Bookmarked Tibor Gánti (1933- 2009): Towards the Principles of Life and Systems Chemistry (Journal of Theoretical Biology | sciencedirect.com)
Edited by Eörs Szathmáry
Volume 381, Pages 1-60 (21 September 2015)
Michael Marshall in He may have found the key to the origins of life. So why have so few heard of him? ()

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Bookmarked Vocabulary of Definitions of Life Suggests a Definition by Edward N. Trifonov (Journal of Biomolecular Structure and Dynamics Volume 29, 2011 - Issue 2)
Analysis of the vocabulary of 123 tabulated definitions of life reveals nine groups of defining terms (definientia) of which the groups (self-)reproduction and evolution (variation) appear as the minimal set for a concise and inclusive definition: Life is self-reproduction with variations.
https://doi.org/10.1080/073911011010524992

Michael Marshall in He may have found the key to the origins of life. So why have so few heard of him? ()

Read He may have found the key to the origins of life. So why have so few heard of him? by Michael MarshallMichael Marshall (Science)
Hungarian biologist Tibor Gánti is an obscure figure. Now, more than a decade after his death, his ideas about how life began are finally coming to fruition.
Good to see Tibor Gánti finally getting some credit. This is a great little article with a nice overview of the Origin of Life problem (and references). The author Michael Marshall has a new book out on the topic.

Peter Molnar in IndieWeb Chat ()

Read - Want to Read: How to Argue with a Racist: What Our Genes Do (and Don't) Say about Human Difference by Adam Rutherford (Experiment)
Race is not a biological reality.
Racism thrives on our not knowing this.
Racist pseudoscience has become so commonplace that it can be hard to spot. But its toxic effects on society are plain to see--feeding nationalism, fueling hatred, endangering lives, and corroding our discourse on everything from sports to intelligence. Even well-intentioned people repeat stereotypes based on "science," because cutting-edge genetics are hard to grasp--and all too easy to distort. Paradoxically, these misconceptions are multiplying even as scientists make unprecedented discoveries in human genetics--findings that, when accurately understood, are powerful evidence against racism. We've never had clearer answers about who we are and where we come from, but this knowledge is sorely needed in our casual conversations about race.
How to Argue With a Racist emphatically dismantles outdated notions of race by illuminating what modern genetics actually can and can't tell us about human difference. We now know that the racial categories still dividing us do not align with observable genetic differences. In fact, our differences are so minute that, most of all, they serve as evidence of our shared humanity.
Read - Want to Read: Metazoa: Animal Life and the Birth of the Mind by Peter Godfrey-Smith (Farrar, Straus and Giroux)
Dip below the ocean's surface and you are soon confronted by forms of life that could not seem more foreign to our own: sea sponges, soft corals, and serpulid worms, whose rooted bodies, intricate geometry, and flower-like appendages are more reminiscent of plant life or even architecture than anything recognizably animal. Yet these creatures are our cousins. As fellow members of the animal kingdom--the Metazoa--they can teach us much about the evolutionary origins of not only our bodies, but also our minds.
In his acclaimed 2016 book, Other Minds, the philosopher and scuba diver Peter Godfrey-Smith explored the mind of the octopus--the closest thing to an intelligent alien on Earth. In Metazoa, Godfrey-Smith expands his inquiry to animals at large, investigating the evolution of subjective experience with the assistance of far-flung species. As he delves into what it feels like to perceive and interact with the world as other life-forms do, Godfrey-Smith shows that the appearance of the animal body well over half a billion years ago was a profound innovation that set life upon a new path. In accessible, riveting prose, he charts the ways that subsequent evolutionary developments--eyes that track, for example, and bodies that move through and manipulate the environment--shaped the subjective lives of animals. Following the evolutionary paths of a glass sponge, soft coral, banded shrimp, octopus, and fish, then moving onto land and the world of insects, birds, and primates like ourselves, Metazoa gathers their stories together in a way that bridges the gap between mind and matter, addressing one of the most vexing philosophical problems: that of consciousness.
Combining vivid animal encounters with philosophical reflections and the latest news from biology, Metazoa reveals that even in our high-tech, AI-driven times, there is no understanding our minds without understanding nerves, muscles, and active bodies. The story that results is as rich and vibrant as life itself.
Read New Clues to Chemical Origins of Metabolism at Dawn of Life by John RennieJohn Rennie (Quanta Magazine)
The ingredients for reactions ancestral to metabolism could have formed very easily in the primordial soup, new work suggests.

they found that the glyoxylate and pyruvate reacted to make a range of compounds that included chemical analogues to all the intermediary products in the TCA cycle except for citric acid. Moreover, these products all formed in water within a single reaction vessel, at temperatures and pH conditions mild enough to be compatible with conditions on Earth. 

Annotated on October 13, 2020 at 10:20PM

Read What Is an Individual? Biology Seeks Clues in Information Theory. (Quanta Magazine)
To recognize strange extraterrestrial life and solve biological mysteries on this planet, scientists are searching for an objective definition for life’s basic units.
I’ve been following a bit of David’s work, but obviously there’s some newer material I need to catch up on. I like the general philosophical thrust of their direction here. I can see some useful abstractions to higher math here, maybe an analogy to a “calculus of biology” which doesn’t look at single points, but rates of change of that point(s).
Darwin Day & Attachment
unopened condition

In honor of Darwin Day: An interior page on natural selection in an unopened original of the Proceedings of the Linnean Society. Note that the octavos in the edition haven’t been cut accounting for the top of the page being curved in the picture (because of the attachment of the adjoining pages). Science changed dramatically that day.

Read Dandelions, Tulips, Orchids and Neurological Pluralism by Ryan BorenRyan Boren (Ryan Boren)
I’m always on the look out for new ways of thinking about and designing for neurological pluralism, especially when it comes in threes. Dandelions, tulips, and orchids designate low-sensitive, medium-sensitive, and high-sensitive people. I like the way this aligns with caves, campfires, and watering holes, the red, yellow, green of interaction badges, and the three speeds of collaboration.
This is a fascinating thesis with some interesting long term effects on evolution.
Listened to How capuchin monkeys learn about food And what that might teach us by Jeremy Cherfas from Eat This Podcast

Cover artwork of female capuchin and young infant. She is holding a rock to crack nuts.When chimpanzees were first seen stripping the leaves off slender branches and inserting them into termite nests to fish for the insects, people marvelled. Our nearest relatives, using tools to get nutritious food. Imagine, then, the surprise among primatologists when capuchin monkeys, not nearly as closely related to us, proved equally adept at tool use. Capuchins select stones that can be half as heavy as they are and carry them long distances to use as nutcrackers.

Elisabetta Visalberghi is a biologist based in Rome, who published the first scientific observations of tool use in capuchins. That is just a part of her far-reaching investigations into how capuchins, which are omnivorous, go about deciding which foods are worth eating and which are best avoided.

The results may surprise you.

Trailer: The Bearded Capuchin Monkeys of Fazenda Boa Vista from Cognitive Primatology_ISTC on Vimeo.

Notes

  1. Cover photo of Chuchu and her infant by Elisabetta Visalberghi.
  2. The video I mentioned in the show is The bearded capuchin monkeys of Fazenda Boa Vista, available from the CNR Primate Center in Rome. There are some other videos on Vimeo.
  3. The CNR Primate Center website.
  4. Cashews really are a problem from the people who have to process them. This article is very recent.
  5. Banner from a photo by Allan Hopkins
  6. How about making a donation to show your love for the show?
This is so fascinating from an anthropological and even socio-economic perspective.

🔖 Origins Of Life | Complexity Explorer

Bookmarked Origins Of Life (complexityexplorer.org)

About the Course:

This course aims to push the field of Origins of Life research forward by bringing new and synthetic thinking to the question of how life emerged from an abiotic world.

This course begins by examining the chemical, geological, physical, and biological principles that give us insight into origins of life research. We look at the chemical and geological environment of early Earth from the perspective of likely environments for life to originate.

Taking a look at modern life we ask what it can tell us about the origin of life by winding the clock backwards. We explore what elements of modern life are absolutely essential for life, and ask what is arbitrary? We ponder how life arose from the huge chemical space and what this early 'living chemistry'may have looked like.

We examine phenomena, that may seem particularly life like, but are in fact likely to arise given physical dynamics alone. We analyze what physical concepts and laws bound the possibilities for life and its formation.

Insights gained from modern evolutionary theory will be applied to proto-life. Once life emerges, we consider how living systems impact the geosphere and evolve complexity. 

The study of Origins of Life is highly interdisciplinary - touching on concepts and principles from earth science, biology, chemistry, and physics.  With this we hope that the course can bring students interested in a broad range of fields to explore how life originated. 

The course will make use of basic algebra, chemistry, and biology but potentially difficult topics will be reviewed, and help is available in the course discussion forum and instructor email. There will be pointers to additional resources for those who want to dig deeper.

This course is Complexity Explorer's first Frontiers Course.  A Frontiers Course gives students a tour of an active interdisciplinary research area. The goals of a Frontiers Course are to share the excitement and uncertainty of a scientific area, inspire curiosity, and possibly draw new people into the research community who can help this research area take shape!

I’m totally in for this!

Hat tip for the reminder to:

Bookmarked Java jig: how birds learn to impress (Economist Espresso)
That many songbirds sing their songs over and over again in an effort to master them before performing in front of potential mates is well known. What has remained less clear is whether they also practise the visual displays that they often use alongside their songs. Research published this week in Royal Society Open Science reveals that they do. The team studied male Java sparrows that dance with bounces and make wiping motions with their bills in an effort to convince females to mate with them. The researchers watched the males in captivity and found that they repeatedly practised dancing early in life in front of their mothers and fathers long before they were ready to breed. While their moves were not particularly good at the start, all males dramatically improved over time, suggesting that the parents may well be providing valuable feedback, and that awkward adolescent dancing may extend beyond Homo sapiens.
Read Dunbar Number by Ton ZijlstraTon Zijlstra (zylstra.org)
In many discussions on social networks the number 150 comes up as a ‘natural’ limit to how much social interaction a person on average can handle. Intuitively I always felt uneasy with this number, and have on several occasions suggested that this could only be a limit in a spe...

📑 Solomon Golomb (1932–2016) | Stephen Wolfram Blog

Annotated Solomon Golomb (1932–2016) by Stephen Wolfram (blog.stephenwolfram.com)

As it happens, he’d already done some work on coding theory—in the area of biology. The digital nature of DNA had been discovered by Jim Watson and Francis Crick in 1953, but it wasn’t yet clear just how sequences of the four possible base pairs encoded the 20 amino acids. In 1956, Max Delbrück—Jim Watson’s former postdoc advisor at Caltech—asked around at JPL if anyone could figure it out. Sol and two colleagues analyzed an idea of Francis Crick’s and came up with “comma-free codes” in which overlapping triples of base pairs could encode amino acids. The analysis showed that exactly 20 amino acids could be encoded this way. It seemed like an amazing explanation of what was seen—but unfortunately it isn’t how biology actually works (biology uses a more straightforward encoding, where some of the 64 possible triples just don’t represent anything).  

I recall talking to Sol about this very thing when I sat in on a course he taught at USC on combinatorics. He gave me his paper on it and a few related issues as I was very interested at the time about the applications of information theory and biology.

I’m glad I managed to sit in on the class and still have the audio recordings and notes. While I can’t say that Newton taught me calculus, I can say I learned combinatorics from Golomb.