Differentiation chapter split into five parts (a, b, c, d, and e) for easier navigation and to improve organization of abstract, basic concepts previously placed apart at the beginning and end of the previous version.  

Uploads to udemy, vimeo done.  lookatphysics.com index and dvd.php updated.  DVD folder updated.  Need: vimeo WE, udemy spotcheck, YouTube update.  

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Turned combinatorics (one video) into parts a, b, c for easier navigation and to reduce echo.  

Uploads to udemy and vimeo complete.  Updated lookatphysics.com index and dvd.php.  DVD folder updated.  W.E. all parts on lookatphysics.com (vimeo).  There’s some noticeable ADR in part b and a slight timing issue (a moment didn’t “land”) in part c.  

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Re-recorded to reduce echo, re-captured in 960x720 resolution to make the reddish font letter c against blue background look clearer (chroma subsampling problem).  

Uploads to udemy and vimeo complete.  Update to lookatphysics.com index.php unnecessary, but dvd.php updated.  DVD folder updated.  W.E. on lookatphysics.com (vimeo).  Small vector graphics error.  

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Packet of videos a, b, c, d, e, f, g (Euler + log) redone to reduce echo (done in car)

Uploads to udemy and vimeo complete.  Updated lookatphysics.com index and dvd.php.  Updated DVD folder.  

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Previous video c renamed video e, and previous video b split into videos b, c, and d.  Corrected use of “measurements” vs. “samples.”  This forces previous video d (sample variance curve fitting) to be renamed video f.  

Uploads to udemy and vimeo complete.  lookatphysics.com index and dvd.php updated.  DVD folder updated.  

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These corrections have been superseded by another set of revisions to the videos on Uncertainty propagation.  

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robotspider:

When you are sad, just remember that jumping spiders sometimes wear water droplets as hats

To be filled out

What are you trying to do? Articulate your objectives using absolutely no jargon.

Teach scientists to use mathematics to think about living things.  

How is it done today, and what are the limits of current practice?

College courses, graduate minicourses in “quantitative biology”

q-Bio summer school

Introductory textbook

Rush to get to example applications

Not enough time teaching reasoning: difficult to develop self-sufficiency (and ability to deciper literature)

Level of algebra and calculus needed not compatible with many biologists

What’s new in your approach and why do you think it will be successful?

Include a review of algebra and calculus in the 

Who cares?

National Cancer Institute Office of Physical Sciences Oncology

Young investigators

Professors

Patient advocates

If you’re successful, what difference will it make?

What are the risks and the payoffs?

How much will it cost?

How long will it take?

What are the midterm and final “exams” to check for success?

Peripheral thoughts:

I was talking to a cancer patient advocate who said that people are starting to notice that there is a lot of research that doesn’t produce rapid progress.  The advocate said that the scientific community needs to find a solution or else public outcry will task CONGRESS to fix the system.  

A clinician explained that part of the problem is that a lot of therapies are not sufficiently beneficial to be adopted as a new official “standard of care.”  That means that placebo can remain the “standard of care,” i.e. “control,” in clinical trials of novel agents.  Hence a few months extension in overall survival over placebo gets FDA approval (repeatedly, if I understand).  This improvement is so poor, that the novel agent, though approved, is not adopted as an official standard of care—lather, rinse, repeat.  

I am concerned that traditional molecular biology does not usually provide quantitative insights suitable for mathematical prediction of effects of dosing regimes.  Superficially, a lot of mol bio papers in Cell, Science, and Nature present network (flowchart) models that look like systems biology math models.  However, the “arrows” are quantitatively meaningless (magnitude, functional form, time scale).  The formula for publication is to identify a funding agency for disease A, phenotype B, and then demonstrate influences on B by molecular entity C, which is activated/inhibited by mRNA/protein/etc. D and E.  Then demonstrate correlations in vitro, and show consistency with histological staining from preclinical or patient samples.  The output {

(1) Alphabet soup interacts with itself in such-&-such ways

(2) Few arrows characterized in quantitative detail b/c reaction rate coefficients no fun to measure

(3) Dynamics information during the first 24 h of process hard to get b/c trypsinization creates artifacts

(4) Paper advertises observation of proliferation and apoptosis, but only reports Ki67 and Annexin-V INDICES, not rates

(5) Obligatory sentence about complexity even though work that actually studies complexity should not have to call attention to it (studying patterns/organization that arise from local interactions without central command—nothing sacred, not “new” law of physics)

}

can be difficult to use in math models.  Some of this is improving with video microscopy and single-cell measurement and interrogation

I feel as though we are obliged to say “complexity” and “emergence” when writing manuscripts and giving talks.  This causes problems.  

1) “We used complexity to understand this system”  

Did you mean: 

“We defined/identified a collection of parts and interactions, squishy as those concepts might be, that allowed us to efficiently understand patterns in space, time, and the structure of connections that arise in this collection, ignoring quite a few details in the parts, and taking into account only a small number of interactions (4 is kind of iffy, 2 or 1 would be great)”

2) “This is emergence” 

Did you mean: 

“Upon being brought together to interact, the interacting parts quickly approach a steady-state pattern (dynamic equilibrium) that quickly reduces the number of degrees of freedom required for useful approximate description.  Statistical physicists will now have fun describing how the ‘underlying’ degrees of freedom collapse into the few effective degrees of freedom, and they’ll tell you about phase transitions.”

or did you mean:

“This effect does not occur with an individual, but occurs by virtue of the presence of more than a lone individual.”  

3) “This is a complex system”

Did you mean:

“We are studying mechanical, chemical, or other interactions between different cellular populations.  Colleagues in our field historically studied gene interactions within cells, so our investigation of interactions between cells is novel, not in recognizing that it can be interesting to conceptualize notions of ‘parts,’ ‘interactions,’ and ‘resultant properties’ at all, but that we recognize the the parts and interactions need not always be intracellular.  We study the microenvironment.”

4) “Our work demonstrates the importance of understanding emergent properties in complex systems”

Did you mean:

“I went to a systems biology conference, and I found out that the words “complexity” and “emergence” are “hot.”  I said the magic words.  Hocus-pocus, publish my paper.”  

If these are what you mean, why on earth don’t you say so?  There is so much vocabulary inflation now that saying “complexity” and “emergence” feels like saying “I have never been a member of the Communist party.”