What Are Organisms?

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Book Reviews

What is an organism?

It’s not an easy question to answer. When faced with such a challenge, it is natural to employ metaphors that help us formulate some preliminary ideas about what it is we’re dealing with. These metaphors relate something that is mysterious to us, like the organism, to one that is well known to us, such as the machine. We know what machines are, and generally how they function, and so this metaphor gives us a point of entry into the analysis of organisms. What are the organism’s parts? How do they interact? When the organism breaks down, what parts must be repaired or replaced? Where does the energy come from that makes it work? And so on and so forth.

The challenge in our reliance on metaphors is that they can limit our understanding as easily as they can expand it. When faced with a subject as tantalizing as the study of organisms, the metaphor can preclude us from noticing essential qualities of their structure or organization, because the map, in its usefulness, inadvertently becomes the territory. It’s not that we don’t recognize these differences—we know that machines do not repair themselves, grow, or reproduce for instance, while organisms do—but there is a tendency to insist the metaphor still holds. A sufficiently complex machine, for instance, might very well do these things. And so we can continue to classify the organism as a machine, albeit an especially profound one, and then continue our search for mechanisms that underlie its various functions. The result can be misleading: the conflation of machinery with life itself, or the reduction of life to apparatus alone.

Machines as we know them today are still rather brute devices that rely on simplistic physical and chemical relationships. Cranks, pulleys and shafts convey forces. Fuel and oxygen combust to release energy in confined spaces. Electricity and magnetism are channeled through tiny circuits, or harnessed to produce linear or rotary motion in subassemblies. And we can do amazing things with this toolkit. But we cannot explain organisms. What if the machine model obfuscates fundamental questions about organisms that might lead to new insights? To what then, might we compare life, if not a machine?

In Mae-Wan Ho’s book The Rainbow and the Worm, she shows that other metaphors of the organism are equally relevant—the jazz band, the liquid crystal, and the rainbow, among others. She focuses on the intersection of twenty-first century physics with modern biology to show that organisms are at least as advanced in the mechanisms they deploy as our present understanding of the natural world allows us to comprehend.

There are two key aspects of biological systems that Mae-Wan highlights. The first is that life exhibits a comprehensive dynamic order at the quantum scale, which none of the machinery we know today does. Quantum mechanics has certainly played a vital role in our technological progress, and is essential to such technologies as GPS, satellite communications, smartphones, computers, and magnetic imaging, but it is not the case that the comprehensive atomic structure of the physical devices we use everyday is contingent upon these functions. For a few discrete subsystems or subassemblies it may be, but for the bulk of the material in a manufactured object, the dynamic interrelationships of the atomic structure are irrelevant to the object’s core function. The classical properties alone are sufficient. This is not the case with organisms.

Quantum mechanics is known today for its spookiness, but at its foundation it resolved a couple of key questions that classical mechanics could not. It’s worth noting that none of these early breakthroughs were based upon the head-scratching quantum mechanics that receives most of the press these days. They were based on the idea that energy, matter and light exist in minimum, discrete quantities. Two key challenges of classical theories that were resolved by this realization were the so-called ultraviolet catastrophe and the mystery of the electron’s orbit around the atom.

The former is the theoretical prediction that the radiant energy emitted from objects at high temperatures should approach infinity, but it does not. The reason is the quantum. With regards to the latter, in classical mechanics the electron should emit electromagnetic radiation as it flies around the atom, causing it to lose energy and crash into the nucleus. But it doesn’t. The reason is that quantum physics only allows electrons to occupy specific orbitals, and they don’t lose energy by zooming around in a given orbital, only by changing orbits, which means atoms don’t arbitrarily collapse.

It turns out that the structure of living organisms is entirely dependent on these aspects of quantum physics. In contrast to systems of relatively disorganized molecules like chicken soup, the atmosphere, or the water in the sea, organisms store a considerably higher fraction of their energy in bound quantum states. By the latter I mean atoms linked together by stable chemical bonds that store a great deal of energy, but are stable because of the quantum physics described above. Life stores energy in molecular trapdoors for later retrieval. Machines do not do this.

Mae-Wan notes that if all of the energy contained in living organisms were converted to thermal energy—as opposed to the electronic form in which it is actually stored and utilized—the human body temperature would be upwards of 3,000 degrees Kelvin. To put this in perspective, the surface of the Earth is about 288 degrees Kelvin, and the surface of the sun about 5,780 degrees Kelvin. Thankfully for us, we are not the thermal engines we thought we were.

Related to this, not only do organisms store energy electronically, they use it electronically. Living organisms utilize energy with close to 100% efficiency when transforming it from one form to another. This is remarkable when one considers that the electricity grid of an industrialized nation operates at about 40% efficiency, plus or minus, when converting the stored chemical energy of fossil fuels to delivered electricity. (Renewable electricity systems are even less efficient, though efficiency is not really a meaningful metric to apply when comparing them to fossil-fuel based technologies.)  The chemical energy of hydrocarbons such as oil and natural gas is in many ways similar to the stored energy in living cells—the energy is contained in the stable bonds that link one atom to the next to form large structures of carbon and hydrogen—but our industrial processes come nowhere close to the efficiency of living organisms in converting such energy into actual work. As organisms, we move our muscles, breath, digest food, sing opera, and think with essentially zero energetic waste. It’s not that organisms don’t use energy. They do. But unlike machines, they use it one quantum at a time.

A second key element of Mae-Wan’s synthesis in The Rainbow and the Worm is long-range order, or coherence. This is a slightly complicated subject in that coherence is a word that could have both classical and quantum physics meanings, but the essence of the two is very similar. Classical coherence is the condition in which a system of oscillators share a common phase. You could imagine several tuning forks, each with the same natural frequency. If you struck them all at roughly the same time, they would each ring with the same tone, but due to inherent variations in when you actually struck each one, they would not initially be in phase. Over some period of time, however, because the energy they exchange with one another through sound waves impacts their vibrations, they would settle into a condition in which they not only rang with the same tone, but did so in phase.

Quantum coherence is more difficult for me to distinguish or fully understand, but real world examples are lasers and superconductivity. In a laser, the light emitted from a large population of atoms is the same frequency, and, like the classical definition above, is completely in phase. This is because all of the electrons that are changing state to emit the light are undergoing a transition from the identical high energy orbit to the identical low energy orbit in their respective atoms. The light they each emit is thus of the same frequency. In a laser, there are mechanisms in place to “pump” the system which results in a synchronicity of the light emissions. (Interestingly, Mae-Wan notes that the organisms may utilize metabolic “pumping” for similar purposes in the body.) Superconductivity occurs when electricity can be conveyed through a conductor with zero resistance. This also is related to a global phase relationship in the electrons within the material. This type of coherence exists at the quantum scale, but is quite similar to the classical coherence described above.

But in the quantum world there is another sort of coherence, and this occurs when various possible states of a system are in phase. This is where we get into the spookier realities of quantum mechanics, in which, for instance, one atom or electron can be said to occupy multiple states simultaneously. This state is a coherent one, because all the possible states are in phase, and it is only when we make a measurement, or when the system otherwise interacts with the environment, that a particular state is selected. It does this by “de-cohering”, or breaking phase with the other possible states. It is this type of coherence that we are attempting to leverage in quantum computing. I believe it is this type of coherence that has been observed in the photosynthetic systems of organisms.

I think the important aspect of this topic overall is what coherence affords to the systems in which it exists. Mae-Wan points to several salient features of coherent systems. She writes, “Coherent excitations can account for many of the most characteristic properties of living organisms that I have drawn your attention to at the beginning of this book: long range order and coordination; rapid and efficiency energy transfer, as well as extreme sensitivity to specific signals.”

A couple of key examples Mae-Wan uses are the sensitivity of the human eye to an individual photon, which relies on the amplification of the signal by thousands of receptors with virtual simultaneity, and the processes associated with muscle contraction, in which billions of molecular operations per second are carried out with perfect coordination. With regards to the latter, she cites an experiment in which the energy from individual ATP molecules was utilized by four cycles of cross-bridge formation between actin and myosin—the fundamental, repeated action associated with muscle contraction. How could the energy from one molecule be shared over four individual cycles? Through coherence, she says, which allows for multi-mode storage and transfer of energy in both space and time.

This is where the jazz band analogy comes into play. Various members of an ensemble may depart temporarily from a common beat, but after enough measures there will be a return to the original “heartbeat” of the piece. The jazz band metaphor is about multiple rhythms occurring simultaneously without loss of the overarching unity that forms the whole. In the example of the muscle contraction, energy is dispersed over all of the various modes of the system, which allows it to be used in non-linear ways.

This might all sound like science fiction, but there is beautiful physical evidence for this idea. Using a microscopy technique known to reveal the crystalline order of various mineral specimens, Mae-Wan and her collaborators showed that the molecular structure of living tissue exists in a liquid crystalline state. The molecular order of this state is visible as dynamic bands of color within the living tissue—colors that are visible because the tissue exhibits the property of birefringence (which it loses quickly when the tissue dies).  The images on the cover of her book below were developed using this microscopy technique. Speaking of this discovery, she writes, “The colour generated and its intensity (the brightness) depends respectively on the structure of the particular molecules (the intrinsic anisotropy of the molecules) and their degree of coherent order.” (Emphasis contained in the original.)

So what is an organism then? Who knows!? What we can say is that unlike any machinery we’ve invented to date, it is a self-directed energetic structure of nested, multi-modal order. It is something like a symphony, or a jazz band—a dynamically evolving wholeness in which each part is an integral expression of the wholeness itself. What I love most about The Rainbow and the Worm is Mae-Wan’s demonstration that our understanding of life is limited only by our imagination…


  1. You seem to really like exploring deep philosophical ideas and science. I applaud your comprehension of such deep matters Michael. I seem to have a block to reading and understanding those topics. I like to boil things down to the simple overview and summary.

    Liked by 1 person

    • I hear you, Brad! You’re right, though, I do enjoy a mix of things. Science as well as literature, etc. Both sides of the brain need some exercise once in a while! I’m probably out of step with the experts in each field, but enjoy a diversity. It’s interesting to me to understand what we know and how we know it, and the latter is not always easy to find. Experts in a field know where the cracks in the wall are, and it can be challenging to find popular science writers who carefully illuminate those areas of interest. Mae-Wan is one of those, I think. I like reading Lee Smolin’s books on physics, too, which are pretty in-depth but also fairly honest (I think) about the challenges that physicists are trying to resolve. Anyway, I do enjoy learning about a wide range of things, Brad!


      Liked by 2 people

  2. ‘It is something like a symphony, or a jazz band—a dynamically evolving wholeness in which each part is an integral expression of the wholeness itself.’ – Excellent, that would be my nutshell and I very much enjoyed reading through all the machinations that led to it Michael *beams*

    – Esme Cloud sending quantum joy to him.

    Liked by 1 person

    • Thank you, Esme! For reading the novella first of all. Haha. It’s wholeness that is for me that intangible something else that life displays. Call it beauty. Call it order. Call it wholeness… Whatever it is or isn’t, it’s extraordinary. And I do like my science with a bit of appreciation for the wonder of it all…

      Hope you are well, Esme! Thanks for the quantum joy and right back at you!

      Liked by 1 person

  3. I think you did such a marvelous job with this. I felt the underlying structure of this book in how quantum mechanics (funny how there’s the word ‘mechanics’ again, as we are getting away from the mechanistic analogy). The idea that organisms are so efficient that they don’t waste energy is so beautiful–the most beautiful aspect of life to me right now. That a single ATP molecule is available over 4 cycles of actin and myosin filament glides is amazing. I’m still trying to understand how coherence makes this possible.

    I’m wondering which came first the understanding for quantum mechanics or the invention of quantum computing. I pose it like this because I think things get figured out as they are built and used. We learn from trying to re/create.

    I’m wondering about how understanding can become more efficient, zero wasted efforts. That would be nice. I’m wondering about how the human body’s energy in terms of a thermal vs. electronic energy works? Pending that I understand the difference between electrical and electronic, how the idea is that the human body has a thermal output in kelvins that’s about half the surface of that of the sun’s thermal output? I think a lot of this has to do with storage. Is electronic moreso the continuous flow of electrons? This needs to be defined for me as a reader.

    When we get to rainbows, I get excited and think back to the first astronomy class I took when I learned that the elements that a star was burning off could be perceived by its colorful spectra. That color represented the stage of the star’s life. It was another instance of “art of science” and the “science of art” are the same. The universe IS a magnificent painter. I like what you say about imagination in the end of your article. We don’t want to be limited by our analogies, so maybe the best way is to make so many of them and try them all out? What do you think?

    This is my second time writing this comment. I missed some thoughts I had in the original. It was wiped away somehow. I tried to bring my energy into this second comment, but I missed a lot.

    Liked by 1 person

    • Hello Ka,

      Thanks for the note and I’m sorry you lost your first attempt. That has happened to me before–to all of us I imagine–and it’s so frustrating! So I appreciate your finding the energetic reserves to try again…

      With regards to your question, the term electronic was one that Mae-Wan used. Describing different forms of energy can be tricky, but thermal energy, which we call heat when it is flowing, is generally related to the relative velocities of atoms and molecules. Heat transfer has virtually nothing to do with the subtlety of electron orbitals around atoms, and all to do with how fast the little particles in a gas or liquid are zinging around (or jiggling in a solid). When we use this type of energy in machinery it is, compared to how the body uses energy, pretty clumsy. It involves heating a gas, and when that gas tries to expand, using a cylinder or turbine wheel to convert that “work” of the gas into a motion we can use. Although there is a lot of energy in all the particles zooming around in a hot gas, they’re all going different directions and so it can’t be harnessed easily, but a turbine wheel or piston at least converts that into a specific motion that we can predict, and utilize.

      This description kind of gives the key to it. Not all forms of energy are equal. A spinning combustion turbine shaft can be used to grind grain, turn the axle of a vehicle, turn a pump shaft, etc. But the random movements of a hot gas have to be “organized” by a heat engine into a form of energy we can use. In the body, though, there’s just very little “randomness” to energy use. Energy is not stored in high-speed molecules banging around, but in “compartments” that are electron orbitals and bonds between molecules. Unlike thermal energy, which is basically just molecules flying around, these “compartments” do not leak energy to the environment by bumping into other molecules. Instead, they keep it relatively “insulated” from the environment, and dole it out only as needed.

      I hope that makes sense, Ka! I think the difference between electrical energy and electronic energy is that electricity like we use in our homes is the flow of many, many electrons in the form of electric current, and the electronic form is more like using one electron at a time in a very specific way…

      As to your closing, I’ve often the thought the universe has just as many patterns and logics and forms of order as we’ll ever be capable of identifying. That is really what is so profound about it to me. There’s nothing we see that doesn’t at least hint at the fact that the whole universe is profoundly ordered, and that it functions in ways that really astound us with their profundity. We need imagination to grasp these types of order! And to see the order that is all around us, but which we’ve not even begun to understand yet…

      Hope you are well, Ka!
      Thanks for the note!


  4. Your words did make sense enough to me. I found the idea of compartments to be interesting though. I’m reading it as the potential energy is available in the bonds that exist in the molecules in living organisms. The different types of energy thermal vs. mechanical seems like the basis laid down in a general 101 class that I have not yet taken. Again since we are talking about processes in motion all the time, we can’t exactly talk about it in snap-shots of action. I think a lot of this is about defining terms in order to have a conversation, but I think we are navigating it alright for our purposes here. The need to have imagination to see how things really are (ordered!) is a very interesting one. It’s a little bit philosophical, but it’s also proven in so many experimental ways…

    Eager to hear more from you: how you met Mae Wan Ho and what is EZ water…?


    Liked by 1 person

  5. I really enjoyed this, Michael. It evokes the wonder I felt as a kid peering into my very own red Tasco microscope. I spent alot of time collecting all kinds of things from a pond in the farmer’s field from behind our house, for example. Biology was my 1st science love. Such amazing images you shared and I appreciate your bringing together Mae Wan Ho’s synthesis and physics in a way that makes these topics more accessible to folks like me who are not necessarily steeped in physics. Inspiring, deep material.

    Amen, well said: “…it is a self-directed energetic structure of nested, multi-modal order. It is something like a symphony, or a jazz band—a dynamically evolving wholeness in which each part is an integral expression of the wholeness itself. What I love most about The Rainbow and the Worm is Mae-Wan’s demonstration that our understanding of life is limited only by our imagination…”

    Thanks for the gift of time & care you put into everything you share here!

    Liked by 1 person

    • Lanessa! So nice to hear from you. Hope you are well.

      I’ve been working from home this week. I find it can be intense–not the location part, but my work has not slowed down, and the constant bombardment of texts, e-mails, video chats and teleconferences has been crazy. I’ve been in that zone of answering one thing while the next two roll in, and without team members in adjacent desks to commiserate with–when I have to purposefully press the time to goof-off button I find it doesn’t get pressed. I’ve gotten a lot done, but the days are intense.

      Glad you enjoyed this post. Your younger self’s amazement with the world is something our great scientists never lose I feel. I think Mae-Wan was one of those. And since I had undergraduate coursework in physics and thermodynamics, I’m able to follow her discussion fairly well… I forget not everyone has this training! Thermo was the “weed-out” course in engineering at AU. The basic ideas are formidable, but relevant to both hard physical sciences and life sciences both, and Mae-Wan does an excellent job of bringing all of that together.

      Hope you and the extended yours are all well…

      With Love


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