User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/09/03

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Some reflexions on robustness

Yesterday I wrote something about the possible structure of robustness in biological system, and I argued something about a proposed nested nature of robustness. When speaking about robustness I previously thought the following things:

  1. The evolutionary history is embedded in the structure of robustness.
  2. Highest robustness corresponds to oldest biological structures.

Because of these arguments I thought that being the transcriptional mechanisms older than the sensory mechanism, transcription would be more robust that sensing.

  1. However, it seems that some transcriptional mechanism are not very robust, when conceived as isolated processes, but they become robust when being part of a network which includes not only transcription.
  2. It seems then robustness is not a nested property in terms of evolutionary history. I conjecture then that robustness is a modular property -I suppose that under certain conditions the nested property is present-.

Meeting with Alexander de Luna

Alexander de Luna is a posdoctoral fellow working here at HMS in the Roy Kishony laboratory. In his own words: "I currently use a combination of theoretical and experimental approaches to study genetic interactions—interactions which illustrate how mutations affect the phenotypic consequences of each other. We first used a flux balance model to simulate the genetic interaction network of yeast and extended the concept of genetic interaction from the gene-gene level to the system level. More recently, we have developed an automated experimental tool based on fluorescence measurements to achieve high-throughput, yet very accurate, quantification of phenotypes in yeast. Using this powerful phenotyping methodology, we plan to study further aspects of the structural and functional design of genetic networks."

Alexander seems to be a very good possible collaborator on robustness issues, in particular because he is involved in experimental activities. I asked him to send me his last papers. He is coming back to Mexico to set a laboratory at Cinvestav -Langebio-. His research seems to be veru approiate to tackle the phenomenon of modularity of the robustness property.

Some ideas about Systems Biology at Cinvestav

I must propose a Systems Biology program to René Asomoza as soon as possible. I must target both biotechnoloy and synthetic biology addressing pharmaceutical issues. I ellaborated a perilimary version of the proposal, and it is here: Media:sysbio.doc.

Organizing the future work

  1. Analyze the friction model for the AKT signaling pathway process.
  2. Contact Pilipel for the robustness and redundancy issue.
  3. Develop the GUI for the Simulink application.
  4. Contact Walter Fontana for the Kappa issue and the MIT contacts.
  5. Read de Wagner book.
  6. Write the introductory text for Cristina.
  7. Contact Moisés and Alberto for the thesis proposals (prepare the proposals).
  8. Study the mTOR question and prepare the meeting with Pamela and David.
  9. Contact Uri Alon and read his book.
  10. Build the GUI for the Mathematica application.
  11. Study the Little B system and contact Aneil Mallavarapu.
  12. Fix the Gaston question.
  13. Read some text on modularity.

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