Link – Page 201 – Chris Aldrich

Bookmarked From bit to it: How a complex metabolic network transforms information into living matter by Andreas Wagner (BMC Systems Biology)

Background

Organisms live and die by the amount of information they acquire about their environment. The systems analysis of complex metabolic networks allows us to ask how such information translates into fitness. A metabolic network transforms nutrients into biomass. The better it uses information on available nutrient availability, the faster it will allow a cell to divide.

Results

I here use metabolic flux balance analysis to show that the accuracy I (in bits) with which a yeast cell can sense a limiting nutrient's availability relates logarithmically to fitness as indicated by biomass yield and cell division rate. For microbes like yeast, natural selection can resolve fitness differences of genetic variants smaller than 10-6, meaning that cells would need to estimate nutrient concentrations to very high accuracy (greater than 22 bits) to ensure optimal growth. I argue that such accuracies are not achievable in practice. Natural selection may thus face fundamental limitations in maximizing the information processing capacity of cells.

Conclusion

The analysis of metabolic networks opens a door to understanding cellular biology from a quantitative, information-theoretic perspective.

https://doi.org/10.1186/1752-0509-1-33

Received: 01 March 2007 Accepted: 30 July 2007 Published: 30 July 2007

Hat tip to Paul Davies in The Demon in the Machine

Bookmarked Statistical Physics of Self-Replication by Jeremy L. England (J. Chem. Phys. 139, 121923 (2013); )

Self-replication is a capacity common to every species of living thing, and simple physical intuition dictates that such a process must invariably be fueled by the production of entropy. Here, we undertake to make this intuition rigorous and quantitative by deriving a lower bound for the amount of heat that is produced during a process of self-replication in a system coupled to a thermal bath. We find that the minimum value for the physically allowed rate of heat production is determined by the growth rate, internal entropy, and durability of the replicator, and we discuss the implications of this finding for bacterial cell division, as well as for the pre-biotic emergence of self-replicating nucleic acids.
https://doi.org/10.1063/1.4818538

Syndicated copy also available on arXiv: https://arxiv.org/abs/1209.1179

Hat tip to Paul Davies in The Demon in the Machine

👓 Graying Out | Tim Bray

Read Graying Out by Tim Bray (tbray.org)

For many years I’ve interacted with my fellow humans, I think perhaps more than any other way, via the medium of Internet chat. But in my chat window, they’re fading, one by one. This problem is technical and personal and I felt it ought not to go unrecognized.

An interesting piece about the death of chat clients in lieu of social media. He’s got a list of some interesting people here, many of whom can be found on their own websites now.

👓 Medium import for Micro.blog | Manton Reece

Read Medium import for Micro.blog by

Manton Reece (manton.org)

Micro.blog can now import blog posts from Medium. You can request a .zip archive of your content from Medium.com, then go to Posts → Import on Micro.blog to upload the file. Because Medium no longer supports custom domain names, we don’t think it’s a good long-term solution for blogging. If yo...

This is some awesome news, particularly for all the people fleeing Medium. Now they can own their own data on their own domain a whole lot easier. I wouldn’t be surprised to see more of the #DoOO crowd joining Micro.blog as an option too.

👓 Defining the DNA of collaboration | The Open Co-op

Read Defining the DNA of collaboration (The Open Co-op)

As a species, human beings are barely more intelligent than kindergarten kids. We revel at our place at the top of the food chain, and praise our technological ingenuity but, let’s face it, we’ve barely begun to work life out. We’ve created one directional extractive systems that undermine our own life support systems, like kindergarten …

There’s some interesting philosophy here. It dances around the idea of fitness landscapes, but doesn’t mention them directly, though this is essentially what the article is exploring from the perspective of businesses.

👓 A ‘Creepy’ Assignment: Pay Attention to What Strangers Reveal in Public | New York Times

Read Opinion | A ‘Creepy’ Assignment: Pay Attention to What Strangers Reveal in Public (New York Times)

An exercise I gave my students helps illustrate the risks to privacy in our everyday, offline lives.

I saw some on Twitter say that this was a terrible assignment and that they can accomplish the same goal without being so creepy, but naturally they neglected to give any details about improving on it.

👓 ‘I can get any novel I want in 30 seconds’: can book piracy be stopped? | The Guardian

Read 'I can get any novel I want in 30 seconds': can book piracy be stopped? by Katy Guest (the Guardian)

As publishers struggle with ‘whack-a-mole’ websites, experts, authors and Guardian readers who illegally download books, assess the damage

👓 Neuroscience Readies for a Showdown Over Consciousness Ideas | Quanta Magazine

Read Neuroscience Readies for a Showdown Over Consciousness Ideas by

Philip Ball (Quanta Magazine)

To make headway on the mystery of consciousness, some researchers are trying a rigorous new way to test competing theories.

Many of these ideas of consciousness seem ridiculous to me. I suppose that people need to be thinking about these ideas, iterating, and even doing some philosophy to ever get around to some better ideas and science, but it’s still very early days on the topic. I am glad that they’re actively attempting to come up with some actual science and testing of some of these theories to find a better answer.

If nothing else, this article does a reasonable job of giving an overview of some of the most recent schools of thought. And of course, it’s Philip Ball, so who could resist reading it…