If you want to understand life, don't think about vibrant, throbbing
gels and oozes, think about information technology.
--- Richard Dawkins, The Blind Watchmaker, 1986,
Norton, p. 112.
The grand Question which every naturalist ought to have before him
when dissecting a whale or classifying a mite, a fungus or an
infusorian is "What are the Laws of Life"
-- Charles Darwin
B Notebook B229
is to seek fundamental knowledge about the nature and
behavior of living systems and the application of that knowledge to
enhance health, lengthen life, and reduce illness and disability.
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were invented here!
were invented here!
how DNA gets information!
Sphere packing -
Molecular efficiency -
a measure of biological states
Z. Qian, A. Trostel, D. E. A. Lewis, S. Jun Lee, X. He, A. M. Stringer, J. T.
Wade, T. D. Schneider, T. Durfee, and S. Adhya.
Genome-Wide Transcriptional Regulation and Chromosome Structural
Arrangement by GalR in E. coli
Front Mol Biosci, 3:74, 2016.
as of 2016 Nov 21
has been upgraded
so that multi-part sequence walkers are now completely connected
using vertical lines along with the rainbow horizontal connections:
as of 2016 Oct 15
"Information Theory in Biology"
at the meeting
Department of Electrical Engineering
Indian Institute of Technology, Kanpur, India,
Wednesday, October 19th, 2016.
Speaker: Thomas Schneider, National Institute of Health, USA
In this talk I will sweep across the major ideas I have developed
using information theory to understand biology (see
We will begin with measuring the
information of protein or RNA binding sites on DNA or RNA (Rsequence,
bits per site) using Claude Shannon's information theory. The
resulting information curve can be displayed by the now-popular
graphical method of sequence logos which we invented. The total
information of binding sites (area under a logo) is predicted by the
genome size and number of sites (Rfrequency, bits per site), and this
leads to a model for the evolution of binding sites which you can run
I will then introduce how
to apply the same theory to individual binding sites, sequence
walkers. An important question is the relationship between binding
site information and the binding energy. This lead to my discovery
that many molecular systems are 70% efficient. Surprisingly, the
mathematics that explains 70% efficiency applies to all biological
systems that have distinct states.
US Patent No. 8,703,734 Issued April 22, 2014,
Ilya Lyakhov, Thomas D. Schneider, and Danielle Needle.
as of 2014 Apr 28.
An important paper was published confirming for the first time
my 70% efficiency discovery:
Analysis of DevR regulated genes in Mycobacterium tuberculosis.
Bandyopadhyay A, Biswas S, Maity AK, Banik SK.
Syst Synth Biol. 2014 Mar;8(1):3-20.
preprint at arxiv.)
They observed that the DevR protein has 66% isothermal efficiency.
as of 2014 Mar 11
Peter K. Rogan.
Rapid and comprehensive identification of prokaryotic organisms.
In this patent Pete Rogan made a clever use of sequence logos.
See figure 2: this is a logo of 16S rRNAs. Pete
used the logo to
chose well conserved parts (into which to put PCR primers)
surrounding less conserved parts (which are different for
Thus the sequence of the fragment obtained can rapidly
identify a bacterial species.
The patent will issue on December 13th as US Pat 8,076,104.
as of 2011 Sep 17.
Keywords for indexing:
70 percent efficiency,
DNA binding site,
fundamental mathematics of biology,
National Cancer Institute,
National Institutes of Health,
T. D. Schneider,
Thomas D. Schneider,
limits of computers,
mathematics of biology,
mathematics of living things,
molecular information theory,
theory of biology,
theory of molecular machines,
what is information theory,
what is information
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