I have often mentioned this but when I sit down and explain it to people they often are surprised and don’t realize how nature leverages quantum mechanics to accomplish probably the single most important thing to life.
Without photosynthesis everyone should realize that life would likely be a lot less interesting. Plants are the food for animals. Without plants we would have mainly bacteria.
What is Photosynthesis?
Nobody could explain photosynthesis for many years. It is obvious at a high level what happens. H2O (water), CO2 (carbon dioxide) are combined to release O2 (through a multi-stage reaction) and the remaining atoms form glucose which is the sugar used to build the plant structure.
We have known for some time that the location of this trick of nature is in a cell called the chloroplast. The chloroplast is composed of a complex of unique elements. Essential to the operation is something we call pigments. Pigments are where the sun’s photons are collected.
There are several variations of these pigments with varying efficiencies and wavelengths of light they absorb energy from.
Most chloroplasts of most plants are composed of chlorophyll-a and b pigments. These pigments have been given another name – Chromophores. These chromophores are located in a region of the chloroplast cell facing the sun. Photons hit the chromophores and create excitations of the molecules which then somehow gets transferred to the “reaction center” where the multiple reactions that take place to produce the life giving chemicals essential to most life on Earth.
From the reaction center the byproducts are ferried to the rest of the plant.
The problem is that until recently we didn’t know how the energy from the sun was delivered to the reaction center in detail. As late as 2014 it was still conjecture and assumed a classical mechanism was involved.
- This paper and others since show that the processes CANNOT be explained by classical physics.
The way this was shown is to show that the molecules in the chloroplast attain a state that has a negative probability of occurring. In other words they could not get into that state. Yet they do.
This is a great example of the limits of our science today.
We are still cavemen in some respects with science
Before 1900 (or thereabouts) we had only a gross ability to observe the human body. We could see there was a heart, lungs, bladder but how they worked was a mystery. As we learned about chemistry we could take samples from the body and tear them apart. Unfortunately such analysis lacks a determination of the purpose of each chemical and the processes to get from one chemical to another.
By the start of the 21st century we know there are 100,000 chemicals and 30,000 genes and 3 billion base pairs in the human system.
An incredible amount of science has been done to try to deduce the processes and steps of various reactions but even with all the work we have done vast numbers of things are unknown.
We have only the smallest understanding of the role of 99% of these 100,000 chemicals. We have 30,000 genes and 3 billion DNA base pairs. 99% of this is basically unknown. We only discovered the 3 billion base pairs contain a new language that describes how to regulate the genes and we know 0.001% of this.
We are still cavemen operating with stone knives. The biggest problem we have is our inability to watch what happens in real time at the chemical level and the fact we have so little theoretical understanding of how different structures could work.
Thus we have to try to deduce from fragmentary and in many cases what is circumstantial evidence.
We notice a certain macro phenomenon such as a disease and notice the prevalence of certain molecules. How those chemicals are involved is conjecture.
We can’t tell you if taking vitamin D will extend your life. We really have no idea how the body operates except in the most extreme deprivation situations.
What we have are still stone tools. This makes the incredible amount of work to understand very laborious and slow.
Nature is by its nature inscrutable at this scale
What’s worse is even with our best microscopes and devices we face a theoretical problem. Quantum mechanics says that we can’t observe what is happening even if we wanted to. The tricky stuff of quantum mechanics happens under the covers while in the “super-position” phase. By definition we can’t see what is happening in this portion of time because as soon as we try to observe we force a break out of superposition.
Scientists are skeptical of applying quantum mechanics
The reasons scientists have been skeptical to ascribe behaviors in nature to quantum mechanics are:
- Scientists believe we should always choose the simplest explanation for something before reaching for something extraordinary. Quantum mechanics is considered extraordinary.
- We don’t see typically quantum phenomenon exhibited at the macro level and because of the same problem discussed above if we did have a chance to see it would go away as soon as we looked.
- Most quantum phenomenon we have observed (indirectly) happen in cold near absolute zero temperatures not warm temperatures of life.
- Most scientists don’t understand quantum mechanics and thus couldn’t understand or explain things with it.
Thus, almost always we try to understand things according to classical physics. Yet at the bottom of everything we know quantum mechanics rules and thus every chemical reaction is in reality actually a quantum phenomenon.
What I’m talking about with Photosynthesis is not this derivative way of thinking about quantum mechanics but a truly tricky phenomenon called quantum tunneling.
Quantum tunneling is the phenomenon that we have leveraged in much electronics for a long time. What happens is that for a short period something happens that is classically impossible.
Imagine you have a stream. We all know streams go downhill. Thus if a stream has to face a mountain it will not go up the mountain even if the ocean is beyond the mountain it cannot climb the mountain to get to the ocean. Water can’t go uphill for any time normally.
In the same way an electron should not be able to penetrate an opposing electric field that is greater than the energy it has. However, in quantum mechanics all things are possible. The electron can “borrow” energy from the universe to push its way past the barrier and show up at the other side. The probability it will do this is dependent on among other things if the energy state at the other side is lower than the energy state if it doesn’t cross the barrier.
In other words nature seems to somehow know that if it could pierce the barrier it could get to a lower state. However, how could it know that without actually doing it? Well quantum mechanics postulates that in effect all possible paths of the particle are tried simultaneously and the ones with highest probability of occurring are the ones which result in the most energy reduction.
So, how does the particle get past the barrier. The theory most described is that other particles are created out of nowhere. Particles called virtual particles. These virtual particles are like helpers. They can add energy to one particle for a short time as long as there is a negative particle created at the same time. Almost any particle or combination of particles could emerge from nowhere in this “superposition phase” and provide all kinds of possible paths.
I am not making this up. I am not joshing you. This is the way nature really works. All possible combinations of paths are tried or examined by nature and a probability matrix of all possible paths is created and then one of them is chosen randomly and we see the result. The result is most likely the most probable path. However, if you do the experiment enough times you will see all the paths emerge. All of them.
You may think this is poppycock. However, quantum mechanics is right. I say this without hesitation because we have done so many trillions trillion of these experiments that we have shown that the particles and things that happen can be predicted by quantum mechanics to 12 digits of precision at least. No other theory has been verified or tested this well in human history. Not even close. If there is only one thing humans know it is that quantum mechanics is right. Everything else we can definitively say is less known.
Nature does appear to somehow while we can’t look shuffle all the possibilities of things that could happen if things appeared out of nowhere and shook things up. I have come to the conclusion this is actually one of the most important aspects of our reality and why we exist, why nature exists, why the world works. The constant shuffling and injection of randomness and possibility keeps the world dynamic and makes evolution work. It is the core of why life evolves and why it persists. In my opinion a world without quantum mechanics would not have life in it.
I believe this bizarre phenomenon that seems so hard to understand is the most crucial aspect of why there is life. A universe without quantum mechanics would never have found the combination of chemicals, materials and eventually DNA that forms life. DNA is in effect a mimicking of the quantum universe. The constant recombination and trying of all kinds of permutations is a reflection of underlying reality. In other words, DNA is just a higher order mimicking of the underlying fabric of the physics of the universe. It should not be surprising that nature leverages tricks of quantum mechanics to make life more efficient. It seems likely to me we will discover that nature uses many tricks of quantum mechanics to solve thorny problems in nature.
Why? Well, this article is not about that, but let me say that nature and quantum physics basically say that you only observe the universe when it is not in the “searching superposition of all possibilities phase.” During this phase called superposition we can know nothing just like we can’t know what is behind the event horizon of a black hole. It is a theoretical impossibility.
The inverse of this tautology is that the universe doesn’t exist unless there is something to observe it. In other words, the universe by definition supports life and consciousness because without consciousness the universe would not exist. It would forever be in a state of searching for possibilities, trying everything possible to construct a world where something could look and go “Aha, I see you.”
(There are variations on quantum mechanics that defy this need for consciousness. Roger Penrose himself has proposed a unification theory that says that gravity causes reality and decoherence.)
So, here I am talking about a philosophy at this time. Don’t take the above couple paragraphs as known science but simply my “interepretation” of why Quantum mechanics and the existence of life may be tied.
Let’s get back to the chromophore molecule.
So, the chromophore part of the chlorophyll molecule absorbs a single photon of energy and has to deliver that energy to the reaction center of the chloroplast. The exact mechanics is still not understood precisely (see above how stupid we are still) and yet somehow nature finds a way to deliver it because at the end of the day if it can deliver it then the chloroplast will divide the co2 molecule, combine it with H2O and release energy.
In other words, the lowest energy state is when the energy is delivered to the reaction center and so it is a high probability even though it means borrowing energy from the universe to do it and picking a path for the electron that has negative probability of occurring and 1 in a million chance of occurring in classical physics.
Nature thus uses quantum mechanics to be 1,000,000 times more efficient than classical physics at delivering the energy. It is easy to see with that kind of barrier without quantum tunneling the photon would never be enough energy to produce a plant and almost all life on the earth wouldn’t exist.
What is hard for many to swallow about this is that plants exist in a high energy state. Such a state of fluid water, excited air molecules banging into everything seems to prohibit a quantum phenomenon. We don’t fully understand this. It’s apparent that quantum mechanics plays in warm environments.
The fact we only experiment with quantum phenomenon in a cold environment where we can isolate and observe it carefully doesn’t mean that it isn’t in operation in everyday things all the time. By definition we know that everything that happens fundamentally is quantum. The fact we can’t observe using the instruments we have doesn’t mean it doesn’t happen.
I believe we will find quantum mechanics is involved in many complex phenomenon. I believe that nature would use quantum mechanics to solve a number of problems simply because that would be the simplest way to do it and quantum mechanics provides some very convenient tools to solve some problems and make life vastly more interesting.
1. All the senses
will end up having very quantum mechanical basis. There are a lot of reasons to believe that smell is a quantum mechanical phenomenon for instance. It seems that bird homing may use quantum mechanics at least in some birds.
All our senses have to be ultra keen to defeat the other creatures. Thus having better sensors is hugely advantageous. Thus any way to use a trick of quantum mechanics to improve a sense would make a lot of sense. I have to believe that if nature uses QM anywhere it is senses.
It’s not surprising our eyes use the same chromophore molecule to detect light. This makes our eyes more sensitive than any camera we have built so far.
2. The Brain – Pattern matching and memory
Almost all living creatures need some form of learning, adaptation and innovation to survive. From even single cell creatures up there is a need for more ways to figure out the environment. Clearly you need senses but then if you apply a “deterministic” algorithm to process that sensory information another deterministic algorithm of another creature once it figured out the weakness of that deterministic algorithm would be able to eliminate all instances of the other deterministic algorithm. Thus, deterministic algorithms have a problem that they are not creative.
QM is not necessarily creative but inevitably what it does is try every possible path. We see even with creatures of every type variations in behavior that exceeds the capability of simple deterministic machines.
It can’t be explained entirely as DNA variations produced by random choices. We find that very quickly as we go up from a single neuron that creatures start to exhibit a remarkable awareness and variability in behavior. I recently saw a paper that showed even fruit flies demonstrated a capability to learn and variation that couldn’t be explained as genetic difference alone. Each Fruit fly even with identical or close to identical DNA had variations in its behavior when faced with certain phenomenon. This is obviously critical for survival. If it isn’t QM it is damn interesting how such small living things can survive.
I believe we will find that memories are somehow stored and searched using quantum mechanics. QM has in its sleeve of tricks as I described a way of finding out of a huge range of possibilities the path that leads to X. This trick can be used easily to find something in a large set of numbers.
Essentially you can store a huge number of numbers in superposition by having a number of superposed states. By representing a “memory” as a combination of states of some particles in coherence you can store a lot of memories simultaneously in the same particles. One of the important principles of QM is that particles can be in superposition meaning they can attain not just X or Y but particles can essentially remember nearly an infinite number of possible states in the log of the number of states number of particles. If you want to remember a billion things you can do it with 20 or 30 particles in superposition.
A single strand of some particles could “remember” lots of possible states. This is theoretically possible however, how to do this in a real machine we are just now doing in our own quantum computers we are building today. Of course the way we do this and the way nature may do it could be dramatically different and frankly we don’t understand how the brain or neurons might encode this.
Roger Penrose has proposed along with a doctor friend of his that memories could be stored on highly stable microtubules that we find in neurons.
A QM machine can then search all the possible states looking for the one that closest matches a search using a method of encoding the memories that is similar to quantum tunneling. In normal quantum mechanics reading out the answer would probably destroy the memory. However, we are so early in building quantum computers we are still trying to figure out tricks. The point is that it is something QM is good at. Searching is something it does in every quantum interaction. So, guessing that nature uses some aspect of QM to do searching of memories and pattern matching is no big leap. It’s certainly something to look into.
A human brain has been called a pattern matching machine. It is one of the primary functions we understand. The brain is constantly getting streams of inputs and it is matching that stream against previously observed streams looking for expected results. When the next input from the world is what the brain is expecting it is happy and continues matching. When the bit is different is where the thinking happens.
When the match occurs the brain then proposes some corresponding output that has been associated with positive results in the past. If that fails then that is where the thinking occurs. In any case pattern matching is a critical feature and something that QM happens to do well. It also is good at storing vast amounts of data in small number of particles and being able to search it quickly and efficiently.
Frankly, we have no other way of explaining how memory might work. There is the potentiation of chemicals at neuron meeting points (called synapses) that is part of the problem of memory but the actual memory is different and QM is as good a theory as any considering we don’t have any.
If we think about it, our consciousness and thinking process is also another variation of pattern matching. That will be left for the reader to see.
3. The Immune System
It is my theory that problems that involve competitive advantage and recognition are particularly well suited to QM tricks. Thus the immune system seems like a likely area. We have seen in T-lymphocytes a neuron and synapse like memory capability.
Our immune system is incredibly sophisticated and something not well explained with classical chemical processing. Our immune system has to wander through the body matching constantly against things it sees that it considers friends and things it considers foes. It does this by looking at the outer layers of cells looking for key configurations that identify what the cell or virus fragment does. The immune system has to keep a memory of a vast array of cells and virus segments it has seen and which ones to fight and which ones are friendly.
We don’t know much about how this system works but when one of these t-cells recognizes an enemy it has to produce a specific response to attack that enemy. It signals to the rest of the army that it should replicate t-cells and other armies of attack machines that have been programmed to find and destroy that invader.
Our immune system has to remember the invading signature and to manufacture enough enemies to fight it should the enemy reappear. This isn’t something that is easy to imagine how a straight chemical system does with classical chemical reactions and relatively deterministic state machine type capabilities.
I suspect we will find “brain” like features of our immune system the more we look into it. This is where the fight of life is at its most intense. The constant assault of the body by invaders and the constant need to innovate against ever varying enemies requires the best of the best smarts. It’s not something we are overtly conscious of but down at the cellular level a lot of smarts are at war everyday and it is hard to imagine that nature doesn’t use QM to find a way to fight the war smarter and more efficiently.
Of course if I believe that the Brain and senses and immune system use QM trickery it is extremely likely that our most basic of all and important system of record and primitive brain of sorts, our DNA probably also utilizes some quantum trickery.
It is not clear how it would do so. There is a lot of stuff going on here.
4.1 Genes themselves
Genes are encoding instructions to manufacture protein machines. The protein machines are the workhorses of the DNA. The machines transport chemicals, process chemicals, do recognition, lots of things. The protein machines are amazing deft and possibly smart. They seem to be able to do several things each. The construction of the protein machines is a bit of a mystery. How the various chemicals fold in constructing the machine varies its purpose dramatically. Like all molecular structures the exact way it is shaped seems to affect its operation.
If we are right then things like smell are associated with genes then the genes produce protein machines that use QM tricks but the production of the machine does not necessarily involve QM. It is likely that the folding process itself has QM elements.
4.2 Epigenetic code
A recent discovery in DNA is that 98% of our DNA is not junk (as was thought) but actually an entirely new form of information encoding representing the instructions when to encode genes and make proteins.
Since we figured out that Genes are simply the machines the body uses to do the stuff it does the question has always been to me that the encoding of when and why to activate a gene and how much to activate it and when to stop must somehow still be missing. The epigenetic code is that programming.
This programming tells how a human body is built from the beginning and then maintained over time and possibly eventually disposed of. How this coding changes or responds to the environment is unclear.
DNA is believed to be wrapped in spirals. Some of these spirals are deactivated by what appears to be what we call chromatin. Chromatin is a substance that is a form of information coding too. We don’t understand precisely but the chromatin changes its shape over time allowing portions of the DNA to be visible and then not. Chromatin is believed to be involved in regulating the construction of the body allowing the building of the body to progress in stages and triggering different genes as the chromatin changes shape. How this happens is unclear and if it is under regulation of the epigenetic code.
I feel we will find that the epigentic code has a learning capacity and memory capacity somehow utilizing QM trickery.
4.3 RNA fragments
Less well known is that throughout the cell are independent fragments of DNA that aren’t from the DNA. In fact, sometimes it appears these RNA fragments can be acquired after a creature is born and they get divided when the cell gets divided like the DNA. This actually gives the possibility for cells to acquire new features after it has divided. In a sense this violates strict evolutionary thoughts that everything is in the DNA.
We don’t know the roles of all these RNA fragments.
4.4 fungible DNA areas
There appears to be parts of the genetic code that are temporary or “testing area” where new DNA is allowed to reside. This allows DNA to be augmented after the cell divides and possibly also violates strict evolutionary concepts as this area allows for between division changes to occur to a cell. I have not read much about this and don’t know if this is still a supported theory.
Both these things above tell us that evolution as we were taught in school isn’t strictly the law of the land in the real world. Cells can acquire new fragments of DNA one way or another and they participate in the splitting of the cell. This means that evolution during a cell or creatures lifetime is possible. It may be minimal and not transferred to babies possibly but it is intriguing the body/cells have this capability and one wonders what it is useful for.
One of the most important parts of the cell is the mitochondria which provides the universal energy chemical ATP. ATP is used as energy for virtually everything the cell does. Almost every gene encoded protein uses ATP to power its functions. ATP is used to power the machines that transport chemicals in and out of the cell. Mitochondria are invaders. They invaded cells about 1 billion years ago and a happy biodependence has transpired. The cell depends on these host organisms inside all our cells.
The Mitochondria themselves have their own DNA and reproduces independently of the cell. From looking at the DNA in our mitochondria we can determine sometimes things like where you were born.
4.5 ER – endoplastic reticulum
One of the most amazing parts of cell biology which has been mysterious is the Endoplastic Reticulum (ER) which is where many of the chemicals the body and cell makes and uses are made.
What is most astounding about the ER is its incredible plasticity. In a matter of hours the ER of a cell can remake itself and produce an entirely different set of chemicals on demand. What triggers the cells sudden desire to change what chemicals it produces is a mystery. This is again one of those areas that I believe is incredibly complex and we are clueless why it happens, mostly how it happens and what triggers it to stop.
In order to do the changes required to reshape the ER seems like it would require a massive amount of energy. Sort of like a car factory deciding to make Maserati’s one day and F150s the next. The ER makes this transition in hours and apparently reusing almost everything without wasting hardly anything.
Anytime you find that nature is incredibly efficient is a sign that possibly some QM trick might be being used. How could the ER reshape itself so incredibly from one hour to the next without consuming vast amounts of energy? I hope we figure it out.
4.6 Cell communication, detection – Intra and inter
The cells themselves have to detect levels of chemicals of all types and this detection has to somehow be transmitted to the DNA where it has to decide what to do about it. Some things seem to be automatic and not require central authority. Other things seem to get sent as signals that involves a particular epigenetic response. All of this is a mystery. Anything that involves sensing usually seems to involve something to do with QM trickery.
All of the above I realize is largely hypothesis and guessing. It is hardly science. I put it in the category of “educated guess” based on mathematics to some extent. I think the way to do these things described above is very difficult to imagine as a classical system. I also postulate that it is unlikely that nature wouldn’t use QM if there is any possibility because as we are finding with Quantum computers it represents a way to make a “quantum leap” in processing capability.
The reason QM is so useful is that it allows nature to short circuit things by searching a wide range of possible paths using tools such as borrowing energy from the universe to get something done.
It also introduces a perfect random variation into everything. This doesn’t mean everything is random because nature still likes to do the most probable thing and the most probable thing is what we see all the time but with QM nature reserves the possibility to pull a trick out of its hat every now and then and try something unexpected that might produce a better result. Sometimes it might not but it gives that variation that allows nature to escape the monotony and sure fire death of finite state deterministic classical chemistry.