March, 2019 | Chris Aldrich

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

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

Replied to Bookmark: Using Inoreader as an IndieWeb feed reader by

Frank Meeuwsen (Digging the Digital)

Ik onderzoek weer hoe ik deze pagina’s beter kan gebruiken als een commonplace book, een plaats waar ik allerlei gedachten, ideeën en losse flodders kan plaatsen met minimale barrieres. Het is een rode draad in mijn blog-ontwikkeling en ik denk dat het een belangrijk element wordt op de IndieWebC...
[Rough English translation for convenience]
I am researching how I can better use these pages as a commonplace book , a place where I can place all kinds of thoughts, ideas and loose pieces with minimal barriers. It is a common thread in my blog development and I think it will be an important element at the IndieWebCamp barcamp for me.

Frank, in case you haven’t come across it yet, there is a stub page on the IndieWeb wiki about using our websites as digital commonplace books. Hopefully it will have some useful information, articles, and examples for you to use as you continue hacking. Feel free to add your own thoughts to it as you experiment.

While I do like the way that WordPress makes it easy for one to create link previews by simply putting a URL into the editor (as in your example), I’ve generally shied away from it as it relies on oEmbed and doesn’t necessarily put the actual text into your site. (Not all websites will provide this oEmbed functionality either.) I mention this because a lot of the benefit of having a commonplace is the ability to easily search it. If your post only has a title and a URL, without careful tagging it may be much harder to come back and discover what you were searching for later.

I’ve started an article on how I’m using my website as one, but still have a way to go before I finish it. A big portion of my workflow relies on the Post Kinds Plugin and its available bookmarklet functionality. There are also a lot of nice Micropub clients like Omnibear that making bookmarking things quick and easy too.

In the erstwhile, I ‘ll note that on my own site, I tag things relating to my own commonplace (thinking about and building it) as “commonplace book” and for examples of other peoples’ commonplaces, I usually use the plural tag “commonplace books“. These may also give you some ideas.

With respect to the Medium article which you linked, I’ve seen a recurring theme among bloggers (and writers in general) who indicate that they use their websites as “thought spaces”. Others may use similar or related phraseology (like “thinking out loud”) but this seems to be the most common in my experience. Toward that end, I’ve been bookmarking those articles that I’ve read with the tag “thought spaces“. Some of those notes and websites may also give you some ideas related to having and maintaining an online commonplace book.

👓 Inoreader is meer dan een RSS lezer | Digging the Digital | Frank Meeuwsen

Read Inoreader is meer dan een RSS lezer by Frank Meeuwsen (Digging the Digital)

Ik gebruik Inoreader al een paar jaar maar ik wist niet dat het mogelijk was om er nieuwsbrieven in te ontvangen. Je kunt een specifieke tag aanmaken waarna je een uniek mailadres krijgt. Met dat mailadres kun je je op allerlei nieuwsbrieven abonneren en deze dus in je feedreader krijgen. https://di...

I use Inoreader a lot and never noticed it did emails to pull in newsletters! This is awesome!

Replied to Context challenges between #indieweb and social media silos by

David Mead (David John Mead)

My utopian dream of owning all my content would be to post it on my blog first. Syndicating to whatever social media silo's I choose afterwards.

This isn't a reality as some of these silos (Instagram) don't allow posting apart through their apps.

This forces me to accept their context for my content if I consume it into my site, from them.

This context piece David Mead is talking about is a far bigger issue than most people might give it credit for. Most don’t even notice it because their lives are split up so tragically online that they simply have never had any other experiences. Seeing things from a different perspective, I can guarantee that they’re missing out.

I’m reminded of chef Alton Brown who regularly gives the cooking advice that one should never buy unitasker kitchen tools, but instead get multi-taskers that can do a variety of jobs. This typically cuts down on a lot of the mess and fuss in one’s kitchen and generally makes it a nicer place to prepare food. Nine times out of ten the unitasker is a much more expensive and infrequently used tool and ultimately gets lost in a junk drawer. More often than not, there are one or multi-taskers that can do a better job for far less.

In some sense social silos like Twitter (with functionality for notes and bookmarks), Instagram (photos), Facebook (notes, photos, links, etc.), Swarm (locations and photos), etc. are just like those unitaskers in the kitchen. They only do one (or sometimes a very few) thing(s) well and generally just make for a messier and more confused social media life. They throw off the mise en place of my life by scattering everything around, making my own content harder to find and use beneficially. On my own website, I have all of the functionalities of these four examples–and lots more–and its such a much better experience for me.

As time goes by and I’m able to post more content types (and cross link them via replies) on my own website and even to others’, I do notice that the increased context on my website actually makes it more interesting and useful. In particular, I can especially see it when using my “On This Day” functionality or various archive views where I can look back at past days/months/years to see what I had previously been up to. This often allows me to look at read posts, bookmark posts, photos, locations to put myself back in the context of those prior days. Since all of the data is there and viewable in a variety of linear and non-linear manners, I can more easily see the flow of the ideas, where they came from and where they may be going. I can also more easily search for and find ideas by a variety of meta data on my site that would probably have never been discoverable on disparate and unrelated social sites. That article I read in July and posted to Twitter could never be grouped again with the related photo on Instagram or the two other bookmarked journal articles I put on Diigo or the annotations I made with Hypothes.is. But put all that on my own website, and what a wonderful exploding world of ideas I can immediately recall and continue exploring at a later date. In fact, it is this additional level of aggregation and search that makes my website that much more of a valuable digital commonplace book.

I’ll note, as a clever bit of of search and serendipity to underscore the discussion of context, it’s nearly trivial for me to notice that exactly two years ago today I was also analogizing social media and food culture. Who knows where those two topics or even related ones from my site will take me next?