Archive for March, 2015

Gordon Conference on Animal Microbe Symbioses: Hologenome Theory of Evolution

After almost 30 years of thinking and occasionally speaking about the hologenome  theory  I’m registered for the Gordon Conference in New Hampshire in June.  I hope I can meet some open minded and thoughtful people with whom to discuss these thoughts.

Since Gordon Conferences operate under what amounts to Chatham House Rule, and communications can’t be quoted (not that I am likely to publish much at this rate) I thought I’d at least post my abstract here in the dusty old blog.

RA Jefferson “Hologenome Theory” Abstract, Gordon Conference on Animal-Microbe Symbiosis, June 21-26 2015

The Hologenome Theory of Evolution: The origins, logic and implications of a ‘cloud genetics’.

Richard A. Jefferson, Professor of Biological Innovation, Queensland University of Technology (QUT), Brisbane, Australia & Cambia, GPO Box 3200, Canberra, Australia

The hologenome theory of evolution developed by Jefferson (1994, 2007) proposes that natural selection occurs at the level of a holobiont, comprising the population of microbial constituents together with a replication-competent macro-apobiont; in essence a populated scaffold. It asserts that the genetic composition of the holobiont comprises the genetic contributions of the micro- and macro-biota in a form called the hologenome and that this ‘hologenotype’ is optimized by natural selection for its performance and persistence over time, but also for its plasticity and responsiveness to change.

The origins of the theory hinge on studies of glucuronide metabolism by diverse vertebrate-associated microbes. The concentration and bio-availability of virtually all the steroid hormones that modulate, regulate or control reproductive performance, mate choice and ontogeny of vertebrates depends on the microbial processing of conjugated intermediaries, including steroid glucuronides. This occurs in microbially-rich complex ecosystems including intestine and surface epithelia, and is mediated by glucuronidases, arylsulfatases, permeases and other enzymes encoded by an extraordinary diversity of microbial constituents, and allows levels of these circulating hormones (and countless other metabolites) to be adjusted by action of a dynamic population of microbes that in turn are intrinsically sampled from and sampling the environment.

The implications from this premise are many, and in many ways, non-trivial. The ability to alter and modulate, amplify and suppress, disseminate and recruit new capabilities as microbially-encoded ‘traits’ means that sampling, sensing and responding to the environment become intrinsic features and emergent capabilities of the holobiont, with mechanisms that can provide rapid, sensitive, nuanced and persistent performance changes. Hologenome theory is essentially probabilistic. The population of microbes associated with the performant microbiome of a holobiont is neither fixed nor necessarily predictable, with the holobiont behaving as an indeterminate, temporally persistent standing wave.

Just as quantum theory (quantum field theory and quantum mechanics) allows a more accurate and generalizable description of physical phenomena at small and large scale both in time and space, so hologenome theory accommodates observations of the ubiquity and function of microbial populations, but also exposes observational and cognitive bias that has hitherto dominated our thinking about evolution and life sciences and their applications to society and the environment. This includes obvious impacts on health and agricultural improvement strategies, but curiously also economics and social institutions. The now classical ‘New Synthesis’ of evolution is by extension, basically a ‘Newtonian’ view of evolution and has fostered a scholarship of symbiosis that focuses on individual interactions rather than probabilistic, synergistic and dynamic populations and the complex and resilient systems these produce.

In this presentation I will review the biochemical and molecular genetic experimental work underlying the articulation of the theory, and describe some of the implications of its probabilistic nature that neither requires nor supports the intellectual construct and memes of ‘host’ and ‘symbiont’.

RA Jefferson (1994) The Hologenome in “’A Decade of PCR: Celebrating 10 Years of Amplification,’ Proceedings of a Symposium” Video released by Cold Spring Harbor Laboratory Press, 1994. ISBN 0-87969- 473-4.

RA Jefferson (2007) “The Hologenome & Hologenomics: a Different lens on evolution” in Science as Social Enterprise.