picture
RJR-logo

About | BLOGS | Portfolio | Misc | Recommended | What's New | What's Hot

About | BLOGS | Portfolio | Misc | Recommended | What's New | What's Hot

icon

 

Image can be zoomed with the mouse or touch-screen gestures or the controls in the upper right.

Krishtalka, L, and Robbins, RJ. 2012. Quantum biology and biological dark matter: Uprooting this view—and tree—of life. Poster presented at: Gordon Research Conference: Microbial Ecology in the Era of OMICS. 2012 Jun 24–29; Lucca, Italy. Retrieved from: http://www.rj-robbins.com/portfolio/publications/gordon-poster/

Quantum Biology and Biological Dark Matter

Gordon Research Conference: Microbial Ecology in the Era of OMICS

Lucca (Barga), Italy: 24–29 June 2012

Leonard Krishtalka & Robert J. Robbins

Abstract: Physics has a fundamental duality: quantum mechanics, which describes all of physical reality (albeit in a profoundly strange and counter-intuitive manner) and classical mechanics, which describes macro-scale physical properties and behavior. Classical mechanics is a derived and constrained subset of quantum mechanics and, as such, cannot be extended to describe quantum phenomena. Biology has realized a similar duality, demanding nothing less than a new view of life. Classical biology, typically restricted to macro-scale, eukaryotic organisms, is a highly derived and constrained subset of what we call quantum biology — the micro-scale prokaryotic realm. Macro-scale organisms evolved out of a subset of microbial ancestors — or at least a committee of microbial ancestors — via endosymbiosis and its simultaneous consequences: eukaryotic multicellularity and the emergence of the soma. As with the classical/quantum discontinuity in physics, the concepts and tenets of classical eukaryotic biology cannot be extended to quantum biology. Continuing the physics analogy, "Biological Dark Matter (BDM)," akin to cosmological dark matter, is an apt descriptor for the large, micro-scale, prokaryotic component of the biosphere. The term reflects our realization that the prokaryotic realm comprises at least half of the planet's biomass and most of its diversity, yet until recently has remained effectively invisible and intractable to direct study. Now made visible with metagenomic tools, this realm is proving to be profoundly and fundamentally different from macro-scale, classical biology. Central to classical biology is the notion of an "individual" organism, which is characterized by: (a) complete differentiation of somatic tissue from germ-line tissue, with increasing, massive somatic dominance to protect the germ line and ensure reproduction (e.g., in a stable mammalian population, each "individual" is a collection of approximately 1013 somatic cells that, during its life time, will send only two gametes successfully into the future); (b) a mechanical relationship of the soma to the external environment; and (c) a highly managed, regulated, and stable genome to accomplish a coherent ontogeny of the soma. Essentially, classical biology is the biology of the soma — the study of multicellular, eukaryotic life has been the study of highly specialized somatic tissues. These three properties of an "individual" organism simply do not exist in the microbial world of quantum biology, in which: (a) there is no soma, just a germ line; (b) absent a soma, every cell maintains a direct biochemical, rather than mechanical relationship with the external environment; and (c) absent a somatic ontogeny, genome constraint and regulation is minimal — just enough for biochemical activity to hold off entropy. Essentially, absent the specialized and highly constrained needs of an "individual" built of somatic tissue, quantum biology phenomena are no more "mini versions" of macro-scale phenomena than is quantum physics a mini version of classical mechanics. Consequently, the fundamental, predictive ideas in macro-scale biology do not apply to quantum biology, such as genetic transmission from parent to progeny, ontogenetic development of the soma through regulated gene expression — and the resultant body of biological theory. Neither do Linnaean or modern species concepts, nomenclature, taxonomy, or a tree of life. Rather, understanding quantum biology will require a novel theoretical framework and a suite of new concepts.

RJR Experience and Expertise

Researcher

Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.

Educator

Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.

Administrator

Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.

Technologist

Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.

Publisher

While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.

Speaker

Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.

Facilitator

Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.

Designer

Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

21454 NE 143rd Street
Woodinville, WA 98077

206-300-3443

E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

RJR Picks from Around the Web (updated 11 MAY 2018 )