👓 Frans de Waal Embraces Animal Emotions in ‘Mama’s Last Hug’ | New York Times

Read Frans de Waal Embraces Animal Emotions in ‘Mama’s Last Hug’ (New York Times)
In his new book, the renowned ethnologist argues that emotions are key to understanding both human and animal behavior.

Acquired The Emergence of Biological Organization by Henry Quastler

Acquired The Emergence of Biological Organization by Henry Quastler (Yale Univ Press; First Edition edition (1964))

In 1964 Quastler's book The Emergence of Biological Organization was published posthumously. In 2002, Harold J. Morowitz described it as a "remarkably prescient book" which is "surprisingly contemporary in outlook". In it Quastler pioneers a theory of emergence, developing model of "a series of emergences from probionts to prokaryotes".

The work is based on lectures given by Quastler during the spring term of 1963, when he was Visiting Professor of Theoretical Biology at Yale University. In these lectures Quastler argued that the formation of single-stranded polynucleotides was well within the limits of probability of what could have occurred during the pre-biologic period of the Earth. However, he noted that polymerization of a single-stranded polymer from mononucleotides is slow, and its hydrolysis is fast; therefore in a closed system consisting only of mononucleotides and their single-stranded polymers, only a small fraction of the available molecules will be polymerized. However, a single-stranded polymer may form a double-stranded one by complementary polymerization, using a single-stranded polynucleotide as a template. Such a process is relatively fast and the resulting double-stranded polynucleotide is much more stable than the single single-stranded one since each monomer is bound not only along the sugar phosphate backbone, but also through inter-strand bonding between the bases.

The capability for self-replication, a fundamental feature of life, emerged when double-stranded polynucleotides disassociated into single-stranded ones and each of these served as a template for synthesis of a complementary strand, producing two double-stranded copies. Such a system is mutable since random changes of individual bases may occur and be propagated. Individual replicators with different nucleotide sequences may also compete with each other for nucleotide precursors. Mutations that influence the folding state of polynucleotides may affect the ratio of association of strands to dissociation and thus the ability to replicate. The folding state would also affect the stability of the molecule. These ideas were then developed to speculate on the emergence of genetic information, protein synthesis and other general features of life.

Lily E. Kay says that Quastler's works "are an illuminating example of a well reasoned epistemic quest and a curious disciplinary failure". Quastler's aspiration to create an information based biology was innovative, but his work was "plagued by problems: outdated data, unwarranted assumptions, some dubious numerology, and, most importantly, an inability to generate an experimental agenda." However Quastler's "discursive framework" survived.

Forty-five years after Quastler's 1964 proposal, Lincoln and Joyce described a cross-catalytic system that involves two RNA enzymes (ribosymes) that catalyze each other's synthesis from a total of four component substrates. This synthesis occurred in the absence of protein and could provide the basis for an artificial genetic system.

The Emergence of Biological Organization

There was a single used copy in the UK for $12.49 and all the rest are $149.00+ so I snapped it up. Should be an interesting read in and of itself, but I suspect it’s got an interesting niche of the history of science covered with respect to bit history, complexity, and biological organization.

Should arrive some time between March 13 – March 25.

🔖 Information Theory in Biology by Henry Quastler (editor) | University of Illinois Press (1953)

Bookmarked Information Theory in Biology (University of Illinois Press (1953))

I’d love to have a copy of this book that I don’t think I’d heard of before. I’ve got his later Symposium of Information Theory In Biology (1958) already. That volume gives credit to this prior book as inspiration for the symposium.

I suspect based on the Wikipedia article for Quastler that this may also be the same book as the slightly differently titled Essays on the Use of Information Theory in Biology. (Urbana: University of Illinois Press, 1953). There’s also a 1955 review of the text with this name available as well.

Google uses the first title with 273 pages and the Symposium text specifically cites Information Theory in Biology as the correct title several times.

The tough part seems to be that there are very few copies available online and the ones that are are certainly used, in poor condition, and priced at $100+. Ugh…

🔖 davidgchristian tweet: We humans have reduced the biomass of life on earth by 50%

Bookmarked a tweet by David Christian (Twitter)

🎧 “The inside story” | Our Daily Bread | Eat This Podcast

Listened to The inside story | Our Daily Bread 12 by Jeremy CherfasJeremy Cherfas from Eat This Podcast

That kernel of wheat isn’t actually a seed or a berry, at least not to a botanist. I have no intention of getting into the whole pointless is it a fruit or a vegetable debate, so lets just agree that no matter what you call it, the wheat thing is made up of three major parts: bran, endosperm and germ. In this episode, a little about each of those parts and what they do for wheat.

🎧 “Dwarf wheat: On the shoulders of a giant” | Our Daily Bread | Eat This Podcast

Listened to Dwarf wheat: On the shoulders of a giant | Our Daily Bread 10 by Jeremy CherfasJeremy Cherfas from Eat This Podcast

Norman Borlaug created the wheats that created the Green Revolution. They had short stems that could carry heavy ears of wheat, engorged by loads of fertiliser. They were resistant to devastating rust diseases. And they were insensitive to daylength, meaning they could be grown almost anywhere.

All three traits had been bred into wheat 40 years before Borlaug got going, by the Italian pioneer Nazareno Strampelli.

Photo is a 1933 medal to honour Nazareno Strampelli.

I’d never heard the quote from the episode, but it is a painful, but wonderful, concept to contemplate. Here’s an alternate, but somewhat more flowery translation:

History celebrates the battlefields whereon we meet our death, but scorns to speak of the ploughed fields whereby we thrive; it knows the names of king’s bastards, but cannot tell us the origin of wheat. That is the way of human folly.

Jean Henri Fabre in Les Merveilles de l’Instinct Chez les Insectes: Morceaux Choisis (The Wonders of Instinct in Insects: Selected Pieces) (1913), page 242.

👓 Scientists Gave MDMA to Octopuses—and What Happened Was Profound | Gizmodo

Read Scientists Gave MDMA to Octopuses—and What Happened Was Profound (Gizmodo)
When humans take the drug MDMA, versions of which are known as molly or ecstasy, they commonly feel very happy, extraverted, and particularly interested in physical touch. A group of scientists recently wondered whether this drug might have a similar effect on other species—specifically, octopuses, which are seemingly as different from humans as an animal can be. The results of their experiment, in which seven octopuses took MDMA, were “unbelievable.”

🔖 Supramolecular Chemistry. Concepts and Perspectives. Von J.‐M. Lehn. | Angewandte Chemie – Wiley Online Library

Bookmarked Supramolecular Chemistry. Concepts and Perspectives by Jeremy K. SandersJeremy K. Sanders (Angewandte Chemie)
Von J.‐M. Lehn. VCH Verlagsgesellschaft, Weinheim, 1995. 271 S., geb. 128.00 DM/Broschur 58.00 DM. ‐ ISBN 3‐527‐29312‐4/3‐527‐29311‐6 https://doi.org/10.1002/ange.19951072130

🔖 The “Hard Problem” of Life by Sara Imari Walker & Paul C.W. Davies

Bookmarked The "Hard Problem" of Life (arXiv)
Chalmer's famously identified pinpointing an explanation for our subjective experience as the "hard problem of consciousness". He argued that subjective experience constitutes a "hard problem" in the sense that its explanation will ultimately require new physical laws or principles. Here, we propose a corresponding "hard problem of life" as the problem of how `information' can affect the world. In this essay we motivate both why the problem of information as a causal agent is central to explaining life, and why it is hard - that is, why we suspect that a full resolution of the hard problem of life will, similar to as has been proposed for the hard problem of consciousness, ultimately not be reducible to known physical principles. Comments: To appear in "From Matter to Life: Information and Causality". S.I. Walker, P.C.W. Davies and G.F.R. Ellis (eds). Cambridge University Press

🔖 Origins of Life: A Problem for Physics

Bookmarked Origins of Life: A Problem for Physics by Sara I. Walker (arXiv)
The origins of life stands among the great open scientific questions of our time. While a number of proposals exist for possible starting points in the pathway from non-living to living matter, these have so far not achieved states of complexity that are anywhere near that of even the simplest living systems. A key challenge is identifying the properties of living matter that might distinguish living and non-living physical systems such that we might build new life in the lab. This review is geared towards covering major viewpoints on the origin of life for those new to the origin of life field, with a forward look towards considering what it might take for a physical theory that universally explains the phenomenon of life to arise from the seemingly disconnected array of ideas proposed thus far. The hope is that a theory akin to our other theories in fundamental physics might one day emerge to explain the phenomenon of life, and in turn finally permit solving its origins.

A new fossil could push back the start of life on Earth | The Economist

Read A new fossil could push back the start of life on Earth (The Atlantic)
The putative fossils formed just a few hundred million years after Earth itself

Continue reading “A new fossil could push back the start of life on Earth | The Economist”

IPAM Workshop on Regulatory and Epigenetic Stochasticity in Development and Disease, March 1-3

Bookmarked IPAM Workshop on Regulatory and Epigenetic Stochasticity in Development and Disease (Institute for Pure and Applied Mathematics, UCLA | March 1-3, 2017)
Epigenetics refers to information transmitted during cell division other than the DNA sequence per se, and it is the language that distinguishes stem cells from somatic cells, one organ from another, and even identical twins from each other. In contrast to the DNA sequence, the epigenome is relatively susceptible to modification by the environment as well as stochastic perturbations over time, adding to phenotypic diversity in the population. Despite its strong ties to the environment, epigenetics has never been well reconciled to evolutionary thinking, and in fact there is now strong evidence against the transmission of so-called “epi-alleles,” i.e. epigenetic modifications that pass through the germline.

However, genetic variants that regulate stochastic fluctuation of gene expression and phenotypes in the offspring appear to be transmitted as an epigenetic or even Lamarckian trait. Furthermore, even the normal process of cellular differentiation from a single cell to a complex organism is not understood well from a mathematical point of view. There is increasingly strong evidence that stem cells are highly heterogeneous and in fact stochasticity is necessary for pluripotency. This process appears to be tightly regulated through the epigenome in development. Moreover, in these biological contexts, “stochasticity” is hardly synonymous with “noise”, which often refers to variation which obscures a “true signal” (e.g., measurement error) or which is structural, as in physics (e.g., quantum noise). In contrast, “stochastic regulation” refers to purposeful, programmed variation; the fluctuations are random but there is no true signal to mask.

This workshop will serve as a forum for scientists and engineers with an interest in computational biology to explore the role of stochasticity in regulation, development and evolution, and its epigenetic basis. Just as thinking about stochasticity was transformative in physics and in some areas of biology, it promises to fundamentally transform modern genetics and help to explain phase transitions such as differentiation and cancer.

This workshop will include a poster session; a request for poster titles will be sent to registered participants in advance of the workshop.

Speaker List:
Adam Arkin (Lawrence Berkeley Laboratory)
Gábor Balázsi (SUNY Stony Brook)
Domitilla Del Vecchio (Massachusetts Institute of Technology)
Michael Elowitz (California Institute of Technology)
Andrew Feinberg (Johns Hopkins University)
Don Geman (Johns Hopkins University)
Anita Göndör (Karolinska Institutet)
John Goutsias (Johns Hopkins University)
Garrett Jenkinson (Johns Hopkins University)
Andre Levchenko (Yale University)
Olgica Milenkovic (University of Illinois)
Johan Paulsson (Harvard University)
Leor Weinberger (University of California, San Francisco (UCSF))

🔖 How Life (and Death) Spring From Disorder | Quanta Magazine

Bookmarked How Life (and Death) Spring From Disorder (Quanta Magazine)
Life was long thought to obey its own set of rules. But as simple systems show signs of lifelike behavior, scientists are arguing about whether this apparent complexity is all a consequence of thermodynamics.

This is a nice little general interest article by Philip Ball that does a relatively good job of covering several of my favorite topics (information theory, biology, complexity) for the layperson. While it stays relatively basic, it links to a handful of really great references, many of which I’ve already read, though several appear to be new to me. [1][2][3][4][5][6][7][8][9][10]

While Ball has a broad area of interests and coverage in his work, he’s certainly one of the best journalists working in this subarea of interests today. I highly recommend his work to those who find this area interesting.

References

[1]
E. Mayr, What Makes Biology Unique? Cambridge University Press, 2004.
[2]
A. Wissner-Gross and C. Freer, “Causal entropic forces.,” Phys Rev Lett, vol. 110, no. 16, p. 168702, Apr. 2013. [PubMed]
[3]
A. Barato and U. Seifert, “Thermodynamic uncertainty relation for biomolecular processes.,” Phys Rev Lett, vol. 114, no. 15, p. 158101, Apr. 2015. [PubMed]
[4]
J. Shay and W. Wright, “Hayflick, his limit, and cellular ageing.,” Nat Rev Mol Cell Biol, vol. 1, no. 1, pp. 72–6, Oct. 2000. [PubMed]
[5]
X. Dong, B. Milholland, and J. Vijg, “Evidence for a limit to human lifespan,” Nature, vol. 538, no. 7624. Springer Nature, pp. 257–259, 05-Oct-2016 [Online]. Available: http://dx.doi.org/10.1038/nature19793
[6]
H. Morowitz and E. Smith, “Energy Flow and the Organization of Life,” Santa Fe Institute, 07-Aug-2006. [Online]. Available: http://samoa.santafe.edu/media/workingpapers/06-08-029.pdf. [Accessed: 03-Feb-2017]
[7]
R. Landauer, “Irreversibility and Heat Generation in the Computing Process,” IBM Journal of Research and Development, vol. 5, no. 3. IBM, pp. 183–191, Jul-1961 [Online]. Available: http://dx.doi.org/10.1147/rd.53.0183
[8]
C. Rovelli, “Meaning = Information + Evolution,” arXiv, Nov. 2006 [Online]. Available: https://arxiv.org/abs/1611.02420
[9]
N. Perunov, R. A. Marsland, and J. L. England, “Statistical Physics of Adaptation,” Physical Review X, vol. 6, no. 2. American Physical Society (APS), 16-Jun-2016 [Online]. Available: http://dx.doi.org/10.1103/PhysRevX.6.021036 [Source]
[10]
S. Still, D. A. Sivak, A. J. Bell, and G. E. Crooks, “Thermodynamics of Prediction,” Physical Review Letters, vol. 109, no. 12. American Physical Society (APS), 19-Sep-2012 [Online]. Available: http://dx.doi.org/10.1103/PhysRevLett.109.120604 [Source]