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.
I’d love to hear more about that. Do you have any good examples?
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.
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
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."
No. I’m not really sure how you’re trying to define entropy, but you’ll probably have quite a bit of difficulty with endothermic processes if you try to think about entropy like this. For example, if you sprinkle sodium acetate in water, the sodium acetate dissolves, and the solution absorbs heat in the process, thus increasing the energy of the system.
In general, entropy increases but energy just moves around.
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...