Publications

Mariscal C 2022: “Introduction to Philosophy of Science”
Mind, Cognition and Neuroscience: Benjamin Young & Caroline Dicey Jennings (eds.). Routledge

Download.

Mariscal C 2021: “Life.” Stanford Encyclopedia of Philosophy

Read

Abstract: Open a textbook in biology and you’ll find a purported definition of life, usually in the form of a list of characteristics that apply to organisms, their parts, their interactions, or their history. Often these definitions will be nothing more than descriptions or rely on more controversial theoretical commitments.

Like many basic concepts, it is difficult to non-controversially define life. Most people simply avoid the issue by ignoring marginal cases, accepting the vagueness of the boundary cases, or setting aside the whole issue as beyond their scope. Nonetheless, there are many people whose work seems to require a rigorous demarcation of life, especially in new scientific contexts, such as astrobiology, origins of life, or synthetic biology. As such, the nature of life continues to be a hotly debated topic.

This article focuses on the subject matter of biology: life. The first half of this article will focus on attempts to characterize life by both philosophers and scientists. The first section will describe alternative accounts of definitions, its two subsections will cover historical and contemporary definitions, and section 2 covers the recent countertrend in skepticism toward definitions of life. Because the various stakeholders have different goals, the second half will focus on those goals. Sections 3, 4, and 5 cover topics that some believe require a definition of life: artificial and synthetic life, the origin(s) of life, and the search for life in the Universe. Section 6 covers entities that are much larger or smaller than organisms, while section 7 covers the role life takes in the context of society, especially with respect to questions raised by new technology.

Stull KE, Bartelink EJ, Klales AR, Berg GE, Kenyhercz MW, L’Abbe EN, Go MC, McCormick K, Mariscal C: “Moving Beyond a Lost Cause: Forensic Anthropology and Ancestry Estimates in the United States” 2020
Journal of Forensic Sciences 65(5): 1791-2. doi: 10.1111/1556-4029.14616

Download.

Conclusion: Bethard and DiGangi’s letter to the editor does not acknowledge the long-standing trend in biological anthropology to rebut typological approaches and to interpret human biological diversity as impacted by complex sociocultural forces and microevolutionary processes. In the same way that Bethard and DiGangi challenged us to find datadriven support that ancestry inferences aid investigative outcomes, we also should be seeking data-driven support for the claimed negative impacts of ancestry on investigations. Asking, and adequately answering, these big-picture, real-world application questions is an essential part of any scientific discipline and certainly would inform the future practice of forensic anthropology in a positive way, regardless of the conclusions.
Is there more work to be done? Yes, most certainly. Can we envision a biological profile without ancestry? For many of us, the answer is conditionally no. We believe abandoning the estimation of ancestry without proper evaluation within our discipline and consultation with our stakeholders could harm cultural redress in our society and stagnate and dogmatize our discipline. Nevertheless, we agree that there should be conversation and research conducted on these issues as a means to best combat complacency in an imperfect system. We call on our colleagues to (a) continue to understand the genetic and environmental facets of the traits, features, and measurements we assess for all aspects of the biological profile; (b) contextualize the practice of ancestry estimation within the biological and cultural frameworks in which it exists today; (c) continue to educate ourselves, the public, law enforcement, students, and others on the evolutionary framework of human populations and the historic circumstances that lead to racial ideologies; (d) be engaged professionals and be active advocates for our cases; (e) implement best practices to ensure quality case results and traceability; (f) reject manuscripts that contain racialized and racist science when submitted to scientific journals; and (g) have a conversation regarding the responsibility anthropologists bear to redress this systemic problem.

• Mariscal C, Brunet, TDP 2020: “What are Extremophiles? A Philosophical Perspective”
Social and Conceptual Issues In Astrobiology: Kelly C. Smith, Carlos Mariscal (eds.). Oxford University Press, Oxford.

Download.

In the 1970s, R. D. MacElroy coined the term “extremophile” to describe microorganisms that thrive under extreme conditions (MacElroy, 1974). This hybrid word transliterates to “love of extremes” and has been studied as a straightforward concept ever since. In this chapter, we discuss several ways the term has been understood in the scientific literature, each of which has different consequences for the distribution and importance of extremophiles. They are, briefly, human- centric, at the edge of life’s habitation of morphospace, by appeal to statistical rarity, described by objective limits, and at the limits of impossibility for metabolic processes. Importantly, these concepts have coexisted, unacknowledged and conflated, for decades. Confusion threatens to follow from the wildly varied inclusion or exclusion of organisms as extremophiles depending on the concept used. Under some conceptions, entire kinds of extremophiles become meaningless. Since our understanding of how life works is shaped by what we take to be its extremes, clarifying extremophily is key for many large- scale projects in biology, biotechnology and astrobiology.
In what follows, we proceed as if a noncontroversial account of life is possible and that it is possible to find complex chemistry in the universe that is similar enough to life on Earth such that both may be considered instances of “life” (but see Mariscal & Doolittle, 2018). We raise, but do not address, the questions of whether the distribution of life on Earth is representative of what we may find elsewhere in the universe, whether the same kinds of extremophiles would exist given a replay of the tape of life. Additionally, each of these concepts assumes life based on some sort of biochemistry in this universe, effectively ruling out claims made by some artificial life proponents that their digital organisms are genuine examples of life (Langton, 1989; Ray, 1995). On the distinction between extremophilic and extremotolerant, we note that all accounts will accept the latter as a broader category than the former, since tolerance of extreme conditions is a prerequisite for extremophily under any conception. Indeed, there will be many extreme environments where tolerance is the only option (e.g., Bacillus marismortui was extracted and grown from 250- million- year- old salt crystals in the Permian Salado Formation in an inactive yet persistent state; Vreeland et al., 2000). The nature of the environment precluded any organisms thriving.
We also note that extremophily, as a functional category, is potentially applicable at many levels of the biological hierarchy. Extremophily at one level does not necessarily extend to higher and lower levels. For instance, a microorganism in isolation might be quite intolerant to certain environmental conditions yet flourish when subjected to the same conditions in the presence of a natural biofilm.
Alternatively, a protein molecule might be quite active under certain conditions even if the optimal environment for the organism containing it is far more mesophilic. There is an industry of artificially selecting organisms and proteins to adapt to extreme environments (see van den Burg & Eijsink, 2002), providing some justification to consider “functioning at extremes” as a worthwhile category of investigation.
Finally, we also note certain physico- chemical ranges are rarely considered with respect to extremophily (e.g., time span, size, nutrient availability; Hoehler & J rgensen 2013), as well as some biological parameters (abundance, isolation, competition, etc.). Perhaps scientific interest must also come into play as to the reason these criteria are not considered relevant. We return to this and other issues later.
In the next section, we give five definitions of extremophily and show their benefits, drawbacks, and unintended consequences. These arguments are summarized in Table 10.1 and represented visually in the three figures. Given research on polyextremophiles, it seems Figure 10.2 is a more plausible representation of the state of current knowledge than the idyllic Figure 10.1 (Harrison et al., 2013). Apparently, life is patchily distributed across various dimensions, which may reflect its contingent history, poor sampling, fundamental limits, or something else. Figure 10.3 shows the conceptual flowchart for all of these views.
In the following section, we take a step back to ask whether we should choose between these definitions and how such a judgment could be made. We argue for a limited pluralism, in which some, but not all, of the concepts are acceptable relative to certain practical and theoretical aims.

• Mariscal C, Barahona A, Aubert-Kato N, Aydinoglu AU, Bartlett S, Cárdenas ML, Chandru K, Cleland C, Cocanougher BT, Comfort N, Cornish-Bowden A, Deacon T, Froese T, Giovannelli D, Hernlund J, Hut P, Kimura J, Maurel M-C, Merino N, Moreno A, Nakagawa M, Pereto J, Virgo N, Witkowski O, Cleaves II HJ: “Hidden Concepts in the History and Philosophy of Origins of Life Studies: A Workshop Report” 2019
Origins of Life and Evolution of Biospheres 49(3), 111-145.

Download.

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up”
approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin.We also describe another family of paths motivated by a” circularity” approach to life, which is guided
by such thinkers as Maturana & Varela, G nti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research.
This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question.

• Mariscal C, Doolittle WF: “Life and Life Only: A Radical Alternative to Life Definitionism” 2018
Synthese. doi: 10.1007/s11229-018-1852-2

Download.
Abstract: To date, no definition of life has been unequivocally accepted by the scientific community. In frustration, some authors advocate alternatives to standard definitions. These include using a list of characteristic features, focusing on life’s effects, or categorizing biospheres rather than life itself; treating life as a fuzzy category, a process or a cluster of contingent properties; or advocating a ‘wait-and-see’ approach until other examples of life are created or discovered. But these skeptical, operational, and pluralistic approaches have exacerbated the debate, rather than settling it. Given the failure of even these approaches, we advocate a new strategy. In this paper, we reverse the usual line of reasoning and argue that the “life problem” arises from thinking incorrectly about the nature of life. Scientists most often conceptualize life as a class or kind, with earthly life as a single instance of it. Instead, we advocate thinking about Earth’s Life (with a capital ‘L’) as an individual, in the way that species are now thought to be. In this view, Life is monophyletic clade that originated with a Last Universal Common Ancestor (LUCA), and includes all its descendants. We can continue to use the category ‘life’ (lower case ‘l’) pragmatically to refer to similarities between various phenomena and Life. But the relevant similarities are a matter of debate, not discovery. The search for other life in the Universe, then, is merely a search for entities that resemble parts of Life in whatever sense astrobiologists find most appealing (e.g. metabolism, evolution, information, etc.). This does not mean that the search for evolved complexity elsewhere in the universe or its creation in the lab are futile endeavours, only that debates over what is or is not alive are. Ironically, finally abandoning the concept ‘life’ may make our searches for evolved complexity more fruitful. We explain why.

• Mariscal C, Fleming L:”Why We Should Care About Universal Biology” 2017
Biological Theory. doi: 10.1007/s13752-017-0280-8

Download.
Abstract: Our understanding of the universe has grown rapidly in recent decades. We’ve discovered evidence of water in nearby planets, discovered planets outside our solar system, mapped the genomes of thousands of organisms, and probed the very origins and limits of life. The scientific perspective of life-as-it-could-be has expanded in part by research in astrobiology, synthetic biology, and artificial life. In the face of such scientific developments, we argue there is an ever-growing need for universal biology, life-as-it-must-be, the multidisciplinary study of non-contingent aspects of life as guided by biological theory and constrained by the universe. We present three distinct, but connected ways of universalizing biology—with respect to characterizing aspects of life everywhere, with respect to the explanatory scope of biological theory, and with respect to extending biological insights to the structure of nonbiological entities. For each of these, we sketch the theoretical goals and challenges, as well as give examples of current research that might be labeled universal biology.

Mariscal, C. & Petropanagos, A. 2016. “CRISPR as a Driving Force: The Model T of Biotechnology.” Monash Review of Bioethics 34(2), 101-116. doi: 10.1007/s40592-016-0062-2

Download.

Abstract: The CRISPR system for gene editing can break, repair, and replace tar- geted sections of DNA. Although CRISPR gene editing has important therapeutic potential, it raises several ethical concerns. Some bioethicists worry CRISPR is a prelude to a dystopian future, while others maintain it should not be feared because it is analogous to past biotechnologies. In the scientific literature, CRISPR is often discussed as a revolutionary technology. In this paper we unpack the framing of CRISPR as a revolutionary technology and contrast it with framing it as a value- threatening biotechnology or business-as-usual. By drawing on a comparison between CRISPR and the Ford Model T, we argue CRISPR is revolutionary as a product, process, and as a force for social change. This characterization of CRISPR offers important conceptual clarity to the existing debates surrounding CRISPR. In particular, conceptualizing CRISPR as a revolutionary technology structures regu- latory goals with respect to this new technology. Revolutionary technologies have characteristic patterns of implementation, entrenchment, and social impact. As such, early identification of technologies as revolutionary may help construct more nuanced and effective ethical frameworks for public policy.

Booth, A., Mariscal, C. and Doolittle, W.F., 2016. “The Modern Synthesis in the Light of Microbial Genomics.” Annual Review of Microbiology, 70(1), 279-297. doi: 10.1146/annurev-micro-102215-095456

Download.

Abstract: We review the theoretical implications of findings in genomics for evolutionary biology since the Modern Synthesis. We examine the ways in which microbial genomics has influenced our understanding of the last universal common ancestor, the tree of life, species, lineages, and evolutionary transitions.
We conclude by advocating a piecemeal toolkit approach to evolutionary biology, in lieu of any grand unified theory updated to include microbial genomics.

• Scharf C, Virgo N, Cleaves HJ, Aono M, Aubert-Kato N, Aydinoglu A, Barahona A, Barge LM, Benner SA, Biehl M, Brasser R, Butch CJ, Chandru K, Cronin L, Danielache S, Fischer J,
Hernlund J, Hut P, Ikegami T, Kimura J, Kobayashi K, Mariscal C, McGlynn S, Menard B, Packard N, Pascal R, Pereto J, Rajamani S, Sinapayen L, Smith E, Switzer C, Takai K, Tian F, Ueno Y, Voytek M, Witkowski O, Yabuta H: “A Strategy For Origins of Life Research” 2015
Astrobiology 15(12): 1031–1042. doi: 10.1089/ast.2015.1113
Write Up: Scharf C, Virgo N, Cleaves HJ: “Collaboration: Come together to study life’s origins” 2016
Nature 529(25): 25. doi:10.1038/529025e

Download.

Abstract. A workshop was held August 26–28, 2015, by the Earth-Life Science Institute (ELSI) Origins Network (EON,see Appendix I) at the Tokyo Institute of Technology. Thismeeting gathered a diverse group of around 40 scholars re-searching the origins of life (OoL) from various perspectiveswith the intent to find common ground, identify key questionsand investigations for progress, and guide EON by suggestinga roadmap of activities.Specific challenges that the attendees were encouraged toaddress included the following: What key questions, ideas,and investigations should the OoL research community ad-dress in the near and long term? How can this communitybetter organize itself and prioritize its efforts? What rolescan particular subfields play, and what can ELSI and EONdo to facilitate research progress? (See also Appendix II.)The present document is a product of that workshop; awhite paper that serves as a record of the discussion thattook place and a guide and stimulus to the solution of themost urgent and important issues in the study of the OoL.This paper is not intended to be comprehensive or a bal-anced representation of the opinions of the entire OoL re-search community. Itisintended to present a number ofimportant position statements that contain many aspirationalgoals and suggestions as to how progress can be made inunderstanding the OoL.The key role played in the field by current societies andrecurring meetings over the past many decades is fully ac-knowledged, including the International Society for theStudy of the Origin of Life (ISSOL) and its official journalOrigins of Life and Evolution of Biospheres, as well as theInternational Society for Artificial Life (ISAL).

Powell R, Mariscal C. 2015. “Convergent Evolution as Natural Experiment: The Tape of Life Reconsidered”
Journal of the Royal Society Interface 5(6): 20150040 . doi: 10.1098/rsfs.2015.0040

Download.

Abstract: Stephen Jay Gould argued that replaying the ‘tape of life’ would result in radically different evolutionary outcomes. Recently, biologists and philosophers of science have paid increasing attention to the theoretical importance of convergent evolution—the independent origination of similar biological forms and functions—which many interpret as evidence against Gould’s thesis. In this paper, we examine the evidentiary relevance of convergent evolution for the radical contingency debate. We show that under the right conditions, episodes of convergent evolution can constitute natural experiments that support inferences regarding the counterfactual stability of macroevolutionary outcomes. However, we argue that proponents of convergence have problematically lumped causally heterogeneous phenomena into a single evidentiary basket, in effect treating all convergent events as if they are of equivalent theoretical import. As a result, the ‘critique from convergent evolution’ fails to engage with key claims of the radical contingency thesis. To remedy this, we develop ways to break down the heterogeneous set of convergent events along several dimensions based on the nature of the generalizations they support. Adopting this more nuanced approach to convergent evolution allows us to differentiate iterated evolutionary outcomes that are probably common among alternative evolutionary histories and subject to law-like generalizations, from those that do little to undermine, and may even support, the Gouldian view of life.

Mariscal, C. 2015 “Universal Biology: Assessing Universality from a Single Example” In: Dick, S.J. (ed.), The Impact of Discovering Life Beyond Earth, Cambridge: Cambridge University Press.

Download.

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), W hler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin. We also describe another family of paths motivated by a” circularity” approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that
produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research.
This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question.

• Mariscal C, Doolittle WF. 2015 Eukaryotes first: how could that be? Phil. Trans. R. Soc. B 370: 20140322. http://dx.doi.org/10.1098/rstb.2014.0322

Download.

Abstract: In the half century since the formulation of the prokaryote : eukaryote dichotomy, many authors have proposed that the former evolved from something resembling the latter, in defiance of common (and possibly common sense) views. In such ‘eukaryotes first’ (EF) scenarios, the last universal common ancestor is imagined to have possessed significantly many of the complex characteristics of contemporary eukaryotes, as relics of an earlier ‘progenotic’ period or RNAworld. Bacteria and Archaea thus must have lost these complex features secondarily, through ‘streamlining’. If the canonical three-domain tree in which Archaea and Eukarya are sisters is accepted, EF entails that Bacteria and Archaea are convergently prokaryotic.We ask what this means and how it might be tested.

Mariscal C (February 2021). “A Pragmatic Account of Universal Biology”
Daily Nous: News for and About the Philosophy Profession

Mariscal C (2017). “Universal Biology Does Not Prescribe Planetary Isolationism”
Theology and Science, 15(2), 150-152. doi: 10.1080/14746700.2017.1299384

Mariscal C, Petropanagos A (February 2016). “Response to Genome Editing: Open Call for Evidence” Nuffield Council on Bioethics

Mariscal C, Petropanagos A (October 2015). “Not Your Grandpa’s Biotechnology”
Impact Ethics: Making a Difference in Bioethics

Mariscal C, Lerner A: “Five Chances in Evolution” 2018
Studies in the History and Philosophy of Science A DOI: https://doi.org/10.1016/j.shpsa.2018.02.004

Powell R, Mariscal C 2014: “There is Grandeur in This View of Life: the Bio-Philosophical Implications of Convergent Evolution by George McGhee”
Acta Biotheretica 62: 115-121 DOI: https://doi.org/10.1007/s10441-014-9211-2