Unreal Nature

March 2, 2013

Between Living and Non-Living

Filed under: Uncategorized — unrealnature @ 7:14 am

… A further stream of reflection sees no contradiction in regarding viruses as alternating between living and non-living phases.

This is from Processes of Life: Essays in the Philosophy of Biology by John Dupré (2012). This chapter was co-written with Maureen O’Malley:

Viruses are often deemed not to be alive on the grounds that they cannot reproduce themselves autonomously, and nor can they metabolize. They can, however, carry out such biologically impressive activities as entering cells, co-opting the transcription and translation machinery of the cell, and picking up and moving about DNA from the organisms with which they interact. And by exploiting or collaborating with cellular organisms in these ways, they very effectively reproduce themselves and have no need of autonomous metabolism.

Thinking about viruses and their relegation to the realms of non-living and non-organismal entities necessitates a consideration of whether organism and living entity are identical categories, and whether a minimal account of life has to begin with cells. Such thoughts then invite further reflection on other biological entities that seem to have some autonomy but are almost never described as living organisms. Joshua Lederberg, a pioneer in molecular biology who first formulated the term ‘plasmid,’ places these biological entities in the same category of ‘symbiotic organisms’ as he does mitochondria and chloroplasts. For him, they comprise part of ‘the organic whole.’ He argues more broadly that any scheme of life has to work out where to place prions, plasmids, integrons (gene capture and integration systems), and transposons — mobile genetic elements in a genome, sometimes called ‘jumping genes.’

We will take our cue from Lederberg and start our examination of life with a discussion of some of the biological entities that inhabit this grey area between living and non-living, specifically prions, plasmids, organelles, endosymbionts, and reduced extracellular symbionts. As we move along the continuum of biological organization to entities whose living status is never questioned (micro- and macro-organisms), we will investigate whether these instances of entities possess some of the most frequently cited life-endowing characteristics, such as spatial boundaries, reproduction, metabolism, and evolvability, and how our criterion, collaborativity, relates to these characteristics. We will also argue that our account of cellular and subcellular entities fits very well with origin-of-life scenarios that stress chemical collaboration and community. Our bottom-up perspective, starting at the microscopic level of biology, rather than top-down from its most complex and undisputed exemplars, will suggest that much standard thinking is based on quite restricted and even covertly normative conceptions of what life is. This perspective will ultimately challenge the view that entities such as viruses are not alive and that the minimal definition of life must be cellular.

Regretfully, I skip over the discussion of prions, plasmids, organelles, endosymbionts, and extracellular symbionts (all of which are fascinating). I will stick to just their coverage of viruses, starting with a description of how they work, in case you aren’t familiar viruses:

Viruses are typically very small packages of single- or double-stranded DNA or RNA (often just a few genes), wrapped up in a coating of protein and sometimes an additional lipid envelope. They are prolific, highly diverse, and ancient, although there is incomplete agreement about their evolutionary origins (as we shall see below).

Viruses have well-defined life cycles that are often described as consisting of ‘developmental’ stages. The cycle begins with virions, the inert form of viruses, which are transformed into the next stage of adsorption, when viruses or phages (the viruses with affinities for prokaryotes rather than eukaryotes) ‘dock’ onto the outer cell membrane of their hosts and either enter the cell or have their DNA absorbed into it. Their protein coats dissolve or are discarded, after which the viruses co-opt the host’s cellular machinery to express genes that lead to genome replication, maturation (in which the new genomes are wrapped in freshly synthesized protein), and, finally, release from the intact or lysed cell. A number of plant viruses move actively from cell to cell, using virus-encoded movement proteins. Some viruses have an extra developmental stage in which they remain dormant in the host cell or genome as prophages or proviruses and are inherited. Endogenous retroviruses, which are viruses that have integrated permanently into the host chromosomes and are inherited vertically, have left their mark on many organismal genomes, including our own. Included amongst these viruses are those that are crucial for the development of the placenta in mammals.

Phage_injecting_its_genome_into_bacteria_svg
Some bacteriophages inject their genomes into bacterial cells (not to scale) [image and caption from Wikipedia]

… There are three main hypotheses about the origins of viruses: primeval pre-cellular life (the virus-first or primordial hypothesis), degenerate intracellular parasites (the reduction or regression hypothesis), and as renegade prokaryote genes (the escape hypothesis). The most popular is currently the third one, which is that viruses are actually genetic elements that opted out of cellular organization and are thus true instantiations of ‘selfish’ genetic material. However, new versions of the primordial hypothesis are also being promoted. They shift the discussion back to the pre-cellular ‘unselfish’ gene pool and give viruses major roles as evolutionary innovators. Whatever their origins, viruses have made extraordinary contributions to the evolution of non-viral life through their proclivity for mutation and recombination, and their ability to pick up and move genes from one organism to another (transduction) and integrate their own and other genetic material into host genomes.

[ ... ]

… A further stream of reflection sees no contradiction in regarding viruses as alternating between living and non-living phases.

Outside the host cell, poliovirus is as dead as a ping-pong ball. It is a chemical that has been purified … and crystallized … with its physical and chemical properties largely determined … and its three-dimensional structure solved. Just like a common chemical, poliovirus has been synthesized in the test-tube. Once poliovirus, the chemical, has entered the cell, however, it has a plan for survival. Its proliferation is then subject to evolutionary laws: heredity, genetic variation, selection towards fitness, evolution into different species and so forth — that is, poliovirus obeys the same rules that apply to living entities. [E. Wimmer, 2006]

The inertness of virions outside the cell leads us to think that viruses are similar to prokaryotes with spore stages as well as to plant seeds and fungal spores.

[ ... ]

… Single animal or plant cells are only truly alive when they are collaborating with other cells. Whether prokaryote or eukaryote, micro-organismal or macro-organismal, cells work together in a great variety of ways, collectively structuring their activities through numerous mechanisms. In the same way that cellular life-forms are only fully functional when collaborating with other cells, so are viruses, plasmids, and prions. Is there a hard line worth drawing between different modes of cellular and subcellular collaboration — between collaboration and exploitation? We think not.

… Perhaps the most widely agreed criteria for being a living thing are metabolism, or energy transformation, and reproduction, the capacity of entities to make more of themselves. Biochemical transformation of energy from the environment, first to maintain their own structural and functional integrity, and second to reproduce themselves, is a plausible general account of what living things most fundamentally do. Metabolism, then, is a basic means of survival for anything alive. For many biologists, this is the most fundamental biological process and the true demarcator of living and non-living entities. An internal capacity for self-sustainability on the basis of the processing of external resources is a common understanding of organismal function.

Our reservations about this criteria are not about whether metabolism is a basic characteristic of living systems, but whether it can effectively be deployed to make the kinds of distinctions into discrete living entities that are generally expected by theorists of biology. The reason for this is that metabolism is typically a collaborative activity involving many of the things that are generally supposed to be discrete living entities. It is generally supposed, for example, that a human, qua discrete biological entity, consists of a lineage of cells deriving in a series of divisions from an original zygote. But a functional human consists also of very large numbers of symbiotic bacteria, in fact amounting to 90 percent of the cells in the total human system. These microbial cells are deeply involved in the metabolic processes, most obviously digestion, that maintain the functioning of the system. Hence, a human, conceived in the way just described, is not capable of performing autonomously the metabolic processes essential for its survival. If it is considered sufficient merely to carry out independently some metabolic processes, but not all those necessary for the survival of the entity, then organelles and endosymbionts will count as living entities.

While we noted earlier that reproduction is a necessary feature of life, we also mentioned its inadequacies for a full understanding of life. As we have shown, viruses, organelles, and even prions reproduce themselves. The reproduction criterion is sometimes tied to autonomous reproduction, so that viruses and the like, though they are very effective replicators, are often taken to fail this criterion because they do not reproduce independently and must use ‘true’ organisms from different lineages to achieve their reproduction. However, it is doubtful whether even paradigmatic multicellular organisms can meet the criterion of lineage-exclusive autonomous reproduction. Those insects in which reproduction is substantially under the control of endosymbiotic Wolbachia are one obvious counterexample. But more generally, in so far as reproduction requires the deployment of metabolic processes, as it surely must, it depends also on endo- and exosymbiotic microbes.

… Evolutionary history suggests that life involves a range of co-evolving hierarchies, and that non-life and life share a huge and biologically significant territory that buffers and makes more complex any account of either. Ecology presents us with scenarios of collaboration at least as compelling as those that highlight competition, and the former are rapidly increasing our understanding of the microbial and macrobial world. Thinking of life as the result of the intersection of lineage-forming, metabolically collaborative matter, organized within different interacting levels, allows a smooth transition from the earliest living matter to standard examples of life and beyond them all the way up to contemporary ecosystems.

My most recent previous post from Dupré’s book is here.

-Julie

http://www.unrealnature.com/

4 Comments

  1. The end point, of course, is a conclusion that “life” has no specific meaning … it is, like any other signifier, a generalised concept defined by its usage – and defined with a certainty which declines as precision increases.

    Comment by Felix — March 2, 2013 @ 1:53 pm

  2. You can stand that on its head; invert it, run it backwards and … choose to see the cause instead of the effect — as generative, not dilutive, of signification. Or something like that; inverting while standing on my head seems to discombobulate the gravity of my thoughts.

    Comment by unrealnature — March 3, 2013 @ 7:09 am

  3. JH> … choose to see the cause instead of the effect…

    Or question whether cause and effect are, in fact, distinct?

    JH> …as generative, not dilutive, of signification…

    Definitely … or both?

    But seriously, folks … I do question whether “life” has a precise meaning which does not evaporate when used as more than a general idea.

    Comment by Felix — March 3, 2013 @ 7:17 am


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