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You can read the genome and build a human being

Secrets, disease and beauty are all written in the human genome, the complete set of genetic instructions needed to build a human being.

Scientist and entrepreneur Riccardo Sabatini shows us, we have the power to read this complex code, predicting things like height, eye color, age and even facial structure — all from a vial of blood.

And soon, Sabatini says, our new understanding of the genome will allow us to personalize treatments for diseases like cancer.

We have the power to change life as we know it. How will we use it?

Behold, the encyclopedia of a single person:

We have the power to change life as we know it.
t.ted.com| Riccardo Sabatini. Scientist, entrepreneur. He applies his expertise in numerical modeling and data to projects ranging from material science to computational genomics and food market predictions. Full bio

For the next 16 minutes, I’m going to take you on a journey that is probably the biggest dream of humanity: to understand the code of life.

0:20 So for me, everything started many years ago when I met the first 3D printer. The concept was fascinating.

A 3D printer needs three elements: a bit of information, some raw material, some energy, and it can produce any object that was not there before.

I was doing physics, I was coming back home and I realized that I actually always knew a 3D printer. And everyone does. It was my mom.

My mom takes three elements: a bit of information, which is between my father and my mom in this case, raw elements and energy in the same media, that is food, and after several months, produces me. And I was not existent before.

So apart from the shock of my mom discovering that she was a 3D printer, I immediately got mesmerized by that piece, the first one, the information. What amount of information does it take to build and assemble a human? Is it much? Is it little? How many thumb drives can you fill?

 I was studying physics at the beginning and I took this approximation of a human as a gigantic Lego piece.

So, imagine that the building blocks are little atoms and there is a hydrogen here, a carbon here, a nitrogen here. So in the first approximation, if I can list the number of atoms that compose a human being, I can build it. Now, you can run some numbers and that happens to be quite an astonishing number.

the number of atoms, the file that I will save in my thumb drive to assemble a little baby, will actually fill an entire Titanic of thumb drives — multiplied 2,000 times. This is the miracle of life. Every time you see from now on a pregnant lady, she’s assembling the biggest amount of information that you will ever encounter. Forget big data, forget anything you heard of. This is the biggest amount of information that exists.  

2:25 But nature, fortunately, is much smarter than a young physicist, and in four billion years, managed to pack this information in a small crystal we call DNA. We met it for the first time in 1950 when Rosalind Franklin, an amazing scientist, a woman, took a picture of it.

But it took us more than 40 years to finally poke inside a human cell, take out this crystal, unroll it, and read it for the first time. The code comes out to be a fairly simple alphabet, four letters: A, T, C and G. And to build a human, you need three billion of them. Three billion. How many are three billion? It doesn’t really make any sense as a number, right?

I was thinking how I could explain myself better about how big and enormous this code is. But there is — I mean, I’m going to have some help, and the best person to help me introduce the code is actually the first man to sequence it, Dr. Craig Venter. So welcome onstage, Dr. Craig Venter.

Not the man in the flesh, but for the first time in history, this is the genome of a specific human, printed page-by-page, letter-by-letter: 262,000 pages of information, 450 kilograms, shipped from the United States to Canada thanks to Bruno Bowden, Lulu.com, a start-up, did everything. It was an amazing feat.

 But this is the visual perception of what is the code of life. And now, for the first time, I can do something fun. I can actually poke inside it and read. So let me take an interesting book … like this one. I have an annotation; it’s a fairly big book. So just to let you see what is the code of life. Thousands and thousands and thousands and millions of letters. And they apparently make sense. Let’s get to a specific part. Let me read it to you:

“AAG, AAT, ATA.”

To you it sounds like mute letters, but this sequence gives the color of the eyes to Craig. I’ll show you another part of the book. This is actually a little more complicated.

 Chromosome 14, book 132:  

“ATT, CTT, GATT.”

5:19 This human is lucky, because if you miss just two letters in this position — two letters of our three billion — he will be condemned to a terrible disease: cystic fibrosis. We have no cure for it, we don’t know how to solve it, and it’s just two letters of difference from what we are.

A wonderful book, a mighty book, a mighty book that helped me understand and show you something quite remarkable. Every one of you — what makes me, me and you, you — is just about five million of these, half a book. For the rest, we are all absolutely identical. Five hundred pages is the miracle of life that you are. The rest, we all share it. So think about that again when we think that we are different. This is the amount that we share.

now that I have your attention, the next question is: How do I read it? How do I make sense out of it? Well, for however good you can be at assembling Swedish furniture, this instruction manual is nothing you can crack in your life.  

 in 2014, two famous TEDsters, Peter Diamandis and Craig Venter himself, decided to assemble a new company. Human Longevity was born, with one mission: trying everything we can try and learning everything we can learn from these books, with one target — making real the dream of personalized medicine, understanding what things should be done to have better health and what are the secrets in these books.

An amazing team, 40 data scientists and many more people, a pleasure to work with. The concept is actually very simple. We’re going to use a technology called machine learning.

On one side, we have genomes — thousands of them.

On the other side, we collected the biggest database of human beings: phenotypes, 3D scan, NMR — everything you can think of. Inside there, on these two opposite sides, there is the secret of translation. And in the middle, we build a machine. We build a machine and we train a machine well, not exactly one machine, many, many machines — to try to understand and translate the genome in a phenotype.

What are those letters, and what do they do? It’s an approach that can be used for everything, but using it in genomics is particularly complicated. Little by little we grew and we wanted to build different challenges. We started from the beginning, from common traits. Common traits are comfortable because they are common, everyone has them.

we started to ask our questions: Can we predict height? Can we read the books and predict your height?

we actually can, with five centimeters of precision. BMI is fairly connected to your lifestyle, but we still can, we get in the ballpark, eight kilograms of precision. Can we predict eye color? Yeah, we can. Eighty percent accuracy. Can we predict skin color? Yeah we can, 80 percent accuracy. Can we predict age? We can, because apparently, the code changes during your life. It gets shorter, you lose pieces, it gets insertions. We read the signals, and we make a model.

 an interesting challenge: Can we predict a human face? It’s a little complicated, because a human face is scattered among millions of these letters. And a human face is not a very well-defined object. So, we had to build an entire tier of it to learn and teach a machine what a face is, and embed and compress it. And if you’re comfortable with machine learning, you understand what the challenge is here.

15 years after we read the first sequence — this October, we started to see some signals. And it was a very emotional moment. What you see here is a subject coming in our lab. This is a face for us. So we take the real face of a subject, we reduce the complexity, because not everything is in your face — lots of features and defects and asymmetries come from your life. We symmetrize the face, and we run our algorithm. The results that I show you right now, this is the prediction we have from the blood.

In these seconds, your eyes are watching, left and right, left and right, and your brain wants those pictures to be identical. So I ask you to do another exercise, to be honest. Please search for the differences, which are many. The biggest amount of signal comes from gender, then there is age, BMI, the ethnicity component of a human.

And scaling up over that signal is much more complicated. But what you see here, even in the differences, lets you understand that we are in the right ballpark, that we are getting closer. And it’s already giving you some emotions.

This is another subject that comes in place, and this is a prediction. A little smaller face, we didn’t get the complete cranial structure, but still, it’s in the ballpark. This is a subject that comes in our lab, and this is the prediction.

So these people have never been seen in the training of the machine. These are the so-called “held-out” set. But these are people that you will probably never believe. We’re publishing everything in a scientific publication, you can read it.

But since we are onstage, Chris challenged me. I probably exposed myself and tried to predict someone that you might recognize. So, in this vial of blood — and believe me, you have no idea what we had to do to have this blood now, here — in this vial of blood is the amount of biological information that we need to do a full genome sequence. We just need this amount.

We ran this sequence, and I’m going to do it with you. And we start to layer up all the understanding we have. In the vial of blood, we predicted he’s a male. And the subject is a male. We predict that he’s a meter and 76 cm. The subject is a meter and 77 cm. So, we predicted that he’s 76; the subject is 82. We predict his age, 38. The subject is 35. We predict his eye color. Too dark. We predict his skin color. We are almost there. That’s his face.

Now, the reveal moment: the subject is this person.

And I did it intentionally. I am a very particular and peculiar ethnicity. Southern European, Italians — they never fit in models. And it’s particular — that ethnicity is a complex corner case for our model. But there is another point. So, one of the things that we use a lot to recognize people will never be written in the genome. It’s our free will, it’s how I look.

Not my haircut in this case, but my beard cut. So I’m going to show you, I’m going to, in this case, transfer it — and this is nothing more than Photoshop, no modeling — the beard on the subject. And immediately, we get much, much better in the feeling.

 why do we do this? We certainly don’t do it for predicting height or taking a beautiful picture out of your blood. We do it because the same technology and the same approach, the machine learning of this code, is helping us to understand how we work, how your body works, how your body ages, how disease generates in your body, how your cancer grows and develops, how drugs work and if they work on your body.

This is a huge challenge. This is a challenge that we share with thousands of other researchers around the world. It’s called personalized medicine. It’s the ability to move from a statistical approach where you’re a dot in the ocean, to a personalized approach, where we read all these books and we get an understanding of exactly how you are. But it is a particularly complicated challenge, because of all these books, as of today, we just know probably two percent: four books of more than 175.

And this is not the topic of my talk, because we will learn more. There are the best minds in the world on this topic. The prediction will get better, the model will get more precise. And the more we learn, the more we will be confronted with decisions that we never had to face before about life, about death, about parenting.

we are touching the very inner detail on how life works. And it’s a revolution that cannot be confined in the domain of science or technology. This must be a global conversation. We must start to think of the future we’re building as a humanity.

We need to interact with creatives, with artists, with philosophers, with politicians. Everyone is involved, because it’s the future of our species. Without fear, but with the understanding that the decisions that we make in the next year will change the course of history forever.

Re-Creating a “cohort” of Neanderthal species: It is feasible, but Why?

Our current human species is uniform. The mono-culture is source of extinction when facing worldwide epidemics and a serious degradation in climatic changes.

Consequently, re-introducing a former species that was wiped out 30,000 years ago might regulate the survival of mankind.

It appears that the Neanderthal species had a larger brain (but we are not sure if the network of his synapses was complex enough to match this current species).

A skeletal, up to one million years old, can be useful for the re-introduction of a lost species.

Scientist George Church (58 of age)  would recuperate the DNA to submit it to the sequencing of its genome.

The genome is later cut into 10,000 fragment to be synthesized.

These synthetic fragments are introduced in a stump cell. By repeating the operation as often as necessary, the descendants are generated from the stump cells.

These cells will be inserted in the uterus to develop.

Et voila! Neanderthal species coming back to live among us and protect mankind from a potential extinction.

Church is a pioneer in synthetic biology, a discipline trying to unite complex systems which function Not necessarily according with existing ones in Nature.

In the 1980’s, this professor in Harvard was at the origin of the Human Genome Project, the decryption of DNA of human body.

Church explains:

“All the information in the world (about 1.8 zettabit) can be stored in 4 grams of DNA. The DNA storage can resist desert climate for 400,000 years.

The scientists of Boston are using an decryption archive system that needs no cells to work, and a coding system that enables the location of the DNA extract in the files.

Thus, strong with the availability of DNA sequencer and a computer, the files could be read.

A mother chimpanzee could be substituted in the cloning process.

A long journey to learn the evolution of the Past.

Note: Mankind relationship with Nature

A great ‪#‎cartoon‬ capturing the cruelty of man and our morbid reality: http://t.co/CfNX6WIMmu

An animation showing a man in a relationship with nature.
Shocking but plausible with an ending that does justice.
wtvideo.com

Son of Man: Margin for Freedom

Does heredity define to great extent every individual?  

Is every one of us the product of long lines of successive unions?

Yet, the probability of identical persons is nil among the billions upon billions of human kinds that roamed earth.

Every person that dies is never replaced and his unique set of characteristics, and the identical set is gone for ever. 

Maybe our margin for developing certain characteristics is limited. Even then, what could be modified a little by nature, environment, social conditions, and personal thrive will have an impact in defining future generations.

We have always attributed our reality to act of God, His will, our Destiny. We have been sons of God until recently

Research and technology are altering many genomes for a healthier man, even before he is born, even when he is a fetus, even by sorting out and selecting one among the many embryos to re-insert in the mother’s uterus. 

Man has started to affect genetically future generations.  God is no longer the sole and exclusive owner of man

Mankind is becoming part owner, though with a tiny share so far. 

As long as man is not able to tamper with the brain on a large-scale, then God will still have the bigger share in man. 

When you partially own a person then you are responsible for the whole entity

We tended to let God off the hook for too long.  If man has to be taken to court for wrong doing or designing and manufacturing defective products, then it is about time that God be taken to court after each war, each genocide, each apartheid systems designed for the suffering and humiliation of fellow men.

We have always attributed to God all the good values, even the immoral values in our daily realities.  We have tried hard to interpret God frequent calamities in a lenient manner. 

If God exists, and he should exist, then God has to be taken to the International Tribunal for crimes against humanity. 

That is the margin of liberty that we still own; to study, read, reflect, have our own opinions, take hold of our personal responsibilities, and act accordingly.  When a person denies his own share of responsibility and stop reflecting and studying… all he does is then but wind. 

I have published many “poems” and I selected two that might be representative for this article.

I Say

I say, every one must have his identity:

Death has forced on us the I.

I say, what exists must be discovered:

Death impressed on us to know.

I say, every feeling must be experienced:

Death created stages for us to grow.

I say, there must be a meaning to life:

Death did not leave us a choice in that.

A Gentle Touch*

Prettier than white dust

You shall never be.

Uglier than a skeleton

You can never be.

Toward the scared souls, scared of death,

Scared in living,

Let your stretched hand

Be gentler, your voice softer.


Son of Man: Margin for Freedom (February 25, 2009)

            Heredity defines to great extent every individual.  Every one of us is the product of long lines of successive unions and yet the probability of identical persons is nil among the billions upon billions of human kinds that roamed earth. Every person that dies is never replaced and his unique set of characteristics is gone for ever.  Maybe our margin for developing certain characteristics is limited; even then, what could be modified a little by nature, environment, social conditions, and personal limited will have an impact in defining future generations.

            We have always attributed our reality to act of God, His will, our Destiny; we have been sons of God until recently.  Research and technology is altering many genomes for a healthier man, even before he is born, even when he is a fetus, even by sorting out and selecting one among the many embryos to re-insert in the mother’s uterus.  Man has started to affect genetically future generations.  God is no longer the sole and exclusive owner of man. 

Man is becoming part owner, though with a tiny share so far.  As long as man is not able to tamper with the brain on a large scale, then God will still have the bigger share to man.  When you partially own a person then you are responsible for the whole entity.  We tended to let God off the hook for too long.  If man has to be taken to court for wrong doing or designing and manufacturing defective products, then it is about time that God be taken to court after each war, each genocide, each apartheid systems of suffering and humiliation.

We have always attributed to God all the good values, even the immoral values in our daily realities, and attributed to God, we have tried hard to interpret then in a lenient manner.  If God exists, and he should exist, then God has to be taken to the International Tribunal for crimes against humanity.  That is the margin of liberty that we still own; to study, read, reflect, have our own opinions, take hold of our personal responsibilities, and act accordingly.  When a person denies his own share of responsibility and stop reflecting and studying then all he does is but wind.  I have published many “poems” and I selected two that might be representative for this article.

I Say

 

I say, every one must have his identity:

           Death has forced on us the I.

I say, what exists must be discovered:

           Death impressed on us to know.

I say, every feeling must be experienced:

           Death created stages for us to grow.

I say, there must be a meaning to life:

           Death did not leave us a choice in that.

 

 

A Gentle Touch*

 

Prettier than white dust

            You shall never be.

Uglier than a skeleton

            You can never be.

Toward the scared souls, scared of death,

            Scared in living,

Let your stretched hand

            Be gentler, your voice softer.

“Nature versus nurture”: Introspection  #58

I am interested in the effects of the dichotomy “nature versus nurture”.

What cause individuals to accede at recognition in social spheres? What is normal behavior? What is meant by being a beneficial member to society? What hobbies and skills keep people happy and alert throughout their life?

The field of “nature versus nurture” should be a scientific specialty but, objectivity set aside, I may state my position based on my individual experience.

What I am is anchored on feeling healthy, though I was not born a healthy person:  I was not supposed to survive.

Mother persisted and after a day of struggle I had my first tit-sucking experience.  I attended school for 3 months when I was almost 5 of age before the terrible illness of Typhus that lasted 4 months, and I had to re-learn walking…  

Within 3 months I had mastered the multiplication tables; thus, I was endowed with some mental potentials; that is a lot of grace already.

I was nurtured in an environment that conveyed a sense of security and warmth in my first critical four years, though my parents were far from feeling in security:  They were robbed four times in less than two years as they were starting to raise a family. May be that is why I could attempt adventures that were not planned?

I could keep faith that I will manage one way or another in critical conditions.

In the summer of 1975, I flew to the USA, my first trip outside my country. I was not even accepted at any university.  I knew no one, had no connections and had no information on the State or universities.

At the end of 1984, I departed for the USA without any planning whatsoever. Both times to escape the rot: I was out of a job or not perceiving any opportunity for a job.

In 1991, I literally ran away to San Francisco after graduation. I had no money; I had no plans, and didn’t have connections.

In 1979, I decided on a foolish scheme which got me in terrible troubles. The consequences of this decision must have affected me deeply, but for years I failed to acknowledge its influence.

What I am not is solely the culprit of consistent disadvantageous nurturing conditions later on: such as in family, schooling programs, society, and environment.  

Living in a religious boarding school for six years, in a new country, and having to learn a new language are not catalysts for normal upbringing.  I tried to learn many skills when it was too late to acquire.

I enrolled in music classes when I was over thirty. I bought a classical guitar and an accordion to prove my incompetence. I could have been successful at many skills and hobbies when it was proper and effective at an early age. What I acquired young I kept at it.

I can admit clearly that my failure is the consequence of my incapacity for long-term planning.

This failure is mainly due to my lack of hunger for anything considered essential by society. Hunger is an acquired quality before the age of four. 

Most of those who have a hunger are successful at acquiring “recognition”, not mainly because of the focused energy toward their targeted hunger but because their hunger is their lightening rod that keeps them focused.

There is nothing wrong with striving for recognition

It is the means employed to destroying many spirits along the way to the target that need to be judged and blamed.

Many marriages fail because the emotional instability of the hungry people takes over and destroy the best stabilizing environment that keep them on track.  The hungry people who manage to salvage marriages are those who wizened up to just wearing the mask of patriarchal attitude.  They know that they are not fooling their closest relatives and friends but that would do for the outsiders, to those who count for nurturing “recognition”.  The saying “No prophet is recognized by his people” means that the mask that ends up identifying us would never fool our community.

I feel helpless starting a business and abhor law regulations.

I could be a flourishing director or manager of an already established institution.

I could have been as successful as many individuals who inherited businesses.

I could have learned to acquire a taste for luxury. I could spend money in profusion when I had it. I enjoy reading abundantly and have been writing lately.

I like to share my reading books and my writings. Who cares reading anymore?  I do.

Someone has to share the work of a few good writers.

My temerity broke the vicious cycles several times but I lacked the tools: Sound behaviors, skills, and capabilities are acquired early on in life. I never despaired.  I lacked the talent to grab good opportunities or retaining potential ones.

I re-invent myself any which way.

I could have turned better. I know from key events in my life that I could have been a successful man. When I was 12, I was transferred to a totally different schooling system. It was a system that emphasized French as the primary language which I had completely forgotten though it was my first language. By the end of the year, I was among the five best students in French among the three other sections. The following two years I was still better than even the French-born students.

When I was 14, the school organized this single ceremony at the end of the year: The entire student body was trained for intricate exercises to be performed in the dark. We carried two lighted colored torches.  I liked these exercises. During summer, I used the two confectioned small sand bags that hold doors, and exercised every day. I thus managed to build up the muscles of my arms and forearms. These parts of my body looked disproportionate with my shriveled body at the time, like Popeye the Spinach man.

When I was 21, I enrolled in a session of Tak Wan Doo, a Korean martial art. Throughout the training I was clumsy and appeared unfit.  Most of the group were more sportive, taller, and better built-in stature and shape. At exam time, it turned out that I was the sole graduate to earn the green belt because I trained at home and had confidence.

I still dream of a change in situation. I am ready to face harsher problems and realities.

Note: We are no different from the other mammalian kinds. Maybe we started with a couple of DNA genomes that differed from most of the other mammals. Most probably, we nurtured these discriminating genomes to warp other genomes into a qualitative difference. It is not our mental agility that sets us apart from other mammals (that would be the external realities), but it is mainly our ability to wear masks and believing that the mask is our identity.


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