Key points that are mostly missing so far

1
Key points that are (mostly) missing so far
Nigel Goldenfeld, University of Illinois at
Urbana-Champaign

• View of biology is too limited.
• Hallmark of condensed matter physics is the study
  of collective phenomena
• Should look beyond the obvious molecular and
  cellular level
• Emergence, dynamics of spatially-extended systems
  and collective behaviour.
• Examples metabolic scaling laws, ecology
  (microbial ecology in particular) population
  biology, invasions and epidemics, genome
  dynamics, social organization, interaction of
  biological organisms with environment.
• Taught course on biological information and
  complexity (Fall 2001)
• Problem selection more important in biology than
  condensed matter because biology is broad and
  shallow
• What are key areas where physicists can answer
  questions that biologists already care about?
• Where do the biologists seek our help?
• Ask biologists
• Ask the NSF

2
Where do biologists seek our help?

• Steven Jay Gould, New York Times, Feb 19, 2001
• Homo sapiens possesses between 30,000 and 40,000
  genes... In other words, our bodies develop under
  the directing influence of only half again as
  many genes as the tiny roundworm ....
• The collapse of the doctrine of one gene for one
  protein, and one direction of causal flow from
  basic codes to elaborate totality, marks the
  failure of reductionism for the complex system
  that we call biology.
• First, the key to complexity is not more genes,
  but more combinations and interactions generated
  by fewer units of code and many of these
  interactions (as emergent properties, to use the
  technical jargon) must be explained at the level
  of their appearance, for they cannot be predicted
  from the separate underlying parts alone.

3
Where do biologists seek our help?
NSF Solicitation 00-22 Biocomplexity

• Biocomplexity arises from dynamics spanning
  several levels within a system, between systems,
  and/or across multiple spatial (microns to
  thousands of kilometers) and temporal
  (nanoseconds to eons) scales.
• This special competition will specifically
  support Research Projects which directly explore
  nonlinearities, chaotic behavior, emergent
  phenomena or feedbacks within and between systems
  and/or integrate across multiple components or
  scales of time and space in order to better
  understand and predict the dynamic behavior of
  systems.

4
What do we have to offer?

• Biology reductionism vs. holistic approach
• Physics high energy physics (fundamental),
  condensed matter (holistic)
• Analogy BEC atomic physicists used to dealing
  with single particle properties, now benefiting
  from the superfluid community (collective
  phenomena)
• Education
• Scaling laws
• Biological systems range of scaling dwarfs that
  of critical point phenomena, yet very poorly
  understood
• Metabolic scaling, species-area law,
• Strong fluctuations
• Biological probability distributions frequently
  not normal strong fluctuations ? heavy-tailed
  distributions
• Ecosystem stability (rainforests, financial
  markets, )
• Spatially-extended dynamical systems
• Ecological modelling current hot topic is role
  of space!!
• Emergent properties population dynamics,
  epidemics
• Systems biology large-scale modelling of cell
  and organism dynamics
• How can you measure all the rate constants?
• Systems reduction goal of systems biology should
  be to find minimal models that capture most
  important dynamics, not excessive realism.

5
Challenge

• Funding how do we protect embryonic advances
  made by condensed matter physics?
• - Should we seek funding in regular biological
  areas of NSF once we have got started? How do we
  gain appreciation for our perspective from the
  existing biologists?
• - Is DMR the right place, beyond providing small
  amount seed money?
• I read so many biology papers and have been
  doing so much biology, that I am starting to
  think like a biologist.
• And that means I am losing the special viewpoint
  I bring to the subject
• -Taekjip Ha (experimentalist in single-molecule
  techniques at Illinois)

6
Biocomplexity Mammoth hot springs at Yellowstone
National Park

• Does microbial metabolic activity plays a
  significant role in the deposition of these
  travertine terraces by the degassing of CO2?
• Can we use observation of certain geological
  structures to infer the existence of microbial
  life?
• On Earth?
• On Mars?
• Answering question ?
• Geomorphological pattern formation
• genomic ecology of microbes and metagenomics
• evolutionary dynamics of microbial genomes