Category Archives: Biology

A macroscopic view of the Schrödinger cat

From the analysis carried out in the previous post, it can be concluded that, in general, it is not possible to identify the macroscopic states of a complex system with its quantum states. Thus, the macroscopic states corresponding to the dead cat (DC) or to the living cat (AC) cannot be considered quantum states, since according to quantum theory the system could be expressed as a superposition of these states. Consequently, as it has been justified, for macroscopic systems it is not possible to define quantum states such as |DC⟩ and |DC⟩. On the other hand, the states (DC) and (AC) are an observable reality, indicating that the system presents two realities, a quantum reality and an emerging reality that can be defined as classical reality.

Quantum reality will be defined by its wave function, formed by the superposition of the quantum subsystems that make up the system and which will evolve according to the existing interaction between all the quantum elements that make up the system and the environment. For simplicity, if the CAT system is considered isolated from the environment, the succession of its quantum state can be expressed as:

            |CAT[n]⟩ = |SC1[n]⟩ ⊗|SC2[n]⟩ ⊗…⊗|SCi[n]⟩ ⊗…⊗|SCk[n][n]⟩.

Expression in which it has been taken into account that the number of non-entangled quantum subsystems k also varies with time, so it is a function of the sequence n, considering time as a discrete variable. 

The observable classical reality can be described by the state of the system that, if for the object “cat” is defined as (CAT[n]), from the previous reasoning it is concluded that (CAT[n]) ≢ |CAT[n]⟩. In other words, the quantum and classical states of a complex object are not equivalent. 

The question that remains to be justified is the irreducibility of the observable classical state (CAT) from the underlying quantum reality, represented by the quantum state |CAT⟩. This can be done if it is considered that the functional relationship between states |CAT⟩ and (CAT) is extraordinarily complex, being subject to the mathematical concepts on which complex systems are based, such as they are:

  • The complexity of the space of quantum states (Hilbert space).
  • The random behavior of observable information emerging from quantum reality.
  • The enormous number of quantum entities involved in a macroscopic system.
  • The non-linearity of the laws of classical physics.

Based on Kolmogorov complexity [1], it is possible to prove that the behavior of systems with these characteristics does not support, in most cases, an analytical solution that determines the evolution of the system from its initial state. This also implies that, in practice, the process of evolution of a complex object can only be represented by itself, both on a quantum and a classical level.

According to the algorithmic information theory [1], this process is equivalent to a mathematical object composed of an ordered set of bits processed according to axiomatic rules. In such a way that the information of the object is defined by the Kolmogorov complexity, in a manner that it remains constant throughout time, as long as the process is an isolated system. It should be pointed out that the Kolmogorov complexity makes it possible to determine the information contained in an object, without previously having an alphabet for the determination of its entropy, as is the case in the information theory [2], although both concepts coincide at the limit.

From this point of view, two fundamental questions arise. The first is the evolution of the entropy of the system and the second is the apparent loss of information in the observation process, through which classical reality emerges from quantum reality. This opens a possible line of analysis that will be addressed later.

But going back to the analysis of what is the relationship between classic and quantum states, it is possible to have an intuitive view of how the state (CAT) ends up being disconnected from the state |CAT⟩, analyzing the system qualitatively.

First, it should be noted that virtually 100% of the quantum information contained in the state |CAT⟩ remains hidden within the elementary particles that make up the system. This is a consequence of the fact that the physical-chemical structure [3] of the molecules is determined exclusively by the electrons that support its covalent bonds. Next, it must be considered that the molecular interaction, on which molecular biology is based, is performed by van der Waals forces and hydrogen bonds, creating a new level of functional disconnection with the underlying layer.

Supported by this functional level appears a new functional structure formed by cellular biology  [4], from which appear living organisms, from unicellular beings to complex beings formed by multicellular organs. It is in this layer that the concept of living being emerges, establishing a new border between the strictly physical and the concept of perception. At this level the nervous tissue [5] emerges, allowing the complex interaction between individuals and on which new structures and concepts are sustained, such as consciousness, culture, social organization, which are not only reserved to human beings, although it is in the latter where the functionality is more complex.

But to the complexity of the functional layers must be added the non-linearity of the laws to which they are subject and which are necessary and sufficient conditions for a behavior of deterministic chaos [6] and which, as previously justified, is based on the algorithmic information theory [1]. This means that any variation in the initial conditions will produce a different dynamic, so that any emulation will end up diverging from the original, this behavior being the justification of free will. In this sense, Heisenberg’s uncertainty principle [7] prevents from knowing exactly the initial conditions of the classical system, in any of the functional layers described above. Consequently, all of them will have an irreducible nature and an unpredictable dynamic, determined exclusively by the system itself.

At this point and in view of this complex functional structure, we must ask what the state (CAT) refers to, since in this context the existence of a classical state has been implicitly assumed. The complex functional structure of the object “cat” allows a description at different levels. Thus, the cat object can be described in different ways:

  • As atoms and molecules subject to the laws of physical chemistry.
  • As molecules that interact according to molecular biology.
  • As complex sets of molecules that give rise to cell biology.
  • As sets of cells to form organs and living organisms.
  • As structures of information processing, that give rise to the mechanisms of perception and interaction with the environment that allow the development of individual and social behavior.

As a result, each of these functional layers can be expressed by means of a certain state. So to speak of, the definition of a unique macroscopic state (CAT) is not correct. Each of these states will describe the object according to different functional rules, so it is worth asking what relationship exists between these descriptions and what their complexity is. Analogous to the arguments used to demonstrate that the states |CAT⟩ and (CAT) are not equivalent and are uncorrelated with each other, the states that describe the “cat” object at different functional levels will not be equivalent and may to some extent be disconnected from each other.

This behavior is a proof of how reality is structured in irreducible functional layers, in such a way that each one of the layers can be modeled independently and irreducibly, by means of an ordered set of bits processed according to axiomatic rules.

Refereces

[1] P. Günwald and P. Vitányi, “Shannon Information and Kolmogorov Complexity,” arXiv:cs/0410002v1 [cs:IT], 2008.
[2] C. E. Shannon, «A Mathematical Theory of Communication,» The Bell System Technical Journal, vol. 27, pp. 379-423, 1948.
[3] P. Atkins and J. de Paula, Physical Chemestry, Oxford University Press, 2006.
[4] A. Bray, J. Hopkin, R. Lewis and W. Roberts, Essential Cell Biology, Garlan Science, 2014.
[5] D. Purves and G. J. Augustine, Neuroscience, Oxford Univesisty press, 2018.
[6] J. Gleick, Chaos: Making a New Science, Penguin Books, 1988.
[7] W. Heisenberg, «The Actual Content of Quantum Theoretical Kinematics and Mechanics,» Zeit-schrift fur Physik. Translation: NASA TM-77379., vol. 43, nº 3-4, pp. 172-198, 1927.

Why the rainbow has 7 colors?

Published on OPENMIND August 8, 2018

Color as a physical concept

Visible light, heat, radio waves and other types of radiation all have the same physical nature and are constituted by a flow of particles called photons. The photon or “light quantum” was proposed by Einstein, for which he was awarded the Nobel Prize in 1921 and is one of the elementary particles of the standard model, belonging to the boson family. The fundamental characteristic of a photon is its capacity to transfer energy in quantized form, which is determined by its frequency, according to the expression E=h∙ν, where h is the Planck constant and ν the frequency of the photon.

Electromagnetic spectrum

Thus, we can find photons of very low frequencies located in the band of radio waves, to photons of very high energy called gamma rays, as shown in the following figure, forming a continuous frequency range that constitutes the electromagnetic spectrum. Since the photon can be modeled as a sinusoid traveling at the speed of light c, the length of a complete cycle is called the photon wavelength λ, so the photon can be characterized either by its frequency or its wavelength, since λ=c/ν. But it is common to use the term color as a synonym for frequency, since the color of light perceived by humans is a function of frequency. However, as we are going to see, this is not strictly physical but a consequence of the process of measuring and interpreting information, which makes color an emerging reality of another underlying reality, sustained by the physical reality of electromagnetic radiation.

Structure of an electromagnetic wave

But before addressing this issue, it should be considered that to detect photons efficiently it is necessary to have a detector called an antenna, whose size must be similar to the wavelength of the photons.

Color perception by humans

The human eye is sensitive to wavelengths ranging from deep red (700nm, nanometers=10-9 meters) to violet (400nm).  This requires receiving antennas of the order of hundreds of nanometres in size! But for nature this is not a big problem, as complex molecules can easily be this size. In fact, the human eye, for color vision, is endowed with three types of photoreceptor proteins, which produce a response as shown in the following figure.

Response of photoreceptor cells of the human retina

Each of these types configures a type of photoreceptor cell in the retina, which due to its morphology are called cones. The photoreceptor proteins are located in the cell membrane, so that when they absorb a photon they change shape, opening up channels in the cell membrane that generate a flow of ions. After a complex biochemical process, a flow of nerve impulses is produced that is preprocessed by several layers of neurons in the retina that finally reach the visual cortex through the optic nerve, where the information is finally processed.

But in this context, the point is that the retinal cells do not measure the wavelength of the photons of the stimulus. On the contrary, what they do is convert a stimulus of a certain wavelength into three parameters called L, M, S, which are the response of each of the types of photoreceptor cells to the stimulus. This has very interesting implications that need to be analyzed. In this way, we can explain aspects such as:

  • The reason why the rainbow has 7 colors.
  • The possibility of synthesizing the color by means of additive and subtractive mixing.
  • The existence of non-physical colors, such as white and magenta.
  • The existence of different ways of interpreting color according to the species.

To understand this, let us imagine that they provide us with the response of a measurement system that relates L, M, S to the wavelength and ask us to establish a correlation between them. The first thing we can see is that there are 7 different zones in the wavelength, 3 ridges and 4 valleys. 7 patterns! This explains why we perceive the rainbow composed of 7 colors, an emerging reality as a result of information processing that transcends physical reality.

But what answer will a bird give us if we ask it about the number of colors of the rainbow? Possibly, though unlikely, it will tell us nine! This is because the birds have a fourth type of photoreceptor positioned in the ultraviolet, so the perception system will establish 9 regions in the light perception band. And this leads us to ask: What will be the chromatic range perceived by our hypothetical bird, or by species that only have a single type of photoreceptor? The result is a simple case of combinatorial!

On the other hand, the existence of three types of photoreceptors in the human retina makes it possible to synthesize the chromatic range in a relatively precise way, by means of the additive combination of three colors, red, green and blue, as it is done in the video screens. In this way, it is possible to produce an L,M,S response at each point of the retina similar to that produced by a real stimulus, by means of the weighted application of a mixture of photons of red, green and blue wavelengths.

Similarly, it is possible to synthesize color by subtractive or pigmentary mixing of three colors, magenta, cyan and yellow, as in oil paint or printers. And this is where the virtuality of color is clearly shown, since there are no magenta photons, since this stimulus is a mixture of blue and red photons. The same happens with the white color, as there are no individual photons that produce this stimulus, since white is the perception of a mixture of photons distributed in the visible band, and in particular by the mixture of red, green and blue photons.

In short, the perception of color is a clear example of how reality emerges as a result of information processing. Thus, we can see how a given interpretation of the physical information of the visible electromagnetic spectrum produces an emerging reality, based a much more complex underlying reality.

In this sense, we could ask ourselves what an android with a precise wavelength measurement system would think of the images we synthesize in painting or on video screens. It would surely answer that they do not correspond to the original images, something that for us is practically imperceptible. And this connects with a subject, which may seem unrelated, as is the concept of beauty and aesthetics. The truth is that when we are not able to establish patterns or categories in the information we perceive it as noise or disorder.  Something unpleasant or unsightly!

Biology as an axiomatic process

The replication mechanisms of living beings can be compared with the self-replication of automatons in the context of computability theory. In particular, DNA replication, analyzed from the perspective of the recursion theorem, indicates that its replication structure goes beyond biology and the quantum mechanisms that support it, as it is analyzed in the article Biology as an Axiomatic Process.

Physical chemistry establishes the principles by which atoms interact with each other to form molecules. In the inorganic world the resulting molecules are relatively simple, not allowing establishing a complex functional structure. On the other hand, in the organic world, molecules can be made up of thousands or even millions of atoms and have complex functionality. It highlights what is known as molecular recognition, through which the molecules interact with each other selectively and which is the basis of biology.

Molecular recognition plays a fundamental role in the structure of DNA, in the translation of the genetic code of DNA into proteins and in the biochemical interaction of proteins, which ultimately form the basis on which living beings are based.

The detailed study of these molecular interactions makes it possible to describe the functionality of the processes, in such a way that it is possible to establish formal models, to such an extent that they can be used as a computing technology, as is the case of DNA-based computing.

From this perspective, this allows us to ask if the process of information is something deeper and if in reality it is the foundation of biology itself, according to what is established by the principle of reality.

For this purpose, this section aims to analyze the basic processes on which biology is based, in order to establish a link with axiomatic processing and thus investigate the nature of biological processes. For this, it is not necessary to describe in detail the biological mechanisms described in the literature. We will simply describe its functionality, so that they can be identified with the theoretical foundations of information processing. To this end, we will explain the mechanisms on which DNA replication and protein synthesis are based.

DNA and RNA molecules are polymers formed from the ribose and deoxyribose nucleotides, respectively, bound by phosphates. On the basis of this nucleotide chain, one of the four possible nucleic acids can be linked. There are five different nucleic acids, adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U). In the case of DNA, nucleic acids that can be coupled by covalent bonds to nucleotides are A, G, C and T, whereas in the case of RNA they are A, G, C and U. As a consequence, molecules are structured in a helix shape, fitting the nucleic acids in a precise and compact way, due to the shape of their electronic clouds.

The helix structure allows the nucleic acids of two different strands to be bound together by hydrogen bonds, forming pairs A-T and G-C in the case of DNA, and A-U and G-C in the case of RNA, as shown in the following figure.

Base-pairing of nucleic acids in DNA

As a result, the DNA molecule is formed by a double helix, in which two chains of nucleotides polymers wind one on top of the other, remaining together by means of hydrogen bonds of nucleic acids. Thus, each strand of the DNA molecule contains the same genetic code, one of which can be considered the negative of the other.

Double helix structure of DNA molecule

The genetic information of an organism, called a genome, is not contained in a single DNA molecule, but is organized into chromosomes. These are made up of DNA strands bound together by proteins. Thus, in the case of humans, the genome is formed by 46 chromosomes, and so, the number of bases in the DNA molecules that compose it being about 3×109. Since each base can be encoded by means of 2 bits, the human genome, considered as an object of information, is equivalent to 6×109 bits.

The information contained in the genes is the basis for the synthesis of proteins, which are responsible for executing and controlling the biochemistry of living beings. The proteins are formed by the bonding of amino acids, through covalent bonds, which is done from the sequences of the bases contained in the DNA. The number of existing amino acids is 20 and since each base codes 2 bits, 3 bases (6 bits, 64 combinations) are necessary to be able to code each one of the amino acids. This means that there is some redundancy in the assignment of base sequences to amino acids, in addition to control codes for the synthesis process (Stop), as shown in the following table.

Translation of nucleic acids (Codons) to amino acids

However, protein synthesis is not done directly from DNA, since it requires the intermediation of RNA. This is called the translation process and involves two types of different RNA molecules, the messenger ARM (mRNA) and the transfer RNA (tRNA). The first step is the synthesis of mRNA from DNA. This process is called transcription, in such a way that the information corresponding to a gene is copied into the mRNA molecule, which is done through a process of recognition between the molecules of the nucleic acids, carried out by the hydrogen bonds, such as shows the following figure.

DNA transcription

Once the mRNA molecule is synthesized, the tRNA molecule is responsible for mediating between mRNA and amino acids to synthesize proteins, for which it has two specific molecular mechanisms. On the one hand, tRNA has a chain of three amino acids called anticodon at one end. On the opposite side, tRNA binds to a specific amino acid, according to the translation table of nucleic acid sequences into amino acids. In this way, tRNA is able to translate mRNA into a protein, as shown in the figure below. 

Protein synthesis (mRNA translation)

But perhaps the most complex process is undoubtedly DNA replication, so that each molecule produces two identical replicas. Replication is performed by unwinding each strand of the molecule and inserting the nucleic acid molecules on each of the strands, in a similar way to that shown in the mRNA synthesis. DNA replication is controlled by enzymatic processes supported by proteins. Without going into detail and in order to show its complexity, the table below shows the proteins involved in the replication process and their role.

The role of proteins in the DNA replication process

The processes described above are defined as the central dogma of molecular biology and are usually schematically represented schematically as shown in the following figure. It also depicts the reverse transcription that occurs in retroviruses, which synthesizes a DNA molecule from RNA.

Central dogma of molecular biology

The biological process from the perspective of computability theory

Molecular processes supported by DNA, RNA and proteins can be considered from an abstract point of view as information processes. As a result, input statements corresponding to a language are processed resulting in new output statements. Thus, the following languages can be identified:

  • DNA molecule. Sentence consisting of a sequence of characters corresponding to a 4-symbol alphabet.
  • RNA molecule – protein synthesis. Sentence consisting of a sequence of characters belonging to a 21-symbol alphabet.
  • RNA molecule-reverse transcription. Sentence composed of a sequence of characters belonging to a 4-symbol alphabet.
  • Protein molecule. Sentence composed of a sequence of characters belonging to a 20-symbol alphabet.

This information is processed by the machinery established by the physicochemical properties of control molecules. To better understand this functional structure, it is advisable to modify the scheme corresponding to the central dogma of biology. To do this, we must represent the processes involved and the information that flows between them, as shown in the following block diagram.

Functional structure of DNA replication

This structure highlights the flow of information between processes, such as DNA and RNA sentences, where the functional blocks of information processing are the following:

  • PDNA. Replication process. The functionality of this process is determined by the proteins involved in DNA synthesis, producing two replicas of DNA from a single molecule.
  • PRNA. Transcription process. It synthesizes a RNA molecule from a gene encoded in DNA.
  • PProt. Translation process. It synthesizes a protein from an RNA molecule.

This structure clearly shows how information emerges from biological processes, something that seems to be ubiquitous in all natural models and allows the implementation of computer systems. In all cases this capacity is finally supported by quantum physics. In the case of biology in particular, this is produced from the physicochemical properties of molecules, which are determined by quantum physics. Therefore, the information process is something that emerges from an underlying reality and ultimately from quantum physics. This is true as far as knowledge goes.

This means that, although there is a strong link between reality and information, information is simply an emerging product of reality. But biology provides a clue to the intimate relationship between reality and information, which are ultimately indistinguishable concepts. If we look at the DNA replication process, we see that DNA is produced in several stages of processing:

DNA → RNA → Proteins → DNA.

We could consider this to be a specific feature of the biological process. However, computability theory indicates that the replication process is subject to deeper logical rules than the physical processes themselves that support replication. In computability theory, the recursion theorem determines that replication of information requires at least the intervention of two independent processes.

This shows that DNA replication is subject to abstract rules that must be satisfied not only by biology, but by every natural process. Therefore, the physical foundations that support biological processes must verify this requirement. Consequently, this shows that the information processing is essential in what we understand by reality.