History of science. The revolution in the life sciences

Science in One Health: A new journal with a new approach

One Health recognizes the close links and interdependence among human health, animal health and environmental health. With the pandemic of COVID-19 and the risk of many emerging or reemerging infectious diseases of zoonotic nature as well as the spreading antimicrobial resistance, One Health has become one of top concerns globally, as it entails the essential global public health challenges from antimicrobial resistance over zoonoses, to climate change, food security and societal well-being. Research priorities in One Health include the study on interactions of human-animal-plants-nature ecology interface, systems thinking, integrated surveillance and response systems, and the overall One Health governance as part of the global health and sustainability governance. The now launched journal, Science in One Health, aims to be a resource platform that disseminates scientific evidence, knowledge, and tools on the One Health approaches and respective possible socio-ecological interventions. Thus, aims at providing fruitful exchanges of information and experience among researchers, and decision makers as well as public health actors.

Biomolecular Basis of Cellular Consciousness via Subcellular Nanobrains

Cells emerged at the very beginning of life on Earth and, in fact, are coterminous with life. They are enclosed within an excitable plasma membrane, which defines the outside and inside domains via their specific biophysical properties. Unicellular organisms, such as diverse protists and algae, still live a cellular life. However, fungi, plants, and animals evolved a multicellular existence. Recently, we have developed the cellular basis of consciousness (CBC) model, which proposes that all biological awareness, sentience and consciousness are grounded in general cell biology. Here we discuss the biomolecular structures and processes that allow for and maintain this cellular consciousness from an evolutionary perspective.

Deep Learning in Mining Biological Data

Recent technological advancements in data acquisition tools allowed life scientists to acquire multimodal data from different biological application domains. Categorized in three broad types (i.e. images, signals, and sequences), these data are huge in amount and complex in nature. Mining such enormous amount of data for pattern recognition is a big challenge and requires sophisticated data-intensive machine learning techniques. Artificial neural network-based learning systems are well known for their pattern recognition capabilities, and lately their deep architectures-known as deep learning (DL)-have been successfully applied to solve many complex pattern recognition problems. To investigate how DL-especially its different architectures-has contributed and been utilized in the mining of biological data pertaining to those three types, a meta-analysis has been performed and the resulting resources have been critically analysed. Focusing on the use of DL to analyse patterns in data from diverse biological domains, this work investigates different DL architectures' applications to these data. This is followed by an exploration of available open access data sources pertaining to the three data types along with popular open-source DL tools applicable to these data. Also, comparative investigations of these tools from qualitative, quantitative, and benchmarking perspectives are provided. Finally, some open research challenges in using DL to mine biological data are outlined and a number of possible future perspectives are put forward.

The metamorphosis of analytical chemistry

Defining analytical chemistry as the measurement of isolated compositional features in a selected study object ignores the unique perspective that analytical chemists bring to twenty-first century science and society. In this feature article, we will discuss some of the existing preconceptions and misinterpretations of analytical chemistry that occur at present and will tackle them from the more up-to-date perspective of science in the Big Data Era. This will place their influence in context while simultaneously enlarging the scope of the discipline analytical chemistry to its well-deserved prevalent position in present-day science and technology. Graphical abstract.

Applications of Deep Learning and Reinforcement Learning to Biological Data

Rapid advances in hardware-based technologies during the past decades have opened up new possibilities for life scientists to gather multimodal data in various application domains, such as omics, bioimaging, medical imaging, and (brain/body)-machine interfaces. These have generated novel opportunities for development of dedicated data-intensive machine learning techniques. In particular, recent research in deep learning (DL), reinforcement learning (RL), and their combination (deep RL) promise to revolutionize the future of artificial intelligence. The growth in computational power accompanied by faster and increased data storage, and declining computing costs have already allowed scientists in various fields to apply these techniques on data sets that were previously intractable owing to their size and complexity. This paper provides a comprehensive survey on the application of DL, RL, and deep RL techniques in mining biological data. In addition, we compare the performances of DL techniques when applied to different data sets across various application domains. Finally, we outline open issues in this challenging research area and discuss future development perspectives.

Receptor visualization and the atomic bomb. A historical account of the development of the chemical neuroanatomy of receptors for neurotransmitters and drugs during the Cold War

This is a historical account of how receptors for neurotransmitters and drugs got to be seen at the regional, cellular, and subcellular levels in brain, in the years going from the end of the World War II until the collapse of the Soviet Union, the Cold War (1945-1991). The realization in the US of the problem of mental health care, as a consequence of the results of medical evaluation for military service during the war, let the US Government to act creating among other things the National Institute for Mental Health (NIMH). Coincident with that, new drug treatments for these disorders were introduced. War science also created an important number of tools and instruments, such as the radioisotopes, that played a significant role in the development of our story. The scientific context was marked by the development of Biochemistry, Molecular Biology and the introduction in the early 80's of the DNA recombinant technologies. The concepts of chemical neurotransmission in the brain and of receptors for drugs and transmitters, although proposed before the war, where not generally accepted. Neurotransmitters were identified and the mechanisms of biosynthesis, storage, release and termination of action by mechanisms such as reuptake, elucidated. Furthermore, the synapse was seen with the electron microscope and more important for our account, neurons and their processes visualized in the brain first by fluorescence histochemistry, then using radioisotopes and autoradiography, and later by immunohistochemistry (IHC), originating the Chemical Neuroanatomy. The concept of chemical neurotransmission evolved from the amines, expanded to excitatory and inhibitory amino acids, then to neuropeptides and finally to gases and other "atypical" neurotransmitters. In addition, coexpression of more than one transmitter in a neuron, changed the initial ideas of neurotransmission. The concept of receptors for these and other messengers underwent a significant evolution from an abstract chemical concept to their physical reality as gene products. Important steps were the introduction in the 70's of radioligand binding techniques and the cloning of receptor genes in the 80's. Receptors were first visualized using radioligands and autoradiography, and analyzed with the newly developed computer-assisted image analysis systems. Using Positron Emission Tomography transmitters and receptors were visualized in living human brain. The cloning of receptor genes allowed the use of in situ hybridization histochemistry and immunohistochemistry to visualize with the light and electron microscopes the receptor mRNAs and proteins. The results showed the wide heterogeneity of receptors and the diversity of mode of signal transmission, synaptic and extra-synaptic, again radically modifying the early views of neurotransmission. During the entire period the interplay between basic science and Psychopharmacology and Psychiatry generated different transmitter or receptor-based theories of brain drug action. These concepts and technologies also changed the way new drugs were discovered and developed. At the end of the period, a number of declines in these theories, the use of certain tools and the ability to generate new diagnostics and treatments, the end of an era and the beginning of a new one in the research of how the brain functions.

The Academic Tree of Howard V. Malmstadt: From Early Scientific Exploration to Modern Analytical Chemistry

Over the last several decades, science has benefited tremendously by the implementation of digital electronic components for analytical instrumentation. A pioneer in this area of scientific inquiry was Howard Malmstadt. Frequently, such revolutions in scientific history can be viewed as a series of discoveries without a great deal of attention as to how mentorship shapes the careers and methodologies of those who made great strides forward for science. This paper focuses on the verifiable relationships of those who are connected through the academic tree of Malmstadt and how their experiences and the context of world events influenced their scientific pursuits. Particular attention is dedicated to the development of American chemistry departments and the critical role played by many of the individuals in the tree in this process.

Planar cell polarity: the Dachsous/Fat system contributes differently to the embryonic and larval stages of Drosophila

The epidermal patterns of all three larval instars (L1-L3) ofDrosophilaare made by one unchanging set of cells. The seven rows of cuticular denticles of all larval stages are consistently planar polarised, some pointing forwards, others backwards. In L1 all the predenticles originate at the back of the cells but, in L2 and L3, they form at the front or the back of the cell depending on the polarity of the forthcoming denticles. We find that, to polarise all rows, the Dachsous/Fat system is differentially utilised; in L1 it is active in the placement of the actin-based predenticles but is not crucial for the final orientation of the cuticular denticles, in L2 and L3 it is needed for placement and polarity. We find Four-jointed to be strongly expressed in the tendon cells and show how this might explain the orientation of all seven rows. Unexpectedly, we find that L3 that lack Dachsous differ from larvae lacking Fat and we present evidence that this is due to differently mislocalised Dachs. We make some progress in understanding how Dachs contributes to phenotypes of wildtype and mutant larvae and adults.

Heredity and self-organization: partners in the generation and evolution of phenotypes

In this review we examine the role of self-organization in the context of the evolution of morphogenesis. We provide examples to show that self-organized behavior is ubiquitous, and suggest it is a mechanism that can permit high levels of biodiversity without the invention of ever-increasing numbers of genes. We also examine the implications of self-organization for understanding the "internal descriptions" of organisms and the concept of a genotype-phenotype map.

The scientific quest for lasting youth: prospects for curing aging

People have always sought eternal life and everlasting youth. Recent technological breakthroughs and our growing understanding of aging have given strength to the idea that a cure for human aging can eventually be developed. As such, it is crucial to debate the long-term goals and potential impact of the field. Here, I discuss the scientific prospect of eradicating human aging. I argue that curing aging is scientifically possible and not even the most challenging enterprise in the biosciences. Developing the means to abolish aging is also an ethical endeavor because the goal of biomedical research is to allow people to be as healthy as possible for as long as possible. There is no evidence, however, that we are near to developing the technologies permitting radical life extension. One major difficulty in aging research is the time and costs it takes to do experiments and test interventions. I argue that unraveling the functioning of the genome and developing predictive computer models of human biology and disease are essential to increase the accuracy of medical interventions, including in the context of life extension, and exponential growth in informatics and genomics capacity might lead to rapid progress. Nonetheless, developing the tools for significantly modifying human biology is crucial to intervening in a complex process like aging. Yet in spite of advances in areas like regenerative medicine and gene therapy, the development of clinical applications has been slow and this remains a key hurdle for achieving radical life extension in the foreseeable future.

Current advances in systems and integrative biology

Systems biology has gained a tremendous amount of interest in the last few years. This is partly due to the realization that traditional approaches focusing only on a few molecules at a time cannot describe the impact of aberrant or modulated molecular environments across a whole system. Furthermore, a hypothesis-driven study aims to prove or disprove its postulations, whereas a hypothesis-free systems approach can yield an unbiased and novel testable hypothesis as an end-result. This latter approach foregoes assumptions which predict how a biological system should react to an altered microenvironment within a cellular context, across a tissue or impacting on distant organs. Additionally, re-use of existing data by systematic data mining and re-stratification, one of the cornerstones of integrative systems biology, is also gaining attention. While tremendous efforts using a systems methodology have already yielded excellent results, it is apparent that a lack of suitable analytic tools and purpose-built databases poses a major bottleneck in applying a systematic workflow. This review addresses the current approaches used in systems analysis and obstacles often encountered in large-scale data analysis and integration which tend to go unnoticed, but have a direct impact on the final outcome of a systems approach. Its wide applicability, ranging from basic research, disease descriptors, pharmacological studies, to personalized medicine, makes this emerging approach well suited to address biological and medical questions where conventional methods are not ideal.

Pragmatic turn in biology: From biological molecules to genetic content operators

Erwin Schrödinger‘s question “What is life?” received the answer for decades of “physics + chemistry”. The concepts of Alain Turing and John von Neumann introduced a third term: “information”. This led to the understanding of nucleic acid sequences as a natural code. Manfred Eigen adapted the concept of Hammings “sequence space”. Similar to Hilbert space, in which every ontological entity could be defined by an unequivocal point in a mathematical axiomatic system, in the abstract ”sequence space” concept each point represents a unique syntactic structure and the value of their separation represents their dissimilarity. In this concept molecular features of the genetic code evolve by means of self-organisation of matter. Biological selection determines the fittest types among varieties of replication errors of quasi-species. The quasi-species concept dominated evolution theory for many decades. In contrast to this, recent empirical data on the evolution of DNA and its forerunners, the RNA-world and viruses indicate cooperative agent-based interactions. Group behaviour of quasi-species consortia constitute de novo and arrange available genetic content for adaptational purposes within real-life contexts that determine epigenetic markings. This review focuses on some fundamental changes in biology, discarding its traditional status as a subdiscipline of physics and chemistry.

At the dawn of a new revolution in life sciences

In a recently published article Sydney Brenner argued that the most relevant scientific revolution in biology at his time was the breakthrough of the role of “information” in biology. The fundamental concept that integrates this new biological “information” with matter and energy is the universal Turing machine and von Neumann’s self-reproducing machines. In this article we demonstrate that in contrast to Turing/von Neumann machines living cells can really reproduce themselves. Additionally current knowledge on the roles of non-coding RNAs indicates a radical violation of the central dogma of molecular biology and opens the way to a new revolution in life sciences.

Evolutionary biology and anthropology suggest biome reconstitution as a necessary approach toward dealing with immune disorders

Industrialized society currently faces a wide range of non-infectious, immune-related pandemics. These pandemics include a variety of autoimmune, inflammatory and allergic diseases that are often associated with common environmental triggers and with genetic predisposition, but that do not occur in developing societies. In this review, we briefly present the idea that these pandemics are due to a limited number of evolutionary mismatches, the most damaging being 'biome depletion'. This particular mismatch involves the loss of species from the ecosystem of the human body, the human biome, many of which have traditionally been classified as parasites, although some may actually be commensal or even mutualistic. This view, evolved from the 'hygiene hypothesis', encompasses a broad ecological and evolutionary perspective that considers host-symbiont relations as plastic, changing through ecological space and evolutionary time. Fortunately, this perspective provides a blueprint, termed 'biome reconstitution', for disease treatment and especially for disease prevention. Biome reconstitution includes the controlled and population-wide reintroduction (i.e. domestication) of selected species that have been all but eradicated from the human biome in industrialized society and holds great promise for the elimination of pandemics of allergic, inflammatory and autoimmune diseases.