02 December 2020

Nobelprize winner Paul Nurse: viruses are alive! and dead!

Paul Nurse 2019 lecture The Royal Institution

Sir Paul Nurse received The Nobel Prize in Physiology or Medicine 2001 for his discoveries of key regulators of the cell cycle together with Leland Hartwell and Tim Hunt. According to the Nobel committee: 

"From the beginning organisms evolve from one cell, which divides and becomes new cells that in turn divide. Eventually different types of cells are formed with different roles. For an organism to function and develop normally, cell division has to occur at a suitable pace. Paul Nurse has helped to show how the cell cycle is controlled. Through studies of yeast in the mid-1970s, he was able to show that a special gene [cdc2] plays a decisive role in several of the cell cycle's phases. In 1987 he identified a corresponding human gene [CDK1]." (Nobel prize organization)

 

Paul Nurse (2020) What is life?
Paul Nurse (2020)
What is life?

In 2020 Paul Nurse published What is Life? [1]. In the first chapters he explains biology for non-biologists: the cell, the gene, evolution, biochemistry, DNA. These chapters constitute the foundation for the final chapter in which he develops a definition of life. Almost casually Nurse tells about his discovery that led to the Nobel prize 20 years later. In the last chapter he defines life with 3 principles. Any entity which operates according to those three principles can be deemed to be alive.

  1. The ability to evolve through natural selection. To evolve, living organisms must reproduce, they must have a hereditary system, and that hereditary system must exhibit variability. Any entity that has these features can and will evolve.
  2. life forms are bounded, physical entities.
  3. living entities are chemical, physical and informational machines. They construct their own metabolism and use it to maintain themselves, grow and reproduce. These living machines are co-ordinated and regulated by managing information, with the effect that living entities operate as purposeful wholes. 

Whenever I encounter proposals for the definition for life, I can't help comparing them with the definition of life of the Hungarian theoretical biologist and biochemist Tibor Gánti. Years ago Gánti proposed a definition of life that stood the test of time. I refer to my description and discussion of Gánti's defitinition of life on my WDW website [1]. Reading and listening to Nurse made me thinking again about the definition of life.

The first principle, the ability to evolve, Nurse adopted from Nobelprizewinning geneticist Hermann Muller. According to Gánti evolvability belongs to the Potential life criteria. That means evolvability is not a necessary property of an entity to be alive. But Nurse does not make the distinction between actual (absolute) and potential life criteria. There are a few practical problems with his first principle. According to evolutionary biologist Szathmáry evolution is not a property of an individual, but of a population. Also, variability is not a property of an individual, but of a population. The principle also causes difficulties when applied to a somatic body cell of an animal or plant. All somatic body cells will eventually die when the organism dies, and they leave no descendants in the next generation. Nobody would deny that somatic cells are living. But at the same time one cannot say that somatic cells in your body have the evolvability property. Only germline cells are involved in reproduction. On the level of an animal there can be also a problem. Mules are infertile, so no reproduction and no evolvability, but they are alive. Finally one comment about evolvability. Nurse's first principle suggests that the only function of the hereditary subsystem is evolvability. Nurse does not state explicitly that the informational subsystem "is useful for the whole" (Gánti's 4th absolute life criterion) and controls metabolism.

His second principle is:'life forms are bounded, physical entities'. This equals Gánti's Chemical boundary system. What is the boundary? Unfortunately, the concept boundary is used in an ambiguous way. For cells the boundary is the cell membrane (animals) or cell wall (plants). But viruses have a capsid which is clearly distinct from the semi-permeable membrane of a cell. A capsid does not have the functions a cell membrane has. This has consequences.

His third principle is complex. It is almost a complete definition of life because two of the three Gánti subsystems are included: a Chemical information system (for example DNA) and a Chemical motor system (metabolism). Nurse also included growth and reproduction in his third principle. According to Gánti growth and reproduction are Potential life criteria. Adults don't grow, and a non-dividing cell –for example a neuron– is not dead. That's why growth and reproduction are not necessary for being alive. They are a potential characteristic of life. The properties 'co-ordinated and regulated' and 'maintain themselves' equal Gánti's third Absolute criterion: "A living system must be inherently stable".
 

Are viruses alive? We all agree that bacteria, plants and animals are alive. Paul Nurse says viruses are alive too. I disagree. The most important reason I think why viruses are not alive is that viruses are not cells and they never become cells. Not being a cell means not having a semi-permeable membrane which enables transport of molecules in and out of the cell. Since viruses are not cells, they don't know cell division. And they don't have Nurse's famous Nobel prize winning cdc2 gene. Viruses are a sort of stripped-down cells. Stripped down to the bare essentials: RNA or DNA with a protein coat.

Although Nurse's principles include an abstract 'boundary', in his talk he said: "the cell is the basic structural and functional unit of life" [3]. That is Robert Hooke's cell theory. Nurse is serious about the cell theory. Rightly so. In the first chapter The Cell: Biology's Atom he writes "What I mean by this is that cells are the smallest entities that have the core characteristic of life. (...) The cell is the simplest thing that can be said, definitely, to be alive" [5]. Since viruses are definitely smaller than cells, viruses cannot be alive. Viruses are dead RNA or DNA molecules!

In response to a question from the public Nurse says "viruses are dead outside the cell and alive inside a cell". This is a unsatisfying compromise. It reflects the fact that viruses outside a cell are chemically inert; they cannot defend themselves against outside disturbances and degradate by physical forces (UV light, heat,etc). They have no metabolism. They are passive entities subjected to physical forces. But in a cell they are active and replicate. But if Nurse wants to claim a replicating virus (which is just a piece of RNA or DNA) is alive, than a chromosome or nucleus must be alive too? Because a thousands times more DNA replication takes place during cell division. The property 'being alive' belongs to a higher level than molecular level. It is a property at the level of the cell. Just as being conscious is at the level of the whole organism, not at the neuron level.


A car is a vehicle on wheels, with an engine, steering wheel, gas pedal, brakes, fuel tank, seats, etc. that moves autonomously. If we strip the car of everything except the wheels, what do we get? Is it a stripped-down car or something quite different? Yes, the trailer is connected to a car and has wheels and it moves ... when attached to the car. Is that a reason to call a trailer a car? I admit: a trailer is an independent entity when disconnected, but then it doesn't move. Yes, a car is dependent on fuel which is not produced by the car itself. Does it mean we have a continuum from car to trailer? Of course we can subsume both car and trailer as non-overlapping subclasses in a higher order class called 'vehicles with wheels'. Cars and trailers share the property 'having wheels' without making them both cars.

 

Virus: a stripped down cell?

Similarly, do we call viruses alive just because they can be viewed as stripped down versions of a cell? Viruses are somehow connected the Tree of life. That's true. The most profound reason for this -I think- is that they use the same genetic code (the code that translates DNA sequences in to protein sequences) as all life. They need to have the same code, because otherwise their genes would be gibberish for the cell and they won't be able to replicate and produce new virus particles. Furthermore, viruses adapt to their hosts. For example the SARS-CoV-19 is perfectly adapted to the human ACE2 receptor. There is no doubt viruses are evolving entities. But one has to distinguish between evolving entities and living entities:

Viruses are evolving but not alive.
James Griesemer & Eörs Szathmáry [2].

When accepting the view that viruses are maximally stripped-down versions of cells, could we conclude from that that RNA or DNA are the bare essentials of evolution? The virus is a set of selfish genes. There you have it: the common property of cells and viruses is: replicating RNA or DNA. The classes of viruses and cells do not overlap, but are included in a higher class of replicating entities. Is this a rediscovery of the essence of Darwinism? I think so. It's all about replicating entities! Replicating entities that make errors and evolve. The 'units of life' are cellular. The 'units of evolution' are strings of DNA or RNA. 

 

Concluding: Nurse is absolutely right that the cell is the simplest unit that can be said to be alive. We now understand why the cell is the smallest life form: only a cell can integrate the three necessary components of life: a semi-permeable boundary, a hereditary information system and a metabolism. A logical consequence is that a virus cannot be said to be alive, neither inside nor outside a cell. I disagree that this is an arbitrary decision. It just follows from the cell theory. Furthermore, Nurse is absolutely right about the profound interconnectedness of all life. And, I fully agree, viruses are intimately and necessary connected to life. They speak -so to say- the same language. But that does not make them living.

I thank Paul Nurse for writing such a stimulating book!



Notes

  1. Paul Nurse (2020) What is Life. Understand Biology In Five Steps, David Fickling Books. It is a popular science book without footnotes, index, and literature list. -I don't know whether the hardback is illustrated, but my e-book is not. Here is a short interview with Paul Nurse about the book.
  2. The Principles of Life. superior insights into the nature of life. (about Tibor Ganti'a definition of life.)
  3. What is Life? Sir Paul Nurse - 2020 James Martin Memorial Lecture youtube 6 Mar 2020. Please note that being a cell is not included in his three principles.
  4. Biography of Paul Nurse at Nobel website. Contains many interesting details about his life.
  5. Paul Nurse: "What I mean by this is that cells are the smallest entities that have the core characteristic of life. This is the basis of what biologists call cell theory: to the best of our knowledge, everything that is alive on the planet is either a cell or made from a collection of cells. The cell is the simplest thing that can be said, definitely, to be alive". (22/360 e-book)

See also:

Paul Nurse: The Royal Institution 2019 lecture What is Life?


07 November 2020

Low Photosynthetic Efficiency? Replacing the agricultural paradigm with the evolutionary paradigm

Dr Matt Johnson: Why is Photosynthesis so inefficient?

I was searching for authors complaining about the low efficiency of photosynthesis. This is a good example:

"Why is Photosynthesis so inefficient? Only 5% of the sunlight that hits this field ends up in these grains. Given that plants have a head start of about a billion years, why haven't they already evolved photosynthesis to be more efficient? ...(Plants have different priorities than us!)" (Dr Matt Johnson)

Dr Matt Johnson asks the question Why is Photosynthesis so hopelessly inefficient? while sitting in a field of grain! Not in a tropical rainforest. Clearly, the question arises in an agricultural context. The human point of view. We need to produce more food for the growing world population and end hunger. Higher photosynthetic efficiency means more food for us humans. Plants don't meet human needs.

Wild strawberry Fragaria vesca
wikipedia Ivar Leidus - Own work, CC BY-SA 3.0,
 

cultivated strawberry (source)
 

When we think of strawberries we automatically think of the big strawberries in the supermarket. But we tend to forget that our big, delicious strawberries started long ago as small wild strawberries. See pictures above. In fact, all our modern cultivated fruit and vegetable species were once small. But, we want bigger tomatoes, bananas, potatoes and grains. This is the standard agricultural paradigm nearly everybody is unconsciously using when we see percentages of photosynthetic efficiency which are closer to 0% than 100%.

This agricultural point of view can also be found in a supposedly neutral wikipedia article about the efficiency of photosynthesis:

"Many plants lose much of the remaining energy on growing roots."

Lose energy? How can a plant exist without roots? Something is seriously wrong here. This is a myopic agricultural view of plant anatomy and physiology. The wikipedia article is apparently written from an anthropocentric point of view: roots of most crop plants are not eaten and thus a waste! Why plants need roots follows directly from the definition of photosynthesis (see below).

Although the Britannica gives a neutral definition of photosynthesis, and there is some attention to 'the needs of the whole plant', the agricultural context is already present in the introduction ('agricultural revolutions').

The Life of a Leaf
The Life of a Leaf
But we can also find the idea of low photosynthetic efficiency outside the agricultural context. Biologist Steven Vogel writes:

"Photosynthesis consumes no more than perhaps 5 percent of that energy [= after rejecting almost all the near-infrared portion of sunlight], an amount we'd dismiss as negligible were it not for life's total dependence on it. That other 95 percent makes trouble. Odd idea, admittedly –light as bad for leaves." The Life of a Leaf, 447/990.

This is remarkable and unexpected, because Vogel wrote a insightful book about plants The Life of a Leaf  in which he exhaustively lists all physical constraints of leaves and the adaptations to deal with them [1]. I will return to him.

Karo Michaelian

Physicist Karo Michaelian observes that photon dissipation into heat accounts for 99,9% of the free energy in sunlight and only 0,1% is used for photo-synthesis:

"This represents an extremely poor efficiency for a photosynthetic system that has had the opportunity to evolve for at least 3,500 million years considering that humans have developed systems capable of converting up to 40% of the free energy in sunlight into usable electrical energy within only 40 years of technological innovation." [2], [19]

Many claims in one sentence! I will debunk all of them. 

An authoritative article in Science states that:

"Solar energy conversion efficiencies for crop plants in both temperate and tropical zones typically do not exceed 1%" [18]. Please note the agricultural context: crop plants [25].

When all the reported photosynthesis efficiencies seem to be low, that is for me a reason to dig deeper. Because it is somewhat surprising.


A number between 0 and 100

For a start, such a simple thing as expressing photosynthetic efficiency as a percentage from 0 to 100 can be quite misleading. It suggests that 100% is the maximum efficiency. Wrong. The calculated theoretical maximum energy efficiency of photosynthesis is 26 percent [7]. So, we should not express the efficiency as a fraction of a physical impossible maximum of 100%, but of the maximum that is set by the laws of physics and biochemistry. Those laws cannot be broken. They set the absolute upper limit. If we use the upper limit, the 26% is the maximum and in a sense represents 100%. So, the 5% efficiency is in fact 20% (5/26). If we use the value 11% in wikipedia [8], than photosynthesis achieves 42% of the maximum. So, it makes more sense to express the efficiency relative to what is physically possible. Karo Michaelian uses 0,1% efficiency which is 1/1000. Indeed, that is negligible! (Hmmm, my income is negligible compared to that of a billionaire.)


Why are solar panels so inefficient?

wikipedia solar panels

We must first debunk the 'solar-panels-are-more-efficient-than-photosynthesis' claim before we can make any progress. The following statements can be found on a website of a company that produces solar panels (a company that hardly can be accused of being pessimistic about performance): 

"Most typical silicon solar cells have a maximum efficiency of around 15 percent. (...) excess energy will be released as heat. This is one of the reasons that solar cells have such a low efficiency; they only need a very specific amount of energy in order to work. (...). 23 percent of the energy from the sun has a wavelength too long to be useful to solar panels. (...) Other wavelengths have some excess energy. In fact, another 33 percent of the sun's energy is excess energy that is also unusable for silicon solar cells. Therefore, this leaves only 44 percent of the sun's energy available to silicon solar cells. More of this energy is lost due to reflection and other processes in the cell itself. Hence, while the theoretical maximum efficiency may be higher, the real efficiency of silicon cells is usually around 15 percent." [16]. [my emphasis]

That means that 85% of the solar energy is wasted! Karo Michaelian (2016) quotes the highest efficiency for solar panels he could find: 40% efficiency. For photosynthesis he chose the lowest value he could find: 0.1%. That is a biased and abstract description. Real-life conditions of solar panels must be included in the calculation such as seasons, weather, the accumulation of dust, grime, and pollen and the problem of shade. No surprise, solar panels and photosynthesis have some efficiency problems in common caused by the laws of physics.

Finally, if engineers are able to produce solar panels with 40% efficiency in 40 years [19], why are engineers unable to do the same for photosynthetic efficiency? Why didn't engineers improve photosynthesis efficiency to 40%? If photosynthesis is so poor, wouldn't it be easy to improve? Be assured: scientists are trying very hard! And the stakes are high. I will elaborate on this later.

 

The difference between solar panels and photosynthesis

As we have seen, in only one sense solar panels can be compared with photosynthesis, but in all other respects the comparison breaks down. By simply looking at the formula of photo-synthesis we see that it is a chemical synthesis:

Photosynthesis (wikipedia)

Photo-synthesis is a chemical synthesis of sugar with input carbon-dioxide, water and light. Solar panels fail in all these respects:

  • solar panels have zero percent efficiency for sugar production
  • solar panels have zero percent efficiency for water splitting
  • solar panels have zero percent efficiency for oxygen production
  • solar panels have zero percent efficiency for energy storage
Solar panels fail completely in these respects simply because solar panels are not designed to produce sugar or oxygen or split water. Solar panels only require light (the only limiting factor) and only produce electricity. Plants store the energy  in chemical bonds (sugar).

Water is often plenty available, but not everywhere on earth. Certainly not in areas such as deserts. Typically, deserts would be great for solar panels, but not for plants precisely because of the lack of water. Water can be a limiting factor. And if water is available it has to be transported to the leaves. This definitively shows the difference between solar panels and plants. Further, water uptake requires roots. Roots have to be grown.

CO2 is –despite climate warming– present in very low concentrations in the atmosphere: 415 parts per million, that is just 0.04% [15]. A plant cannot actively grab CO2 from the air. Animals have active breathing and are only interested in oxygen which is present in the atmosphere in a comfortable concentration of 21%. That is more than 500 times higher than carbon-dioxide! Plants don't have active breathing [3]. CO2 ends up inside plant cells mainly by simple diffusion [4]. That CO2 is really a limiting factor is shown when CO2 is experimentally increased: plant growth is stimulated [5]. So, both the concentration of carbon dioxide and the passive diffusion are limiting factors for the rate of photosynthesis. Natural selection can do a lot, but not increasing atmospheric CO2 concentration!

CO2 concentration
figure 1 (source).

Law of Limiting Factors

The Law of limiting factors states that the rate of a physiological process will be limited by the factor which is in shortest supply. Any change in the level of a limiting factor will affect the rate of reaction. (source). In photosynthesis light, temperature and CO2 are limiting factors alone and in combination. Above we have seen the CO2 effect. Here is the temperature effect:

figure 2 (source).

Here is the combination of CO2 and temperature:

 

figure 3 (source).

 

Below the effect of light is shown (figure 4).
 


CO2 / O2 balance is crucial for photosynthesis

 
Above the law of the limiting factors there is an evolutionary legacy. Earth history and biochemistry show that the relative levels of oxygen and carbon-dioxide in earth’s atmosphere are important. Plants require a minimum level of carbon-dioxide and at the same time not too much oxygen. This is because the enzyme involved in photosynthesis (rubisco) doesn't work when carbon-dioxide levels are below 40-65ppm at 21% oxygen level. At 1000ppm carbon-dioxide photosynthesis works very efficiently. At the same time at 2-5% oxygen photosynthesis works well, while at the current level of 21% oxygen there is 25% inhibition of photosynthesis. The oxygen/carbon-dioxide balance has changed during the lifetime of the planet and that has its effect on photosynthesis. The core photosynthesis enzyme rubisco has been adapted to the past [21]
 

Too much sunlight!

Steven Vogel (quoted above) already noted that too much sunlight is bad for plants. Direct full sunlight is needlessly bright. He measured leaf temperature on a hot day: 55°C (130°F)! That is clearly outside the range photosynthesis works best: 20° – 35° C (68° – 95°F). Plants manage to survive those harsh conditions. Why aren't they dead?

figure 4 (source).

Rates of photosynthesis in bright sunlight sometimes exceed the needs of the plants, resulting in the formation of excess sugars and starch. When this happens, the regulatory mechanisms of the plant slow down the process of photosynthesis, allowing more absorbed sunlight to go unused [14].

Although light is required for photosynthesis, too much light can be harmful. To protect the photosynthetic apparatus from oxidative damage, photosynthetic systems possess antioxidant systems that scavenge reactive oxygen species, as well as mechanisms that regulate photosynthesis to minimize their production [20].

At high light the absorption of light energy exceeds a plant's capacity for CO2 fixation [20].

Carotenoids are part of a cycle that renders excess energy beyond the level of light saturation harmless, effectively serving as “lightning rods” in the process [14].

These effects explain why photosynthesis rate has a ceiling.


Plants in natural conditions

“People often think that nature is very efficient. It is, but only in natural conditions. The crops we grow were not born for agriculture; we took them from the forests and placed them in fields. If they had completely adapted to these new conditions they would perform much better." ( wur.nl )

According to photosynthesis researcher Vincent P. Gutschick the components of photosynthesis in wild plants have been nearly optimized by natural selection [10]. That explains why breeding for photosynthesis has enabled few discrete gains in yield. Breeding for higher yield has trade-offs such as lower water-use efficiency.

The authors of an article in Science conclude: "the main evolutionary pressure on photosynthetic organisms is that they survive, not that they have the optimum thermodynamic efficiency!" [17]. Very important.

Recently, researchers claim to have eliminated 3 bottlenecks in photosynthesis in tobacco, thereby increasing yield significantly. They are trying to apply the findings to food crops as cassava, cowpea, maize, soybean and rice [11]. The question arises: if this is good for the plant species, why has natural selection not removed these bottlenecks? The answer can only be found when we find out what the evolutionary reasons are. One example is a wasteful process called photorespiration. It's long been thought that more than 30% of the energy produced during photosynthesis is wasted in the process. Now, a new study suggests that photorespiration wastes little energy and instead enhances nitrate assimilation. The researchers propose that something else is going on that shows plants aren't so stupid [9]. Again, digging deeper is rewarding.


Evolution and adaptation

A leaf is not a simple 'solar panel'. A leaf has many functions: "Assuring access to light, providing mechanical support, coping with heat, deploying from a bud, dealing with wind, getting atmospheric carbon dioxide into the cells, extracting water from soil and raising it upward, deterring herbivores" [22].

Pinus
All these functions often require compromises. Furthermore, evolution designed different life-cycle strategies: annual, biennial, perennial. Each of these lifestyles imply different compromises such as fast or slow growing, making many small leaves or few big leaves, producing seed once in the growing season, or every year; deciduous trees (shed leaves in the autumn), conifers (evergreen). For example, deciduous trees show that trees make choices, they shed their leaves and they don't photosynthesise the whole year. Why? Think about that. Clearly, they don't maximize photosynthesis. Otherwise they wouldn't shed their leaves. Apparently, climatological circumstances make it unprofitable to have leaves the whole year.
Something similar holds for conifers. They have long, thin
'leaves' (needles). That is a very small surface compared to 'normal' leaves. Think about it: why do they do that?

 

Summary of main points

  • In an agricultural context photosynthetic efficiency is meaningful and important because it is all about food production
  • In an evolutionary context photosynthesis efficiency is only one of several factors that contribute to survival and reproductive success.
  • Reporting photosynthesis efficiency is meaningless without a precise description of how it is measured: plant species, wild or domesticated, light spectrum considered (Photosynthetically Active Radiation or all wavelengths), how photon flux is measured, which end-product measured [12], water-use efficiency, CO2 levels, minerals, temperature, which 'losses' are included, in the lab or in the field, duration.
  • Limiting factors are: light, CO2, water,  temperature, nutrients [14]. Evolution cannot improve the physical environment!
  • Whenever a feature of a plant in nature looks wasteful and inefficient, we should study the species to find out why [9].

 

Final thoughts

Is photosynthetic efficiency low? First, use your common sense. Whatever the efficiency, it is a fact that plants are able to grow, survive and multiply. That is a remarkable fact. Photosynthesis has existed for some 3.5 billion years. Plants are the evolutionary success story. They made the earth habitable for animals including humans. Plants produce oxygen. Without atmospheric oxygen animals would not exist on earth [24]. The earth is the only known planet with life. Apparently photosynthesis is powerful enough for the existence of 8 million species on earth [23]. We should not ignore the obvious.

Is photosynthetic efficiency low? It is really too simplistic to conclude that 0.1% is low just because the percentage is low. Period. In this blog I introduced the chemical formula of photosynthesis. Many things follow from that formula. Important: carbon-dioxide. To know what the effect of carbon-dioxide is, one has to know what the history of carbon-dioxide and relative CO2/O2 concentrations were in the history of the earth. Those concentrations formed the selection pressures of the core enzyme rubisco. Further, one has to know what the biochemical sensitivity of rubisco is for different concentrations in order to understand the current efficiency of that molecule. Finally, one has to find out if there exists selection pressure at all for higher efficiency of photosynthesis in the wild. That's why it is wrong to say that "0,1% is an extremely poor efficiency for a photosynthetic system that has had the opportunity to evolve for at least 3,500 million year".

Is photosynthetic efficiency low? A better question would be: how are plants adapted to their natural environment? Plants are not adapted to human needs. From an evolutionary point of view agriculture is unnatural. Wild plants have been taken from their natural environment and transported to a different continent with a different climate. Plants are modified in order to redirect their resources to human goals. We want different parts of the plant: the root, stem, leaves, seeds, fruits, and modify plants accordingly. Plants did not evolve to meet human needs.

 

Acknowledgments

I would like to thank Kasper van Gelderen en Thijs Pons.


Notes

  1. Steven Vogel The Life of a Leaf. A second quote about leaves: "These relatively inefficient solar panels provide all the energy a tree can invest in growth, reproduction, and dispersal - the three central concerns of every organism that has ever lived." (505/506)
  2. Karo Michaelian (2016) Thermodynamic Dissipation Theory of the Origin and Evolution of Life, p.312) paperback (see a previous blog). Karo is right about one thing: "Photosynthesis was well-established on the earth at least 3.5 thousand million years ago." (source). In a next blog I will refute Dissipation theory with evolutionary biology.
  3. CO2 is not always passively transported. C4 plants use a biochemical pump to concentrate CO2 at the locations within the leaf where the RUBISCO enzyme mediates incorporation of CO2.
  4. Andrew Bocarsly of Princeton University: "We've been studying CO2 chemistry for a long time, more than 100 years, and there's very little evidence that we could do what a leaf does."
  5. Effects of Carbon Dioxide on Photosynthesis, Plant Growth, and Other Processes
  6. see wikipedia article Measuring ancient-Earth carbon dioxide concentration.
  7. Energy efficiency of photosynthesis, Britannica (free article)
  8. The theoretical maximum efficiency of solar energy conversion is approximately 11% (wikipedia).
  9. Shedding light on the energy-efficiency of photosynthesisSciencedaily, 2018. "a new study suggests that photorespiration wastes little energy and instead enhances nitrate assimilation,".
  10. Vincent P. Gutschick (1997) Photosynthesis, Growth Rate, and Biomass Allocation, Ecology in Agriculture, 1997 
  11. Third breakthrough demonstrates photosynthetic hacks can boost yield, conserve water. August 10, 2020
  12. End-product: "Only 5% of the sunlight that hits this field ends up in these grains"! (Dr Matt Johnson). "if only agricultural products (e.g., seeds, fruits, and tubers, rather than total biomass) are considered as the end product of the energy-conversion process of photosynthesis, the efficiency falls even further." (source)
  13. C4 plants: "The C4 metabolic pathway is a valuable recent evolutionary innovation in plants, involving a complex set of adaptive changes to physiology and gene expression patterns." (wikipedia).
  14. Britannica. "Several minerals are required for healthy plant growth and for maximum rates of photosynthesis. Nitrogen, sulfate, phosphate, iron, magnesium, calcium, and potassium are required in substantial amounts".
  15. Industrial carbon capture from the air is costly because CO2 has a low concentration in the air and lots of water are required! Just like photosynthesis!
  16. The Average Photovoltaic System Efficiency, Sciencing, April 25, 2017
  17. quoted in this blog Is photosynthesis highly efficient? 2012
  18. Comparing Photosynthetic and Photovoltaic Efficiencies and Recognizing the Potential for Improvement, Science,  13 May 2011. (a pdf can be downloaded here)
  19. On page 223 of his book he writes "in only 25 years" for the solar panels and "after more than 3.8 Ga years of biological evolution" for photosynthesis, making the difference still bigger! Exaggeration!
  20. Photosynthesis, R.C. Leegood, in Encyclopedia of Biological Chemistry (Second Edition), 2013.
  21. Evolution on Planet Earth, page 21.
  22. Steven Vogel The Life of a Leaf., 28/990 (ebook)
  23. How many species on Earth? About 8.7 million, new estimate says. Science daily 2011.
  24. "Animals depend on oxygen because they need it to release energy from sugars, fats and proteins. In strict chemical terms, cellular respiration reverses the reaction at the core of photosynthesis. Sugar and oxygen react with each other to make water and carbon dioxide, releasing a lot of energy." Paul Nurse (2020) What is Life? 22 Nov 2020
  25. Nobel prize winner Paul Nurse (2020): "If we could re-engineer plants to carry out photosynthesis even more efficiently than they do..." in: What is Life? 306/360 24 Nov 2020


Previous blogs about photosynthesis


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) [5]. 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.
  5. Later I find out that in the chemoton model of Tibor Gánti there are no enzymes. So it appears that both Gánti and Kauffman define simple forms without enzymes and genes.

 

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. 

 

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