomic musical hitting Growlway!

Genomic Entertainment: Ghouls Genome Project The Musical.


For Martin Wincker and Eric Topol MD: enjoy this nutty'n girly piece of fan art!
MonsterHigh Institute of Tech (MIT Salem), January 2014:


This morning, Operetta is rehearsing a song by Birdy: "People help the people", because she believes it to be the essence of what Internet-minded people call "2.0".
==> Operetta singing "People help the people": download audio file. 

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.

Why don't you run along and play with your chemistry set
http://www.flickriver.com/photos/nataloons/random/
"Things that are just patently absurd and impossible today turn out to be just hard a year or two from now, and turn out eventually to be a high school lab project a decade and a half from now or something like that. That's what modern biology is." Eric Lander PhD, one of the leaders of the Human Genome Project.

Genomic musical hitting Growlway?!? That's all very well (and madly ambitious), but how do you get all the way from the science of the human genome to some kind of genomic musical hitting... Growlway? Sounds like a nutty idea, doesn't it?

Well, I wanna try to tell you the whole story. I wanted to write something about our genes and about people helping the people, thanks to the Internet.

It all started with that writing assignment a friend of mine -- a Canadian writer and MD -- gave me last summer.

"Monster High", the Ughsome Musical! A writing (and singing) assignment:

==>  LINK

What happened next was... this: the ghouls thought their Mad Science teacher deserved a No-Bel Prize and they wanted to help him get it. How? Well thanks to their nutty secret project:

"The Monster High Genome Project" : Genomic musical hitting Growlway!

Special Halloween 2013! MIT Salem Students help their PhD Prof get No-Bel Prize with Genomic Musical in Growlway! 

==> LINK

But hey, wait a second! How do you get from Mad Science to some cool gene groove? I just don't get it... Well, here would be a good place to start:  

Working hard in biochemistry today... 

==> LINK

Our favorite ghouls just knew one thing: "What is in my body belongs to me. My genes belong to me. My body, my data."


"But mad science data does not translate into music, does it?," asked Operetta. She wasn't sure... How could you possibly listen to the music of your genes? 

"My Body My Data My Music": Gene Groove, The first Genomic Music App Ever!
 
==> LINK  

"Evolution is all about competition", says Clawdia, who new a thing or two about competition, as the teenager ghoul wanted nothing more than to set-up her own fashion empire. "I wanna be a smash, Marilyn wanted it, the cells in my body want it..." 

Marilyn & Marilyn and the "Evolution is about Competition" theory
 
==> LINK

That's all very well, but you know what? Mad science is made of 2% of talent plus 98% of hard work, where most people think that if you want to get a No-Bel Prize, you need 98% of talent and 2% of work (redefined as "serendipitous luck").

Oh, and just one last thing: if you want to learn how the MIT Salem ghoul students came to meet the One Direction boys band -- and then what happened?? -- I'm afraid you'll have to read... this:

The Ghoulfriends are having it their way!

==> LINK


"Well, choose me!"


https://www.facebook.com/catherine.coste

"Let me be your star" -- Bombshell/Smash, the Musical

=> Download audio file here.

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.

Or: you can download MP3 version of audio file here.

Lyrics



Not a scientist? Become one in four months with MIT 7.00x MOOC: "The Secret of Life", starting June 17, 2014. Enrol now, it's free!

MIT MOOC 7.00x "The Secret of Life"?! What's that?? To answer your question, here's the best read I was able to find:
This course will be live in June 2014! Enrol now!

https://www.edx.org/course/mitx/mitx-7-00x-introduction-biology-secret-1768#.U1eeLVfSmVq

Now, about my own experience: becoming gene savvy in four months?! How do you do that?

Healthcare consumers will need to become increasingly savvy regarding their genes...



Not a scientist? Become one in four months with MIT 7.00x MOOC: "The Secret of Life"
 (PDF Doc, 4 pages).


==> Software Tools that are being used for MIT Genomics courses: see here


Amazing!! With the help of this really "Awesome Sreenshot" software, I've been able to print each and every screen/page, with all the problem sets and midterm and final exams, including correction! 101 documents that will come in handy whenever I will feel like I need to review some or all of this stuff that gave me so much fun and challenge -- and that I came to love ;-)

When Will Genomics Cure Cancer?

IN DUE COURSE "Genomics is just picking up steam, the Broad Institute's Eric Lander tells The Atlantic. As a comparison, Lander notes that it took some 75 years to go from understanding that microbes cause infectious diseases to the widespread implementation of antibiotics to treat those diseases. 'With genomics, we're maybe halfway through that cycle — something like the situation around 1915, when early, highly imperfect antibiotics were first introduced,' he says.
Currently, genomics is working on getting a sort of parts list together for what genes are involved in certain diseases and how those genes interact in networks. While Lander says that this is not a cure for any disease, having such knowledge is influencing treatment, though it is still early days there too.
New targeted drugs for cancer, he tells The Atlantic, have been able to make certain tumors disappear, though as the tumors mutate, they find a way to recur. But now, he says, researchers can target those new mutations as well and take a lesson from how HIV has been treated to turn it into a chronic disease.
'What made it become a chronic, treatable disease? It was a combination of three drugs. Any one of those drugs alone, the virus could mutate its way around,' Lander says. 'But with the combination of all three, the chance that a virus could find its way around all of them was vanishingly small. That's what's going to be happening in cancer.' He adds, though, that it will take time and investment."

Genome Web: The Daily Scan, Jan. 09/2014

Hospitals launch genome sequencing programs to get ready for the future of medicine

Marketing and Patent (not "patient") strategy instead of R&D: no wonder we're running short of new molecules. We just have stopped looking for them...

OUR HEALTHCARE SYSTEM IS PATENT CENTERED -- NOT PATIENT CENTERED:  

"Financing Drug Research: What are the issues?"
==> http://www.cepr.net/documents/publications/intellectual_property_2004_09.pdf

How to sequence the human genome - Mark J. Kiel



View full lesson: http://ed.ted.com/lessons/how-to-sequ...

"Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence."

Lesson by Mark J. Kiel, animation by Marc Christoforidis.

Eric Lander PhD, Geneticist: "Please share your data! The Cancer Genome Project."

MITx 7.00 MOOC "Intro to Biology - The Secret of Life". Lecture week 13.Instructor: Eric Lander PhD.


Eric Lander, PhD, involved in the Human Genome Project, MIT Professor:

"What has been so cool, in the past four or five years, as we talked about DNA sequencing, it's gotten so cheap that you could sequence every patient's own cancer and compare it to their normal DNA. And find that patient's mutations. And you can imagine a world where every patient will have their genome sequenced and their tumor sequenced. And a physician could use that information, as we collect more of it, to figure out which drugs to be using in which combinations. And that's a world we're all imagining right now, a world where that could happen. It's going to take a lot of work to get there. And in my opinion, it's going to take a lot of sharing.

Because we're going to need information pooled from patients around the world. Because we're going to have to learn which patients respond well to which drugs as a function of which mutations they have. And if they have a relapse and the cancer becomes resistant to the drug, which mutations have happened? We're going to need to pool all that, which means I think we're going to need to have some kind of common, agreed upon data sharing mechanisms where patients can voluntarily-- it's up to them-- but voluntarily say, 'count me in. I'm willing to share my data with other people sharing their data so we can build a big enough data set that we can learn what works best.' And I wouldn't be surprised over the next couple of years we see a kind of alliance across many institutions in the world and patients in many countries to try to create that knowledge base. It's kind of like a human cancer Genome Project, but where it's the humans who are involved who are doing it, or the patients who are doing it. And I think it's going to be a really important thing."

MITx 7.00 MOOC "Intro to Biology - The Secret of Life". Lecture week 13.

DNA Forensics: How To Use DNA To Exonerate Wrongfully Convicted People. "The Innocence Project"

DNA Forensics... How to use DNA to exonerate wrongfully convicted people... If the legal system does not allow this, then this can only mean one thing: the system is broken and needs a reboot -- thanks to the science of the human genome. The "Innocence Project" is here to fix things...

Jumping Into Your Genes

"Rational Medicine in Cancer" - "The Secret of Life" MITx 7.00

What if we can no longer hide from... data? What if people were in charge of their own health? Should we become the risk manager of our own genome? Wouldn't that give us the Wilis, sorry, I meant to say, the willies?

National Ballet’s Giselle: Why the Wilis give you the willies

"In the United States, we see about 1.2 million new cases per year of which half of these people will go on to die from their cancer. Actually, all are going to die, but half of them are going to die from their cancer. And this accounts for, we all die, but half are dying of their cancer, and this accounts for about a quarter of deaths in the United States. This is a serious big deal. Now, when cancers begin to grow, it's a single cell. And a single cell, there-- so, I mean, first off, usually, cancers derive from a single cell. That's the first thing to be said is cancers usually-- and many things I'll say tonight are usually-- usually derive from a single cell that goes bad. And it divides and divides and divides and divides and divides, and it's lost its control of its growth. But you won't know it, because when there's two cells there or 100 cells there, it's way too tiny for you to know. You only can see a cancer in an X-ray when it's about 10 to the 8th cells. So only when you get to about 10 to the 8th cells is it detectable by radiography, for example. By imaging. When It gets to 10 to the 9th cells, you can actually feel it. It's what they say, palpable. So this is on the order of maybe one centimeter or so in diameter. By the time you've got 10 to the 12th cells, the patient is usually dead. So you have all these logs of growth that are essentially invisible, and then these logs of growth can become fatal at that point.

By the way, this indicates why it would be really good if you could detect cancers at 10 to the 4th cells and 10 to the 6th cells. And people are working on ways that they might be able to do that.

Now, these cancer, when I say they derive from a single cell, I also want to say that they arise because of mutations in the genome of a single cell. So the cancers usually arise from mutations in the genome. When you think about it, in your body from the time that you were a fertilized egg to now, you've had a total of about, well, during your lifetime, about 10 to the 16th cell divisions, give or take. That's what you've got; in your life, there's probably 10 to the 16th cell divisions, and the chance of a mutation arising in any particular gene per cell division is about 10 to the minus 6th: this is the chance of a mutation in a given gene. That varies between genes and all that, but that's a good guess. So if you had 10 to the 16th divisions and 1 in 10 to the 6th chance of mutation in a given gene per division, every gene has had mutations in it. Every gene has had mutations in it, despite the impressive fidelity of DNA replication that we talked about earlier in the course, that only one error per 10 to the 9th bases. A gene is 10 to the 3rd bases long. So that's about 1 in 10 to the 6th, and you've got 10 to the 16th divisions. That's a lot. Now, these mutations, most of them are happening during development. Some of them could happen before birth. You could have inherited some critical mutations as well. But the mutations can happen by chance, or you can accelerate your rate of mutations. (...)

Cancers usually start by random mutations in a single cell. Some mutations create a protein that fails to function properly increasing the likelihood for additional mutations. For example, if a protein in the mismatch repair pathway did not function properly, then more mutations would occur during replication. Cancers develop as a result of a variety of mutations. Although mutant forms of some proteins are found more commonly in cancers. Some mutations that occur in one cell can increase the likelihood of additional mutations occurring in the same cell." Eric Lander PhD. "Intro to Biology. The Secret of Life" MITx 7.00 MOOC.