
Granular convection - glcheetham
https://en.wikipedia.org/wiki/Granular_convection
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dekhn
I remember a journal club where we read a paper in which they demonstrated the
inverse brazil nut effect
([http://large.stanford.edu/courses/2007/ph210/spector2/](http://large.stanford.edu/courses/2007/ph210/spector2/)).
The scientists built a physical nut shaker- like, a huge tube that they
bounced. that's when I realized I had picked the wrong field (theoretical
biology instead of experimental physics).

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technoplato
What do you do in theoretical biology?

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dekhn
Nothing anymore- I became disillusioned with modern scientific research,
especially biology, because I believe that most of what is published is simply
false or wrong (it's much harder to publish false crap in experimental physics
because everybody knows more math, is better at analyzing experiment design,
and the systems are "simpler"). Now I work on software engineering related to
neural network performance (focusing on things that have worked well for
years).

That said, things I've worked on include: classifiers to identify genes in
DNA, molecular dynamics simulations of proteins and nucleic acids, methods to
discover new drugs, analysis of protein function from an evolutionary
perspective, protein design.

~~~
crgwbr
> I became disillusioned with modern scientific research, especially biology,
> because I believe that most of what is published is simply false or wrong

I’d love to hear more about that. Do you have any good examples?

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dekhn
Sure, there was a paper about yeast. They created a collection of 6000 clones-
each one had a "single gene deletion" and nothing else. THey were able to
study each clone and explain whether the gene deletion was fatal (IE, if you
delete this gene that is essential for yeast to grow, the clones all die).

I was tasked to analyze the paper results, specifically a table that listed
"all the genes we newly discovered that, when removed, are fatal".

Since I'm interested in overlapping genes, I took the list of new genes and
intersected it with all the other known genes, and noticed that for each gene
they newly discovered had a fatal outcome, it intersected a gene that was
already known to be necessary for yeast to live (housekeeping genes, essential
enzymes, dna checkpoint repair, etc).

The most likely conclusion from this is that when they deleted the gene, they
also truncated or deleted the other gene, which abolished the function of the
known-necessary gene. Therefore, they didn't discover anything new- they just
disabled things that we already knew broke yeast, by accident, by ignoring the
fact that genes overlapped.

I showed this to my advisor, who said "Good catch, why don't you write them a
letter?" So I sent them a letter showing my results, never got a response
back. They published a paper a year later, totally unapologetically, saying
how they had "discovered interesting interactions between overlapping
genes"...

You can also look back at the original human genome sequencing papers, they
were massively overestimating the accuracy of the assembly and the
representation of the genome (compared to the wider population). It took
decades of additional large-scale sequencing to verify this, but it still
bothers me just how overly egotistical and self-confident the folks who worked
on the human genome project were.

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phkahler
Farmers know the rocks come to the suface over the winter.

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itronitron
interesting, I suppose if the top 6 inches of a field freezes then it slightly
expands in volume and when the soil thaws the smaller soil particles would
then have an opportunity to fall beneath the rock... not sure if this is
dependent on the top or bottom thawing first though...

~~~
no_protocol
In many places, the frost line is more like 3 to 6 feet, than 6 inches.

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malcolmhere
This is a recurring problem in the animal feed industry. Easiest explanation
for the phenomena: the small particles fall through the gaps gaps between the
large particles.

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tgb
My first instinct would be that this is due to entropy rather than minimizing
energy, but the article doesn't mention that hypothesis. Is it easy to rule
this out?

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ggus
Isn't "minimizing energy" a definition for entropy?

My idea is that, when shaking, all pieces try to move. Big pieces can only go
upwards, while small pieces can go sideways (and take the space that was
previously taken by a big piece). This ends up with the effect of big pieces
floating to the top

~~~
jjoonathan
> Isn't "minimizing energy" a definition for entropy?

No. If you have a system with a well-defined energy/entropy exchange rate
(temperature) you can use it to put entropy in units of energy, add it to your
energy term, and model the combined system behavior on the basis of this "free
energy." The free energy is not a fundamental quantity, though, and it doesn't
define entropy. That's why the first two laws of thermodynamics are "Energy is
Conserved" and "Entropy Increases," not "Free Energy decreases."

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cr0sh
Here I was this morning just thinking about this - weird how that happens.

My wife got this gift recently, that at first looks like a snowglobe, but
actually has fine sand and seashells inside. You can kind of shake it or
rotate it about, and the seashells that "rise" to the top on the sand change
as you do it.

For some reason, that got me thinking about this topic. Then I see it on HN...

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Abishek_Muthian
Maybe OP bought pack of assorted nuts for Christmas and wondered the same.

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ptah
this also has application in mixed spice grinders. you can shake it right side
up or upside down to get the desired effect

