Biology by the Numbers
Developing Intuition: What Sets the Scale of X?
Drawing Inspiration From McClintock’s “A Feeling for the Organism”
…one must have the time to look, the patience to ‘hear what the material has to say to you”, the openness to “let it come to you”. Above all, one must have a “feeling for the organism”.
from chromosomal structure to macroscopic phenotype
Developing an Extra Sense
sometimes you cannot know if you should be surprised or not without a quantitative dissection of the problem
What Does It Mean to Get a Feeling for the Organism in the Age of “Big Data”?
Science is built up of facts as a house is built up of bricks, but a mere accumulation of facts is no more a science than a pile of bricks is a house…
Henri Poincare
Schmidt, Heinemann, Nat. Biotech.
Understanding What the Data Mean �Using Simple Estimates
Challenge: You’re on a Desert Island and You Have Nobody but Wilson
Biological Numeracy for Cell Biology
Knowing the Facts: Bionumbers
See Sanjoy Mahajan,
Street Fighting Mathematics
See Lawrence Weinstein and John Adam,
Guesstimation
Making Simple Estimates Using the Geometric Mean
Biology by the Numbers
(Talk in pairs)
The Cell as a Bag of X
The Cell as a Bag of Genes
(Talk in pairs)
Distribution of Protein Sizes Across Species
Cell Biology by the Numbers
Protein Sizes in Different Organisms
The Cell as a Bag of mRNA
The Cell as a Bag of mRNA
(Berman et al.)
The Single-Cell Sequencing Revolution
The Tabula muris project
A Suite of Different Ways to Count RNA
One of the Ways to Count mRNAs Is Using a Microscope!
Counting mRNAs by RNA-Seq
The Cell as a Bag of Proteins
A Suite of Different Ways to Count Proteins
a key rule of thumb: relating molarity to molecular counts
The Molecular Census of E. coli and the Importance of Reproducibility
Mass spectrometry
Microscopy
A Brief Reflection on Our Aspirations as Experimentalists
Taking the Protein Census
The Cell as a Bag of Ribosomes
Your Turn: Number of Ribosomes in E. coli using EM
Baumeister lab, MPI
Cryo Electron Microscopy image of Spiroplasma melliferum
Ribosomes and Growth Rate
Number of Ribosomes in E. coli
E. coli and Salmonella handbook
Calculating from the dry mass
Growth of a Single Cell
Campos et al. ‘14
Fidelity in biological polymerization: Key question, are we surprised?
The Insufficiency of Equilibrium Molecular Recognition
A Toy Model of Translation
The Kinetic Proofreading Idea: Energy to Fuel Error Correction
One Version of Developing Intuition: “What Sets the Scale of X?”
Personal view: if I can’t answer this question of what sets the scale in a problem, I don’t understand it.
See Sanjoy Mahajan,
Street Fighting Mathematics
See Lawrence Weinstein and John Adam,
Guesstimation
Slide Left Blank Intentionally