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Sat Jun 23, 2018, 11:38 AM

Open source paper on "Defining Life."

As I age and more and more come face to face with the inevitably of dying, I wonder more and more, having experienced the real beauty of being alive, of whence life came to be.

I have always wanted to read Schroedinger's famous book, "What is Life?" but probably will never find the time.

Nevertheless, I resolved to spend some time reading this review article, Prebiotic Systems Chemistry: New Perspectives for the Origins of Life (Kepa Ruiz-Mirazo†, Carlos Briones‡, and Andrés de la Escosura*§ Chem. Rev., 2014, 114 (1), pp 285–366), when, not far in, I came across the following text:

The complete picture and implications of this issue come out only when we try to specify the requisites that, in principle, any type of system (i.e., not only an organic chemical one) should actually fulfill to be considered alive. Opening or generalizing the problem of the nature of life, and thus of its origins, makes it richer, wider, and more challenging, as can be reflected in the recent merging of the traditional field of origins of life and the younger ones of synthetic biology and astrobiology. Indeed, the main questions addressed by astrobiology are the origins, evolution, and distribution of life in the universe.6−8

However, we do not aim to discuss here in detail the issue of defining life: the reader is referred to a special issue of the journal Origins of Life and Evolution of Biospheres,9 or to a comprehensive anthology of articles on this subject.10

When I see references I'd like to pick up, I always email them to myself for my library time, and I usually send the reference as a link to the paper when possible so I can use my library time efficiently.

But when I generated the link to reference 9, I found that it opened at home, and thus is open sourced.

It's 244 pages on the question of "What is life," updated from Shroedinger, 85 years ago.

If you're interested, here it is:

Defining Life: Conference Proceedings.

Perhaps I don't know what life it, other than whatever it, it is extraordinarily beautiful, even with the pain, and very much worth living.

Have a great weekend!

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Reply Open source paper on "Defining Life." (Original post)
NNadir Jun 2018 OP
Loki Liesmith Jun 2018 #1
defacto7 Jun 2018 #2
NNadir Jun 2018 #3
Loki Liesmith Jun 2018 #4
NNadir Jun 2018 #5

Response to NNadir (Original post)

Sat Jun 23, 2018, 11:58 AM

1. Life is a cancer of matter

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Response to Loki Liesmith (Reply #1)

Sat Jun 23, 2018, 12:33 PM

2. How uplifting.

The statement does create a curious visual.

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Response to Loki Liesmith (Reply #1)

Sat Jun 23, 2018, 11:13 PM

3. I once got to spend an amazing afternoon with Freeman Dyson in his office.

I took my two sons and a friend of one them. They were kids, but they will probably treasure the photographs taken with the great man until they are very old

It was an afternoon I will never forget.

At one point in the discussion, the subject turned somehow to self organizing systems and I mentioned that Stuart Kaufmann described life as "an eddy in thermodynamics."

It came as no surprise that Dyson actually knew Kaufmann personally, but indicated he had not heard that description, "life is an eddy in thermodynamics," but he nonetheless approved instantly of the description, calling it "perfect."

It is, I think, a more beautiful and probably accurate description of what life is then a description of it as a "cancer." There are those who argue that matter has no meaning without life. The argument may be metaphysical to an extent, but it seems to me it could be correct.

That issue, the fact that life is thermodynamically unstable, is, as I work through it, the central point of the Chem Rev paper cited in the OP through which I am working my way.

It's a wonderful review article by the way, very enlightening.

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Response to NNadir (Reply #3)

Sun Jun 24, 2018, 12:20 AM

4. I've had several conversation with Stu

and his former Santa Fe Institute colleague Doyne Farmer and they are sharp guys. But I still think cancer is an excellent model. Life hijacks the chemical machinery of matter to propagate itself, just like cancer does for cells.

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Response to Loki Liesmith (Reply #4)

Sun Jun 24, 2018, 08:26 AM

5. Well, it's probably a matter of semantics but...

...the chemical machinery of cancer - in which I have some career involvement - tends to disorder and dysfunction. Cancer's not really "hijacking" so much as it is breakdown and loss of function and control. Cancer cells, particularly in the genomic sense, are higher entropy than normal cells. They are about disorder, not order, and one of the problems of treating advanced cancers is the control machinery continues to degrade even after the initial genetic breakdown occurs.

I get your point, I suppose, but I still like "an eddy in thermodynamics" better to describe life. Life, as far as we can tell, is rare, and is certainly not in a position to take over the universe and destroy it. We might destroy this planet, but not the universe, which is a comforting thought.

It is therefore comforting, if still speculative, to think that life is an inevitable property of matter, at least on a scale that seems to involve infinities.

I haven't thought very much about the origin of life in many years, although it's a fascinating subject in which I invested some time to think about years ago, and I probably read Kaufmann's "Origin of Order" close to the time it came out.

I was inspired to think about it again though because I've been thinking about certain molecular machinery involved in the proteomic control of the genome, specifically proteins that control PTMs.

In normal cells, this machinery is awe inspiring, and one wonders how it arose, so it drove me to look again.

I was also inspired to look again because this consideration coincided with some organizational work I was doing in my files whereupon I came across papers I'd collected in 2010 on the subject of the Murchinson Meteorite.

One of the points made in the review involves mechanisms of energy flows and combinatorial diversity and the stabilization of intermediates against degradation.

While reading the review, I learned about a set of experiments about which I knew nothing, John D. Sutherland's work on pyrimidine ribonucleotides from a systems chemistry perspective, which suggests a way through the difficult thermodynamic problem of coupling sugars to nucleobases.

I'm definitely going to pick up this paper, which is now nearly ten years old: Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions (Sutherland et al, Nature volume 459, pages 239–242 (14 May 2009))

I'm definitely going to collect some of this guy's more recent papers, as well as citing papers for the original. I would not be surprised to hear of this guy getting a Nobel some day, although I'm personally nowhere near the level to offer input about who does and does not get that prize.

It's very cool.

Thanks for your comment.

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