21ST CENTURY BIOLOGY: Uncovering the Code Delusion and the Cellular Mind with No Brain

Thursday, October 31, 2013

Brain_Image

|| By: Bhakti Niskama Shanta, Ph.D. ||

Sri Chaitanya Saraswat Institute, New Pal Para (Netaji Sarani), Hayder Para, Siliguri – 6, West Bengal, India. Email: bns@scsiscs.org, Phone: +91-9748906907 (M)

Abiology, “Easy Problems” and “Hard Problem” of Consciousness

In the past, philosophers, scientists, and people in general, had no problem in accepting the existence of consciousness in the same way as the existence of the physical world. After the advent of Newtonian mechanics (the notion that everything can be explained mechanistically), science embraced a complete materialistic conception about reality. Scientists started proposing hypotheses like abiogenesis (origin of first life from accumulation of atoms and molecules) and Big Bang theory (the explosion theory for explain the origin of universe), which failed to find the material basis for consciousness. Modern science hypothesizes that manifestation of life on Earth is nothing but a mere increment in the complexity of matter—and hence is an outcome of evolution of matter (chemical evolution) following the Big Bang. After the manifestation of life, modern science believed that chemical evolution transformed itself into biological evolution, which then had caused the entire biodiversity on our planet. Scientists suggest that the early living organisms must have resembled the unicellular organisms—like bacteria present on Earth today. In chemical evolution, scientists basically make an attempt to explain how simple matter evolved into three new basic characteristics (that they believe as the characteristics of life): (1) a spectacular permeable membrane that separates organisms from its environment, (2) genetic material that facilitates organisms to replicate (reproduce), and (3) proteins that represents the so called building blocks of life, for which the phonotypical development instructions are in the codes of organisms’ genetic material. However, the fact is that in a dead cell all three of these may be in proper condition and yet the cell cannot display the living symptom. Scientists can collect all the necessary components necessary for a cell from the existing living cells and yet they do not have a mechanism to produce a living cell from those components. Robert Shapiro stated in Nature,[1]

In June 2005, a group of international scientists clustered around a small, near-boiling pool in a volcanic region of Siberia. Biochemist David Deamer took a sample of the waters, then added to the pool a concoction of organic compounds that probably existed 4 billion years ago on the early Earth. One was a fatty acid, a component of soap, which his laboratory studies suggested had a significant role in the origin of life.

Over several days, Deamer took many more samples. He wished to see whether the chemical assembly process that he had observed in his laboratory, which eventually produced complex ‘protocell’ structures, could also take place in a natural setting. The answer was a resounding no.

Modern science leaves no room for the subjective aspect of consciousness in its attempt to know world as the relationships among forces, atoms, and molecules. This mechanistic approach created the duality between the experience and the experiencer – “easy problems” and the “hard problem” of consciousness.[2] David Chalmers first highlighted that the problems in the study of consciousness can be divided into two separate types: the “easy problems” and the “hard problem” of consciousness.[3] One should not be mislead by the term “easy problems” of consciousness because the problems under this category are very far from having been solved. What Chalmers meant by the “easy problems” of consciousness is that, for the problems in this category, scientists can imagine some mechanism to explain the phenomena. For example, scientists may try to explain the injury suffered by the body of an organism as the cause of the pain experienced by that organism. To find further details, scientists may explain that pain reception in an organism happens through a certain type of nerve fibers. In this way scientists try to construct some type of mechanistic explanation to explain the organism’s subjective experiences, like hearing, vision, smelling, memory, and so on. Because this type of approach is in line with the classical methods of scientific observation and experimentation, they call this category “easy problems.” However, merely knowing the mechanistic explanations, like neurophysiological processes, functions, states, and operations that are necessary for the sense perception cannot fully elucidate another much more complex conscious realm—selfhood. The questions: “how sensations acquire characteristics, such as colors and tastes?” and “how an organism develops a sense of self?” cannot be addressed by any mechanistic explanations. Because of this, scientists consider this problem under the category of “hard problem” in connection to consciousness. Thomas Nagel describes the difficulty[4]:

Thomas NagelIt isn’t easy to absorb the fact that I am contained in the world at all. It seems outlandish that the centerless universe, in all its spatiotemporal immensity, should have produced me, of all people – and produced me by producing TN [i.e., Thomas Nagel]. There was no such thing as me for ages, but with the formation of a particular physical organism at a particular place and time, suddenly there is me, for as long as the organism survives. In the objective flow of the cosmos this subjectively (to me!) stupendous event produces hardly a ripple. How can the existence of one member of the species have this remarkable consequence?

The life principle cannot be understood properly without overcoming the subject-object duality. There cannot be any content-part (object of consciousness) without a subject-part (conscious self) and vice versa. Traditionally, in both Eastern and Western philosophy, life is understood as a cognitive or sentient principle. Sentience cannot be manufactured artificially by any noble mechanical and chemical arrangements of inanimate atoms and molecules. Every sentient living entity comes only from a preexisting sentient living being. Ancient Eastern philosophy, based on the Vedantic or Bhagavat paradigm, provides the concept of “Organic Wholism,” as found, for example, in the invocation of Sri Isopanishad[5]om purnam adah purnam idam purnat purnam udacyate purnasya purnam adaya purnam evavasishyate–The “Organic Whole” produces “organic wholes.” An “organic whole” cannot arise from parts that have to be assembled. That process can only produce inorganic, mechanical machines or chemical processes, not living organisms. A similar conclusion was made by Rudolph Virchow[6] in 1858, “omnis cellula e cellula” (“every cell comes from a cell”). In 1864, Louis Pasteur also demonstrated that life cannot arise from non-life (abiogenesis is impossible) and with experimental evidence established the theory of biogenesis: Omne vivum ex vivo – life comes from life. Modern science adopts a naive approach to comprehend life and that is why it had continuously failed to explain how consciousness comes about. This irrational approach to study life is in reality a misrepresentation of the term that we understand as biology. Therefore, to differentiate the real biology from this misconception, we are calling it as “a-biology.” A scientific understanding of consciousness requires a completely different rational approach from those naive approaches that we find within abiology. Scientific theories and empirical analyses will certainly help us to substantiate that there is consciousness, but we need a very different approach to understand further how conscious beings experience things and how they make their choices. Therefore, we need new theories on “origin of life” and “origin of universe,” which can accommodate consciousness and freewill.

Code Delusion

Influenced by the grand success of computer sciences, life sciences have also adopted the concept of code in genetics and also in neuroscience to explain the sentient principles of livings organisms. This is also an outcome of modern science’s mechanistic thinking. The following two subsections discuss how recent empirical evidence disproves this illusionary code concept in genetics and neuroscience.

1. Genetic Code Delusion

Following abiology, researchers are busy taking organisms apart and analyzing their cells. Following this reductionistic process of disassembling cells they cataloged and characterized the molecular parts of the cells, they found that cells are made of four main types of macromolecules: (1) proteins, (2) sugars, (3) nucleic acids (genetic material), and (4) fats (lipids). Proteins are the principal elements of all cells and the molecular links of protein are made of amino acid molecules. Different amino acids have their unique shape and when they linked collectively in a chain to form proteins, it gives them the ability to fold into a complex 3-dimensional wire sculptures. A living cell has the ability to balance the electromagnetic charges along the protein’s chain, which helps to guide the final form of the complex protein sculpture. When proteins chemically couple with other molecules, it alters the distribution of electromagnetic charges and therefore causes a change in the shape of the protein. Living cell uses this mechanism to alter the shape of the protein from one conformation to another conformation. This change in shape of protein causes motion and cell uses this motion of protein to do work. A group of proteins may interact together in a specific manner to execute a specific function and that is known as pathway. In living organism different protein pathways helps in different functions like digestion, excretion, respiration, reproduction, and so on. Guided action of proteins helps in the development of the bodily structure of the organism and its function. Like parts in a machine, proteins also wear out when they are utilized within the living organism and the pathway stops when the wear out proteins are not replaced. Therefore, within living organism the wear out proteins are constantly replaced. A mere chemistry of random actions of protein is not useful for the life principle. In abiology, scientists are trying hard to find out the mechanism that guides the protein functions within a living organism. They presume that behavior of organism can be controlled by controlling different proteins in the pathways. They believe that there is a code or a mechanically stored memory within DNA that guides these functions of protein within the living organism.

Crick initially laid the foundation of central-dogma: two linear information flows: DNA —> DNA during replication and DNA —> RNA —> protein during protein synthesis. Later, in 1970, evidence (Mizutani and Temin’s work established that reverse transcriptase activity can copy RNA back into DNA) forced Crick to revise his unidirectional formulation.[7] Crick had to allocate an additional arrow from RNA to DNA in his dogmatic proposal. However, he adamantly rejected any possibility of transfers of information from protein to nucleic acid or from protein to protein: [8]

. . . sequence information cannot be transferred from protein to either protein or nucleic acid and the discovery of just one type of present day cell which could carry out any of the three unknown transfers (protein —> DNA, protein —> RNA, protein —> protein) would shake the whole intellectual basis of molecular biology . . .

Following this “genetic determinism,” many believed the idea that the secret of every sentient organism is coded in their genes (see for example, “Deciphering the code of life”[9]). The Human Genome Project is an outcome of this code delusion in genetics. Many scientists were calling DNA the “Book of Life,” but subsequent evidence established the imprudence of such claims. Even Craig Venter, president of Celera Genomics and the corporate arm of the DNA sequencing project, stated[10], “genes can’t possibly explain all of what makes us what we are.” We now know that in a living cell every genome function includes inputs and information-processing networks. Cells can rearrange their genomes—thereby writing information that influences all features of genome function. Cell regulatory functions, such as the DNA proofreading/repair mechanisms and alternative splicing of pre-mRNA, clearly disprove the simplistic central dogma, and thus significantly modify our understanding of information dynamics. Therefore, cell functioning cannot be explained by reducing it to any single molecule like, DNA or RNA. Shapiro[11] stated in his book Evolution: a view from the 21st century, “it seems that “the intellectual foundations of molecular biology” have indeed been shaken—and shaken hard.” Similarly, referring several examples from studies in molecular biology and genomics, Stephen L. Talbott expertly summarized the demise of abiology in his article[12], “Getting Over the Code Delusion.” At the end of the article he states:

There is a frequently retold story about a little old lady who claims, after hearing a scientific lecture, that the world is a flat plate resting on the back of a giant tortoise. When asked what the turtle is standing on, she invokes a second turtle. And when the inevitable follow-up question comes, she replies, ‘You’re very clever, young man, but you can’t fool me. It’s turtles all the way down.’”

As a metaphor for the scientific understanding of biology, the story is marvelously truthful. In the study of organisms, “It’s life all the way down.

2. Neural Code Delusion

Like geneticists, neurologists also presumed the material basis of cognition and therefore they want to establish neurons in brain as the basis of consciousness. They have the notion that there is a “neural code”[13] that represents the mind of the organism and helps the brain to manage synaptic modulation over wide areas of cortex. They believe that the complex brain function is as simple as the operation of a man-made machine—robot—and therefore they hope that in future they can control the living organisms just like a robot. Delgado stated in this book Physical Control of the Mind[14]:

There are basic mechanisms in the brain responsible for all mental activities, including perceptions, emotions, abstract thought, social relations, and the most refined artistic creations. . . . Predictable behavioral and mental responses may be induced by direct manipulation of the brain.

We will discuss in this subsection some of the empirical facts from recent scientific findings to explain how all these believes are only a misunderstanding about brain functioning and consciousness. First question will be, does any neural code exists in reality, or it is only in the minds of neurologists? It is reported that coding occurs in context and hence, the meaning aspect should be considered strictly in the context of the subject’s behavior. An individual living entity selects according to his behavior only those aspects of neural firing that make sense for its behavior. Therefore brain function is controlled by the behavior of the living being. Apart from the behavior of organism whose brain is under study, interpretations of neural action are also very much influenced by the brain states of the neuroscientists. Eggermont[15] explains this difficulty:

The information encoded in a train of neural action potentials is interpreted by higher order neurons and it is also interpreted by the neuroscientist who designed and performed the experiments. There need not be any correspondence between these two interpretations. . . . The interpretation by the neuroscientist, however, may be influenced by the ruling paradigm in the particular field of research.

Code, by its meaning, is a predetermined representation of information that is independent of the sender, receiver, and mechanisms of transmission.[16] Influenced by the concept of neural coding and decoding, neurologists think the brain as an information processing system. However, unlike inert man-made information processing systems, the behavior of a sentient living being adds a semantic aspect to the brain information processing. Moreover, information obtained from an organism’s sensory stimulation is utilized to constantly renew the brain’s internal image of the world.[17], [18] Therefore, neural codes must change with time through conscious learning, which implies that same neural spike sequence may represent a different behavior at different times. For several such reasons, the concept that there is just one mode of neural signaling represented by a single “neural code” is certainly false.

Extracting ethologically significant neural representation requires very specialized cells, or populations of neurons, that merge each individual feature. Different qualitative and quantitative stimulus attributes of sentient living organism are represented by different neural codes—and therefore, unlimitedly, many neural codes are necessary. Moreover, entirely different coding is necessary for stimulus attributes from computational processes (spatial position of a sound and depth of a visual scene).[19] Neurologists also do not know whether coding is performed by individual neurons or by nervous system.[20] There are several such questions like, What reads the code and decodes the message?; Is the reader a distributed system or is it a “cardinal cell”?; Is there a local decoder or is there an integral sensori-motor system that is genetically set up to react appropriately?; and so on, for which abiology does not have any tangible answers. The simplistic mechanistic approaches have limited applications in these studies because unlike classical information transmission systems, the sensori-motor coordination systems, are feedback systems. Therefore there is no unidirectional flow of information. That is why Erlich[21] stated:

Extensive investigation of the brain’s synaptic connectivity, the presumed material basis of cognition, has failed to explain how the brain thinks. Further, the neural code that purportedly allows the brain to coordinate synaptic modulation over wide areas of cortex has yet to be found and may not exist.

Cell Sentience- Mind with No Brain

French philosopher René Descartes is known for encouraging mistreatment of animals because he argued that only humans are conscious.[22] From the 17th century onwards, after René Descartes, many furthered this misconception—that only humans are conscious and that no animals are conscious. Fortunately, findings in the twenty-first century help to remove this error of judgment.[23] Recently, several prominent scientists signed the Cambridge declaration at the First Annual Francis Crick Memorial Conference, stating, “… the weight of evidence indicates that humans are not unique in possessing the neurological substrates that generate consciousness. Nonhuman animals, including all mammals and birds, and many other creatures, including octopuses, also possess these neurological substrates.”[24] However, the statement unfortunately perpetuates further misunderstandings, that, “neurological substrates … generate consciousness”.

The “identity theory” explains that states and processes of the mind are alike to states and processes of the brain. Therefore, scientists and philosophers following the concept of identity theory believing that that the brain secretes thought as the liver secretes bile.[25],[26] That is why, till now the major focus of consciousness studies are focused on brain research. However, all these materialistic theories in abiology are completely disproven by twenty-first century biology. Twenty-first century biology shows that even the smallest cells (brainless) are also conscious entities.[27]

monkey  humanIn multicellular organisms, the brain is assumed to be the organ controlling life. Using the same analogy—and with the notion of code delusion—scientists consider the cell nucleus (because DNA and genes are within the cell nucleus) as an equivalent to the brain of a cell. The demise of code delusion ascertains that abiology’s assumption that DNA controls life is wrong. By considering brain as the source of consciousness, it was believed that if the brain is detached from any organism, the instantaneous and indispensable outcome of that action is the organism’s death. However, for over forty years, research in medical science has proven this wrong. In 1970, Robert White and his team successfully transferred the head of a rhesus monkey to the headless body of another monkey. The monkey survived for eight days.[28] Researchers are also attempting to perform the same scenario with human beings.[29] It is reported that if a human head has been detached under controlled conditions, it must be reconnected to the circulatory flow of other person’s body within one hour.[30] The same is also true for the brain of the cell, i.e., a cell can sustain an enucleation operation (the operation in which a cell’s nucleus is removed). In fact, cells are found to be more robust towards brain removal than multicellular organisms. It has been reported that enucleated cells continue to survive and display a regulated control of their biological processes for up to three months.[31] Therefore, for both single-cell and also multicellular organisms, the brain is not the source of life. Many researchers influenced by abiology doubt the cell cognition and hence, to help clarify, we will discuss below some of the findings from 21st century biology that prove cell cognition:

1. Cell Sentience from the Prospective of Organismal Behavior

Quorum_SensingStudies on cognitive processes, like perception, learning, memory, decision making, and so on, based on observations from the behavior of animals are well known.[32] However, in recent times, the similar cognitive studies on organismal behavior have been done for the cases of many unicellular organisms such as bacteria, protozoa[33], amoeba[34], unicellular algae (cyanobacteria)[35] and unicellular fungi (slime mold)[36], and archaea[37]. Many biologists still believe that Darwinian competition is the prime feature of life. However, this is contradictory. Cooperation is the very nature of all living organisms[38] –from humans, colonial insects, like ants and bees and even microorganisms, including bacteria display cooperation.[39] Monod’s pioneering studies revealed how E. Coli chooses the best sugar to eat.[40] It is well known that bacteria carry out intricate communications enabling them to tackle a difficult environment. Quorum sensing is the language that Bacteria utilize to communicate important information and coordinate bacterial populations into supracellular colonies.[41] Bacterial actives in colonies are similar to that of multicellular organisms[42] and they also communicate with eukaryotic hosts.[43] Bacteria exhibit cognitive activities[44] and intelligent behavior[45] to smartly sense various parameters from their environment—and hence can display amazing resistance to diverse antibiotics through innovation, anticipation and learning.[46] Apart from bacteria, green algae use cognitive photo-induced intracellular electric signals and their motor motoric flagella in eye-apparatus.[47] In an experimental setup, amoeba can answer geometric problems.[48] Unicellular organisms display learning, memory, anticipation, risk management, and other aspects of cognitive behavior.[49]

Not only unicellular organisms can perform these functions, but also the individual cells in the multicellular organisms also exhibit individual cognitive behavior. Gametes of multicellular living entities display sentient cell-cell communication and chemotaxis.[50] Sperm cells and oocytes use several cognitive transmitters.[51] Even plants cells also have sensory perception and integration of these multiple sensory perceptions into adaptive actions helps them in signaling and communication.[52] Plant cells and neurons in other multicellular organisms produce sentient action potentials.[53] Root cells of plants exhibit sentient features at the transition zone interpolated between the apical meristem and elongation region.[54]

2. Cell Sentience from the Prospective of Cell Functions

There is ample empirical evidence that establish cell sentience from the prospective of cell functions. Cells can cognitively read their environment, analyze the received information and then execute the necessary action to continue their survival.[55] This coordinated cell action is known as cell signaling, and also substantiates that cell also has a mind. Living cell regulates practically every cell function, including DNA synthesis, RNA synthesis, protein synthesis, cell division, cell differentiation, morphogenesis, and neuroendocrine regulation.[56] Cell cognitively monitors different cellular processes and if there is either a mistake or damage, a cell can detect the problem. A cell activates a checkpoint and stops the entire cycle until all has been set accurately to further progress the cycle.[57] Cells execute programmed cell death where they perform suicide by following an organized cascade of events, known as apoptosis.[58] Cells of multicellular organism use various cell receptors for various functions. To coordinate functions in cell communities, they use integration-receptors which respond to information signals. In different environments, using intercellular signaling molecules cells can select and execute various essential actions.[59] Identity receptors are also known as self-receptors, or histocompatibility-receptors, and they help cells to have individual and collective identity.[60] Therefore, they help cellular communities to collectively respond to a central command—and are used by the immune system in the multicellular organisms to discriminate self from invader. Self-receptors also play an important role in the functioning of organs or tissues. If our tissues and organs recognize a requirement for protection, they can compromise their growth activities. Completely dismissing central-dogma, cells can rewrite existing gene programs in an attempt to surmount stressful conditions.[61] All such evidence clearly acknowledges that all living cells are also individual cognitive entities.

Conclusions

Soon after the beginning of the scientific revolution, Francis Bacon defined the goal of modern science. Following Bacon, the main objective of modern science was to dominate and control Nature. This mentality has already created havoc in society and is self-threatening in the form of environmental pollution, dangerous nuclear weapons, genetic modification of food, and so on. To attain this goal of science, scientists have attempted to know what controls a living organism’s form, function, and behavior. Researchers influenced by abiology try hard to apply the principles of Newtonian mechanics to understand living organisms. Newtonian mechanics based abiology presumes that the living organism is a mere collection of parts (matter) and therefore in the literature of abiology there is no place for studies on consciousness and its source—the soul. Abiology only encourages futile studies on materialism. Twenty-first century biology has revolutionized our understanding about living organisms and helped remove the illusion that our health and fate is preprogrammed in our genes (genetic determinacy). Srimad Bhagavad-Gita explains that consciousness is the symptom of the existence of the soul; the soul of each individual living entity is eternal and therefore has no material basis. We have shown in this article that empirical evidence in twenty-first century biology substantiates that life requires cognition at all levels. Moreover, we have also seen that the source of our consciousness – soul is beyond the interaction of neurons in our brain. This further ascertains that there is no part in the body of a living organism which we can call as the source of our consciousness and therefore soul is a non-material entity. Modern science was dominated by atheistic dogmas and therefore it was a general practice to dismiss the concept of soul as an object of religious belief. However, revolutionary twenty-first biology and its new understandings of consciousness have thoroughly challenged this unscientific attitude.

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