Tag Archives: Medicine

How to sequence the human genome

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Paperscape

paperscape

Paperscape is a tool to visualize papers in Arxiv (Arxiv is a free open archive for scientific papers and preprints), but not the information inside the papers, the relation between papers. Each paper is represented by a circle, and the size of the circle represent how many citations it has. To group together the papers they use an algorithm based on the common citations between papers.

So basically, is a tool to see what is going on in physics and what are the important things in your area.

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Ok, let’s give it a try.

I’m going to look for Neural Network,s my old topic (hope to go back soon).

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Nice, they lay close to quantitative biology.

And now my new topic, magnetic domain walls.

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Not bad! Pretty close actually! And  computer science is in between!

Hope you like it.

ZOOniverse

Yesterday I discovered a web page that makes real one of my visions for the future. One day neural networks will perform tasks that are impossible nowadays for actual algorithms. Until that, why not use internet and the power of thousands of humans to perform that tasks? Well, It has been done, and the name of it is Zooinverse.

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On this web page you can access to many different projects and help them. The main task is classification. Human brain capability to identify patterns and classify them has not yet been achieved by computers, so that is what this web page ask the users, help in classification tasks.
And at the same time, is like a small game, so it’s funny to help.

Those are the projects involved.

  • Classification of galaxies from Hubble images. It seems an easy task, but Hubble has been taking photos for a long time and the better the clasiffication the better the stellar population profile can be achieved, and that can help to study the evolution of the universe. For more information about Hubble, please visit the HubbleSite.

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  • Classification of craters on the Moon. Check images to distinguish between craters and mounds. To know more about the Lunar Reconaisance Orbiter, you can visit it’s NASA webpage here.

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  • Tracking solar storms to it’s origin. This is quite funny, because before any classification tasks, we are trained to do it. This job will help to predict the evolution of solarm storms, which are a big danger to earth and specially to satellites and electronic devices. I can say that this one is the most difficult so far. Helping in this project is no kids game, each survey has to be done with time tracking, front and ahead stereo vision… For more information about the STERO mission, visit the wikipedia article.

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  • Look for planets. Yeah, little green men, are you there? Kepler mission measures the brightness of a star. That measure is not constant, there is many reasons for the amount of light from a star to be variable. One of them is that the star has a planet near by. Basically, each time the planet moves between the star and the earth, the brightness of the star decreases. This is very difficult to spot because of the noise in the measure and the variability on the data. It’s almost impossible to fit the brightness to a smooth function and look for spikes. For more information about Keppler Spacecraft visit it’s web page.

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  • The next one is to identify different materials in galaxies using infra-red images. This is the link and below is a video tutorial. In this case, identifying materials and it’s evolution through time will help to evolve simulation models. That represents and improvement for universe evolution prediction, but also for other kinds of simulations, because there is many fundamental interactions happening in the evolution of a galaxy, and understanding them can help to improve simulations of more common things on earth (like predicting the temperature of formation of some chemical compound for the chemical industry). Please, visit Spitzer telescope web page to learn more about the tool that is making this possible.

  • The Red Planet! The HiRISE project is dedicated to analyse data from a camera on board the Mars Reconnaissance Orbiter. The main task of this program is to identify dust formations on Mars. That will help to trak sand storms and distinguish between permanent features and weather effects. A part form that, the HiRISE web page has many interesting photos from the earth, don’t forget to visit!

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  • Next step, Speed Factor 12 Mr Data. We are going to help to develop Warp Drive. Well, not exactly, that is what they say in the project, the truth is that we are looking for massive dark objects. According to relativity, the energy of an object can affect the space-time in it’s surroundings, that means that is we have a very massive object in the path of a light ray, the light ray will be deflected. The more mass has the object, the biggest the deflection. In this project they look for that kind of deflection. How it looks like? If you are looking at very far away galaxies, a massive object between you and them will deflect the light and create an optical   illusion. A ring, a pair of object, an arc of light… Detecting them is very difficult, but can help to detect massive object that are invisible to us, yes, black holes.

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  • I think this next project is one of the things I always asked my self about. How is it possible that sometimes studies refer to climate in eras where computer and data logging was not common? One of the answers is indirect measurements, like CO2 concentration in polar ice… but this one… this project consists in help to digitalize handwrite data form old vessels in other to track their travels and the climate changes they faced. I think they idea is nice, but the tasks is massively boring…

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  • Classifying Cyclones can help to prevent them or discover a trend in the data. Are they increasing? Are they becoming more stronger? What can be learned from them?

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  • On the next project we use the Oxyehynchus Papyri collection, and our task is to identify letters and text on that documents. Is a very hard task. I think this one is only interesting to history or arqueological students. To read more about the collection, visit the wikipedia article.

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  • I feel like in Star Trek, mission Save the Earth. The scope of the next project is to identify whale sounds. Looks amazing, but basically, you listen to one sound and try to match it with another sounds.
  • galaxySince my the first time I read 20,000 leagues under the sea I wanted to visit the bottom of the ocean. With this project you can feel how it looks like. Your task is to identify components in sea floor pictures, like kind of soil, fish, sea stars… And with that, help them to classify different kinds of floor. Remember that 2/3 of the planet is ocean, there is more sea floor than normal floor. Imagine what we can expect!galaxy
  • Now we want to monitor the population of bats. In this project we have a series of sounds recorded in different places and we need to identify the sources of sound in the record. Quite simple and nice. And at the same time, it challenges us to listen more carefully at our environment next time we hear something.

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  • Camera traps on the Serengeti!!! I think I like this the most, because the other ones I have a little insigth into them because of my formation, but this one is like diving into David Attenborough documentaries, and at the same time, they are real images took remotely.

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  • This one is very similar to the archaeological ones. There is lots of data from museums that has been stored in paper format and needs to be transcribed. This is a project to transcribe data from plants and insects. It’s not quite interesting, sorry.

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  • Help with cancer. That is a good project. Cancer is one of the worst illness of all times. Now you can help to fight against it. Here we need to classify cell samples and identify different parts on them. This project can help to improve detection techniques and accelerate diagnosis of cancer, preventing them to develop and save many lives.

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  • The latest ones is the most disfgusting. I appolige for that. You need to tarck worms and click “Z” whenever they lay an egg. Puag!galaxy

 

Hope you enjoy the experiments!

 

SUPER Cooperators.

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Original title: Super Cooperators: Altruism, Evolution, and Why We Need Each Other to Succeed.

Title of this edition: Super Cooperators: Altruism, Evolution, and Why We Need Each Other to Succeed.

Author: Martin A. Nowak, Roger Highfield.

Gender: Science Divulgation.

Saga: —.

Editorial: Free Press.

Edition year: 1, 2011.

Prizes: …

Synopsis [Warning: Spoiler]: Martin A. Nowak is Professor of Biology and Mathematics and Director of the Program for Evolutionary Dynamics at Harvard University.

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This book is a small resume of his career and the problems he has been working on. His life has been dedicated to mathematics. His studies are about evolution and cooperation, and how is evolution with cooperation the true game played by life.

Personal Review: I was preparing a course for the Santa-Fe institute about complex systems when we came across this book. Was one of the suggested readings. It´s not a practical book, it´s just a nice travel into the lands of evolution and cooperation.

It´s very dangerous to resume in a few words what the book is about, but I will try to give you an idea. Basically, evolution, the subsistence of the most fitted, it’s not enough to explain some of the things we see in life. What else we need? Cooperation. is cooperation and evolution the key to life. Cooperation gives individuals a emergence power that they are not able to reach by themselves, and that in combination with evolution is what governs life.

To study this combination of evolution and cooperation, the correct tool is game theory, and that is what the book is about. Different experiments of game theory and how Nowak has been working on them and what he has found.

I think is a nice book and I learn quite a loot. Especially, I learn that a huge work has been done in this area, which was not know by me, and that interesting results has been developed.

I came across this video just a second ago. i think is interesting.

on of the most interesting part of the book is when it speaks about different games, and how rules can decide between better strategies. For isntance, if you play a game with other player and you decide to cheat and take advantage of him that strategy is going to work in the long term only if you never play again with him or if there is no way of new players to know about it. If you are supposed to encounter that player again or you reputation indicate you are a defector, then that strategy is terrible bad.

Hmmm maybe Nowak himself can explain this better.

I suggest to get a copy of the book and read it. It’s nice, its short and is written in a way accessible for all.

(And now I must prepare to my final test on the course, which is already on-line).

 

Gibberellin a plant growth hormone.

I was readding an Asimov’s book about the brain and he came to growth hormones in plants. First he talk about Auxins and later about Gibberellins. He says about Gibberellins:

“Sprayed upon plants, it encourages a too rapid and too disorganized growth, killing them, trougth what practically amounts to an induced cancer”.

It was so interesting that I needed to learn more. So, first stop, PubChem for a view of 3D structure and some data. (If you want to get fast info about molecules or proteins, PubChem is a very nice place with cool graphs and lots of data, so, please, take a look).

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To learn something on what is Asimov talking about, we need to review somethings.

Cancer is when cells grow without control, and a such rate that cells in the end tend to die and accumulate into other places making other cells to also die or making imposible for them to work. (I’m not biologist, so that’s the best I can say).

Point two. Aminoacids are structures of between 10 and 30 atoms. Proteins are structures made of aminoacids, usually have from 1000 to 1000000 atoms. Such huge amount of atoms is quite dificult to study, and many groups are working quite hard to develop new techniques to understand how proteins fold (thanks to Ludovica for introducing me to this fascinating world ;) ).

Part three. Hormones are a especial tipe of proteins that a living organism uses to comunicate different parts of the body or trigger some mechanism. Enzymes are other kind of proteins which task is to destroy, specifically, other proteins.

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(Human enzyme glyoxalase I.)

How they work together?

The common scenario is that a glandula (an part of the body where hormones are produced, we have many), recives the order to produce some kind of hormone.  For example, the amount of sugar in the blood triggers the production of insulin in the pancreas. Once liberated, the insulim helps to sintetice the sugar into other compounds. If the sugar level is too high, the pancreas can read it’s level, and a enzyme called glucagon is produced and it compensates insulin raising sugar level.

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And what have to do Gibberellin in this?

Gibberellin is an growth hormone for plants. That means that its the way plants transmit the message “grow” to different parts of their body. But it’s not the only one. Other hormones are Auxin, Citokinin, Abscisic acid and ethylene gas.
(Thanks to: http://www.biologie.uni-hamburg.de/b-online/library/plant_physiology/Seedgerm.html )

hormones

Each of then is generated in different parts and control the growth of the plant. For example, Auxin is created mostly in the stems, can controls elongation, and can be destroyed by solar rays. So… if we have a stem inside a box and the sun enters in one of the sides of the box, the Auxin in this side is going to be destroyed, while in the other side makes the plant grow… and blend the stem towards the sun… That means… a mechanism to grow towards the sun!

And what Gibberellin controls?

Well it changes a little bit from plant to plant, and also depending on the growing state of the plant, but among the things that this hormone controls, the most important one is the Growing speed of seeds.

So… that means that if the levels of Gibberellin inside the plant are raised, than the plant can grow bigger. And if they rise enough, the growing becames uncontrolled and then cancer appears.

Biology is cool. But much more. Did you know that Gibberellin can be synthesized artificially? And actually is a very common aditive in many farms to make plants and fruits grow bigger.

Ok, cool good, we get bigger food. and what about the cancer? Well that’s the interesting point. if you see the whole video lesson, we can understand that obviously we are tackling the limit of a very delicated order, and if we go too far cancer appears, but if we learn how to compensate overgrowth, we can still have bigger plants and make them healthy!And that’s where theoretical biology, numerical simulations biology and experimental biology enters. And it’s going to be (it’s not finished yet) an amazing voyage.

So.. thanks biologist for all this things. And thanks Asimov once again to point to another interesting thing.

To read about japanese farmers and how Kurosawa discovered the Gibberellin, go here.

The Situation is Hopeless but Not Serious

situation

Original title: The Situation is Hopeless but Not Serious.

Title of this edition: El arte de amargarse la vida.

Author: Paul Watzlawick.

Gender: Science Ficction.

Saga: Theory of communication.

Editorial: Electronic copy.

Edition year: 1989

Prizes: …

Sinopsis [Warning: Spoiler]: This book is a light and ironic review of the ways that one can find to make his life unhappy… and doing that… making it interesting and something interesting to do.

Personal Review: Last week, someone very close to me, and very special, suggested that I must read this book. And, since in the past I never did what she suggested, this time I did it inmediately. And I realize that this book is very cool, but you need to be free of some of the things it talks about or you will get very angry reading. I mean, this book talks about the kind of things we do to aourselves to make our life more difficult and in this way more interesting to us.
For example, the book explains the ways we can deal with our couple in order to make her crazy about love. “Do you love me?” “Yes” “Do you realy love me?” “Yes realy” “Realy realy?” And in that way the problem is never solved and can be continued forever (Continuing the problem seems to be good at the same time as bad… hey don’t blame at me, if I was able to explain it properly then I will writte the book, not Watzlawick).
It’s strange, because while readding the book, it seems to be at the same time like a bad selfhelp book and at the same time knowing very good what he is talking about. So… I decide to make a little survey about that Paul Watzlawick.

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A little visit to wikipedia showed that he is died… and a little briefing of his theories. interesting. I will try to understand then by trying to explain them here. (Obviously, without reading more books this is going to be very poor, but will be interesting to revisit this post in the future with more knowledge).

The San Francisco Chronicle wrote: “… a philosopher and therapist who believed people create their own misery by trying to force epic, self-defeating solutions to trivial problems of the ego… “.

Before starting, I’m remembering something from one of my teachers “… if a model has enough parameters, then can explain any data…”.

As I understand, his theory of information can be resumed in this diagram that takes some ideas from Feynman diagrams.

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There is 3 main elements in the theory, Systems, Reality (which has also some properties of the systems), and information.

System: Can be anything, depends on what we are analyzing in each moment.

An example of system can be a person, a plant, a TV, or a rock.

System Reality: Is a model of the world (part exists wihout the System and part only exists because the system), and I acts filtering and generating information for the system which it belongs and another system’s reality.

An example of system’s reality can be the model of the world or the model of ourselves that we have in our minds, or can be the laws of the physics that determines how a TV works, or that sets how a rock behaves.

Because some of this things can change roles depending what our description is focused on, it’s quite difficult to translate the theory into examples. So, don’t be too severe whit me.

Information: It is described by it’s interactions with things (like some particles or interactions in particle physics… interesting). Information can be filtered by reality, modifies systems, and can be generated everywhere. Also, information has two types, objective and subjetive. Objetive is if both realities share the coding and decoding of the information. Subjetive is if both realities has different coding and decoding systems, making information depending on what we use for generating it and reading.

In addition, there is some extra rules:

1) Information is lost everywhere, so we can’t never get a prefect transmision.

2) Information paths appear always in pairs.

3) Every possible information path that can exists, exists and contributes to the evolution.

Using this elements and the rules, we have for two systems the diagram that i draw. There you can see that the two systems allways interacts (rule 3). That the information between systems pases trougth the reality of each system. And both system and reality change because of information flowing into them (as information always appears in pairs we only need to take account of flowing out info, becuse allways exists a returning path). And finally, we can only see in the draw the major paths, but you can understand that information can be created from every element, and like a fractal, paths of paths of paths of information appears.

As I said, it’s a poor description, but I did my best this time. Maybe in the future, with more knowledge I came back and tell more things.

For now, just two things, the first one, also from the San Francisco Chronicle:

“… Dr. Watzlawick thought people author their own emotional setbacks by striving to fix themselves. He felt the solution was closer and simpler — adjusting one’s self-image to absorb new experiences. The patient looks outward and harmonizes his relationships with others, actively building knowledge and skill in a learning process called constructivism. Emotional health comes from growth, not from healing…”

And the other one is something that I’ve learned from my eastern friends and actually has some meaning with this book. Ahhh and it’s about movies. For western people, movies has to have action, romance, and a clear distinction between diferent gendres, because in a word, when we go to the movie, we look for something especific that is not in our lives and we want to feel it. For eastern people (Bollywood), films must be a way of relaxing, that’s why all movies has to have part of action, part of romance, part of dancing and lots of music. Because they don’t want to fix part of their life, they want all of them.

Some books for the future:

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And a film?

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