Open question of the day : life and machines
 Does biology aims to uncompress the obfuscated code of Life ?

This question is relative to the nature of Life : are living things made of machines and programs ?
 
I guess not but it is useful to think like that. Thinking living things as machines helps researchers to make retro-engineering on them, and indeed :
- many words used in biology come from engineering, computer sciences and electronics : cell machinery, genetic code, genetic program, molecular motors, connexions ...
- under a microscope, one observe only the things our brain is able to recognise, i.e. well organized structures, things that look like machines,  !


...

The Open Science Door - REBOOT



Dear all,

We are trying to reboot the Open Science Door.

You make science, you have a door, you want to share your scientific ideas, projects, work, code, pictures ... with you office collegues : stick them (not your collegues) on your door, take a picture and post on this blog.

Want to participate : send us an e-mail at nicolas[dot]glade[at]univ[minus]grenoble[minus]alpes[dot]fr

and stick this QR code to your door.






See you soon on OSD

Nicolas

Isochronal sufaces

In 1974, Arthur T. Winfree introduced the notion of isochrons when studying biological oscillators' response to perturbations [1]. Oscillators are physical or abstract systems that evolve in time periodically passing through or nearby a reference state. The time needed to browse the circle of states is the period of the oscillator. Therefore, if you take a reference state, you can define another state by a fraction of the period. This number is called the phase of the oscillator. This is the case of the point which belongs to

the cycle but the system can have other states, perturbed states. For example, one can pull a maintained

spring till reaching a point B greater than the spring maximal elongation in normal conditions.

This new point B can also be described by a period fraction if we extend the notion of phase to latent phase.

The latent phase of the perturbed point B is equal to the phase of a point A on the cycle, if two identical springs one starting from A and the other from B tend to synchronize after some time.

Oscillator 1 (black) starts from A and oscillator 2 (red) starts from B.

After, some time the two springs synchronize.

Original link: http://www.scholarpedia.org/article/Isochron

The set of all the perturbed points having the same latent phase is called an isochron. This set

describes a hyper-surface : a curve in the case of 2D system and a suface in the case of 3D system. This was proved in [2] by Guckenheimer...

Bibliography

[1] Winfree, A.T. : Patterns of phase compromise in biological cycles. J

Math Biol 1 (1974) 73–95

[2] Guckenheimer, J. : Isochrons and phaseless sets. J Math Biol 1 (1975)

259–273

[3] The isochronal fibration : Characterization and impli-

cation in biology. Hedi Ben Amor, Nicolas Glade, Claudio Lobos,

Jacques Demongeot, Acta Biotheoretica (2010) 58, 121142.

The Open Science Door

Hello World,

We are Nicolas Glade and Hedi Ben Amor from the University of Grenoble, France.

We started a new concept we called "The Open Science Door".

We stick our fresh new results on our office door. We think that this can catalyse new local interactions with persons passing by the corridor. Of course, we aim to extend the range of interactions to a more global scale. The present corresponding blog is a virtual mirror of our door(s). It is a good and fun manner to start open collaborations via our door(s)/blog in order to explore new ideas.

We are in the begining of the process, take a look at our own Door.

By the way, if you want to join us, you can send the photo of your Open Science Door to hedi[nospace]ben[nothing here]amor[at]gmail[dot]com or to nicolas[dot]glade[at]gmail[dot]com .

We will upload it here http://www.flickr.com/photos/theopensciencedoor

Researchers and PhD are of course also welcome to contribute to the blog as authors. Just send us an email.

NB: behind our door, we also created a Open Draft Door from where the ideas start to take shape. New concepts should then diffuse in the door throughout its edge !

That's it++,
Have fun :)

Nicolas and Hedi