Life asymmetry
Hello! I do not know about you, but I always wanted not only to know something, but also to understand what I know. The knowledge presented by the education system, in the form of an incoherent set of facts about the world around us, always demanded great efforts to keep them in mind, but it was enough to understand a logical principle or pattern that corresponds to the appearance of these facts and could get rid of them with a clear conscience. only the rule itself is in the head and, if necessary, derive the necessary fact from this principle.
And the sciences most written facts without logical explanations for me have always been those related to organic life and its structure. To see this, open a textbook on biology, for example, in the section on DNA, there will be a detailed description of the structure and functions of DNA, but not words about why this all should work this way and no other way. Perhaps that is why in my knowledge in these subjects there has always been a big failure. This article is about trying to fill in the gaps and bring the facts about organic life into a coherent system that would not only answer the question “how?” But could also give a general direction in which to move to answer the question “why?”. So let's go!
“Symmetry elements may be present in various phenomena, but they are not necessary, for the existence of phenomena only the absence of certain symmetry elements is necessary.” Pierre Curie
“Knowing few principles frees many facts from knowledge.” René Descartes
Content:
What is the most symmetrical you can imagine? Many in this matter imagine a ball, and indeed every point on the surface of the ball is at an equal distance from the center, but if we take another point in depth, then the symmetry is already broken. Surely, the state of symmetry can be considered as an approximate ideal, infinite space consisting of an absolute physical vacuum containing neither fields nor particles, without a center of boundaries, each point of such space will be equivalent to the other, to describe such a space you will need a minimum of information, since essentially nothing to describe.
Fortunately, the state of absolute symmetry is not available in our physical world. The maximum possible in this regard, the state of symmetry is interstellar space, there is practically no matter in it and apparently it is infinite, but unlike the true vacuum, it is permeated with fields that fluctuate constantly and randomly - fluctuate at a speed of about a million billion billions (10 to 24 degrees) once a second on scales comparable to millionths of billions (10 to minus 15 degrees) of a millimeter. We can perceive the largest and most stable oscillations as separate particles, this can be compared with how a tsunami wave can be viewed as a separate object, but this is nothing more than a pumped variation of ripples on the water surface. Thanks to constant fluctuations of the fields, we have such fun and dozens of clever brains that have broken things like the principle of uncertainty and dark energy. More details can be read ina review article on Habré , as well as see a vividly describing video:
https://www.youtube.com/watch?v=Qhowc1PSO4EV
Visualization of fluctuations of the gluon field.
So, we see that our real state of maximum symmetry is quite different from the ideal, and, in contrast, has a maximum uncertainty, i.e. requires maximum information for description or has maximum entropy ( https://ru.wikipedia.org/wiki/Informational entropy ) to see this, let's consider one simple example:
Imagine a plate filled to the brim with water, so that the surface tension forms a convex, symmetrical with respect to the edges of the vessel surface, gently place on this surface, for example, the ball from ping-pong, exactly to the center, to the highest point. There are a huge number of options, in which direction the ball moves along the surface of the water, its direction will depend on the outcome of billions of random collisions with water molecules as a result of thermal movement and to calculate this result you will need to know the speed and direction of all these molecules, you can surely say that this is a very large amount of information and unpredictability (entropy) of this system is also very large (Fig. 1). And what if to break the symmetry of the system? For example, lifting one edge of the plate relative to the other, forces of nature will immediately begin their work to restore this terrible injustice, water will flow out of the vessel leveling out, the outflowing water will carry the ball and its movement can already be described simply recognizing the speed and direction of water flow (Fig. 2) But the flow will not create itself To create a flow, you will have to break the symmetry ie bring energy into the system from the outside.
From here you can derive the following:
“We emphasize once again: the concept of maximum entropy implies the most chaotic, and therefore the most symmetrical state of the system. All spontaneous processes in nature go in the direction of increasing entropy. ” ( Http://cyclowiki.org/wiki/Paradoks_intermixing )
And indeed we can say for sure that all the processes we observe are echoes of a once well broken symmetry, which fortunately is not yet the end has been restored, but you can’t argue against entropy, and sooner or later all systems will come to balance and the pendulums of all hours will stop, or are there any exceptions?
If we consider living organisms from the point of view of entropy, we can see that, unlike all surrounding non-living systems, which at any opportunity roll into chaos, living systems produce more and more complex and ordered structures over time, from the simplest self-replicating molecules to the human brain, demonstrating the reverse movement - reducing the entropy.
To better understand this statement, let us try to very roughly compare the entropy of a biological organism, for example, a person weighing 70 kg, with the entropy of a system consisting of the same number of atoms.
Entropy system consisting of 70 kg. unordered atoms the value is very large and proportional to their number, i.e. to set this system we need to describe a state of about 6.7 * 10 to 27 degrees (6.7 billion billion billion) atoms. What about a living organism? All information necessary for the assembly of the “Man” system is stored in its DNA, a long sequence of several types of identical molecules, i.e. in the case of a living system, it is enough for us to know only the configuration of the DNA chain which consists of only 6 billion molecules each of which consists of about 30 atoms, which is 18 * 10 to the 10th degree, i.e. total 180 billion atoms. Then, by a simple relationship, one can estimate the difference in the order of the entropies of these systems:
6.7 * 10 ^ 27 ÷ 18 * 10 ^ 10 ≈ 3.7 * 10 ^ 16
In total, according to the roughest estimates, the entropy of the living system “Man” with the same mass of matter is less than that of a non-living cluster of atoms 16 orders of magnitude ie tens of millions of billions of times! (You can read more about the entropy of the systems here: studfiles.net/preview/953337/page : 31 /, sernam.ru/book/tp.php?id=104 ). It seems that living systems have lost a good nose entropy. But thanks to what quality they manage such a unique trick?
Since we decided to talk about life, we should turn to the Theory of Evolution as well. in this matter it is an absolute authority. If we reject everything that is superfluous, then basically, this theory states that the development of the whole diversity of living nature we observe is due to the constant transmission and modification of hereditary information between generations of organisms. Successful modifications contribute to more efficient reproduction (self-copying) of their carrier, creating a positive feedback and unsuccessful feedback, on the contrary. Thus, accumulating successful modifications, organisms acquire more and more complex and ordered forms, breaking the primary symmetry more and more.
Proceeding from this key difference of living systems from non-living, in the most general consideration it is possible to imagine all living organisms as simply self-replicating and self-changing DNA programs with the type code:
Instruction1: <create: [Random instructions]>
Instruction2: < execute: [Original instructions] + [Random instructions]>
Instruction3: <write down: [Original instructions] = ([Initial instructions] + [Random instructions])>
Instruction4: <copy: [All instructions above] + [Instruction4]>
As a result of executing such a program, we will get its mutated copy, which will be different from the original by adding random instructions to the original instructions and which then itself will also create its modified copy, etc. If the mutations are unsuccessful and an error occurs during their execution, the program will not reach the copying stage, so they will not be passed on to the next generation.
It is enough to put such a program into an environment suitable for functioning, and to provide oneself, and in just a few billion years, you will receive a whole variety of species evolution, without additional development costs.
Original
The concept of self-replicating programs was proposed as far back as 1951. - Von Neumann is a brilliant mathematician and physicist, a man whose contribution to the science of the twentieth century, it is difficult to overestimate, the father of game theory, the mathematical language of quantum mechanics, and in addition according to the architecture named after him, most computers are now produced. (more about the theory of self-replication in the article from PostScience, as well as in the original article by Von Neumann ).
We have already seen that living systems are continuously becoming more complex and self-organizing due to their ability to accumulate, change and copy their own genetic information. To better understand how these functions work and put them into a logical system, let's as a mental experiment, try to simulate the birth of life and write a program replicator from scratch, imagining that we have at hand only what nature had: the laws of physics, a bunch of different atoms and a few billion years of free time.
Okay, where do we start, after we are well stuck on social networks and watch all the TV shows ever filmed? First of all, in order to write something, we need letters, let's not produce unnecessary entities and take for starters a minimally necessary alphabet, sufficient for encoding any information - these are just two characters: 0 and 1. Let's say that if you combine any or two atoms, then the resulting molecule is referred to as "zero", and if you connect any other two atoms - you get another molecule, which will be called - "unit" and to begin present them the following scheme:
In order to write a text using these letters could be a program widely regarded as one the following minimally necessary requirements:
To fulfill the first requirement, it is enough to match our molecules so that they have two compounds left and right, then they can interlock with each other, forming a continuous chain. And in order to always observe one direction of the chain, it will be enough that the hooks on the letters can connect only the left to the right, this principle is easy to imagine using the example of a chain of people who hold hands, each person holds the neighbor’s right hand with his left hand, thus everyone faces in one direction. United by this principle, each of the molecules of the letters will also be able to stand in a chain only in one direction. Schematically imagine it this way:
Great, now we have our minimum alphabet of 2 letter-molecules that can be connected to stable chains with direction. Let's start writing code.
Because we write a self-replicator, first of all we need to think about a simple and reliable mechanism for self-copying our program. How should it work? Here again, we cannot do without two minimum requirements:
Because we cannot make spaces, our code should consist entirely of one line, but nobody limited us in the number of characters, so this should not be a problem. Further assume that it is possible to choose such a sequence of element molecules so that it performs the following functions only due to interactions between atoms: on the one hand, it would interact in order with a code element (zero or one) and then, after the interaction, would collect from other atoms the same element (copied element), after which I would repeat this action with the next element of the chain, also connecting them together. let's call this sequence the copy mechanism and add it to the code, which can be schematically represented as follows:
0> 1> 0 ... (any number of characters)> (code of the copy mechanism) ... 0> 1>
Excellent, now let's model how our mechanism will work. Being at one end of the chain, he begins to copy the program from the opposite, so our line of code collapses like a snake in the game of the same name, and the mechanism moves forward, gets input and copies the elements of the sequence one by one, completes the copy of the section "... (any number of characters) > "And then stumbles upon the problem of recursion, because in order to read information from its own elements, the mechanism will need to have a copy of itself, and to create a copy of itself, you need to read information from own elements.
Let's somehow get out and for this we consider another way to copy something, not directly, recreating each element, but according to the principle of impression. For example, they make molds for casting bronze statues: they create a prototype, then they make an imprint of the prototype in clay, by filling it with molten metal, you can get a copy of the prototype. It sounds good, we will try to apply this principle in our molecular code. To implement such a copying scheme, we will have to go back to the very beginning and make small changes to our alphabet. Namely: add two more symbols to our zero and one: “2” and “3” and make each symbol an imprint for its pair, zero for two, one for three, and vice versa, leave everything else unchanged : all letters will have the same side hooks and one direction, and in order that the impression and the original always exactly match each other, we will attach a pair of impressions to each letter using new hooks that work on the principle of a puzzle, so that they can only engage each other with their pair 0 with 2, and 1 From 3. New hooks will also be placed in all the letters the same - from the bottom edge. And so we have an alphabet of 4 symbols: 0,1,2,3 each of which has three hooks-connections: on the left, on the right and below, the left hooks will connect only to the right of any symbols, and the lower connections can connect only the symbol with his partner-cast: zero with two and one with three. Schematically, a chain of code from such an alphabet can be represented as follows: who would work on the principle of the puzzle, so that they can only stick together with their pair 0 s 2, and 1 s 3. New hooks will also be placed in all the letters just the same - from the bottom edge. And so we have an alphabet of 4 symbols: 0,1,2,3 each of which has three hooks-connections: on the left, on the right and below, the left hooks will connect only to the right of any symbols, and the lower connections can connect only the symbol with his partner-cast: zero with two and one with three. Schematically, a chain of code from such an alphabet can be represented as follows: who would work on the principle of the puzzle, so that they can only stick together with their pair 0 s 2, and 1 s 3. New hooks will also be placed in all the letters just the same - from the bottom edge. And so we have an alphabet of 4 symbols: 0,1,2,3 each of which has three hooks-connections: on the left, on the right and below, the left hooks will connect only to the right of any symbols, and the lower connections can connect only the symbol with his partner-cast: zero with two and one with three. Schematically, a chain of code from such an alphabet can be represented as follows: to the right and to the bottom, the left hooks will connect only to the right of any symbols, and the lower connections can only connect the symbol with their partner-impression: zero with two and one with three. Schematically, a chain of code from such an alphabet can be represented as follows: to the right and to the bottom, the left hooks will connect only to the right of any symbols, and the lower connections can only connect the symbol with their partner-impression: zero with two and one with three. Schematically, a chain of code from such an alphabet can be represented as follows:
Now we will re-code our program into a 4-character alphabet and re-start writing the code, recording one character from left to right, while at the same time forming the bottom line of the impression. We will get a rather interesting result, a couple of lines of code-cast are not identical, but interconnected. Having any of them available, it is possible to unambiguously restore the second one, while using only one simple rule: attaching a pair of 0 -2 to each letter and 1 -3 to each letter. We say that a separate mechanism will be responsible for the attachment function of the corresponding symbol, then we replace the copy mechanism with it and for brevity we call it the “casting mechanism”, as a result we get:
0> 1> 2> 3 ... (casting mechanism) ………… .. > 0> 1> 2> 3
1 <0 <3 <2 ... (cast of casting mechanism) .... <1 <0 <3 <2
An attentive reader will probably have a question: why is the direction of the bottom line opposite? This is explained by the fact that all letters have an inter-lower hook only from the bottom, and one direction, respectively, in order to connect with the upper symbols of the lower one, turn 180 degrees - “stand on your head”, while their direction changes.
Let's see if our new code implementation can self-copy. First, suppose that the casting mechanism, which is located in the “code” line, follows the “cast” line by sequentially putting matches to each letter, resulting in another “code” line, and accordingly, because of which everything was started, a copy of itself. Then the casting mechanism is traversed by a new line with the code, putting a correspondence to each character, getting a line-cast, and so the self-copying recursion is defeated and as a result we now have two complete sets from the same source.
And it really is very similar to how the very first mechanism of DNA replication could appear. Although in the process of evolution, it was overgrown with many auxiliary mechanisms and improvements, for example, in a cell, you no longer need to worry about the fact that the whole program was in one piece of code, and you can be allowed to make your own “software environment” - to have a separate program for copying, separate for finding and correcting errors, but the principles themselves remained unchanged.
I propose to summarize our mental experiment before moving on. As we could see, within the framework of the theory of self-replicators, many of the principles of Genetics and Cytology fit quite logically, namely:
In the video below, the excellent DNA replication visualization is already closer to real scales and speeds and everything that we see here, no matter how hard it looks, just logically fits into our simple system, for example, the formation of a leading thread (Leading strand) Lagging strand) naturally follows from the fact that the casting mechanism (helicase) can substitute correspondences to each nucleotide in only one direction as well. our threads due to the complementary structure of nucleotides are obtained in different directions (anti-parallel), then one of them, helicase can put the correspondences in the direction of travel, and the second passes a little forward, and then returns along it in the direction of the code.
And when it would seem, everything develops into a rather logical picture, nature throws up another surprise. If we really repeated in the laboratory all the above listed operations for creating a molecular replicator program, starting with the synthesis of our nucleotide letters, having started the program, we would find that chains of our nucleotides are copied with large errors or not copied at all; in the end, they found out that the reason for the errors was that when synthesizing letters-nucleotides not only a certain number of letters we needed were formed, but exactly the same number of their mirror twins, i.e. having the same composition and chemical formula, but all the links within which are rearranged from left to right, for example, if the original has a C-O-H bond, then the mirror twin will have H-O-C.
In a special section of chemistry that studies the properties of the symmetries of various compounds. Stereochemistry, such a uniform mixture of left and right molecules is called racemate, and the left and right molecules themselves are isomers, and very often in the synthesis of organic compounds, for example, drugs it turns out that the properties of right and left isomers differ fundamentally, probably the most famous and tragic incident associated with this is the scandal that arose after the application in the 60s of the last century, a drug called Taliomide, in the process of synthesis of which On the one hand, the second isomer was not removed, which had an unexpected effect when taken by pregnant women, with the result that about 12,000 newborns were born with physical deformities. ( en.wikipedia.org/wiki/Thalidomide )
Then it turns out that the first self-replicating molecules should have been formed from a mixture of 50% of the right and 50% of the left nucleotides. Of course, this would not create particular problems if the nucleotides were symmetrical, such as the H-O-H water molecule, but as we showed above, molecules are necessary for recording and transmitting information, the asymmetry of which determines the presence of direction and complementary compounds, then it turns out that the mirror image of the nucleotide will have the opposite direction, and if at some part of the DNA replication, the mirror nucleotide is inserted, then there will be a gap of one character between it and the correct nucleotide not one of the elements of our puzzle. So, to the joy of various kinds of creationists, the formation in natural conditions of 50/50 left and right molecules,
The question of exactly which conditions made the separation of isomers possible in the primary broth and created the possibility of the origin of life, is still the subject of many studies, and despite the fact that it is already more than 100 years old, a definite answer has not yet been received. (about success in this direction can be read here: elementy.ru/novosti_nauki/432316 ).
Violation of symmetries lies at the very core of living systems, so it would not be superfluous to consider how the asymmetry properties of chemical compounds are used in living systems, for example, to separate their two main systems: informational and functional, or using computer-hardware and software terms.
Indeed, if we consider any organisms on the planet, we will see that all DNA chains - assembly instructions, consist only of the right nucleotide isomers, and at the same time, all proteins - the building blocks of the body, collected according to these instructions, consist only of the left amino acid isomers. This separation ensures strict adherence to another basic principle of genetics:
"The direction of information transfer within the body always goes only in one direction from DNA to proteins."
If you think about it, this principle is really necessary to ensure the stability of any organism, because in the process of its functioning proteins are constantly exposed to aggressive environmental influences, are destroyed and replaced by new ones, and if the whole organism consisted of only one self-copying code, then its permanent damage would have caused , we would not be able to recognize the original protein after several steps of copying, i.e. such an organism would begin to mutate very quickly and uncontrollably. To avoid such situations, a “source code” is needed - DNA, which is stored in the cell itself, protected from harmful effects, in its core, and according to which new proteins are stamped as necessary, and in order to clearly distinguish instructions from building blocks, it is very convenient to have them in the form of opposite isomers.
A description of another application of asymmetry by living organisms, no longer associated with computer science, but with the topology of molecular mechanisms, came into biochemistry from knot theory, a science at the intersection of mathematical analysis and geometry, and is called supercoiling. To understand how this works, you only need two hands and a piece of rope. Take your rope by the ends with both hands, stretch it and begin to break its symmetry. Holding both ends twist one end to the right, after some time the rope will coil into the right helix, thus breaking the symmetry of the left and right you stored energy in the system, now do the next trick - connect without releasing both ends of the rope and watch carefully how the universe itself will restore the broken symmetry and the two right spirals will wrap around each other in the left direction.
This effect underlies the supercoiling process , which is very important for DNA functions , i.e. dense packing in a form, convenient for storage and copying. In this process, the DNA chain initially having a total length of about 2 meters, is twisted many times, changing the direction of spiralization and becoming tens of thousands of times more compact, to then fit in the form of chromosomes in the cell nucleus, so small (6 μm) that on a match head easily accommodate a thousand of these cores.
Living systems stand out vividly against the background of non-living nature in that for more than 3.7 billion years they have been creating more and more complex structures in the course of their evolution, demonstrating a decrease in their total entropy. The uniqueness of living systems is a special relationship between matter and the information that constitutes them, as well as the ability to transmit and modify this information, which also makes it possible to apply the concepts of informatics when describing many processes in living organisms. The mechanism of restoring broken symmetry is the fundamental engine of any processes and life is no exception, but it is life that has learned not only to use this “pendulum of the universe clock” for its own purposes, but also to rock it, with time more and more. Therefore, the study of living systems can give clues in which direction to move,
And the sciences most written facts without logical explanations for me have always been those related to organic life and its structure. To see this, open a textbook on biology, for example, in the section on DNA, there will be a detailed description of the structure and functions of DNA, but not words about why this all should work this way and no other way. Perhaps that is why in my knowledge in these subjects there has always been a big failure. This article is about trying to fill in the gaps and bring the facts about organic life into a coherent system that would not only answer the question “how?” But could also give a general direction in which to move to answer the question “why?”. So let's go!
“Symmetry elements may be present in various phenomena, but they are not necessary, for the existence of phenomena only the absence of certain symmetry elements is necessary.” Pierre Curie
“Knowing few principles frees many facts from knowledge.” René Descartes
Content:
- "Symmetry of chaos" - consider the relationship of symmetry, energy and information;
- “Living systems - violators of disorder” - we investigate the differences between living nature and inanimate in terms of informational entropy;
- "Self-replicator-reasonable" - consider the biological evolution in the framework of the theory of self-replication;
- “Life ++” - we will show how the logical principles necessary for the functioning of the self-applicator are consistent with the basic structure of nucleotides and DNA;
- "Spoon of Chiral Tar" - let's get acquainted with the phenomenon of the chiral purity of organic molecules;
- "Asymmetric source of life" consider how the symmetry breaking of organic molecules is used by living systems;
- Conclusion
Symmetry of chaos
What is the most symmetrical you can imagine? Many in this matter imagine a ball, and indeed every point on the surface of the ball is at an equal distance from the center, but if we take another point in depth, then the symmetry is already broken. Surely, the state of symmetry can be considered as an approximate ideal, infinite space consisting of an absolute physical vacuum containing neither fields nor particles, without a center of boundaries, each point of such space will be equivalent to the other, to describe such a space you will need a minimum of information, since essentially nothing to describe.
Fortunately, the state of absolute symmetry is not available in our physical world. The maximum possible in this regard, the state of symmetry is interstellar space, there is practically no matter in it and apparently it is infinite, but unlike the true vacuum, it is permeated with fields that fluctuate constantly and randomly - fluctuate at a speed of about a million billion billions (10 to 24 degrees) once a second on scales comparable to millionths of billions (10 to minus 15 degrees) of a millimeter. We can perceive the largest and most stable oscillations as separate particles, this can be compared with how a tsunami wave can be viewed as a separate object, but this is nothing more than a pumped variation of ripples on the water surface. Thanks to constant fluctuations of the fields, we have such fun and dozens of clever brains that have broken things like the principle of uncertainty and dark energy. More details can be read ina review article on Habré , as well as see a vividly describing video:
Visualization of fluctuations of the gluon field.
So, we see that our real state of maximum symmetry is quite different from the ideal, and, in contrast, has a maximum uncertainty, i.e. requires maximum information for description or has maximum entropy ( https://ru.wikipedia.org/wiki/Informational entropy ) to see this, let's consider one simple example:
Imagine a plate filled to the brim with water, so that the surface tension forms a convex, symmetrical with respect to the edges of the vessel surface, gently place on this surface, for example, the ball from ping-pong, exactly to the center, to the highest point. There are a huge number of options, in which direction the ball moves along the surface of the water, its direction will depend on the outcome of billions of random collisions with water molecules as a result of thermal movement and to calculate this result you will need to know the speed and direction of all these molecules, you can surely say that this is a very large amount of information and unpredictability (entropy) of this system is also very large (Fig. 1). And what if to break the symmetry of the system? For example, lifting one edge of the plate relative to the other, forces of nature will immediately begin their work to restore this terrible injustice, water will flow out of the vessel leveling out, the outflowing water will carry the ball and its movement can already be described simply recognizing the speed and direction of water flow (Fig. 2) But the flow will not create itself To create a flow, you will have to break the symmetry ie bring energy into the system from the outside.
From here you can derive the following:
- a system with more symmetry has more entropy — uncertainty or a measure of the amount of information required to describe it, and at the same time less energy;
- symmetry breaking reduces entropy and starts the process;
- nature loves symmetry, all systems strive for a state of equilibrium and minimal energy;
- Any processes can be considered as an attempt of the system to return to the state of symmetry or minimum energy.
“We emphasize once again: the concept of maximum entropy implies the most chaotic, and therefore the most symmetrical state of the system. All spontaneous processes in nature go in the direction of increasing entropy. ” ( Http://cyclowiki.org/wiki/Paradoks_intermixing )
And indeed we can say for sure that all the processes we observe are echoes of a once well broken symmetry, which fortunately is not yet the end has been restored, but you can’t argue against entropy, and sooner or later all systems will come to balance and the pendulums of all hours will stop, or are there any exceptions?
Live mess-breaking systems
If we consider living organisms from the point of view of entropy, we can see that, unlike all surrounding non-living systems, which at any opportunity roll into chaos, living systems produce more and more complex and ordered structures over time, from the simplest self-replicating molecules to the human brain, demonstrating the reverse movement - reducing the entropy.
To better understand this statement, let us try to very roughly compare the entropy of a biological organism, for example, a person weighing 70 kg, with the entropy of a system consisting of the same number of atoms.
Entropy system consisting of 70 kg. unordered atoms the value is very large and proportional to their number, i.e. to set this system we need to describe a state of about 6.7 * 10 to 27 degrees (6.7 billion billion billion) atoms. What about a living organism? All information necessary for the assembly of the “Man” system is stored in its DNA, a long sequence of several types of identical molecules, i.e. in the case of a living system, it is enough for us to know only the configuration of the DNA chain which consists of only 6 billion molecules each of which consists of about 30 atoms, which is 18 * 10 to the 10th degree, i.e. total 180 billion atoms. Then, by a simple relationship, one can estimate the difference in the order of the entropies of these systems:
6.7 * 10 ^ 27 ÷ 18 * 10 ^ 10 ≈ 3.7 * 10 ^ 16
In total, according to the roughest estimates, the entropy of the living system “Man” with the same mass of matter is less than that of a non-living cluster of atoms 16 orders of magnitude ie tens of millions of billions of times! (You can read more about the entropy of the systems here: studfiles.net/preview/953337/page : 31 /, sernam.ru/book/tp.php?id=104 ). It seems that living systems have lost a good nose entropy. But thanks to what quality they manage such a unique trick?
Self-locator-reasonable
Since we decided to talk about life, we should turn to the Theory of Evolution as well. in this matter it is an absolute authority. If we reject everything that is superfluous, then basically, this theory states that the development of the whole diversity of living nature we observe is due to the constant transmission and modification of hereditary information between generations of organisms. Successful modifications contribute to more efficient reproduction (self-copying) of their carrier, creating a positive feedback and unsuccessful feedback, on the contrary. Thus, accumulating successful modifications, organisms acquire more and more complex and ordered forms, breaking the primary symmetry more and more.
Proceeding from this key difference of living systems from non-living, in the most general consideration it is possible to imagine all living organisms as simply self-replicating and self-changing DNA programs with the type code:
Instruction1: <create: [Random instructions]>
Instruction2: < execute: [Original instructions] + [Random instructions]>
Instruction3: <write down: [Original instructions] = ([Initial instructions] + [Random instructions])>
Instruction4: <copy: [All instructions above] + [Instruction4]>
As a result of executing such a program, we will get its mutated copy, which will be different from the original by adding random instructions to the original instructions and which then itself will also create its modified copy, etc. If the mutations are unsuccessful and an error occurs during their execution, the program will not reach the copying stage, so they will not be passed on to the next generation.
It is enough to put such a program into an environment suitable for functioning, and to provide oneself, and in just a few billion years, you will receive a whole variety of species evolution, without additional development costs.
Original
The concept of self-replicating programs was proposed as far back as 1951. - Von Neumann is a brilliant mathematician and physicist, a man whose contribution to the science of the twentieth century, it is difficult to overestimate, the father of game theory, the mathematical language of quantum mechanics, and in addition according to the architecture named after him, most computers are now produced. (more about the theory of self-replication in the article from PostScience, as well as in the original article by Von Neumann ).
++ life
We have already seen that living systems are continuously becoming more complex and self-organizing due to their ability to accumulate, change and copy their own genetic information. To better understand how these functions work and put them into a logical system, let's as a mental experiment, try to simulate the birth of life and write a program replicator from scratch, imagining that we have at hand only what nature had: the laws of physics, a bunch of different atoms and a few billion years of free time.
Okay, where do we start, after we are well stuck on social networks and watch all the TV shows ever filmed? First of all, in order to write something, we need letters, let's not produce unnecessary entities and take for starters a minimally necessary alphabet, sufficient for encoding any information - these are just two characters: 0 and 1. Let's say that if you combine any or two atoms, then the resulting molecule is referred to as "zero", and if you connect any other two atoms - you get another molecule, which will be called - "unit" and to begin present them the following scheme:
In order to write a text using these letters could be a program widely regarded as one the following minimally necessary requirements:
- Integrity. For this, it is important that our molecular zero and unit can be firmly interconnected, forming one continuous line, because under the conditions of molecular writing we cannot afford gaps, because around the other molecules and atoms and our molecular the code with spaces immediately breaks into components from collisions with them.
- Sequence. Any program, by definition, should have a sequence of command execution, so, in our example of the self-repeater code described above, the sequence was followed because we read the text in one direction only: from left to right, from top to bottom. This means that the second prerequisite is to unequivocally set the direction for our molecular text.
To fulfill the first requirement, it is enough to match our molecules so that they have two compounds left and right, then they can interlock with each other, forming a continuous chain. And in order to always observe one direction of the chain, it will be enough that the hooks on the letters can connect only the left to the right, this principle is easy to imagine using the example of a chain of people who hold hands, each person holds the neighbor’s right hand with his left hand, thus everyone faces in one direction. United by this principle, each of the molecules of the letters will also be able to stand in a chain only in one direction. Schematically imagine it this way:
Great, now we have our minimum alphabet of 2 letter-molecules that can be connected to stable chains with direction. Let's start writing code.
Because we write a self-replicator, first of all we need to think about a simple and reliable mechanism for self-copying our program. How should it work? Here again, we cannot do without two minimum requirements:
- The mechanism should be contained in the program code.
- The mechanism should, as a result of its work, create a copy of the program code.
Because we cannot make spaces, our code should consist entirely of one line, but nobody limited us in the number of characters, so this should not be a problem. Further assume that it is possible to choose such a sequence of element molecules so that it performs the following functions only due to interactions between atoms: on the one hand, it would interact in order with a code element (zero or one) and then, after the interaction, would collect from other atoms the same element (copied element), after which I would repeat this action with the next element of the chain, also connecting them together. let's call this sequence the copy mechanism and add it to the code, which can be schematically represented as follows:
0> 1> 0 ... (any number of characters)> (code of the copy mechanism) ... 0> 1>
Excellent, now let's model how our mechanism will work. Being at one end of the chain, he begins to copy the program from the opposite, so our line of code collapses like a snake in the game of the same name, and the mechanism moves forward, gets input and copies the elements of the sequence one by one, completes the copy of the section "... (any number of characters) > "And then stumbles upon the problem of recursion, because in order to read information from its own elements, the mechanism will need to have a copy of itself, and to create a copy of itself, you need to read information from own elements.
Let's somehow get out and for this we consider another way to copy something, not directly, recreating each element, but according to the principle of impression. For example, they make molds for casting bronze statues: they create a prototype, then they make an imprint of the prototype in clay, by filling it with molten metal, you can get a copy of the prototype. It sounds good, we will try to apply this principle in our molecular code. To implement such a copying scheme, we will have to go back to the very beginning and make small changes to our alphabet. Namely: add two more symbols to our zero and one: “2” and “3” and make each symbol an imprint for its pair, zero for two, one for three, and vice versa, leave everything else unchanged : all letters will have the same side hooks and one direction, and in order that the impression and the original always exactly match each other, we will attach a pair of impressions to each letter using new hooks that work on the principle of a puzzle, so that they can only engage each other with their pair 0 with 2, and 1 From 3. New hooks will also be placed in all the letters the same - from the bottom edge. And so we have an alphabet of 4 symbols: 0,1,2,3 each of which has three hooks-connections: on the left, on the right and below, the left hooks will connect only to the right of any symbols, and the lower connections can connect only the symbol with his partner-cast: zero with two and one with three. Schematically, a chain of code from such an alphabet can be represented as follows: who would work on the principle of the puzzle, so that they can only stick together with their pair 0 s 2, and 1 s 3. New hooks will also be placed in all the letters just the same - from the bottom edge. And so we have an alphabet of 4 symbols: 0,1,2,3 each of which has three hooks-connections: on the left, on the right and below, the left hooks will connect only to the right of any symbols, and the lower connections can connect only the symbol with his partner-cast: zero with two and one with three. Schematically, a chain of code from such an alphabet can be represented as follows: who would work on the principle of the puzzle, so that they can only stick together with their pair 0 s 2, and 1 s 3. New hooks will also be placed in all the letters just the same - from the bottom edge. And so we have an alphabet of 4 symbols: 0,1,2,3 each of which has three hooks-connections: on the left, on the right and below, the left hooks will connect only to the right of any symbols, and the lower connections can connect only the symbol with his partner-cast: zero with two and one with three. Schematically, a chain of code from such an alphabet can be represented as follows: to the right and to the bottom, the left hooks will connect only to the right of any symbols, and the lower connections can only connect the symbol with their partner-impression: zero with two and one with three. Schematically, a chain of code from such an alphabet can be represented as follows: to the right and to the bottom, the left hooks will connect only to the right of any symbols, and the lower connections can only connect the symbol with their partner-impression: zero with two and one with three. Schematically, a chain of code from such an alphabet can be represented as follows:
Now we will re-code our program into a 4-character alphabet and re-start writing the code, recording one character from left to right, while at the same time forming the bottom line of the impression. We will get a rather interesting result, a couple of lines of code-cast are not identical, but interconnected. Having any of them available, it is possible to unambiguously restore the second one, while using only one simple rule: attaching a pair of 0 -2 to each letter and 1 -3 to each letter. We say that a separate mechanism will be responsible for the attachment function of the corresponding symbol, then we replace the copy mechanism with it and for brevity we call it the “casting mechanism”, as a result we get:
0> 1> 2> 3 ... (casting mechanism) ………… .. > 0> 1> 2> 3
1 <0 <3 <2 ... (cast of casting mechanism) .... <1 <0 <3 <2
An attentive reader will probably have a question: why is the direction of the bottom line opposite? This is explained by the fact that all letters have an inter-lower hook only from the bottom, and one direction, respectively, in order to connect with the upper symbols of the lower one, turn 180 degrees - “stand on your head”, while their direction changes.
Let's see if our new code implementation can self-copy. First, suppose that the casting mechanism, which is located in the “code” line, follows the “cast” line by sequentially putting matches to each letter, resulting in another “code” line, and accordingly, because of which everything was started, a copy of itself. Then the casting mechanism is traversed by a new line with the code, putting a correspondence to each character, getting a line-cast, and so the self-copying recursion is defeated and as a result we now have two complete sets from the same source.
And it really is very similar to how the very first mechanism of DNA replication could appear. Although in the process of evolution, it was overgrown with many auxiliary mechanisms and improvements, for example, in a cell, you no longer need to worry about the fact that the whole program was in one piece of code, and you can be allowed to make your own “software environment” - to have a separate program for copying, separate for finding and correcting errors, but the principles themselves remained unchanged.
I propose to summarize our mental experiment before moving on. As we could see, within the framework of the theory of self-replicators, many of the principles of Genetics and Cytology fit quite logically, namely:
- The structure of nucleotides - 4 letters of our alphabet are 4 nucleotides: 0 - Thymine; 1- Guanin; 2- Adenine; 3-Cytosine, which consists of the DNA of any living organism.
- The scheme of connecting nucleotides into a chain in DNA, which is naturally derived from the need to read and copy information in one order, which is provided by the structure of the “side hooks” which are called the 3 'and 5' ends. (For details on connecting nucleotides: www.youtube.com/watch?v=pzYE3WL_n2I&t=320s )
- The principle of complementarity is our connection rule “0 together with 2, and 1 together 3” - necessary for the functioning of the replication mechanism according to the principle of “casting”. In the original, Thimin is always connected together with Adenin, and Cytosine with Guanine, with the help of special hydrogen bonds — our “lower puzzle-hooks” (the first pair with 2 such bonds, and the second with 3), we were convinced that the necessary minimum for the replication mechanism is exactly 4 nucleotides, which should complement each other in pairs.
- The secondary structure of DNA, which naturally follows from the necessity of copying according to the rule of casting, explains why it is necessary to have exactly two "lines of code" or multidirectional (anti-parallel) threads of nucleotides in DNA, as well as why only one of the DNA strands is coding. ( www.xumuk.ru/biochem/90.html )
In the video below, the excellent DNA replication visualization is already closer to real scales and speeds and everything that we see here, no matter how hard it looks, just logically fits into our simple system, for example, the formation of a leading thread (Leading strand) Lagging strand) naturally follows from the fact that the casting mechanism (helicase) can substitute correspondences to each nucleotide in only one direction as well. our threads due to the complementary structure of nucleotides are obtained in different directions (anti-parallel), then one of them, helicase can put the correspondences in the direction of travel, and the second passes a little forward, and then returns along it in the direction of the code.
Spoon of chiral tar.
And when it would seem, everything develops into a rather logical picture, nature throws up another surprise. If we really repeated in the laboratory all the above listed operations for creating a molecular replicator program, starting with the synthesis of our nucleotide letters, having started the program, we would find that chains of our nucleotides are copied with large errors or not copied at all; in the end, they found out that the reason for the errors was that when synthesizing letters-nucleotides not only a certain number of letters we needed were formed, but exactly the same number of their mirror twins, i.e. having the same composition and chemical formula, but all the links within which are rearranged from left to right, for example, if the original has a C-O-H bond, then the mirror twin will have H-O-C.
In a special section of chemistry that studies the properties of the symmetries of various compounds. Stereochemistry, such a uniform mixture of left and right molecules is called racemate, and the left and right molecules themselves are isomers, and very often in the synthesis of organic compounds, for example, drugs it turns out that the properties of right and left isomers differ fundamentally, probably the most famous and tragic incident associated with this is the scandal that arose after the application in the 60s of the last century, a drug called Taliomide, in the process of synthesis of which On the one hand, the second isomer was not removed, which had an unexpected effect when taken by pregnant women, with the result that about 12,000 newborns were born with physical deformities. ( en.wikipedia.org/wiki/Thalidomide )
Then it turns out that the first self-replicating molecules should have been formed from a mixture of 50% of the right and 50% of the left nucleotides. Of course, this would not create particular problems if the nucleotides were symmetrical, such as the H-O-H water molecule, but as we showed above, molecules are necessary for recording and transmitting information, the asymmetry of which determines the presence of direction and complementary compounds, then it turns out that the mirror image of the nucleotide will have the opposite direction, and if at some part of the DNA replication, the mirror nucleotide is inserted, then there will be a gap of one character between it and the correct nucleotide not one of the elements of our puzzle. So, to the joy of various kinds of creationists, the formation in natural conditions of 50/50 left and right molecules,
The question of exactly which conditions made the separation of isomers possible in the primary broth and created the possibility of the origin of life, is still the subject of many studies, and despite the fact that it is already more than 100 years old, a definite answer has not yet been received. (about success in this direction can be read here: elementy.ru/novosti_nauki/432316 ).
Asymmetrical source of life
Violation of symmetries lies at the very core of living systems, so it would not be superfluous to consider how the asymmetry properties of chemical compounds are used in living systems, for example, to separate their two main systems: informational and functional, or using computer-hardware and software terms.
Indeed, if we consider any organisms on the planet, we will see that all DNA chains - assembly instructions, consist only of the right nucleotide isomers, and at the same time, all proteins - the building blocks of the body, collected according to these instructions, consist only of the left amino acid isomers. This separation ensures strict adherence to another basic principle of genetics:
"The direction of information transfer within the body always goes only in one direction from DNA to proteins."
If you think about it, this principle is really necessary to ensure the stability of any organism, because in the process of its functioning proteins are constantly exposed to aggressive environmental influences, are destroyed and replaced by new ones, and if the whole organism consisted of only one self-copying code, then its permanent damage would have caused , we would not be able to recognize the original protein after several steps of copying, i.e. such an organism would begin to mutate very quickly and uncontrollably. To avoid such situations, a “source code” is needed - DNA, which is stored in the cell itself, protected from harmful effects, in its core, and according to which new proteins are stamped as necessary, and in order to clearly distinguish instructions from building blocks, it is very convenient to have them in the form of opposite isomers.
A description of another application of asymmetry by living organisms, no longer associated with computer science, but with the topology of molecular mechanisms, came into biochemistry from knot theory, a science at the intersection of mathematical analysis and geometry, and is called supercoiling. To understand how this works, you only need two hands and a piece of rope. Take your rope by the ends with both hands, stretch it and begin to break its symmetry. Holding both ends twist one end to the right, after some time the rope will coil into the right helix, thus breaking the symmetry of the left and right you stored energy in the system, now do the next trick - connect without releasing both ends of the rope and watch carefully how the universe itself will restore the broken symmetry and the two right spirals will wrap around each other in the left direction.
This effect underlies the supercoiling process , which is very important for DNA functions , i.e. dense packing in a form, convenient for storage and copying. In this process, the DNA chain initially having a total length of about 2 meters, is twisted many times, changing the direction of spiralization and becoming tens of thousands of times more compact, to then fit in the form of chromosomes in the cell nucleus, so small (6 μm) that on a match head easily accommodate a thousand of these cores.
Conclusion
Living systems stand out vividly against the background of non-living nature in that for more than 3.7 billion years they have been creating more and more complex structures in the course of their evolution, demonstrating a decrease in their total entropy. The uniqueness of living systems is a special relationship between matter and the information that constitutes them, as well as the ability to transmit and modify this information, which also makes it possible to apply the concepts of informatics when describing many processes in living organisms. The mechanism of restoring broken symmetry is the fundamental engine of any processes and life is no exception, but it is life that has learned not only to use this “pendulum of the universe clock” for its own purposes, but also to rock it, with time more and more. Therefore, the study of living systems can give clues in which direction to move,