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Posts tagged with biochemistry

Einstein opined that the great philosophical breakthrough leading to the mental possibility of science was the hypothetico-deductive method.

Which is a jargony way of saying: forget whether A is true or not (measurement of the world)—let’s talk about the separate, purely logical issue, of whetherif A were true, would B necessarily be true as well, as a result of A being true? ⧝

People aren’t great with hypotheticals, though—at least not everyone or not without education.

  • I can get people to agree with my reasoning  by first telling them that  leads to a conclusion they already agree with B.
  • (This is really dastardly because once I’ve judoed someone this far I can get them to agree to even more things, in order to maintain local consistency.)
  • We judge each other on credentials (A).
  • We judge arguments on what other experts think of them.
  • Mathematics is all about the  and most people are either scared to tears by mathematics, bored to tears by mathematics, or think mathematics irrelevant, or all three.
  • People think that if I argue that their reasoning  is wrong, I’m saying their conclusion B is wrong.
  • (Symbolically it’s obvious that A↛B = A⊬B = ¬(A→B) isn’t the same as ¬B. But people regularly interpret “That does not follow” as “That’s wrong”.)

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Whatever it is people do in arriving at their beliefs, it’s not propositional calculus; it’s not Bayesian probability; it’s not “believe whatever mama says”. But it is a little like all of those.

 ⤳⃝

I was riding on a train in Italy. Watching lemon trees out the window. Fantasising of tasting a lemon-based liqueur.

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Lemon trees. Amalfi Coast, Campania, Italy (color)

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My travel partner and I shared a vestibule with an American monk-cum-priest who introduced himself as Father John. Father John was making a pilgrimage from the Carolinas to Vatican City. I don’t know if he always evangelised but, although my partner and I tried to steer the conversation away from religion, Father John wanted to talk about his Catholic faith—specifically in a way that might score some converts.

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I don’t know whether the part of me that makes me debate with strangers online was acting out in its pre-internet form, or whether Fr J’s insistence on having a conversation we clearly did not want to have put me in a pugilistic mood.

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For whatever reason, I started querying him on some of the more outlandish assertions of Catholic doctrine. One thing I challenged him on in particular was transubstantiation.

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Try though the alchemists might they could never transmute lead to gold—but every Sunday around the world, holy men of Christianity transmute sacramental bread and wine into literally the body and blood of Christ.

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The biochemistry involved in going from wheat flour to bone marrow or from pectin to haemoglobin is not discussed in catechism, but the transition is obviously impossible by natural processes. Nonetheless, “the real presence of Christ in the Eucharist is a mystery—something so packed with meaning that we can never fully understand it.”

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I really don’t have a bone to pick with “transubstantiationalists”. I find the deeper reasons he and I think as we do more interesting than what we profess. I don’t go out of my way to attack people or hurt anyone’s feelings—but I do consider it rude to evangelise someone without consent.

So I needled the man. "Come on, you really believe that? Really? It’s not just a symbol? You can’t just have your religion without this physically impossible claim? Why would you insist on invoking the supernatural when that clearly undermines the credibility of everything else you say? Not only is it impossible according to science, even to your own sensory experience it just looks like a normal wafer—not like a hand or a butt or whatever. You literally, actually believe that this wafer literally, actually turns into actual human flesh of a dead man from two millennia ago—using up more body mass than he ever had all over the world every Sunday—really? Really?”

I still remember Father John’s response (which is how I’m able to tell you this story). He said: “OK, I understand your objections. But consider this. What if it were all true? What if the Resurrection, the Virgin Birth, G-d walking among men, the sacred mysteries, all of it were true? Wouldn’t that be wonderful? Wouldn’t that change everything about the way you see the world?”

What-if indeed, Father. What if.




inside the cell

…how fast things happen inside cells.

…a white blood cell responding to inflammation.

Cells are very crowded


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Image: “The structure of the cytoplasm" from Molecular Biology of the Cell. Adapted from D.S. Goodsell, Trends Biochem. Sci. 16:203-206, 1991.

… a synaptic vesicle, which is the part of a neuron that releases neurotransmitters from one neuron to another. …I assumed that the authors crammed all the different proteins into the [diagram]…. But in fact, the diagram below omits ⅓ of the proteins so real membranes are even more crowded…. paper … we should think of membranes as packed with proteins like a cobblestone pavement.
A neural vesicle studded with proteins
Image: “Molecular Model of an Average SV" from Molecular Anatomy of a Trafficking Organelle, Takamori et al, Cell. 2006 Nov 17;127(4):831-46.

Molecules move very very fast

You may wonder how things get around inside cells if they are so crowded. …[M]olecules move unimaginably quickly due to thermal motion. A small molecule such as glucose is cruising around a cell at about 250 miles per hour, while a large protein molecule is moving at 20 miles per hour. Note that these are actual speeds inside the cell, not scaled-up speeds. I’m not talking about driving through a crowded Times Square at 20 miles per hour; to scale this would be more like driving through Times Square at 20 million miles per hour!

Because cells are so crowded, molecules can’t get very far without colliding…. In fact, a molecule will collide with something billions of times a second and bounce off in a different direction. Because of this, molecules are [on] a random walk through the cell … diffusing…. A small molecule can get from one side of a cell to the other in ⅕ of a second.

As a result of all this random motion, a typical enzyme  … interact with 500,000 [molecules] every second. …[Y]ou might wonder how the different pieces just happen to move to the right place. In reality, they are covering so much ground in the cell so fast that they will be in the “right place” very frequently just by chance.

In addition, a typical protein is [spinning] a million times per second. Imagine proteins crammed together, each rotating at 60 million RPM, with molecules slamming into them billions of times a second. This is what’s going on inside a cell.

The incredible speed and density of cells also helps explain why it’s so difficult to simulate what’s happening inside a cell. Even with a supercomputer, there’s way too much going on inside a cell to simulate it without major simplifications. Even simulating a single ribosome is a huge computational challenge.

Molecular motors sprint, not walk

.. Like a mechanical robot with two lumbering feet, a kinesin motor protein can be seen in the video at the 2 minute mark dragging a monstrous bag-like vesicle along a microtubule track. (This should be what you see in the YouTube preview frame at the top of the page.) These motor proteins move cargo through the cell if diffusion isn’t fast enough to get things to their destination, which is especially important in extremely long cells such as neurons. …

… these mechanical walkers…sprint at 100 steps per second. If you watch the video again, imagine it sped up to that rate.

Cells are powered by electric motors spinning at 40,000 rpm

Mitochondria also provide a fascinating look at just how fast things are inside cells. You may know that mitochondria are the power plants of cells; they take in food molecules, process it through the famous citric acid cycle, and then use oxygen to extract more energy… ATP….

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Image from David Goodsell, ATP Synthase, December 2005 Molecule of the Month


… Mitochondria use the energy from oxidizing food to pump protons out of the cell, creating a voltage of 170mV across the cell. This voltage causes a complex enzyme to spin, and the mechanical energy of this spinning enzyme creates the ATP molecules that energize the rest of the cell.

…these enzymes spin at up to 700 revolutions per second, which is faster than a jet engine. …

If you’re interested in more about this mechanical motor, you’ll probably enjoy PDB’s molecule of the month article.

(There’s also a longer narrated version at the BioVisions website.)

The above text is by Ken Shirriff.

It makes sense to me that if my muscles do things on the order of hundredths of seconds, then the chemical interactions to cause something like “arm, go up” has to be happening several orders of magnitude below what my consciousness evolved to notice.

Hearing the speeds of biological molecules made me wonder how heavy / fat these fast-moving molecules are relative to hydrogen (familiar Schroedinger stuff) or quantum chemistry. DNA is apparently 6 orders of magnitude heavier than hydrogen ion.

Follow-up thought on gerontology: If you think on the decades scale, your body starts falling apart after 3 or 4 and is pretty much useless by 8, 9, or 10 — if it even lasts that long. But think about how many molecular things have to happen to make you be yourself for even a minute. Let’s say it’s tens of millions. Then multiply that by 100 trillion cells and a 60×24×365×10 = 6½ orders of magnitude difference between a minute and a decade, for a total O(10^28) molecular thingies to make a life. That’s not so short.




Robert Sapolsky on Language and schizophrenia

  • importance of FOXP2
    http://upload.wikimedia.org/wikipedia/commons/3/37/Protein_FOXP2_PDB_2a07.png
  • Take away FOXP2 from mice and they talk less complexly.
  • Give mice our human FOXP2 and they talk more.
  • Humans missing FOXP2 can’t do they no talkin be wrongly.
  • Babel → pidgin → creole
  • all creoles have the same grammar
  • …smells like…one inherent human language???
    Correlation
  • ecological factors: rainforest & biodiverse ecosystems tend to produce polytheistic cultures (more linguistic diversity, “more diversity” in many areas)
  • 90% of Earth’s languages will be extinct in not so long.
  • hunter-gatherers have a higher frequency of click languages
  • "Language is how we outsmart plants" —Steven Pinker
  • language is sequential; toolmaking is sequential
  • cooperation — game theory — kin selection — and, lying.
  • Dogs put the lid on their fear pheromones by tucking their tails.
  • A lot of the brain controls facial expressions. (important if you want to lie)
  • Game theory with communication, with semanticity, with syntax, with grammar — all traits of our language — improve outcomes in the game.

Minute 23 — Schizophrenia

  • Sequential thinking is impaired. (Can’t tell a story in an order that will make sense to others.) (Actually that sounds like me.)
  • Loose associations. (Can’t keep straight within one sentence whether “boxer” refers to dog or occupation. Gold caddy vs Cadillac)
  • (So I guess homophones differ among languages and thus schizophrenics of different languages tangent predictably based on their language?)
  • Difficulties with abstraction. (Fact vs parable vs rumour) Always interpret as concrete reality.
  • "Apple, banana, orange. What do these words have in common?" "They’re all multisyllabic words." "OK, that’s true. Anything else?" "Yes. They all have letters with closed loops." Symbolic function of language not working for them.
  • "What’s on your mind?" "My hair." "Can I take your picture?" "I don’t have a picture to give." "Can you write a sentence for me?" "A sentence for me."
  • Belief that they participated in historical events.
  • "What do apples, oranges, and bananas have in common?" "They’re all wired for sound."
  • Hallucinations. The defining feature.
  • Most hallucinations are auditory but we don’t know why.
  • People experience very structured hallucinations, not random ones. But neurologically it looks random. epsilon;
  • In fact papers have been published about the most common hallucinations. Commonest voices, in order: Jesus, Satan, the political leader.
  • The story of a schizophrenic Maasai.
  • After a really abhorrent violation of social convention, they locked her away and she died. Sound familiar? Oh well, I guess she knew what was coming to her and ∴ tacitly rationally agreed to her punishment, right?
  • Nuopharmacology evolving from trying to cure hallucinations to trying to cure disordered thought.
  • Elderly schizophrenics lose the positive symptoms (hallucinations, delusions, loose associations) and the negative symptoms (flat affect and withdrawal) dominate.
  • Schizophrenia sets on in late adolescence/early adulthood—make it to  30 without it, you’re probably safe.
  • Anchored in the frontal cortex.

(por StanfordUniversity)




Listen to the doctor
crystilogic:

Kidney, this time with ions and color. It’s a whole crazy world down there. This is one of the thousands of small tubes that urine moves along on its way through the kidney, with all these transport proteins (little circles) and ion channels embedded in the membrane walls to move different things in and out.

Listen to the doctor

crystilogic:

Kidney, this time with ions and color. It’s a whole crazy world down there. This is one of the thousands of small tubes that urine moves along on its way through the kidney, with all these transport proteins (little circles) and ion channels embedded in the membrane walls to move different things in and out.







@IgorCarron blogs recent applications of compressive sensing and matrix factorisation every week.
(Compressive sensing solves underdetermined systems of equations, for example trying to fill in missing data, by L₁-norm minimisation.)
This week: reverse-engineering biochemical pathways and complex systems analysis.

@IgorCarron blogs recent applications of compressive sensing and matrix factorisation every week.

(Compressive sensing solves underdetermined systems of equations, for example trying to fill in missing data, by L₁-norm minimisation.)

This week: reverse-engineering biochemical pathways and complex systems analysis.




The chemistry of living things & Mary Baker Eddy’s Christian Science

It’s obvious that people are completely unalike to liquid mercury, ammonium chloride, and plumbum. Likewise, it stands to reason that frogs, bats, voles, minks, snakes, geckos, sparrows, drosophila, ferns, magnolias, buffalo grass, and juniper; bark, blood, bone, leaf, skin, resin, albumen, tannin, cornea, magenta, phloem, ambergris, and fur are made of different stuff than formaldehyde, bronze, sulphur, colcothar, antimony trichloride, diethyl ether, cinnabar, salt, spiritus nitroaereus, gunpowder, pepsin, shale, ferrous sulphate, saltpeter, rust, ore, coal, granite, magma, lime, silver, mercury, phosphorus, and oyl of vitriol. I mean: animals move with their own vital animus, and dust just gets blown around.

So, according to Scrimgeour & Moran: even though Wöhler synthesised an organic chemical just before the French Revolution, living things were still not generally accepted to be made of chemicals until around 1905 — and that was in scientific circles. As lauded a scientist as Louis Pasteur argued in the late 1800’s that a vital force (unique to living things) was necessary to the fermentation (by yeast) of sugar into alcohol. And remember that Mendeleev’s table wasn’t introduced until 1871.
 
Proving to the common soul that everything is made of chemicals required:
the atomic hypothesis
the periodic table (should I say the proton hypothesis?)
laboratory synthesis of organic matter
the mapping of metabolic pathways, and their reproduction in the lab by non-vital means;
and its acceptance was no doubt speeded by the fantastic successes of 20th-century physics (quantum mechanics, discovery of galaxies, Big Bang and inflationary cosmology) which reshaped philosophy and made way for today’s secular religion of Big Bang + Physics & Logic + Evolution = us.
—so it’s a very modern idea that we are chemical.
Remember, too, that in the 1800’s the Bible was still used to demonstrate objective truths about the universe. (I almost wrote “scientific truths”—but that just shows my 20th-century-ness: thinking that Science yields true facts and Religion functions in a separate magisterium.) And the Great Chain of Being was widely held to not so long before the time of Samuel Coleridge, Harriet Beecher Stowe, Mark Twain, Henry David Thoreau, and Mary Baker Eddy.
 
Evolution and Relativity are glossed as the culture-bending scientific developments which shaped 20th-century minds. But that overlooks the advent of Bio Chemistry — takes for granted the previously disbelieved and extremely surprising fact that living things are made of chemicals.

 
Against that backdrop I find it very hard to critique Mary Baker Eddy’s logic in writing Science & Health, with a Key to the Scriptures and starting the niche religion of Christian Science.
She slipped on the ice in 1866 and continued working out her metaphysical views until her death in 1910. The first version of Science and Health was published in 1875 but the Authoritative version wasn’t finished until 1908. So the periodic table preceded her first draft by 4 years, and the chemical composition of mankind wasn’t definitively proven until 3 years before her death. (I’m counting Buchner’s 1907 Nobel as the date of “proof”.) If you were editing and improving a book about the most relevant spiritual and medical finding in centuries, not to mention giving lectures, and starting and administering a church for your new religion — do you think you would be keeping up on the curiosities turned up by the Royal Society? I wouldn’t.

 
What I’m saying is that it’s totally unreasonable to expect Mary Baker Eddy’s book to take a chemical, atomic, particulate view of mankind and its health — because that viewpoint was barely available during her lifetime. As an octogenarian, yes, she technically could have read up on all the latest science and trimmed Science & Health to a new prevailing wind. But at that point she had already given so many sermons on the question, Is the universe, including man, governed by atomic force?, that it would have taken an unusually flexible person to recant in the remaining year or two before her death.
In a sense, Christian Science looks the fool merely because it was invented historically just prior to the modern Age of Biochemistry. Maybe there is a grander dialectic to this bit of history, in that the same widespread fascination with Science which drove Boyle, Faraday, and Maxwell, impelled Mrs. Eddy to rationally decompose the healing miracles of Christ. Maybe the era’s Romantic hubris and Scientific hubris were the drivers of both innovations (as well as others like the advent of psychology).
On the other hand, if biochemistry hadn’t progressed; if germ theory, atomic theory, the possibility of vaccination, chemical metabolism and most of all DNA hadn’t been proven beyond a reasonable doubt, Christian Science would occupy a very different place in the public imagination. Medicine would probably be about as good as it was in MBE’s time, and the placebo effects of absolute conviction in both metaphysical perfection and the scientific efficacy of prayer would be a compelling sell.

The chemistry of living things & Mary Baker Eddy’s Christian Science

It’s obvious that people are completely unalike to liquid mercury, ammonium chloride, and plumbum. Likewise, it stands to reason that frogs, bats, voles, minks, snakes, geckos, sparrows, drosophila, ferns, magnolias, buffalo grass, and juniper; bark, blood, bone, leaf, skin, resin, albumen, tannin, cornea, magenta, phloem, ambergris, and fur are made of different stuff than formaldehyde, bronze, sulphur, colcothar, antimony trichloride, diethyl ether, cinnabar, salt, spiritus nitroaereus, gunpowder, pepsin, shale, ferrous sulphate, saltpeter, rust, ore, coal, granite, magma, lime, silver, mercury, phosphorus, and oyl of vitriol. I mean: animals move with their own vital animus, and dust just gets blown around.

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So, according to Scrimgeour & Moran: even though Wöhler synthesised an organic chemical just before the French Revolution, living things were still not generally accepted to be made of chemicals until around 1905 — and that was in scientific circles. As lauded a scientist as Louis Pasteur argued in the late 1800’s that a vital force (unique to living things) was necessary to the fermentation (by yeast) of sugar into alcohol. And remember that Mendeleev’s table wasn’t introduced until 1871.

 

Proving to the common soul that everything is made of chemicals required:

  • the atomic hypothesis
  • the periodic table (should I say the proton hypothesis?)
  • laboratory synthesis of organic matter
  • the mapping of metabolic pathways, and their reproduction in the lab by non-vital means;
  • and its acceptance was no doubt speeded by the fantastic successes of 20th-century physics (quantum mechanics, discovery of galaxies, Big Bang and inflationary cosmology) which reshaped philosophy and made way for today’s secular religion of Big Bang + Physics & Logic + Evolution = us.

—so it’s a very modern idea that we are chemical.

Remember, too, that in the 1800’s the Bible was still used to demonstrate objective truths about the universe. (I almost wrote “scientific truths”—but that just shows my 20th-century-ness: thinking that Science yields true facts and Religion functions in a separate magisterium.) And the Great Chain of Being was widely held to not so long before the time of Samuel Coleridge, Harriet Beecher Stowe, Mark Twain, Henry David Thoreau, and Mary Baker Eddy.

 

Evolution and Relativity are glossed as the culture-bending scientific developments which shaped 20th-century minds. But that overlooks the advent of Bio Chemistry — takes for granted the previously disbelieved and extremely surprising fact that living things are made of chemicals.

image

 

Against that backdrop I find it very hard to critique Mary Baker Eddy’s logic in writing Science & Health, with a Key to the Scriptures and starting the niche religion of Christian Science.

She slipped on the ice in 1866 and continued working out her metaphysical views until her death in 1910. The first version of Science and Health was published in 1875 but the Authoritative version wasn’t finished until 1908. So the periodic table preceded her first draft by 4 years, and the chemical composition of mankind wasn’t definitively proven until 3 years before her death. (I’m counting Buchner’s 1907 Nobel as the date of “proof”.) If you were editing and improving a book about the most relevant spiritual and medical finding in centuries, not to mention giving lectures, and starting and administering a church for your new religion — do you think you would be keeping up on the curiosities turned up by the Royal Society? I wouldn’t.

image

 

What I’m saying is that it’s totally unreasonable to expect Mary Baker Eddy’s book to take a chemical, atomic, particulate view of mankind and its health — because that viewpoint was barely available during her lifetime. As an octogenarian, yes, she technically could have read up on all the latest science and trimmed Science & Health to a new prevailing wind. But at that point she had already given so many sermons on the question, Is the universe, including man, governed by atomic force?, that it would have taken an unusually flexible person to recant in the remaining year or two before her death.

In a sense, Christian Science looks the fool merely because it was invented historically just prior to the modern Age of Biochemistry. Maybe there is a grander dialectic to this bit of history, in that the same widespread fascination with Science which drove Boyle, Faraday, and Maxwell, impelled Mrs. Eddy to rationally decompose the healing miracles of Christ. Maybe the era’s Romantic hubris and Scientific hubris were the drivers of both innovations (as well as others like the advent of psychology).

On the other hand, if biochemistry hadn’t progressed; if germ theory, atomic theory, the possibility of vaccination, chemical metabolism and most of all DNA hadn’t been proven beyond a reasonable doubt, Christian Science would occupy a very different place in the public imagination. Medicine would probably be about as good as it was in MBE’s time, and the placebo effects of absolute conviction in both metaphysical perfection and the scientific efficacy of prayer would be a compelling sell.




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Gauß’ divergence theorem states that, unless matter is created or destroyed, the density within a region of space V can change only by flowing through its boundary ∂V. Therefore

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i.e., you can measure the changes in an entire region by simply measuring what passes in and out of the boundaries of the region.

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"Stuff passing through a boundary " could be:

  • tigers through a conservation zone (2-D)
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  • sodium ions through a biological cell (3-D)
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  • magnetic flux through a toroidal fusion chamber
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  • water through a reservoir (but you’d have to measure evaporation, rain, dew/condensation, and ground seepage in order to get all of ∂V)
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  • in the other direction, you could measure water upstream and downstream in a river (no tributaries in between) and infer the net amount of water that was drunk, evaporated, or seeped
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  • probability mass through a set of possibilities
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  • particulate pollution through "greater Los Angeles"
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  • ¿ ideas through your head ? ¿ electrical impulses through your brain ? ¿ feelings through your soul over time ?
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  • ¿ notes through a symphonic orchestra ?
  • chromium(VI) through a human body
  • smoke or steam through an industrial cooling tower or smokestack
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  • imports and exports through an economy
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  • goods or cash through a limited liability company

Said in words, the observation that you can measure change within an entire region by just measuring all of its boundaries sounds obvious, even trivial. Said symbolically, Gauß’ discovery amounts to a nifty tradeoff between boundaries  and gradients . (The gradient  is the net amount of a flow: flow in direction 1 plus flow in orthogonal direction 2 plus flow in mutually orthogonal direction 3 plus…) It also amounts to a connection between 2-D and 3-D.

 

Because of Cartan-style differential geometry, we know that the connection is much more general: 1-D shapes bound 2-D shapes, 77-D shapes bound 78-D shapes, and so on.

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Nice one, Fred.

(Source: ocw.mit.edu)




Man, I wish I had majored in chemical engineering. Then I would be employed, and get to make cool things. I’d probably be disgustingly rich and disgustingly handsome. That’s right, disgustingly handsome.

Topics in this video:

  • size and shape of blood cells (2 × 8 µ microns) and platelets (2 µicron sphere)
  • blood cells are shaped like the Millennium Falcon so they can fit through 2-micron µm capillaries
  • that’s why red blood cells are only part-way filled up
  • they’re not filled full of hemoglobin for that reason
  • if the hemoglobin was just loose in your bloodstream, your blood would be thick and viscous — and hard to pump
  • clotting

Janet Tavakoli majored in chemical engineering, and then she became a world expert on synthetic derivatives.




Mathematical Biofluiddynamics
Covers two very different questions:
How do fluids in an animal’s body flow? Like how does blood squeeze through arteries and veins, how does air (a fluid) flow into and out of sacs during respiration, how do capillaries work, etc?
How do aquatic animals swim themselves along with their tails, fins, hydrodynamic bodies, etc?

Mathematical Biofluiddynamics

Covers two very different questions:

  1. How do fluids in an animal’s body flow? Like how does blood squeeze through arteries and veins, how does air (a fluid) flow into and out of sacs during respiration, how do capillaries work, etc?
  2. How do aquatic animals swim themselves along with their tails, fins, hydrodynamic bodies, etc?

(Source: books.google.com)


hi-res