Scientific MOOCs follower. Author of Airpocalypse, a techno-medical thriller (Spring 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).


Airpocalypso




David Delmare
Florence Cartozo
Please note that this material is under copyright. It will appear in my upcoming medical thriller, French version, "Airpocalypse".

Airpocalypso
Pour Jean-Christophe Victor

La Chine met en service
Deux usines à combustion
De charbon
Chaque mois,
Ce qui conduit
Le pays
A brûler aujourd’hui
50% de la production
Mondiale annuelle
De charbon.
Le C0 2 dans l’air explose,
Les microparticules
De moins de 2,5 micromètres 
De diamètre,
100 fois plus fines qu’un cheveu,
Aussi.

« Particulate Matter 2.5 »
Est le petit nom
De ta bronchite chronique,
De ton cancer du poumon
Ou de ta crise cardiaque.
PM 2.5 s’échappe
Des voitures, des plantes ou
Du charbon,
A Delhi, Patna, Gwalior et Raipur
PM 2.5 made-in-India.
Ou made-in-Pakistan :
Karachi, Peshawar et Rawalpindi.
PM 2.5 made-in-China :
Pékin est sous le smog,
Baoding, Shijiazhuang et Xingtai aussi.
« Particulate Matter 2.5 »
La Chine est le premier marché
De véhicules particuliers
Au monde.

Airpocalypso
L’économie prend son essor
Et la sirène se mord
La queue.

La circulation
Est responsable de 58% des émissions
De monoxyde d’azote
Et de 25% des émissions
De particules fines.
En Chine,
Toujours plus à l’ouest.
Arrivée au Xinjiang,
Airpocalypso
Redevient petite sirène.
Mais à l’est de la Chine,
La concentration de particules fines,
De dix fois supérieure
Au niveau moyen
Recommandé par l’OMS…
Airpocalypso
L’économie prend son essor
Et la sirène se mord
La queue.

Calypso
Et sa toux sifflante
A la COP 21
Puis à la 22,
Surnageant
Dans les vrombissements
Des moteurs
De mobylettes à Marrakech.
Les minarets
De mosquées,
Cheminées enfumées,
Nagent et toussent
Dans les pots d’échappement
De ruelle en ruelle.
A la Médina,
De minaret-fil en minaret-aiguille,
La petite sirène 
Nage dans le désert.

A la 22 il n’y a que
Les cigognes, installées
Sur la paille en haut
Des minarets,
Qui prient,
De fil en aiguille,
Pour Airpocalypso.
Les minarets brodent,
La santé se brade.
La petite sirène
Est un objet en filigrane
D’argent.
Airpocalypso
L’économie prend son essor
Et la sirène se mord
La queue.

Demain est né
D’une sirène 
Pérenne,
Celle qui prend son essor
Tandis que l’économie se mord
La queue.
Calypso.
Demain est né
D’une sirène 
Pérenne,
Celle qui prend son essor
Tandis que l’économie se mord
La queue.

Calypso.

Bossy Missy Meteorology, For Plume Labs App (English version)

Plume Labs App
Telling me 
What’s
Hanging in the air,
The IBM Watson
Of air quality.
Big Data applied
To pollution.

Six types of pollutants:
Particulate matters
Nitrogen Dioxide (NO 2)
Ozone
Sulfur Dioxide
Carbon Monoxide
Volatile organic compounds.

In the course of
Particulate matters
That will stay forever
In my lungs,
Wind and sun
Matter.
Wind can get us rid
Of pollutants.
Ultraviolet light beams
Are transforming
Exhaust gas
At ground level.
As a consequence:
Ozone!
Ozone is a harmful
Pollutant 
At ground level.

Polluting ozone
Found at ground level
Has nothing to do
With ozone from
The upper 
Atmosphere layer,
Protecting us from
UV light beams
Coming from
The sun.

Six types of pollutants:
Particulate matters
Nitrogen Dioxide (NO 2)
Ozone
Sulfur Dioxide
Carbon Monoxide
Volatile organic compounds.

In meteorology,
An inversion
Is a deviation
From the normal change
Of an atmospheric property
With altitude.
It refers to a temperature
Inversion,
Which means
Temperature will increase
With heights.
This will create
In the atmosphere
Some hot air cover
Called inversion layer.
Why should I care?
Bloody inversion layer
Will maintain pollutants
On the ground.

Six types of pollutants:
Particulate matters
Nitrogen Dioxide (NO 2)
Ozone
Sulfur Dioxide
Carbon Monoxide
Volatile organic compounds.

Six types of pollutants.
When their agenda is full,
Be careful.
Don’t take your new baby
On an outing.

Six types of pollutants.
When their agenda is full,
Be careful.
Don’t take your new baby

On an outing.

One Day The Wall Between Genomics and Conventional Medicine Will Fall...

... just like the Berlin Wall did in 1989... I was 20 years old then, living in Berlin...

Pinterest
Singing "D'Allemagne", a song by French singer Patricia Kaas.

--> Link to audio file here. Yup. This is me, singing :-)

"D'Allemagne" is a song about that wall that used to divide Eastern and Western Germany. See lyrics of this song in English and French here.

Medicine and I.T. have merged. Time to learn about it (and if my singing can help)...

NB: I'm a native German speaker ;-)

Thank you Regina Holliday for the great jacket!



Genomic Entertainment

MIT MOOC starting Jan. 10, 2017: Molecular Biology. RNA Processing and Translation

Airpocalypse

Illustration by Florence Cartozo
My medical thriller Airpocalypse will soon be out (French version first). Link to the lyrics for 8 songs I wrote (English) for this fiction: http://ethictransplantation.blogspot.fr/2016/12/crush-test.html

Ninth song: Airpocalypse 


Whenever I have
To wear a breathing mask
In Beijing,
I try to remember this.

Sulfate is a big contributor 
To the fog in Beijing, 
Sulfuric acid particles are formed
From sulfur dioxide, 
Released by coal burning 
For residential use and power plants.

Sulfur dioxide is turned
Into sulfuric acid. 
This deadly process 
Is facilitated by nitrogen dioxide, 
Another co-product of coal burning, 
And occurs initially on natural fog. 
Sulfur dioxide turning into sulfate 
Produces acidic particles. 
The sulfate formation process 
Is only possible 
With ammonia to neutralize the particles.
Natural fog contains larger particles 
Of several tens of micrometers in size, 
(In Beijing the haze starts 
From much smaller nanoparticles)
And the acid formed is sufficiently diluted. 
Evaporation of those fog particles 
Then leave smaller acidic haze particles 
That cover the city.

In China, sulfur dioxide
Is mainly emitted by power plants, 
Nitrogen dioxide is from power plants 
And automobiles, 
And ammonia comes 
From fertilizer use and automobiles.

The right chemical processes 
Have to interplay for the deadly haze 
To occur in China. 
Chinese haze is basically neutral
But it is not neutral to my health.

So whenever I have
To wear a breathing mask
In Beijing,
I try to remember this.

My health is left
Hanging in the air
Airpocalypse
Arpocalypse

Persistent poor air quality 
Often requires people 
To wear breathing masks 
During much of the day.

How about solutions?
Reduction in emissions 
For nitrogen oxides and ammonia 
Is likely effective in disrupting 
This sulfate formation process.

How about solutions?
My health was left
Hanging in the air
Airpocalypse
Airpocalypse

Reduction in emissions 
For nitrogen oxides and ammonia 
Is likely effective in disrupting 
This sulfate formation process.

So here’s my new 
Super duper
Scientific song
To pitch the UN
With brilliant ideas
To solve OMG
The air pollution
The air…
-pocalypse.

My health is left
Hanging in the air
Airpocalypse
Airpocalypse

And please don’t forget
Small particles between 2.5 and 10 microns
When measuring air quality,
Are just as deadly
As particles above 10 microns.

I know it’s a dream,
But just imagine.
Want a microorganism that eats 
Carbon dioxide 
And makes fuel? 
Someday you might be able
To point and click 
And get one delivered.

Engineering biofuels 
With the help of bacteria
In the lab, 
This will replace oil and coal. 
Tata India and Jack Ma China
Combining biofuels and solar energy
For the first zero carbon-emission plane flight.

I know it’s a dream,
But just imagine.

Here’s my new 
Super duper
Scientific song
To pitch the UN
With brilliant ideas
To solve OMG
The air pollution
The air…
-pocalypse.

My health is left
Hanging in the air
Airpocalypse
Airpocalypse

Biofuels using 
Synthetic biology. 
Optimizing the microbes for high-yield, 
Efficient production through 
Genome engineering, 
Matching the microbe 
With appropriate feedstock molecules 
Or micronutrients, 
And then fine-tuning the entire production process
For generating clean fuels 
That are drop-in ready for use 
In the gas tank at costs 
That are competitive with those 
Of natural petroleum products.

And now we did not think 
We were able to produce 
A flammable liquid 
In such a simple way, 
From electricity. 
Ethanol in place of oil. 

In an engine, ethanol is burned. 
This gives carbon dioxide and energy. 
In the factory, the carbon dioxide 
Is captured again 
In order to re-cycle. 
This way of storing electricity
In liquid form 
Is very interesting. 

So here’s my new 
Super duper
Scientific song
To pitch the UN
With brilliant ideas
To solve OMG
The air pollution
The air…
-pocalypse.

My health is left
Hanging in the air
Airpocalypse
Airpocalypse

And now we did not think 
We were able to produce 
A flammable liquid 
In such a simple way, 
From electricity. 
Ethanol in place of oil. 

Oil is the result 
Of photosynthesis 
Millions of years ago.

Trees have grown, 
Captured carbon dioxide 
Through photosynthesis. 

Plants retain carbon and release oxygen. 
Photosynthesis
Means that plants keep the sun, 
Which is the energy that breaks CO2 
Or carbon dioxide
Into carbon on one side 
And oxygen on the other. 
CO2 is a very strong molecule, 
C and O2 are bonded very strongly. 
It takes a lot of energy 
To break this molecule. 
Burning carbon makes it possible
to associate again 
C and O2, 
Carbon and oxygen, 
And releases energy, 
That was previously 
stored in C and O2. 

Energy is not lost 
And is not created. 
It can only be stored or free.

When separating C and O2, 
Energy must be provided 
To separate them. 
When we associate them again, 
This energy is released. 

Think about magnets. 
They are glued to one another 
And it takes energy to separate them. 
Once they are separated, 
It is as if they were storing 
A lot of energy. 
If we bring them closer, 
They will jump over 
Each other and stick together. 

Energy is not lost 
And is not created. 
It can only be stored or free.

The same applies to carbon and oxygen. 
If we have succeeded 
In separating them and then 
Bringing them together, 
There is energy 
That will be released. 

The problem with oil 
Is that photosynthesis 
Took place millions of years ago, 
So it removed a lot of carbon dioxide 
From the atmosphere, 
Which is rich in oxygen. 
Other forms of life 
Have therefore appeared, 
And require oxygen. 
When burning oil, 
Carbon dioxide and energy 
Are produced. 
The released carbon dioxide
Is not consumed, 
Because it is released 
Massively. 
The problem? 
we can see it right away. 
We do not make oxygen. 
And we have a big excess of CO2. 
That's what happens when the trees were burned 
Millions of years ago: 
We do not make enough oxygen 
And we have a large excess of CO2.

So here’s my new 
super duper
scientific song
To pitch the UN
With brilliant ideas
To solve OMG
The air pollution
The air…
-pocalypse.

My health is left
Hanging in the air
Airpocalypse
Airpocalypse

The effect of this carbon dioxide
is to isolate the atmosphere 
and create a greenhouse effect. 
And to acidify the oceans. 

Instead of burning oil 
That can not be duplicated,
We can burn ethanol, 
Which we can reproduce. 
As a result, oxygen is re-circulated 
In the air and CO2 is captured 
Again. 
Bye bye, big excess of CO2. 

The storage of energy 
Called photosynthesis
Can be done with ethanol. 
Then we do not produce carbon and oxygen, 
But ethanol. This can return 
To making carbon 
And oxygen, C + O2. 
C is coal, carbon, wood. 

The pollution in Beijing
Is linked to chemical reactions 
With the atmosphere 
Under certain conditions, 
When combustion of coal happens.
The reaction between carbon and oxygen 
Releases plenty of polluting compounds.

A diesel engine produces solid 
(and non-liquid) 
Microparticles. 
Solid Microparticles 
Have far more health effects 
Than the gases themselves. 
This micro-dust, 
When it enters the lungs, 
Remains there. 
This is also the case for asbestos, 
Which is also a micro-dust. 
In the case of asbestos and diesel, 
It is the accumulation 
That is bad for your health. 
Alcohol is even more refined than petroleum, 
So there are even less odors and soot. 
In the case of diesel, combustion particles 
Produce even more soot than in the case of oil.

So here’s my new 
Super duper
Scientific song
To pitch the UN
With brilliant ideas
To solve OMG
The air pollution
The air…
-pocalypse.

My health is left
Hanging in the air
Airpocalypse
Airpocalypse

So just imagine
Microbial factories for everyday products
Biosensors for food pathogens
Marijuana without the plant
Fixing your genes to cure diseases
The end of synthetic nitrogen fertilizers
And please remember:
Y cancer =f(X pollution lifestyle)

And even fancier:
Know the super-power
Of urine.
From the urine, 
We can reconstruct 
Stem cells of neurons 
(Folks, this means the death of brain death!)
And other undifferentiated stem cells.
The urine also serves 
For the production 
Of hydrogen 
For the cars of tomorrow.

That was my new 
Super duper
Scientific song
To pitch the UN
With brilliant ideas
To solve OMG
The air pollution
The air…
-pocalypse.

My health is left
Hanging in the air
Airpocalypse

Airpocalypse

I know it’s a dream,
But just imagine.
Want a microorganism that eats 
Carbon dioxide 
And makes fuel? 
Someday you might be able
To point and click 
And get one delivered.

My health is left
Hanging in the air
Airpocalypse
Airpocalypse.

Tenth song: Forget Yesterday Remember Tomorrow

Beijing’s sick beating heart
Witnessing pollution
And organ trafficking.
Beijing’s vibrant scientific scene,
Engineering, editing, making and hacking,
Trying to forget yesterday, 
Remember Tomorrow.
Engineering biofuels 
With the help of bacteria
In the lab. Making new drugs 
With the help of gene
Editing tools.
Forget Yesterday 
Remember Tomorrow.
Beijing’s recovering beating heart,
But…

Science is hype is money
I am a buzz word trader
The biggest Ponzi scheme ever
Nothing is forever
Going global, spinning faster
Burnout’s the new pot o’honey
People have started dating their innernet:
«  - Dear pitch-perfect A.I., will you be my Scarlett? »

Science happens by accident
A fungus remote-controlling the insect brain 
leads to . . . cyclosporine, 
The drug allowing physicians to transplant organs.
If the patient’s got an accident,
Doctors will look for the necrosis in his brain
Then another patient gets a new heart.
Medicine also happens by accident.
Is this incremental? Is this exponential?
Wait. I’ll ask the blockchain.
Women’s breasts and organs
Are political objects
In the database of Business Abject.
Digital locks and Rights Management
Are the new stethoscope of madicament,
I mean medicament.

I work in life science
I’m a buzz word trader
Accident is the new blockchain,
Making big data’s head spin.
Human on-a-chip
Hope-hip
I work in life science
I’m a buzz word trader
Accident is the new blockchain
Making big data’s head spin.
I am a buzz word trader
I deal emotions
One keynote at a time
Human on a chip
Hope-hip

Beijing’s anonymous heartbeat,
Hacking into the Operating System
Of Humanity
Writing snippets of code
Encoding more equity
Into the language of evolution
Yeah, revolution, evolution, devolution, religion
You decide.

They call me Anonymous
But that’s just what I write
When asked for my identity
While downloading a file
From some FTP server.
I’m a geek I’m a hacker
And maybe some day
Some anonymous organ donor.
I guess this is the reason
Why they call me Anonymous.

Free and anonymous
I am,
Just like organ donation.
We don’t need more anonymous
Prisoners executed, 
Slaughtered
For their hearts kidneys lungs
Sold for medical transplants.

Bloody Harvest 
Bloody Harvest 
Beijing’s beating heart 
Is bleeding.

We need more gene editing science.
The science of vital organ replacement 
Is paved with accidents and crisis.
Now we need to edit that crisis out
And make amendments thanks to a cool
Crisis editing tool,
Sorry I meant,
Gene editing tool.
Yeah, revolution, evolution, devolution, religion
You decide.

Forget yesterday,
Remember tomorrow.

Hey, rest of the world,
Listen to what China has to say.
Just like the low-cost flight company:
« If you are late, we won’t wait ».
Forget yesterday,
Remember tomorrow.

Beijing’s beating heart,
Telling me what Anonymous means.
It means anyone.
ANYONE 
Can go from concept to execution 
Of coded proteins 
Virtually overnight, 
Through cloudlabs, 
Robot lab assistants, 
And rapid prototyping software. 
Cost is dropping fast. 
Direct-build-and-deploy your personal
– Medicine Farm
– Nanofactory
– Liquid biocomputer

Forget yesterday,
Remember tomorrow.

How about a nice, graphical, 
Web-accessible SaaS 
For compiling genomes, 
With direct printing of DNA 
Via your cloud lab of choice?
'Shapeways for genes' has arrived.
Have fun with the 'mutate random amino acid' function!

Here is gene therapy’s Secret Recipe
(yes I love their raspberry cheesecake too):
Take an adeno-associated virus 
Devoid of toxicity
(typically AAV9) 
In 20% of cases, when you have a sore throat 
It is this type of virus, therefore no sorcery
And introduce corrective action 
Using Crispr / Cas9 
Such that if the virus is swallowed / injected 
It will 'infect' cells 
With the consequence 
That if there is a DNA sequence 
AATCGCGGCGAGCGAG 
(I just made up that one) 
It will be replaced with AATCGCAACGAGCGAG 
Where the central GG
Is replaced by AA,
And trust me 
This should be
No ‘mutate random amino acid' function.

Beijing’s lungs are struggling to breathe
Airpocalypse
Airpocalypse
Lung cancer represents
Two deaths every minute
Worldwide.
So please Airpocalypse xiānsheng,
Don’t tell me bioengineering
Cannot help.

Beijing’s ailing lungs on-chips,
Engineering biofuels 
With the help of bacteria
In the lab.
Want a microorganism that eats 
Carbon dioxide 
And makes fuel? 
Someday you might be able
To point and click 
And get one delivered.

Forget yesterday,
Remember tomorrow.

I work in life science
I’m a maker
Evidence is the new blockchain,
Big data crunching
Snippets of Computer Code
For Human Organs-on-Chips,
Clinical trials going digital 
And exponential.
Big data means
Prices are dropping.

Forget yesterday,
Remember tomorrow
This is Beijing’s beating heart
Sole credo
I can hear it now.

Forget yesterday,
Remember tomorrow
This is Beijing’s beating heart
Sole credo

I can hear it now.

Lyrics of all songs by Catherine Coste, for medical thriller "Airpocalypse". Copyrighted material.

#GenomicEntertainment