Resources for individual classes
ADDED LATE: Optional Reading
Here is a well-written article about how AI has helped out with protein-structure determination.
Before Class #7, please read these stories from The Complete Cosmocomics
• The Spiral
• Blood, Sea
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We did not get to The Spiral last week, but there's plenty to talk about in Calvino's little prelude. The resources below for this story are reprinted are provided again here, from the assignments from Class #6, with a couple of additions at the beginning.
••• After reading The Spiral, study the following resources:
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-- How can natural selection from the products of random mutation produce what looks like evolutionary progress?
Here is a computer simulation that lets you look at the effects of random genetic variation, natural selection acting on the offspring that harbor these variations ("mutations").
If you get bogged down in these instructions, don't waste a lot of time. I'll help out in class.
Click the link and then follow these instructions:
- Scroll down to a black square with a Launch button at its upper left corner and Biomorph Evolve at its center.
- Click "Launch". An array of nine squares appears, each containing a tree-like pattern of connected lines. In most patterns, it's easy to find a single line (a trunk, if you will) which, by branching, produces the whole pattern. Each pattern is called a biomorph, or morph, and represents an organism whose pattern is determined by the numerical values of a handful of variables called "genes". Each gene determines a single feature, such as the number of branches, the branch angle for all branches of that morph, the length of all branches relative to first one, whether the branches ascend or descend, and other simple features. In this first screen, all morphs are given random values for all of their genes, making them highly varied.
- Click once on any morph that looks interesting to you. That morph will move to the center square, and eight similar new ones will appear around it. The central morph is the "parent" you chose, and the eight new ones are its offspring. Each offspring differs from the parent by a small change (mutation) in the value of one, or at most, two genes, so they all resemble, but are not identical to. their parent.
- The same thing happens if you now click any square: the clicked morph moves to center and produces eight new offspring, each genetically very similar to the parent in the center.
Try this. Reload the page to get a new set of random parents (see below** if you don't know how to reload a page.) See if you can evolve a species of morphs that are all very flat and wide. Start by picking the flattest and/or widest first parent, then pick the offspring that you judge to be shorter and widest, and click to make it the next parent. Repeat to make the shortest and widest morph you can.
Then try this. Reload and restart the simulation repeatedly, each time getting nine new random figures. Do you ever find any random morphs that hat are even close to being as short and wide as you can get by selection from promising parents?
You are seeing the difference between the power of random mutation with selection, versus random mutation alone. In a few generations, you can pick a property and enhance much faster than waiting for random mutation to produce it. If you have ever played gin rummy, you have seen the same kind of selection in making exchanges that improve your hand.
I will explain this simulation in class, and show some examples. If you aren't getting anywhere with this, don't waste a lot of time. I'll help out in class.
Have you ever played gin rummy? Do you see any parallels between natural selection acting on natural genetic variation versus your decisions in gin rummy and the stepwise improvement of your gin-rummy hand from a perhaps unpromising hand dealt to you to a winning hand?
••••••
•••After reading Blood, Sea, study these resources
The compositions of sea water and blood plasma (the liquid component of blood, not included the cells, like red and white blood cells), are sometimes said to be similar. But the similarities are very general, mainly in the presence of salts, but less so in the concentrations of these salts. In looking for comparisons online, you mostly find dubious claims for health benefits of sea water or diluted sea water. HERE is s short answer that is not an attempt to sell you something.
Major components of blood are red and white blood cells. Red blood cells contain lots of the protein hemoglobin, which binds to oxygen (actually dioxygen, or O2, and thus makes oxygen more soluble in blood, increasing the amount of oxygen blood can carry from the lungs to tissues that need it, including those hard-working muscle cells, and those hard-thinking brain cells.
What are proteins, anyhow, and how can they do so many jobs in living organisms?
All of the following biological molecules are proteins: enzymes, antibodies, sensors, transporters, structural elements or cells and organs, gates through membranes, signal receptors, DNA copiers, and some (but not all) of the hormones -- and that's just a sample.
At Wikipedia, look over the beginnings of the entries Proteins and Protein Structure, to get a general overview. In class, we will look at the nature of proteins by using computer graphics and moving stepwise from their simplest components to some fairly complex, but understandable, elements of their structure.
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** How to Reload A Web Page
On an Apple computer or iPad, pick Reload Page from the View menu, and Launch again.
On other brands, you will find a Reload command under one of the menus. On an iPhone, click the clockwise arrow on the right of the web-address line. You might have to scroll the page up or down to make the address line appear. On other phones, reloading is just as easy, but I don't have one to figure that out for you. If you succeed with reloading on a non-Apple phone, send me email with instructions and I'll put them here.
