What is life? What separates alive and death? What is the difference between living things and inanimate? These are the questions probably many of us wonder about when we were kids. No one gave me an answer satisfied me, instead provided the concept of evolution and ideas in philosophy. This type of questions is considered as a question in philosophy that is not able to answer or prove in science.
I was told many times in my career, if I want to be a scientist, I need to work on the problems I can solve. A complex issue should be divided and further subdivided into a biteable size. Reductionism. Then, scientists solve each biteable size problem. ‘Solve’ in modern science means that you provide something repeatable and confirmable by others and propose ‘cause and consequence’ as a mechanism that allows us to make predictions. Good scientists are good at making new biteable size problems as well as biting new areas with new technology no one has ever used. The current scientific knowledge is based on many solved biteable size problems that have reconstituted to the original complex issue, as a whole. Very logical and linear progressive thoughts.
I use logic every day. As a PhD holder, I am good at noticing logical gaps. I use logic to convince others including my students. But I have a strong skepticism on its reliability. I do not have a full trust on logic. I feel I conflict myself. Every day I am thinking if it is possible to think logically about outside of logic. I am wondering if ‘solved’ in reductionism is really solving the problems in a whole?
I like a story of “Blind men and an elephant”. Nothing would be wrong what each blind man will say. Probably, each can report very details of their arm’s reach finding. When they combine their findings, they will create a gigantic monster completely different from an elephant. For them, this monster would be their elephant. I also like what Aristoteles said, “the whole is greater than the sum of its parts”. This is opposite to the blindmen’s case. But both indicate the limit of reductionism. Recently, I realized about myself that I carry a strong skepticism on reductionism and logic. With this doubt, I wonder if I can keep working as a scientist? I agree that reductionism has tremendously contributed the advance of modern science. I also believe that logic is important and essential for communication with others. Logic provides a feeling of making sense that is something we like. Probably, this making sense feeling removes uncertainty and anxiety from us. Uncertainty forces us aware and alert. Uncertainty demands more energy and occupies our cognitive resource. Reductionism and logic allow to eliminate (or reduce) uncertainty. At least making us believe that is possible. But I doubt them.
Logic strongly relies on languages. Each language creates own logic. Logic captures time. Without logic, everything will be a moment. Simply just sensation and emotion, ‘pain and pleasure’. ‘Pain and pleasure’ (e.g. fears against predators and pleasures towards foods) should be remembered for better survival. I think this could be the beginning of memory (can also be a simple reflection). Memory permits building logic. Capturing time by logic creates anxiety and anticipation that stimulate emotion. Gaining languages in humans permitted to establish this circle. I believe that this circle is the human consciousness. Without languages, animals can still communicate that permits to build a pack that shares ‘alert’. However, strong logic is difficult to emerge. Without strong logic, time cannot be captured. Connections between two packs or more to build a larger group or society have never evolved because no strong logic has emerged due to no language, except humans.
When a multicellular organism dies, not all cells are dead. When a cell dies, not all components like proteins and etc. are dysfunctional. Their activities are alive. When a protein denatures, all amino acids composing the protein are still there. Nothing is disappeared. But we consider as not alive anymore. Is it possible to make it back as ‘alive’? What is exactly ‘dead’ meaning? We also use ‘alive or dead’ on inanimate, like my computer is ‘dead’. Interestingly, we do not use them on primitive tools like a hammer. No one says my hammer is ‘dead’ but probably ‘broken’. When something has a function through networks within it, we often call ‘alive or dead’. Dysfunction means ‘dead’. Dysfunction without apparent changes outside is ‘dead’. This suggests ‘alive or dead’ is not based on materials but networks in a system. Inanimate with functions can die, but they do not replicate. That is why they are inanimate.
The 2nd law of thermodynamics suggests that the state of entropy should always increase over time. Biology appears against this law. However, Stu Kauffman suggested in his recent book entitled “The world beyond physics” based on the work by Montévil and Mossio that life is ‘a closure of constraints’. By constraining the direction of the increase of entropy by catalysts, this could be enzymes in a cell, the change of entropy becomes a controlled reaction. In biology, we call this as a function. When a network of distinct functions builds a circle (i.e. a closure of constraints), something ‘alive’ emerges. This network with replication is live organisms. A loop of multiple self-assemble and self-organized reactions that each constrains the direction of the increase of entropy. As a whole, it forms a closure of constraints.
I think that the circuits of connected materials (connected in various means) with one replicating machinery is Life. Various types of materials with enough density and random connections. These connections, by chance, creates a circuit. In the field of studying information networks, this is called from Chaos to Small world network. One circuit would make connections with others by chance. The circuits gradually become larger and complex. One big circuit connect with others without merging but forming a loop of multiple circuits. One loop connects other loops and they eventually create a circle of many loops. From DNA replication machinery, metabolite networks, cell-cell interaction to organismal homeostasis. The nested structure of networks. I think that this is Life. The nested structure of networks is Life itself as well as human languages and societies. When the higher-level network is dysfunctional, despite the lower-level networks are fully functional, we call it as ‘death’.
DNA is a very interesting molecule. The complementarity of its double helix makes a perfect material to replicate. More precisely, the property of complementarity as the material permits replication. The most important point is that the DNA double strand helix can be separable! Each strand becomes a template for a new complement strand. The one original double strand can make two identical double strands. Amazingly, this process makes a logic with time. DNA synthesis, completion and then separation, back again to the synthesis. No step can be skipped. Not be able to change the order. A logical progression along time. This is not a simple diffusion equilibrium. Equilibrium creates time but that has an infinite end. From zero to infinity. Probably, infinity is not the time we, humans, can perceive. The DNA replication process creates a repetitive period, one generation. If this process is perfectly replicating the original, nothing is changed. If too many errors, the whole system collapses within several generations. At the right frequency of errors, the system will keep evolving with selection and drift. The replicable system with errors is an evolvable system.
Another interesting property of DNA is that it can form a nested structure. The double helix is twisted. The twisted double strand makes the twisted chromatin structure. Then, the twisted chromatin structure makes a twisted supercoil structure. What makes me interesting is that this nested structure can be formed step by step with simple twisting toward one direction. Imagine keeping twisting a rubber band. At beginning, the change of the rubber band is linear, simply adding more twists. Then, at one point it starts making a supercoil structure. The 3D nested structure of DNA can make order and time. The inside structure of the nested DNA is only accessible after loosening the outer structure.
I used three different words, circuit, loop and circle to explain the layers of a nested structure. Importantly, we cannot make any prediction when and how a new circuit, loop or circle is established and what kind of circuits, loops or circles will be. We only recognize it after it forms. Something unpredictively connecting them suddenly emerges from a small modification of things already exist. Kauffman described this as jerry rigging explained a screwdriver as an example. If it were not a screwdriver, what else we can use it for. It could be a door stopper or heavy chopsticks. Once you name it, a screwdriver suddenly gains new functions. Something did not exist suddenly emerges, from zero to one. If it is incorporated into something else, like a screwdriver attaches to a shoe sole, it can become a blade of skate shoes. Something new not previous existing is born from other pre-existing. Originally a screwdriver but now it is working as a blade of skate shoes. Eventually, a screwdriver may disappear, but a blade could remain. Connections from a dot to a dot eventually makes a circuit of dots. Connections from a circuit to a circuit eventually makes a loop of circuits. Connections from a loop to a loop eventually makes a circle of loops. This forms a nested structure. When a new layer is formed at a higher level, we find strong emergence. This is not reducible. We can probably understand how this happened retrospectively by reductionism. However, we cannot anticipate if this would happen beforehand.
Once something dies, is it possible to make it back alive? It is possible if that is a car or computer by replacing a broken part or reconnecting a network. How about an organism? Recent studies of synthetic embryos from three kinds of stem cells make me think what is ‘alive’ in multicellular organisms. When the highest-level network is dysfunctional, we consider it as ‘dead’ despite all other lower-level networks are intact. In case of synthetic embryos, with correct combinations of lower-level networks we can reactivate the higher-level network. ‘Alive’ from ‘dead’. We already knew we can stop the networks by freezing preimplantation embryos and reactivate them by thawing. Stem cells are separated networks individually maintained. Through interactions with other stem cells, they can rebuild the one-layer higher network to emerge. Like ‘a name to exist’, each part is ‘a connection to exist’. As a whole, something new emerges at the top of a nested structure. I think that is life, multicellular organisms and human consciousness.
REFERENCE:
Stuart Kauffman
A World Beyond Physics: The Emergence and Evolution of Life (2019)
Oxford University Press
Montevil and Mossio
Journal of Theoretical Biology http://dx.doi.org/10.1016/j.jtbi.2015.02.029 (2015)
Tarazi, S. et al. Cell https://doi.org/10.1016/j.cell.2022.07.028 (2022)
Amadei, G. et al. Nature https://doi.org/10.1038/s41586-022-05246-3 (2022)
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