Dear All,

This is to inform that our review paper titled: “Engineering life through Synthetic Biology” has been published in the journal In Silico Biology. The paper can be read here.

Your feedback is welcome.

Regards,
Paras Chopra and Akhil Kamma

This news story writes about a new strategy for combating HIV. The summary of the method is this. A sample of HIV is removed from the patient’s body. Outside the body, the HIV proteins are concentrated, which are then used to train the “killer T-cells”. These trained killer cells are now injected inside the body again to fight the HIV.

Instead of using anti-HIV drugs, the trained immune system does the job of fighting HIV. It reduces the chances of side-effects and is more effective too. Now, that is what I call *good* and *simple* biohacking

Have you heard of the names Tierra, Avida or Nanopond? If you are an evolutionary biologist (or even plainly curious person) and you haven’t heard of them then my guess is that you have missed much.

You might be wondering what on earth does evolution has to do with (digital) software. The general attitude of people is that evolution is a sole property of the material world. This is not entirely true. Believe it or not, the above mentioned software packages are instances of evolution. Yes, you have heard it right. They do not model or simulate evolution rather RUN a real evolution.

The evolving entities here are not the usual DNA, RNA, proteins, organisms, and etc. but tiny computer programs. Their world is composed of memory space where the computer programs spend there lives. The role of energy is taken by CPU cycles in this case hence different programs compete for both memory space and CPU cycles. This competition leads to the ‘survival of the fittest‘, hence evolution is kick-started.

The system starts with randomly generated programs written in a very simple (Assembly like) language. When the generated programs are run, each executed instruction costs some energy. Hence, there is a crunch for energy. Moreover, there is a certain probability that an executed instruction will go wrong which symbolizes the case of mutations in real world. Over the time, thanks to the mutations, self-replicating programs arise. This is the beauty of evolution. Given a substrate allowing self-replication and enough time, self-replicating entities will eventually emerge.

Once the self-replicating programs arise, there is a competition for being slicker. In other words, the selection pressure makes the programs smaller and smaller so that they consume lesser energy while maintaining their self-replicating property. In addition to consuming lesser energy, smaller programs can also multiply multiple times in the same CPU time because they have less number of instructions to execute and copy.

All this is not just plain imagination; the software systems mentioned above have indeed produced excellent results. The evolutionary dynamics seen in these systems closely match to the real world. Hence, these software packages enable one to study evolution at home/lab with ease. You may run an experiment hundreds of times, trace the lineage of an individual, see the whole-population at once, etc. The list of experiments is endless and is only limited by one’s vision and imagination.

A group of researchers have “accidentally” found that the plant Arabidopsis can pass on its ability for greater homologous recombination in case of stressed environment to its offsprings. It is quite intriguing because this increased tendency for recombination is passed on even if the mutation occurs in somatic cells.

This phenomenon can be regarded as if the plant is telling its offsprings to kick-start increased recombination so that they may be saved from stresses such as UV or pests. In other words, the plants are getting ready to evolve!

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Researchers at Georgia Institute of Technology have successful made a two-way communication with a bunch of neurons which they (cryptically) call the animats. The bunch of neurons are interfaced with a computer & live in a virtual environment. The researchers have managed to demonstrate that these animats can stay away from a moving target. They even add that the “clumps have a certain amount of awareness“.. Frightening as it may seem, but always remember there is nothing magical about the human brain or indeed about any biological phenomena.

Click here to read the news.