Evolutionary computing and 3D Virtual Creature Evolution. Check this seminar out.

I think I will definitely have to set up a seminars- dedicated category soon, since there are tons of interesting seminars around. In this one, Evolutionary Computing is explained. Evolutionary Computing is a branch of Artificial Intelligence computing that imports the principles of biological evolution in programming. The best known Evolutionary Computing issue are doubtless genetic algorithms, wich are becoming from year to year more involved in the implementation of algorithms for sequence alignment and structural prediction.

Lee Graham provides a good overview of Evolutionary Computing for the Ottawa Skeptics meeting. This video is quite dated, but still interesting. In order to explain his 3D Virtual Creature Evolution project, Graham gives a very good demonstration of the characteristics and potentials of evolutionary computing.

Basically, I’ve always thought that Evolutionary Computing represents a striking exception in modern science. There is a dogma in Scientific investigation that can be compared to the Molecular Biology Central Dogma. As in Molecular Biology it was originally stated that information flows from DNA to RNA to Proteins. we can say that in Science application is meant to flow from mathematical and base- sciences to Biology. The Molecular Biology Dogma has been denied by the revealing of reverse transcription mechanisms, and this “Science Application Dogma” has been denied by Evolutionary Computing since, at this time, is Logical Mathematics that takes advantage of theoretical principles defined in biology.

You can find other interesting videos in Leo Garham’s youtube channel.


Openworm. Understanding C. elegans by computational modeling

Simple and mysterious. The million times cited nematode Caenorabditis elegans is a small organism with only few hundreds cells in a constant number and a very simple structure. It is the perfect model organism for several wet-lab applications, from molecular biology to neurosciences. Anyways, the basis of its biology are not fully understood yet. An amazing attempt to insight the mechanism of this small worm it is carried on with the Openworm Project. A Java- based environment with a Python scripting interface is designed to build a theoretical model of a living C. elengans. The approach is of the bottom- up kind: observing informations that emerge from a simulation of data derived from scientific experiments in order to build a credible computer model. The software is maintained by a community in a full Open Source philosophy. Collaborations of individuals, researchers and philanthropists is very welcome.

So, if you are a java or python developer, a wet lab scientist, or maybe just a bit courious, consider to join this project. For a preview, the team organizes a Google Plus Hangout every two week. Everyone is invited.

About the creationist stand at the Venice Biennale

The majority of catholic believers has a strange relationship with Darwin’s evolution. Since they can no longer support a full creationist point of view, they try to find reasons to make creation and evolution coexist. How? In someway, the best they can imagine. So, if you talk with an average catholic, he will tell you that evolution is still part of divine plan of creation, or maybe he will purpose the idea that creation really happened, but it will limit the thing to the birth of life on the earth. God started the process, evolution did the rest. This attitude could seem positive and conciliatory, light years away from the dumb american christian fundamentalists and their intransigence. But let’s see what is moving under the hood.

One of the cardinals that spent more efforts into the reconciliation between creationism and evolutionism is Gianfranco Ravasi. The idea he’s proposing since a few years is that the incompatibility of the two theories is no longer acceptable. Evolution doesn’t exclude creation and creation doesn’t exclude evolution. In this spirit, Ravasi organized the first stand dedicated to the Vatican in the history of Venice Biennale the last May. A 40 square meters pavilion completely dedicated to the 11 books of the Genesis. In a few words, we must sadly denote that one of the most important cultural events in Europe reserved 40 square meters to creation. An international team of photographers, visual artists and media groups focused on creation.

Not to mention how despicable a thing like this can be for the Country of Galileo. I just would like to reason about the real sense of the Church’s openings towards the evolutionary ideas. If they kept supporting creationism as it is, and kept denying evolution, the only result they could get would have been making fools of themselves. So, they realized that what they need is a survival strategy, a way to store creationism in a safe place from the unstoppable attacks of Science. Basically this doesn’t differ much from the strategy we have seen with the “intelligent design”. As they discover cell biology, molecular biology and DNA, we try to find a way to modify creationism in order to include the new discovers.

It is remarkable and quite funny to notice how creationism is changing under the pressure of the overwhelming amount of evidences in support to Darwin’s theory. Basically, as any prey, creationism tries to evolve in order to survive to the attacks of its fearsome predator. Maybe they will keep talking about creation for years, but to do it, they will definitely need to choose an evolutionary attitude.

The 6 books you must consider for your very first steps into databases.

Basically one would really avoid this. Biology is already quite hard to keep in mind, and you don’t really need of informatics to keep your brain busy. But, by definition, a bioinformatician is someone who match the two subjects and the best thing to do is to do it the best you can. Learning a powerful programming language such as Python, Ruby or Perl, getting used with markup- languages (XML and derivates) and learning databases are the three things a biologist must do to call himself bioinformatician.

Yes, ok, but how to do it? The standard procedure a computer scientist would enthusiastically prospect you is to find all the information for free and on the web. And he would be right. After all, the hacker philosophy is pretty clear about that: take all the free information you can find, even if this can be quite hard. But, since many of us are romantically devoted to books, and since not everybody is willing to spend time in a fight to the death against information entropy, sometimes release few money for a book it is not that bad idea.

Here are reported some books that can be useful to deepen into the world of databases. Building a database is a really boring thing you might really need. Handling big information is needed for the majority of genomics and structural studies. Building a database, beeing able to build querys or developing scripts to reason with the major genomic or protein databases out there could be really useful and time- saving.

Introduction to Database and Knowledge-base Systems
By S. Krishna

With this book you’ll learn the basics of database theory. Very easy to read and exhaustive.

SQL in a Nutshell A Desktop Quick Reference
By K. Klein

Maybe the best guide to understand Structured Query Language.

SAMS Teach Yourself SQL in 10 Minutes
By B. Forta

A concise guide to SQL. The text is organized into lessons. Easy to read and exhaustive.

MySQL Cookbook
By P. DuBois

900 pages to have a very complete overview on the open source DBMS MySQL. Maybe the best MySQL book around.

Instant PostgreSQL Starter
By D. K. Lyons

Move your first steps in the world of the open source DBMS PostgreSQL.

Database Annotation in Molecular Biology: Principles and Practice
By A. M. Lesk

A very exhaustive guide to Biological databases. Useful for database curators and users.

If you know more, please comment this.

Introducing pyphylogenomics 0.2.0, a python module for phylogenomics.

If we have to find a word to best represent the encounter between informatics and evolutionary biology, that word would definitely be phylogenomics. The large-scale analysis, allowed by the big amount of data made available in the last 20 years, is rapidly imposing the rule that “nothing makes sense in evolutionary biology except in the light of high throughput analysis”. The uptake of the most important evolutionary relationships is subject to large-scale analysis, since the relevant information is often hidden in a mountain of genetic material.

The python module I am going to present is a brand-new module, completely dedicated to phylogenomics, made by Carlos Peña, from the Nymphalidae Systematic Group at the University of Turku (Finland). The package implements several functionalities including blast integration, sequence analysis, fastq- fasta conversions and primer sites finding.

To try it on you python environment you’ll need the modules MySQLdb and biopython installed. Just connect to the pypi page and download the package, then unzip, open the terminal in the unzipped folder and type:

python setup.py build
python setup.py install

Ubuntu users will need to sudo first. For more information check the github page.

Painting Darwin. Evolutionary street art in the Isle of Wight.

Just a small post to share this video. Sometimes human arts meet science and, when they do, the carachters that traced the shape of modern science become popular icons. And when street art is involved, these icons will be on the walls. And walls can talk more than one could expect. In this video we see the street artist Tony Trowbridge painting a Charles Darwin’s portrait on a wall in the Isle of Wight. The artist used an airbrush- stencil technique and realized a colorful, darwinful and amazing wall in the legendary island of Great Britain.

Meet artist’s work

Youtube channel
Google Plus Account

Four billion years old protein 3D structure determined by an Euro- American team. Showing the potential of evolutionary research.

One of the biggest challenges in molecular evolution studies is to gain informations about the evolution of protein tertiary structures. When we try to determine the evolutionary origins of proteins, we basically consider the structure similarities between contemporary proteins, since we don’t generally have enough paleo- materials to analyze. Therefore, we can only abstract a putative model of the ancestors of proteins.

The international team leaded by Sanchez- Ruiz from the spanish University of Granada overcome this problem resolving the x-ray structure of Precambrian thiredoxins. In an earlier paper, Sanchez- Ruiz and his collaborators constructed a phylogenetic tree of thioredoxins- proteins that are present in the three domains of life (archaea, bacteria and eukariotes).

The tree leaded the way for the resurrection of Precambrian proteins in the labotratory and the characterization of their features. In the new study, published on structure the last august 8th,  Sanchez- Ruiz teamed up with Jose Gavira from the Andalutian Institute of Earth Sciences (Spanish National Research Council — University of Granada) to analyze the X-ray chrystal structure of the resurrected proteins. The finidings are simply striking. The present- day thireodoxins are remarkably similar to those that existed 4 billions of years ago, a period really close to the origins of life. This is consistant to the punctuated- equilibrium model of evolution, in wich protein structures changes occur intermittently in short periods, with long periods of conservation.

This work is remarkable because of his capability to show the full potential of theoretical and base- research approaches in biology. The same author underlines it as it follows:

In addition to uncovering the basic principles of protein structure evolution, our approach will provide invaluable information regarding how the 3D structure of a protein is encoded by its amino acid sequence. (…) It could also provide information about how to design proteins with novel structures — an important goal in protein engineering and biotechnology.

For a theoretical biology blog it is very important to remark this. The base research approaches and theoretical contributions play a crucial role for the development of applied fields such as biomedical research and biotechnology.