11 September 2020

Stuart Kauffman: A World Beyond Physics. Review.

A World Beyond Physics
I did not foresee for a moment how the subject of my previous blog The difference between physics and biology is masterfully argued in Stuart Kauffmans' latest book A World Beyond Physics. I added the book title to my previous blogpost without knowing how relevant the book was. This blog is not a complete review of A World Beyond Physics. I will focus on the 'beyond physics' part of the book. Building on his previous books (f.e. At home in the universe) Kauffman significantly extends his collectively autocatalytic set theory, includes several examples of real world chemistry; defines life in a new and profound way; solves the origin of life (in theory); attacks Dawkins' selfish genes and the overemphasis on genes and DNA in evolution; rejects the RNA-world because nobody has shown in 50 years that it works; explains why biology cannot be reduced to physics and why evolution is open-ended and unpredictable. Kauffman is not an anti-Darwinist. However, his account of the origin and evolution of life on earth skips the origin of RNA, DNA and the genetic code. If restricted to the Origin of Life, especially to the origin of protocells, then this omission may be a superb move. It shows how proto-life could exist without genes (in theory). A very intelligent, insightful and visionary book. There is a rare video of a 2017 lecture of Kauffman where he summarizes the ideas in A World Beyond Physics. If one wants to get familiar with Kauffman's worldview, watching both the lecture and reading the book is recommended. 

The book title is 'A world beyond physics' and this is also the title of chapter 11. That chapter contains sections such as 'Entropy and Evolution'; 'Beyond Law: Biology Cannot Be Reduced to Physics'. The first chapter is titled 'The World is not a Machine'. This chapter contains a section titled 'Beyond the Second Law'. One can find the beyond physics theme throughout the book. He is serious about it. The book is not just an update of the current status of Collectively Autocatalytic Set theory.

Especially relevant is the section 'Entropy and persistent self-construction' of chapter 6. It starts with:

"A deep issue is how the biosphere builds up complexity in face of the second law of thermodynamics. This law states that in a closed system, disorder or entropy, can only increase. ... In plants, photosynthesis builds up glucose molecules from carbon dioxide and water. Fine, but if the second law degraded this order faster than it was created, no order could accumulate! How does order accumulate?" (207/359)
Indeed, the scientific problem of life is not how to destroy order or release heat, but exactly the opposite: how to create order in the first place. Please note: in face of the second law. Apparently, the Second Law doesn't help us. On the contrary.  Life is a river flowing uphill. Life is against the flow. Explaining how and why plants dissipate energy is the easier part. But, explaining how plants with complex photosynthetic machinery originated and is maintained in the first place: that is the more difficult question. Where do complex dissipating structures come from? One needs a theory to solve that problem first. Life does not follow from physical laws. Newton and Einstein and all subsequent geniuses, yes, they did explain the universe, but they did not explain life [4].

Kauffman develops a theory of life in which the concept 'constraint' plays a central role. It's too complex a story to summarize it here [1]. He concludes that life is characterized by the construction of constraints on the release of energy in non-equilibrium processes. Those constraints do work and this work is used to construct yet more of the same constraints. This is the harnessing of energy to build up further order. "The constraints, in other words, channel the release of energy into work, not just entropy increase" (p.69). Nowhere Kauffman says the release of energy is important, let alone the driving force of life. This channeling of work is part of how life "beats" the Second Law. Due to constraints, entropy still increases, but more slowly. This is how life surges upward in complexity and spreads this order despite the Second Law." (p.70).

The most characteristic property of life is the continuous 'fight' against disorder (Second Law) in as many ingenious ways as there are species. So, if a physicist claims that the thermodynamic function of organisms is dissipation of heat [2], he highlights what is common between the living and the non-living. However, the difference between living and non-living is lost. The difference is the most important part of the equation. What is common does not and cannot explain how organisms are different. It is the difference that frustrates a straightforward application of physical law to organisms. 

To illustrate the problem: consider a bird and a cannon ball.  

Common buzzard ©GK

Cannon balls

https://en.wikipedia.org/wiki/Trajectory

Are they both subject to gravity? Yes and No. Cannon balls obey the law of gravity, no doubt. Birds also have mass and are somehow subject to gravity. But birds do not behave like cannon balls. The trajectory of a cannon ball can be calculated perfectly, but the trajectory of a bird is impossible to calculate. Even better: consider the chaotic movements of a butterfly! There you have the problem. The application of physical laws to organisms is very complex, if not impossible.

So, it makes no sense to claim that biological species are governed by physical laws, when exactly those physical laws are circumvented by life. 

In Kauffman's own words: "In short, I will claim that no law at all entails the becoming of the biosphere; and that therefore, we cannot reduce biology to physics. The world is not a machine." (Chapter 9).

Chapter 11: "The aim of this chapter, indeed the driving purpose behind this book, is to show that life, though rooted in physics, surges beyond it into myriad unprestatable [3] ways of making a living in the world." (p.294).

So, in this book Kauffman gives more than one reason why biology is different from physics, how life differs from non-life and why this is relevant. I hope I have given just enough information in this short blog post to stimulate readers to check it out for themselves.

Finally, it is still possible that somehow dissipation is a factor in the design of organisms, or even the driving force. A physicist may propose a revolutionary theory about life. However, it is not sensible to do that without profound knowledge of the most fundamental properties of life. Theoretical biologist Stuart Kauffman recently made a strong case that the biological world is A World Beyond Physics.


Notes

  1. His example: An automobile constrains the motion of many parts but does not construct new constraints. Life does! (p.73). In the absence of the cylinder, the hot gas would expand in all directions. In its presence the gas expands only along the cylinder.
  2. Physicist Karo Michaelian, see previous blog.
  3. Kauffman uses the word 'unprestatable' many times, it means possible forms of life can not be enumerated in advance.
  4. Organisms are made of atoms and those atoms are created in stars.  That is absolutely true and very interesting stuff. Ultimately, life depends on the Big Bang. Kauffman does not elaborate the connection between life and the universe in this book. It is the subject of Big History and Astrobiology books.

 

PS: I included a few page numbers in the text. These are relative page numbers of the eBook edition which has 359 pages on my Kobo eReader. 

 

Previous post about the subject

03 September 2020

Nocturnal bird migration at full moon

10 dark spots on the surface of the full moon are in fact 10 birds!
f/8.0 1/3200 sec. ISO speed 800. 1 Sep 2020 22:49
One stop underexposed; some contrast enhancement added.
1000x1000 pixels. Sony A6400; 70-350. Manual focus
Width and height of the Moon itself: 783x779 pixels

What is the probability that birds appear in front of the full moon in a series of only 10 exposures? Close to zero, I would say. I only discovered them the next morning on my computer screen. One or two seconds earlier or later and they would have disappeared into total darkness. If the birds flew a few degrees higher of lower, I would miss them too. You won't spot them in the dark. If the birds flew directly towards the moon it would be harder to make sense of those clustered strange speckles. Luckily the birds did a nice fly-by. It looks like they are flying in one straight line. But they could fly in a V-shape. One cannot tell the difference. In reality the group could be bigger than ten. If there were only one or two birds in front of the moon, I would probably have missed them. If they were still further away from me, they would have been too small to notice at all. I doubt if the chances would be higher if they were significantly closer to me. It would be a hit or miss. At least, it would be less likely to see them all ten together.

Detail. 362x227 pixels (not scaled up)

There is just enough detail visible to conclude that they must be birds. Some have their wings up and some down. These black spots are darker than anything on the moon. I am not sure what species it is. It could be geese. Sheer luck that they entered my exposure. Thanks birds! Have a good trip! To whatever destination!

The position of the moon must have been southeast and the birds must be flying to the south or southwest (location: The Netherlands). They appear to be ascending. This seems unlikely to me. It could be caused by the orientation of my camera. I did not pay attention to that when taking the pictures.



Literature

14 August 2020

The difference between physics and biology.

This blog post originated from a discussion with physicist Karo Michaelian about his book Thermodynamic dissipation Theory of the Origin and Evolution of Life.  The difference between physics and biology is a topic that deserves a blogpost. It will be an informal discussion. 

What is the difference between animals, plants, bacteria and viruses on the one hand and stars, volcanos, clouds, rivers, and rainbows on the other hand? If organisms are just physical objects and must obey the laws of physics, what biological laws could exist? Physicists explained the Universe. Physicists have finally arrived at The Theory of Everything which explains all known physical phenomena in the universe from the smallest to the most massive things [11]. And organisms are in between. If organisms are physical objects, they are also explained by The Theory of Everything. They should also obey physical laws. But then, do we need Darwin? Do we need Mendel? Do we need Watson & Crick? Could the biology department be subsumed in the Physics department and send biologists home? Let's listen to a physicist:

" ...the biologists simply are not trained to think in terms of symmetries and fundamental laws, as physicists are. (...) Biologist want simple answers that can be written out in a single paragraph, with learning as little mathematics as possible, and they found one in the perspective of Darwin (and, of course it is a perspective and nothing more). It works as a nice description for some things, but it is only a poor description of reality and misses completely at understanding the fundamental function of life. The physicist wants to know what is behind this Darwinian description and this thermodynamic view opens a completely new paradigm with a much richer and profound understanding." Karo Michaelian, August 12, 2020

No wonder that physicists –in possession of the Theory of Everything– want to invade and occupy the territory of biology. As if it were a war. There is only one real science. The profitability of mathematics is easily explained. Physics deals with dead things. Dead things behave rather predictably. They are being moved by external forces. Newton! The movements of the planets! [12]. But living objects move themselves. They seem to have a 'free will'. 

The first difference between physics and biology: complexity. There are only 118 chemical elements, but millions of biological species. The chemical elements do not vary, except radioisotopes which behave predictably. Humans have DNA with 3.5 billion bases. All humans differ genetically. There are 67.3 million single-nucleotide polymorphisms in the human  population [4]. A human body has millions of cells, each cell contains in total 42 million protein molecules. The majority of proteins exist within a narrow range - between 1000 and 10,000 molecules. Some are outstandingly plentiful at more than half a million copies, while others exist in fewer than 10 molecules in a cell [1]. And these are only proteins. Physics has no laws for this huge amount of complexity. Physics studies dead and simple things.

A hot cup of tea (source)
A hot mouse (Apodemus sylvaticus) ©GK
 

Most importantly, physicists don't understand the difference between a mouse and a cup of tea. A mouse maintains a temperature difference between its body and the environment. A cup of tea also has a higher temperature than its environment. But what happens with the cup of tea? The temperature difference has gone within an hour. Just obeying the laws of physics. The mouse maintains the temperature difference all its life. Physical laws don't explain the difference in behaviour between a cup of tea and a mouse. Physics cannot explain how the physical object called 'mouse' maintains its temperature. This example alone suffices to suggest that we need a separate science. It's called biology, the science of the living things.

Does a mouse maximize heat loss? Being naked would help! That would very likely maximize heat loss [9]. Heat loss may be a driving force in the abiotic and pre-biotic world. But living organisms have subsystems that control energy uptake, energy production, energy use, energy storage, and heat loss [5]. Those systems by-pass physical laws without violating them. Just as birds and air-planes do not violate the law of gravity.
In the living world, energy is under control, it is regulated: thermo-regulation. Because it is under control, pure physical laws cannot be applied. Therefore, physical laws cannot be the driving force of evolution.

Yes, physical laws constrain the properties of living organisms, but within those constrains there is freedom to shape organisms. And what a shapes there are! Endless forms most beautiful! Heat loss occurs in living organisms, but it is not a driving force, certainly not the driving force. Energy management is one of the fundamental differences between biological and physical systems. This is under genetic control. Genetics is information [6]. The control of chemical and physical processes is the main difference between living and physical systems [2], [5]. It is part of the definition of life.

I add two important reasons why organisms have energy control systems:

  1. without energy control they die. Energy uptake is not maximized, but optimized.
  2. organisms can produce more offspring if they use energy more efficiently. That's the evolutionary reason.

Organisms that are less energy efficient waste energy and cannot invest as much energy in reproduction because that's an energetically very costly process. In general: energy efficient organisms, especially animals, out-compete less energy efficient organisms. Energy efficient organisms are winners, energy wasters are losers [3]. Warm-blooded animals have fat, fur or feathers to prevent heat loss. Whales, dolphins, seals and other marine mammals can generate their own heat and maintain a stable body temperature despite fluctuating environmental conditions. But these animals take thermoregulation to an extreme, enduring water temperatures as low as –2 degrees Celsius and air temperatures reaching –40 degrees C [7]. They have biological inventions that oppose heat loss. That's against the Thermodynamic Dissipation Theory. Life is a successful fight against the Second Law of Thermodynamics, against disorder, against equilibrium [10]. There is certainly no attempt to lose as much heat as possible. That would be insane [13].

Dead Weasel Mustela nivalis ©GK

Even a dead weasel is not quite a dead physical object as can be seen on the picture above. It is teeming with life. Flies are the first organisms to occupy the unfortunate animal. Many follow, including bacteria, worms, beetles, fungi, maybe a fox or a raven [8].

So, if physicists are blind and deaf for the differences between living and dead objects, no useful exchange of ideas between physicists and biologists will happen. Arrogance and ignorance will be deadly for any communication. Only as equal partners in science we will understand life.



Notes

  1. A cell holds 42 million protein molecules, Science daily January 17, 2018
  2. I wrote about that in my review part 2 of Thermodynamic dissipation Theory.
  3. See further 'Not Wasting Energy' in my review part 2. 16 May 2018.
  4. For more details see: Open Questions / Genetic variation in this review.
  5. 'Processes in living systems must be regulated and controlled' is one of 5 Real (absolute) life criteria. See my Ganti review. In engineering it is known as: Control Theory. Heat production in a 'warm-blooded' animal is regulated. Otherwise the animal would be overheated and die. The heat is generated by Brown Adipose Tissue. On the other hand, in some animals their metabolic rate and body temperature drop during the night to conserve energy (torpor). To conserve energy! Regulation! Control!
  6. Information is the difference between life and matter, A review of Hubert Yockey's 'Information theory and molecular biology'. Yockey is a physicist.
  7. How do marine mammals avoid freezing to death? Scientific American, 13 May 2009.
  8. Thousands of unexpected microbes break down our bodies after death, Science, Dec. 10, 2015 
  9. If not maximize and not minimize heat loss (minimize heat loss is against TDT), than anything goes? Any value would be compatible with the Thermodynamic Dissipation Theory? But then it would be unfalsifiable! The theory would not forbid anything. It would not predict anything. It would not say one thing about the world. It would make the TDT non-empirical and theory-less. Worst of all: no mathematics involved! That's a serious matter. 14 Aug 2020 15:09
  10. A friend of mine, Frank Visser, uses this illuminating metaphore: life behaves like a sailboat sailing into the wind. A sail boat has the ability to move forward despite being headed into the wind. Life is also sailing against The Second Law of Thermodynamics dictating that order becomes disorder. 21 Aug 2020;
  11. In a comment Karo Michaelian wrote "Almost all physicists agree that we have discovered all of the fundamental laws of nature needed to begin an attempt at describing complex systems through these formalisms, both living and non-living systems. We do not need new laws." I would like to see how Michaelian derives Mendel's laws from physical laws! 23 Aug 2020
  12. Newton ignored the composition of the planets, the elements, the temperature, the composition of the atmosphere. In short: everything geologists, biologists and climatologists are interested in. Newton used abstract planets. Furthermore, physicists use 'ideal gas' or 'perfect gas' (an ideal gas is a theoretical gas composed of many randomly moving point particles that are not subject to interparticle interactions);  a point particle is an idealization of particles heavily used in physics: it lacks spatial extension; being dimensionless, it does not take up space. So, even dead things are often too complicated for physicists! 27 Aug 2020
  13. To save energy animals go into hibernation or torpor. Some hummingbirds in South America go into torpor: a state of reduced metabolic activity and temperature that is not unlike hibernation, but only one night long. (Nature) 11 Sep 2020


Further Reading

  • Ernst Mayr (2004) What makes Biology Unique? Considerations on the autonomy of scientific discipline. (a defence of the autonomy of biology). See my summary.
  • Stuart Kauffman (2019) A World Beyond Physics: The Emergence and Evolution of Life. Stuart Kauffman is a theoretical biologist. Especially relevant is: Beyond Law: Biology Cannot Be Reduced to Physics in chapter 11.

 

 

Postscript 25 Aug 2020

After writing this blog I discovered the views of theoretical biologist Robert Rosen

"By proposing a sound theoretical foundation for studying biological organisation, Rosen held that, rather than biology being a mere subset of the already known physics, it might turn out to provide profound lessons for physics, and also for science in general".

The wikipedia page contains a rather detailed description of his theories about living systems and how they differ from physical systems. His book Life itself (2005) is still available at amazon. Large parts can be read at google books.