All scientific discoveries contribute towards a better understanding of the universe that we live in. All of this knowledge reinforces our belief that the universe is orderly and that we are at the center. In contrast, there are some scientific revolutions that change how we think about ourselves, as humans. There are some discoveries that shake up our complacency about our importance in the grand scheme of the universe. Such scientific revolutions deserve special merit since by removing our self-centered bias, we get closer to a more universal truth about us and the universe we inhabit. Since our bias for self-centeredness is strong, so are these scientific revolutions. This paper examined five such scientific revolutions and postulates a sixth one that is emerging.
It is easy to define the first of such revolutionary thinking. Thales of Miletus 6th century BCE argued that we should observe physical events without assigning the cause to "god." He argued that there is an underlying process that causes the world to behave the way it does and that we need to work out these hidden processes rather than simply call it the will of god. This revolutionary thinking caused the birth of science.
The second scientific revolution was by the 16th century Nicolaus Copernicus., who in astronomy, removed the earth from the center of the universe and placed it among other planets revolving around the sun. By doing this Copernicus also moved humankind, and not just Earth, from being at the center of the universe and we attained a more peripheral place in the universe.
The third revolution that continued to move humans away from being the center of the universe was by the 19th century Charles Darwin. By publishing his The Origin of Species, Darwin pushed humans off the throne of superior beings and back into our mammalian lineage. The theory asserts that like all other beings, we evolved and share lineage with lower primates and other living things. Like all other animals, we are a work in progress.
The 20th century brought the fourth revolution with Sigmund Freud who emphasized the concept of an unconscious mind. The notion of the unconscious can be traced back to ancient civilizations when dreams were considered to be messages from the gods. Even early philosophers like Plato and Aristotle explored the idea of unconscious mental processes. At the turn of the century, scientists such as Franz Anton Mesmer, Pierre Janet, Alfred Adler, and Carl Jung all worked on this unconscious mind that hid thoughts and decisions from consciousness and therefore from us. But it was Freud that took this concept further and developed a theory of the mind that argued that the unconscious mind is the primary motivator for behavior. The theory put forward the interpretation that we are not in conscious control of our actions.
The later part of the 20th century brought us the fifth revolution with Albert Einstein and his colleagues who developed the idea that the matter is relative. This theory of relativity postulated that gravity and acceleration are indistinguishable, that mass and energy cause gravity and time to curve, and that the acceleration of massive objects causes ripples in spacetime. All of this makes our natural world less rigid, and our reality is determined by context by the locality of the event.
These theories have one thing in common, what we believe about who we are, as humans on Earth, is not true. That we are part of a larger universe, that we evolved from other life forms, and that how we see the world is relative to our position in the universe. There is a locality in our reality. Where we are is important. The sixth revolution takes all these concepts of moving humankind away from being to the center of the universe as it argues that even our body is part of such a locality. That the biological and chemical context that we reside in determines how we function and behave. This environmental physiology, where the environment changes our physiology proposes that although we see ourselves as sovereign entities we are in reality a conglomerate of different processes that are influenced by the world we live in. As such, under this environmental physiology, there is no “us” and “them”, no “me” and the “environment”, as both converge. Environmental physiology highlights the malleability of our physiology. Richard Rorty said this beautifully: “…had physiology been more obvious psychology would never have arisen…if the body had been easier to understand, nobody would have thought that we had a mind.” (p 239).
Most of the developments in environmental physiology highlight human intervention in modifying the body. However, equally impressive, and more instructive, is the evidence showing how nature itself manipulates our bodies. By observing how nature manipulates and modifies our bodies, scientists have learned new techniques that emulate nature. Despite the impressive nature of these technological advances, the underlying theme is how nature has such a powerful force on us by constantly changing and modifying our bodies.
Technological advancements include:
Genetic Engineering and Recombinant DNA technology led to the creation of genetically modified organisms (GMOs);
Polymerase Chain Reaction (PCR) amplified specific DNA segments, making it possible to study and analyze genes and their functions more easily;
Gene Sequencing has led to insights into genetic variations, disease mechanisms, and personalized medicine; Stem Cell Research that promoted regenerative medicine, and tissue engineering;
CRISPR-Cas9 Gene Editing technology allows precise modification of DNA sequences, making gene editing faster, and more accessible;
Synthetic Biology of new biological components, systems, and even entire organisms, with varied applications;
Omics Technologies advancements in how molecules interact within living organisms resulting in contributions to genomics, proteomics, and metabolomics;
Human Embryonic Stem Cells that repair specific damaged organs;
Induced Pluripotent Stem Cells (iPSCs) takes adult cells and reprogram them to an embryonic stem cell-like state; Immunotherapy such as immune checkpoint inhibitors and CAR-T cell therapy, harness the immune system to target and eliminate cancer cells;
Microbiome Research that evaluates the bacterial makeup of the stomach enabling the development of probiotics;
Nanobiotechnology that promotes targeted drug delivery, biosensors, and imaging technologies;
Neuroscience and Brain Imaging such as functional MRI (fMRI), provide insights into the brain's structure and function; and
Artificial Intelligence and Machine Learning in Biology accelerate data analysis, drug repurposing, protein folding predictions, and diagnostics.
Such advancements, impressive as they may seem, are just a small insight into the way that nature itself behaves. Scientists have used this limited knowledge about what we know about how the environment influences our bodies to experiment with coming up with technologies in a short span of time. But it would express a special kind of hubris if we forget to add how nature itself manipulates “us.” There is a vast number of unknown-unknowns, but what we have learned provides enough substantiating evidence to affirm that our context, our environment, changes us. This knowledge has taught us that we are more malleable and receptive than we believe. Nature manipulates our bodies on a daily basis. The sixth revolution in science is knowledge about how nature influences and changes our genes, how genes are expressed, how our body processes food, how we uptake nutrients, how we age, how we think, and how we behave.
Natural influences on the body include:
Epigenetic modifications that determine the expression of specific genes, subdue some and excite others without altering the underlying genetic sequence. Environmental factors, such as diet, stress, and exposure to toxins, can lead to epigenetic modifications, influencing health outcomes;
Plasmids, are small, circular DNA molecules in humans that come from bacteria and archaea and become inserted in human cells. They often carry genes that provide selective advantages, such as antibiotic resistance, leading to the spread of antibiotic resistance genes;
Horizontal Gene Transfer (HGT) is the transfer of genetic material between different organisms, typically bacteria can exchange genetic material-- share beneficial genes, such as antibiotic resistance genes--through processes like conjugation, transformation, and transduction;
Jumping Genes (Transposons) are segments of DNA capable of moving within a genome. They can "jump" from one location to another, potentially affecting gene regulation and function, playing a significant role in shaping the human genome's evolution and diversity;
Retroviruses are individual strands of RNA viruses that can multiply into human cell DNA by integrating their genetic material into the host genome;
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections in our ancestors' germ cells; MicroRNAs (miRNAs) play a crucial role in post-transcriptional gene regulation by binding to messenger RNAs (mRNAs) and either degrade them or inhibit their translation into proteins;
Dysregulation of miRNAs has also been linked to the progression of diseases, such as cancer and neurodegenerative disorders;
Prions are misfolded proteins that can induce the misfolding of other normal proteins, leading to a chain reaction that can propagate disease in the brain and nervous system, such as Creutzfeldt-Jakob disease in humans and bovine spongiform encephalopathy (mad cow disease) in cattle;
Endocrine Disruptors such as Bisphenol A (BPA) are chemicals that can interfere with the endocrine system, disrupting hormonal regulation reproductive and developmental abnormalities;
Gut bacteria break down complex carbohydrates, producing essential vitamins, and regulating immune responses affecting weight, inflammatory bowel disease, and allergies. which can influence our metabolism, immune system, and overall health;
RNA editing such as Adenosine-to-inosine (A-to-I), is a process that alters the nucleotide sequence of RNA after transcription. It is modified by enzymes called ADARs (adenosine deaminases acting on RNA and can impact gene expression, particularly in the nervous system, and is essential for normal brain function;
Genetic recombination is the process of exchanging genetic material between two DNA molecules during meiosis (cell division), homologous chromosomes exchange genetic material through crossing over. It occurs during sexual reproduction and contributes to genetic diversity;
DNA Repair Mechanisms correct errors that arise during replication or as a result of external factors. For example, Nucleotide excision repair (NER) is a DNA repair pathway that removes and replaces damaged nucleotides caused by exposure to ultraviolet radiation;
Hormesis where exposure to low or moderate levels of a stressor or toxin can result in a beneficial or stimulatory response, leading to improved health, resilience, or longevity. In other words, "What doesn't kill you makes you stronger." Hormesis can occur in various biological contexts such as Radiation Hormesis, Exercise Hormesis, Caloric Restriction Hormesis, and Phytochemical Hormesis.
All of these processes, and many others that we still have not discovered, interact. For example, exposure to low or moderate stressors that trigger hormetic responses may lead to epigenetic modifications. A hormetic response could activate specific cellular pathways that, in turn, influence epigenetic modification that changes how some genes are expressed (Vaiserman, 2011). The relationship can also be reciprocal where epigenetic modifications can regulate genes involved in stress response pathways or cellular repair mechanisms. Specific epigenetic changes may enhance or dampen hormetic responses, affecting the magnitude of the beneficial effect elicited by the stressor. In some cases, epigenetic changes induced by hormetic responses may be heritable. Offspring could inherit the altered epigenetic marks from their parents, potentially passing on the beneficial effects of hormesis to subsequent generations (Xavier, et al, 2019). Both hormesis and epigenetics have been linked to aging and longevity (Vaiserman, 2011). Moderate stressors that induce hormetic responses are believed to contribute to lifespan extension in various organisms. Epigenetic changes, on the other hand, can influence the aging process by regulating genes involved in cellular senescence and age-related diseases.
The Sixth Revolution in science moves humans from a homo-centric view of the world to one that places humans as more malleable and porous, allowing for the context, and the environment, to influence and change us.
REFERENCES
Rorty, R. (1979). Transcendental arguments, self-reference, and pragmatism. Transcendental arguments and science: Essays in epistemology, 77-103.
Vaiserman, A. M. (2011). Hormesis and epigenetics: is there a link?. Ageing research reviews, 10(4), 413-421.
Xavier, M. J., Roman, S. D., Aitken, R. J., & Nixon, B. (2019). Transgenerational inheritance: how impacts to the epigenetic and genetic information of parents affect offspring health. Human reproduction update, 25(5), 519-541.
TECHNOLOGICAL INNOVATIONS
Genetic Engineering and Recombinant DNA Technology:
Watson, J. D., & Crick, F. H. (1953). Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature, 171(4356), 737-738.
Cohen, S. N., Chang, A. C., Boyer, H. W., & Helling, R. B. (1973). Construction of biologically functional bacterial plasmids in vitro. Proceedings of the National Academy of Sciences, 70(11), 3240-3244.
Polymerase Chain Reaction (PCR):
Mullis, K. B. (1986). The unusual origin of the polymerase chain reaction. Scientific American, 262(4), 56-61.
Saiki, R. K., Scharf, S., Faloona, F., Mullis, K. B., Horn, G. T., Erlich, H. A., & Arnheim, N. (1985). Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science, 230(4732), 1350-1354.
Gene Sequencing:
Sanger, F., Nicklen, S., & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, 74(12), 5463-5467.
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., ... & Zhu, X. (2001). The sequence of the human genome. Science, 291(5507), 1304-1351.
Stem Cell Research:
Evans, M. J., & Kaufman, M. H. (1981). Establishment in culture of pluripotential cells from mouse embryos. Nature, 292(5819), 154-156.
Takahashi, K., & Yamanaka, S. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell, 126(4), 663-676.
CRISPR-Cas9 Gene Editing:
Doudna, J. A., & Charpentier, E. (2014). Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science, 346(6213), 1258096.
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816-821.
Synthetic Biology:
Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R. Y., Algire, M. A., ... & Venter, J. C. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 329(5987), 52-56.
Khalil, A. S., & Collins, J. J. (2010). Synthetic biology: applications come of age. Nature Reviews Genetics, 11(5), 367-379.
Omics Technologies:
Aebersold, R., & Mann, M. (2003). Mass spectrometry-based proteomics. Nature, 422(6928), 198-207.
Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., ... & Bouvrette, S. (2001). Initial sequencing and analysis of the human genome. Nature, 409(6822), 860-921.
Human Embryonic Stem Cell Research:
Thomson, J. A., Itskovitz-Eldor, J., Shapiro, S. S., Waknitz, M. A., Swiergiel, J. J., Marshall, V. S., & Jones, J. M. (1998). Embryonic stem cell lines derived from human blastocysts. Science, 282(5391), 1145-1147.
Yu, J., Vodyanik, M. A., Smuga-Otto, K., Antosiewicz-Bourget, J., Frane, J. L., Tian, S., ... & Thomson, J. A. (2007). Induced pluripotent stem cell lines derived from human somatic cells. Science, 318(5858), 1917-1920.
Immunotherapy:
Hodi, F. S., O'Day, S. J., McDermott, D. F., Weber, R. W., Sosman, J. A., Haanen, J. B., ... & Urba, W. J. (2010). Improved survival with ipilimumab in patients with metastatic melanoma. New England Journal of Medicine, 363(8), 711-723.
Maude, S. L., Laetsch, T. W., Buechner, J., Rives, S., Boyer, M., Bittencourt, H., ... & Wood, P. (2018). Tisagenlecleucel in children and young adults with B-cell lymphoblastic leukemia. New England Journal of Medicine, 378(5), 439-448.
Microbiome Research:
Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007). The human microbiome project. Nature, 449(7164), 804-810.
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., ... & Wang, J. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464(7285), 59-65.
Nanobiotechnology:
Farokhzad, O. C., & Langer, R. (2009). Impact of nanotechnology on drug delivery. ACS Nano, 3(1), 16-20.
Sweeney, S. M., & Wooley, K. L. (2005). Self-assembling polymers for gene delivery: from laboratory to clinical trial. Advanced Drug Delivery Reviews, 57(15), 2075-2087.
Neuroscience and Brain Imaging:
Ogawa, S., Lee, T. M., Nayak, A. S., & Glynn, P. (1990). Oxygenation-sensitive contrast in magnetic resonance image of rodent brain at high magnetic fields. Magnetic Resonance in Medicine, 14(1), 68-78.
Kandel, E. R., Schwartz, J. H., & Jessell, T. M. (2000). Principles of neural science (Vol. 4). McGraw-Hill, Health Professions Division.
Artificial Intelligence and Machine Learning in Biology:
Alipanahi, B., Delong, A., Weirauch, M. T., & Frey, B. J. (2015). Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nature Biotechnology, 33(8), 831-838.
Topol, E. J. (2019). High-performance medicine: the convergence of human and artificial intelligence. Nature Medicine, 25(1), 44-56.
NATURAL INFLUENCES
Epigenetics
Jirtle, R. L., & Skinner, M. K. (2007). Environmental epigenomics and disease susceptibility. Nature Reviews Genetics, 8(4), 253-262.
Plasmid
Modi, S. R., Lee, H. H., Spina, C. S., & Collins, J. J. (2013). Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature, 499(7457), 219-222.
Horizontal Gene Transfer
Thomas, C. M., & Nielsen, K. M. (2005). Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nature Reviews Molecular Cell Biology, 6(9), 711-721.
Jumping Genes
Chuong, E. B., Elde, N. C., & Feschotte, C. (2017). Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science, 351(6277), 1083-1087.
Retroviruses
Grandi, N., & Tramontano, E. (2018). Human endogenous retroviruses are ancient acquired elements still shaping innate immune responses. Frontiers in Immunology, 9, 2039.
MicroRNAs
Bartel, D. P. (2009). MicroRNAs: target recognition and regulatory functions. Cell, 136(2), 215-233.
Prions
Prusiner, S. B. (1998). Prions. Proceedings of the National Academy of Sciences, 95(23), 13363-13383.
Endocrine Disruptors
Diamanti-Kandarakis, E., Bourguignon, J. P., Giudice, L. C., Hauser, R., Prins, G. S., Soto, A. M., ... & Zoeller, R. T. (2009). Endocrine-disrupting chemicals: an Endocrine Society scientific statement. Endocrine Reviews, 30(4), 293-342.
Gut Bacteria
Sender, R., Fuchs, S., & Milo, R. (2016). Revised estimates for the number of human and bacteria cells in the body. PLOS Biology, 14(8), e1002533.
RNA Editing
Nishikura, K. (2010). Functions and regulation of RNA editing by ADAR deaminases. Annual Review of Biochemistry, 79, 321-349.
Genetic Recombination
Hunter, N. (2015). Meiotic recombination: The essence of heredity. Cold Spring Harbor Perspectives in Biology, 7(12), a016618.
DNA Repair
Lehmann, A. R., & McGibbon, D. (2006). Xeroderma pigmentosum. Orphanet Journal of Rare Diseases, 1(1), 27.
Radiation Hormesis,
Macklis, R. M., & Beresford, B. (1991). Radiation hormesis. Journal of Nuclear Medicine, 32(2), 350-359.
Exercise Hormesis,
Ji, L. L., Kang, C., & Zhang, Y. (2016). Exercise-induced hormesis and skeletal muscle health. Free Radical Biology and Medicine, 98, 113-122.
Caloric Restriction Hormesis,
Turturro, A., Hass, B. S., & Hart, R. W. (2000). Does caloric restriction induce hormesis?. Human & experimental toxicology, 19(6), 320-329.
Phytochemical Hormesis
Son, T. G., Camandola, S., & Mattson, M. P. (2008). Hormetic dietary phytochemicals. Neuromolecular medicine, 10, 236-246.
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