Evolutionary Biology

A new trend in deep learning, represented by Mutual Information Neural Estimation (MINE) and Information Noise Contrast Estimation (InfoNCE), is emerging. In this trend, similarity functions and Estimated Mutual Information (EMI) are used as learning and objective functions. Coincidentally, EMI is essentially the same as Semantic Mutual Information (SeMI) proposed by the author 30 years ago. This paper first reviews the evolutionary histories of semantic information measures and learning functions. Then, it briefly introduces the author’s semantic information G theory with (...) the rate-fidelity function R(G) (G denotes SeMI, and R(G) extends R(D)) and its applications to multi-label learning, the maximum Mutual Information (MI) classification, and mixture models. Then it discusses how we should understand the relationship between SeMI and Shannon’s MI, two generalized entropies (fuzzy entropy and coverage entropy), Autoencoders, Gibbs distributions, and partition functions from the perspective of the R(G) function or the G theory. An important conclusion is that mixture models and Restricted Boltzmann Machines converge because SeMI is maximized, and Shannon’s MI is minimized, making information efficiency G/R close to 1. A potential opportunity is to simplify deep learning by using Gaussian channel mixture models for pre-training deep neural networks’ latent layers without considering gradients. It also discusses how the SeMI measure is used as the reward function (reflecting purposiveness) for reinforcement learning. The G theory helps interpret deep learning but is far from enough. Combining semantic information theory and deep learning will accelerate their development. (shrink)

The increasing importance of computational techniques in post-genomic life science research calls for new forms and combinations of expertise that cut across established disciplinary boundaries between computing and biology. These are most marked in large scale gene sequencing facilities. Here new ways of organising knowledge production, drawing on industrial models, have been perceived as pursuing efficiency and control to the potential detriment of academic autonomy and scientific quality. We explore how these issues are played out in the case of BGI (...) (Beijing Genomics Institute prior to 2008). BGI (in Pinyin, Hua Da Jiyin– Big China Genome) is today the world’s largest centre for gene sequencing research. Semi-detached from traditional academic institutions, BGI has developed distinctive models for organising research and for developing expertise, informed by practices in US Information Technology and Life Science Laboratories, that differ from existing models of interdisciplinary research in academic institutions. (shrink)

Traditional evolutionary theory invoked natural and sexual selection to explain species- and sex-typical traits. However, some heritable inter-individual variability in behaviour and psychology – personality – is probably adaptive. Here we extend this insight to common psychopathological traits. Reviewing key findings from three background areas of importance – theoretical models, non-human personality and evolved human social dynamics – we propose that a combination of social niche specialisation, negative frequency-dependency, balancing selection and adaptive developmental plasticity should explain adaptation for individual differences (...) in psychology – ‘specialised minds’ – explaining some variance in personality and psychopathology trait dimensions, which share various characteristics. We suggest that anthropological research of behavioural differences should be extended past broad demographic factors (age and sex) to include individual specialisations. As a first step towards grounding psychopathology in ancestral social structure, we propose a minimum plausible prevalence, given likely ancestral group sizes, for negatively frequency-dependent phenotypes to be maintained as specialised tails of adaptive distributions – below the calculated prevalence, specialisation is highly unlikely. For instance, chronic highly debilitating forms of autism or schizophrenia are too rare for such explanations, whereas attention-deficit-hyperactivity disorder and broad autism phenotypes are common enough to have existed in most hunter-gatherer bands, making adaptive explanations more plausible. (shrink)

Chemistry is engaged with a subject that is not static but evolving in time, in chemical space, namely, the collection of all substances and reactions reported over time. If we accept that premise, we can identify the path dependencies and self-reinforcing mechanisms that determined its current space and selected it across historical alternatives. In particular, data analysis allows us to identify two crucial turning points. One was the introduction of structural theory in 1860, the other a technological shift around 1980.

Programming languages provide a variety of mechanisms to associate names with values, and these mechanisms play a central role in programming practice. For example, they allow multiple references to the same storage location or function in different parts of a complex program. By contrast, the representations used in current genetic programming systems provide few if any naming mechanisms, and it is therefore generally not possible for evolved programs to use names in sophisticated ways. In this chapter we describe a new (...) approach to names in genetic programming that is based on Holland’s concept of tags. We demonstrate the use of tag-based names, we describe some of the ways in which they may help to extend the power and reach of genetic programming systems, and we look at the ways that tag-based names are actually used in an evolved program that solves a robot navigation problem. (shrink)

Question: Why does Bayes (often) work, even when parameters aren’t randomly generated? Answer: For the same reason that evolution often works. Bayes is natural selection, without mutation, sex, or any of the other good parts. Question: If Bayes is evolution, what is the fitness function? Answer: The relative entropy rate. Bayes is evolutionary search with an information-theoretic objective function. Question: What is this observation good for? Answer: Understanding what happens with mis-specification and dependence.

The role of Boolean functions is prominent in several areas like cryptography, sequences, and coding theory. Therefore, various methods for the construction of Boolean functions with desired properties are of direct interest. New motivations on the role of Boolean functions in cryptography with attendant new properties have emerged during the years. There are still many combinations of design criteria left unexplored and in this matter evolutionary computation can play a distinct role. This paper concentrates on two scenarios for use of (...) Boolean functions in cryptography. The first uses Boolean functions as the source of the nonlinearity in filter and combiner generators. Although relatively well explored using evolutionary algorithms, it still presents an interesting goal in terms of the practical sizes of Boolean functions. The second scenario appeared rather recently where the objective is to find Boolean functions that have various orders of the correlation immunity and minimal Hamming weight. In both those scenarios we see that evolutionary algorithms are able to find high quality solutions where genetic programming performs the best. (shrink)

Both language and genes evolve by transmission over generations with opportunity for differential replication of forms. The understanding that gene frequencies change at random by genetic drift, even in the absence of natural selection, was a seminal advance in evolutionary biology. Stochastic drift must also occur in language as a result of randomness in how linguistic forms are copied between speakers. Here we quantify the strength of selection relative to stochastic drift in language evolution. We use time series derived from (...) large corpora of annotated texts dating from the 12th to 21st centuries to analyse three well-known grammatical changes in English: the regularization of past-tense verbs, the introduction of the periphrastic ’do’, and variation in verbal negation. We reject stochastic drift in favour of selection in some cases but not in others. In particular, we infer selection towards the irregular forms of some past-tense verbs, which is likely driven by changing frequencies of rhyming patterns over time. We show that stochastic drift is stronger for rare words, which may explain why rare forms are more prone to replacement than common ones. This work provides a method for testing selective theories of language change against a null model and reveals an underappreciated role for stochasticity in language evolution. (shrink)

The question of what role sex plays in evolution is still open despite decades of research. It has often been assumed that sex should facilitate the increase in fitness. Hence, the fact that it may break down highly favorable genetic combinations has been seen as a problem. Here, we consider an alternative approach. We define a measure that represents the ability of alleles to perform well across different combinations and, using numerical iterations within a classical population-genetic framework, show that selection (...) in the presence of sex favors this ability in a highly robust manner. We also show that the mechanism responsible for this effect has been out of the purview of previous theory, because it operates during the evolutionary transient, and that the breaking down of favorable genetic combinations is an integral part of it. Implications of these results and more to evolutionary theory are discussed. (shrink)

Biological evolution provides a creative fount of complex and subtle adaptations, often surprising the scientists who discover them. However, because evolution is an algorithmic process that transcends the substrate in which it occurs, evolution’s creativity is not limited to nature. Indeed, many researchers in the field of digital evolution have observed their evolving algorithms and organisms subverting their intentions, exposing unrecognized bugs in their code, producing unexpected adaptations, or exhibiting outcomes uncannily convergent with ones in nature. Such stories routinely reveal (...) creativity by evolution in these digital worlds, but they rarely fit into the standard scientific narrative. Instead they are often treated as mere obstacles to be overcome, rather than results that warrant study in their own right. The stories themselves are traded among researchers through oral tradition, but that mode of information transmission is inefficient and prone to error and outright loss. Moreover, the fact that these stories tend to be shared only among practitioners means that many natural scientists do not realize how interesting and lifelike digital organisms are and how natural their evolution can be. To our knowledge, no collection of such anecdotes has been published before. This paper is the crowd-sourced product of researchers in the fields of artificial life and evolutionary computation who have provided first-hand accounts of such cases. It thus serves as a written, fact-checked collection of scientifically important and even entertaining stories. In doing so we also present here substantial evidence that the existence and importance of evolutionary surprises extends beyond the natural world, and may indeed be a universal property of all complex evolving systems. (shrink)

Return-orientated programming (ROP) identifies pieces of a process’s executable memory ending in a return instruction (gadgets), and enlists them as an instruction set in which a new, “parasitic” program can be written, hijacking the process’s control flow. Since gadgets are already present in executable memory, there is no reliance upon memory being mapped as both writeable and executable, which lets the ROP program (or “chain”) bypass the shellcode attack mitigation known as w ⊕ x. As such ROP represents one of (...) the most difficult exploit mechanisms to mitigate. This thesis explores ROP-chain generation as a domain for evolutionary computation. It describes a system called ROPER (Return-Oriented Program Evolution with ROPER), designed and implemented by the author, which orchestrates the evolution of ROP-chains towards declaratively specified objectives. The author goes on to study the behaviour and ecology of the ROP-chain populations generated by ROPER, and their responses to various environmental pressures. Issues of importance include: 1) establishing a robust environment for evolution to discover ROP solutions, 2) the design of variation operators, 3) emergent strategies for genomic resilience, and 4) the role of speciation through fitness sharing. Case studies are performed using four very different tasks representative of: 1) the functional objective of a bare bones exploit, 2) a supervised learning task, 3) policy discovery for an agent playing ‘Snake’, and 4) an “unwinnable” task in which fitness is gauged randomly, so that the effects of non-selective pressures in the environment can be studied. Taken together this work represents the first time that ROP evolution has been explicitly demonstrated (at least in the public domain), and studied across a range of tasks. (shrink)

We examine the behavior of an evolutionary search on neutral networks in a simple linear genetic programming system of a Boolean function space problem. To this end we draw parallels between notions in RNA-folding problems and in Genetic Programming, observe parameters of neutral networks and discuss the population dynamics via the occupation probability of network nodes in runs on their way to the optimal solution.

In recent years computer viruses have received much attention although their theoretical aspects have been neglected. One such aspect is the possibility of viruses as life, with the attendant characteristics of terrestrial life including evolution. Where this particular idea has been previously considered, it has been judged highly improbable. The author disagrees and argues that viral evolution may not only be possible but inevitable. After an introduction to the biology of computer viruses evidence of viral evolution will be presented as (...) well as examples of how current and future trends in computing could lead to the emergence of sophisticated and novel entities. Finally the author speculates on the consequences of this. (shrink)

Purpose The purpose of this paper is to demonstrate the advancements in artificial intelligence (AI) and conversational agents, emphasizing their potential benefits while also highlighting the need for vigilant monitoring to prevent unethical applications. Design/methodology/approach As AI becomes more prevalent in academia and research, it is crucial to explore ways to ensure ethical usage of the technology and to identify potentially unethical usage. This manuscript uses a popular AI chatbot to write the introduction and parts of the body of a (...) manuscript discussing conversational agents, the ethical usage of chatbots and ethical concerns for academic researchers. Findings The authors reveal which sections were written entirely by the AI using a conversational agent. This serves as a cautionary tale highlighting the importance of ethical considerations for researchers and students when using AI and how educators must be prepared for the increasing prevalence of AI in the academy and industry. Measures to mitigate potential unethical use of this evolving technology are also discussed in the manuscript. Originality/value As conversational agents and chatbots increase in society, it is crucial to understand how they will impact the community and how we can live with technology instead of fighting against it. (shrink)

One potentially extremely fruitful use of the tools of corpus analysis in the philosophy of science is to help us understand disputed terrains within the sciences that we study. For philosophers of biology, for instance, few controversies are as heated as those over the concepts we use in taxonomy to classify the living world, with the definition of ‘species’ perhaps most fundamental among them. As many understandings of biodiversity, in turn, involve counting the number of species present in a given (...) area, these taxonomic concepts thus become crucially implicated in our efforts in conservation biology and our response to climate change. In this chapter, we present a corpus of taxonomic journal papers, and illustrate how it might be used to make progress in the history and philosophy of taxonomy. What parts of the biological world do taxonomists most often study? Are these areas of focus related to other methodological commitments, or perhaps to their underlying conceptual disagreement? Are species that are more important to conservation, or economic concerns, or more important to local cultures, more or less likely to be the target of biological study? Corpus-based methods, we argue, are uniquely powerful for approaching questions such as these, and we hope that the case we present can serve as a fruitful example for others considering their implementation. (shrink)

We study 944 shareholder proposals submitted to 343 U.S. firms on climate change issues during 2009–2022. We use logistic and two-stage regression to estimate the propensity for a firm to be targeted or subjected to a vote at the annual general meeting and, for voted proposals, the determinants of that vote. We also examine whether climate-related proposals affect investor returns and how they relate to firms’ future environmental performance and greenhouse gas emissions. Compared to a matched sample, we first find (...) that activists target larger, more carbon-intensive, and less R&D-active firms. Second, voting likelihood is higher for firms with repeated and operations-related proposals and lower pre-proposal environmental ratings. By contrast, disclosure-related proposals are likelier to be negotiated and withdrawn. Third, repeated and operations-related proposals receive higher votes in favor, whereas votes on carbon-intensive firms do not. Fourth, building on the theory that investors act as if they distinguish among the different shareholder proposals based on the expected cost to the firm, we find evidence to support this idea. We find that investors respond negatively to ex-ante costlier proposals, such as those that relate to emissions reduction and target carbon-intensive firms. Fifth, targets’ future environmental performance rating is almost twenty percent higher after a proposal than before compared to the matched sample, whereas emissions do not budge appreciably. (shrink)

This paper focuses on the nonlinear self-interaction of gravitational waves and explores its impact on the spectrum of the resulting gravitational wave. While many authors primarily investigate the nonlinear effects within the framework of "gravitational memory," we take a different approach by conducting a comprehensive analysis of harmonic generation. Theoretical analysis indicates that higher harmonics do not possess suitable conditions for energy accumulation. However, our study presents intriguing evidence supporting the concept of "nonlinear gravitational memory": the conversion and accumulation of (...) gravitational wave energy into a persistent metric deformation in the background space (specifically referred here to as zero harmonics). In simpler terms, a wave leaves a lasting imprint on the background space, even after the gravitational pulse subsides. Furthermore, our study estimates the significance of this effect and demonstrates that it should not be disregarded. (shrink)

Many environmental ethicists think evolutionary processes are good or, put differently, that they are morally valuable. Furthermore, many claim this value can be compromised when humans disrupt or cause a break in these processes. In this paper, I argue this account is mistaken. Evolution is not good. Furthermore, evolution cannot be “broken” by mere human involvement. There is no preordained trajectory in evolution; randomness, genetic drift, and historical contingency influence all evolutionary histories. Additionally, to think humans necessarily undermine so-called “natural” (...) processes and turn them artificial is to ignore Vogel (2011, 2015), and insist on pre-Darwinian dualism. There is no morally meaningful distinction between natural selection and artificial selection; they are both simply selection. Furthermore, animals shape their own evolutionary trajectories, their progenies’, and those of other organisms through their intentions and choices—as is illustrated in the theory of niche construction. Human involvement in evolutionary processes does not “break” them nor does it necessarily reduce the value of the end products of those processes. (shrink)

The evolutionary origins of deception and its functional role in our species is a major focus of research in the science of human origins. Several hypotheses have been proposed for its evolution, often packaged under either the Social Brain Hypothesis, which emphasizes the role that the evolution of our social systems may have played in scaffolding our cognitive traits, and the Foraging Brain Hypothesis, which emphasizes how changes in the human dietary niche were met with subsequent changes in cognition to (...) facilitate foraging of difficult-to-acquire foods. Despite substantive overlap, these hypotheses are often presented as competing schools of thought, and there have been few explicitly proposed theoretical links unifying the two. Utilizing cross-cultural data gathered from the Human Relations Area Files (HRAF), we identify numerous (n = 357) examples of the application of deception toward prey across 145 cultures. By comparing similar behaviors in nonhuman animals that utilize a hunting strategy known as aggressive mimicry, we suggest a potential pathway through which the evolution of deception may have taken place. Rather than deception evolving as a tactic for deceiving conspecifics, we suggest social applications of deception in humans could have evolved from an original context of directing these behaviors toward prey. We discuss this framework with regard to the evolution of other mental traits, including language, Theory of Mind, and empathy. (shrink)

_One of the enduring queries in the development of human intellectual thought is, "What is human nature?" What does it mean to be a human tends to be defined by all disciplines, including religion? We all need theories about what makes people tick in order to predict how they will respond to their environment in various situations. Indeed, how we view human nature affects a number of things. People utilize it in their private lives to govern their daily routines, manage (...) their relationships, raise their children, and influence others. Additionally, our policies in areas of collective social life like politics, law, and education are influenced by how we view human nature. Steven Pinker critically explains the modern view of human nature and its theoretical presuppositions in his widely read book The Blank Slate: The Modern Denial of Human Nature. Pinker contends that this contemporary account of human nature faces significant challenges in light of recent developments in the fields of biology, genetics, evolution, and the brain sciences. Because it is built on axioms that we cannot accept in light of the advancements in science over the past few decades, the current theory of human nature is conceptually unsound. This research performs a comparative analysis between Pinker’s View of Human Nature and Dupré’s Critique of Evolutionary Psychology on the principles which serve as the foundation for the influential idea of human nature, and contributes significantly in our contemporary intellectual life._. (shrink)

The present paper discusses and studies Plantinga's intended context and meaning regarding the Evolution Theory - which we have named as "God-based Evolution" - based on the foundations and premises of reformed epistemology which is one of the examples of his religious scientific theories; in the next part of the paper Dennett's criticisms as a New Darwinian atheist on Plantinga's "God-based Evolution" have been modified and finally, the writer evaluates and judges the views of these two philosophers in order to (...) reach a final conclusion. In order to briefly explain these two views, it must be said that according to Plantinga Evolutionism and Creationism are cultural concepts that act as ideological indicators; in contrast, Dennett accepts an exclusively secular or godless view in order to understand evolution. According to him, Darwin's idea regarding the Evolution Theory is dangerous and is like a cosmological acid that absorbs the concepts of God, religion and later the "Theory of Creationism" into itself. But Plantinga, in defense of his view, believes in the existence of Divine action from evolutionary biology which is important in contemporary discussions about the relation between biology, philosophy and theology. (shrink)

The concept of democracy is fraught with ambiguity. There are none who know what democracy means, where it came from or indeed where it is going despite it being the system of governance that is most widely heralded for its modernity and promotion of equality. For example, the theory and principles that underpin democracy are unimaginably complicated while its institutions across time and space are contradictory. The stark reality is that democracy is imprisoned by parochialism, subjectivity and myopia with humanity (...) being governed by a system that is does not fully understand. If democracy is everywhere and everyone wants it, then how do we not know what it means? If we do not know what democracy means, then why is it forcefully driving our politics and societies? This extremely ambitious and illuminating book offers a way out by answering these important questions and by exploring democracy in its purest form and as such has been nominated for the 2013 Stein Rokkan Prize. Evolutionary Basic Democracy has been nominated for the 2013 Stein Rokkan prize. This extremely prestigious award is presented by the International Social Science Council, The University of Bergen and the European Consortium for Political Research. For more details please click the link below."--Publisher's website. (shrink)

This comprehensive qualitative literature study examines the profound impact of Auguste Comte's philosophy on the evolution of knowledge, specifically focusing on the analysis of philosophical perspectives regarding the classification of science. Through a systematic and critical analysis of diverse and reputable sources, this study explores Comte's thoughts and ideas, employing a philosophical approach to understand the influence of his philosophy on the organization and development of scientific knowledge. The findings highlight the hierarchical classification of science proposed by Comte, emphasizing the (...) interdependence of scientific disciplines and the role of philosophy in synthesizing knowledge. The study contributes to our understanding of Comte's contributions and their implications for the evolution of knowledge. (shrink)

Extraterrestrial Altruism examines a basic assumption of the Search for Extraterrestrial Intelligence (SETI): that extraterrestrials will be transmitting messages to us for our benefit. This question of whether extraterrestrials will be altruistic has become increasingly important in recent years as SETI scientists have begun contemplating transmissions from Earth to make contact. Technological civilizations that transmit signals for the benefit of others, but with no immediate gain for themselves, certainly seem to be altruistic. But does this make biological sense? Should we (...) expect altruism to evolve throughout the cosmos, or is this only wishful thinking? Is it dangerous to send messages to other worlds, as Stephen Hawking has suggested, or might humankind benefit from an exchange with intelligence elsewhere in the galaxy? Would extraterrestrial societies be based on different ethical principles, or would we see commonalities with Earthly notions of morality? Extraterrestrial Altruism explores these and related questions about the motivations of civilizations beyond Earth, providing new insights that are critical for SETI. Chapters are authored by leading scholars from diverse disciplines—anthropology, astronomy, biology, chemistry, computer science, cosmology, engineering, history of science, law, philosophy, psychology, public policy, and sociology. The book is carefully edited by Douglas Vakoch, Director of Interstellar Message Composition at the SETI Institute and professor of clinical psychology at the California Institute of Integral Studies. The Foreword is by Frank Drake. This interdisciplinary book will benefit everybody trying to understand whether evolution and ethics are unique to Earth, or whether they are built into the fabric of the universe. (shrink)

This paper endeavors to appraise scholarly works from the 1940s to the contemporary era, examining the scientific quest to transpose human cognition and consciousness into a digital surrogate, while contemplating the potential ramifications should humanity attain such an abstract level of intellect. The discourse commences with an explication of theories concerning consciousness, progressing to the Turing Test apparatus, and intersecting with Damasio’s research on the human cerebrum, particularly in relation to consciousness, thereby establishing congruence between the Turing Test and Damasio’s (...) notions of consciousness. Subsequently, the narrative traverses the evolutionary chronology of transmuting human cognition into machine sapience, and delves into the fervent endeavors to metamorphose human minds into synthetic counterparts. Additionally, theoretical perspectives from the domains of philosophy, psychology, and neuroscience provide insight into the constraints intrinsic to AI implementations, contentious hypotheses, the perils concealed within artificial networks, and the ethical considerations necessitated by AI frameworks. Furthermore, contemplation of prospective repercussions facilitates the refinement of strategic approaches to safeguard our future Augmented Age Realities within AI, circumventing the prospect of inhabiting an intimidating technopolis where a mere 30% monopolize the intellect and ingenuity of the remaining 70% of human minds. (shrink)