Finally a whole cell computational model

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Published on: July 20, 2012

An entire organism is modeled in terms of its molecular components
Complex phenotypes can be modeled by integrating cell processes into a single model
Unobserved cellular behaviors are predicted by model of M. genitalium
New biological processes and parameters are predicted by model of M. genitalium

Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. An integrative approach to modeling that combines diverse mathematics enabled the simultaneous inclusion of fundamentally different cellular processes and experimental measurements. Our whole-cell model accounts for all annotated gene functions and was validated against a broad range of data. The model provides insights into many previously unobserved cellular behaviors, including in vivo rates of protein-DNA association and an inverse relationship between the durations of DNA replication initiation and replication. In addition, experimental analysis directed by model predictions identified previously undetected kinetic parameters and biological functions. We conclude that comprehensive whole-cell models can be used to facilitate biological discovery.

More info  [The Science Direct Link] [The Link]

Is Society Becoming Over-Medicalized? (Ivan Oransky)

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Published on: July 16, 2012

An interesting talk @TEDMED 2012 by Ivan Oransky.

Also, interesting interview in medgadget: [Interview Transcript here]


Interesting interview with Stephen Wolfram [theeuropean-magazine]

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Published on: July 5, 2012

Here is an interesting interview with Stephen Wolfram of Mathematica, WolframAlpha from theeuropean-magazine. Couple questions that I found interesting in the interview.

The European: The New York Times Magazine recently published a profile of Craig Venter, who led the team that decoded the human genome. Two things about it struck me as very interesting: One, he argued that the main challenge for innovation is not to do more, but to spread the benefits of innovation around the globe. Two, the best way to do that is through private enterprises and not through academic research. What’s your take on that?
Wolfram: I was an academic for a while, but I really like energetically doing projects. What I tried to do is build a very efficient mechanism to turn ideas into things. Right now, entrepreneurial companies seem to be the best way to do that. I look at my friends in academia and think: “Wow, things moved so slowly there in the last 25 years!” When we hire academics to work on WolframAlpha or Mathematica, the biggest shock for them is always how quick everything moves. We sit down, and an hour later we have decided what we are going to do and moved on. We can do crazy projects! If you want an immediate impact on the world, that’s what you need.


The European: So there are limits to the intrusiveness of data searches that violate personal privacy. Is there a similar limit where we might say: Even if it were technologically possible to automate most everyday processes, we should not do so for the sake of intuition or creativity.
Wolfram: It’s interesting that you mention creativity. We did an experiment a few years ago where we randomly plucked music from the universe of possible musical arrangements, and it actually sounded quite decent. I have been hearing from composers that they use that website for inspiration, which is the exact opposite of what I had expected. But the question remains what we humans should do if everything became automated. The answer, I think, is that we figure out what we should do. Let’s assume that everything is automated and wonderful. What do you choose to do in that case? As humans and as individuals, we have certain purposes that we are trying to achieve and which cannot be automated. Highly advanced artificial intelligence can be programmed to have a particular purpose but it cannot answer the question of what’s the right purpose to have. I find it highly interesting to figure out how human purposes evolved and how technology might affect them. At different times in history, we have said that our purpose is religion, or maximizing pleasure, or maximizing money. Some of the purposes we have today would seem rather bizarre from a historical perspective. Imagine a paleolithic ancestor trying to figure out why someone would walk on a treadmill indoors! So when lots of things are automated and possible, what purposes will we value? My personal and rather bizarre answer is that future generations will return to the wisdom of the ancients. The times we live in right now mark the first time in human history that data is permanently recorded on a large scale, so future generations can study us and say: “These people lived finite lives and had to make tough choices. So maybe those choices can tell us something about what it means to be human, and about what endpoints our idea of progress should aspire to.”


More of this here: [The Link]





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