Showing posts with label biology. Show all posts
Showing posts with label biology. Show all posts

Sunday, 20 December 2015

Size Does Matter

Prerequisite: none

I had a curiosity for gigantic organisms. Gigantic, as in dinosaurs, eighteen meter sharks and five meter sloths. Then I came across the right book. Here are the highlights of John Tyler Bonner's book Why Size Matters: From Bacteria to Blue Whales.

First of all, we all love pictures. This book has tons of cute illustrations. This diagram compares the sizes of various species in the eukaryotic domain. Adorable, especially specimen number 10..


That is a tapeworm.

Some other awesome organisms introduced, such as the rotor flagellum bacteria. Just when you thought humans were cool for using wheels and axles, these bacteria were born with it!

And then some maths. Roughly. The little fishlike squiggle (∝) means "proportional to". This is a summary of general trends that organisms follow:


Some other trends are (diameter ∝ height) and (size ∝ distribution distance). In fact, most organisms seem to aim for a common size-distance ratio. That is very mind blowing.

This book also introduces the Reynolds number, defined as the ratio of inertial force and viscous force. It points out that although microorganisms appear to swim relatively fast with their rapidly beating cilia, that is not actually the case. If you were one of these puny germs, the Reynolds number would be extremely low as viscous environment has way more effect on your microscopic inertial mass.

And my very favourite, this graph:


Organisms of one centimeter appear to be the slowest in the race, while the two extremes of the size spectrum are incredibly fast. So you see, size does matter.

Saturday, 14 November 2015

Cactus Chronicles

Prerequisite: none

This baby is coming home with me!


Wandered around Cicada Night Market, Hua Hin on a Friday night. Adopted this buddy for fifty baht. Barely half a pinky wide, with only a few white spots indicating where spikes will sprout. There were many bloomed cacti to choose from, but I am in for a surprise with this youngster.

The care is apparently very simple. Water once a week, to the point where water gushes out of the pot base. The cactus does not die abruptly but turns yellow or white first, so that there is time for saving. It needs some four hours of sunlight every day. I suppose a cactus can withstand drastic temperature changes as a desert's environment is such.

Great companion plant for lazy people like me. Go get one now~

Will update on a separate blog: Cactus Chronicles.

Monday, 17 August 2015

Knot Theory and Polynomials

Followup of Braid Theory

Prerequisite: algebra 2

Mathematics is broad and wide. Nonmathematicians have probably never heard of topology, which is about the properties of deformed objects and spaces. Under topology is knot theory.

Receive an introduction from Numberphile:
https://www.youtube.com/watch?v=aqyyhhnGraw

And take up some basics from this site. I love the commutativity and associativity of knots. Simple yet mindblowing:
http://www.popmath.org.uk/exhib/knotexhib.html

I was at this awkward stage where the understandable information are too easy and the advanced information are too difficult. Then I found Knots: Mathematics with a Twist by Alexei Sossinsky. It tells of ways people applied rules to discover invariants, consistent properties that suggests an underlying truth. I bent my brains a little, but at least it is still topologically the same brain..

Conway's Skein Relation

A knot is topologically the same no matter how you stretch and tangle it. But once you cut and reattach sections, it is no longer the same knot. There are three possible ways to attach two sections, eerily reminiscent of topoisomerase and their work on DNA strands.


In order to attach numerical value to knots, three rules are established (pardon me for using N instead of L). The upsidedown ∆ denotes "the polynomial of" whatever is in the bracket.


I. Two knots are the same if their polynomials are the same.
II. The polynomial of the unknot is 1.
III. Conway's Skein Relation: [the polynomial of N+] minus [the polynomial of N-] is [x times the polynomial of N˚].

Rule III is better understood with this diagram, where the intersection/break is the only point of difference between these three knots.


If we plug in the unknot into Conway's Skein Relation, we get 1 - 1 = 0x, which is just 0. From rules II and III we found that the polynomial of a double ring is 0.


If you still have not figured out how Conway's Skein Relation works, notice how the parts outside the dashed circles are the same, and the insides are N+, N-, and N˚.

Conway's Skein Relation is as easy as algebra. If we plug in the double ring and unknot along with their polynomials, we get ∆(H+) - (0) = x(1). The polynomial of the hopf link is x.


We can bring it even further. You need to stretch your imagination a little more in this example. (1) - ∆(T) = x(x), do the algebra, and figure that the trefoil knot is -(x^2)+1.


Note that rule I applies all the way.. so far. The problem with Conway's polynomials is that a trefoil knot and its mirror image have the same polynomial. They are topologically different because one cannot be deformed into the other without breaking, and Conway's polynomials do not express that. More advances will be made to solve this problem.

Kauffman Bracket

The revised rule I is another form of Conway's Skein Relation. In rule II <KUO> denotes a knot added to an unknot. Rule III states again that the polynomial of an unknot is 1.


You can figure that <00> is (-a^2 - a^-2) by rule II. Let K be an unknot, which is linked to another unknot. (-a^2 - a^-2)<1> is just (-a^2 - a^-2). <00> = (-a^2 - a^-2).

Here are some more polynomial assigning that you can do according to Kauffman's revision. More algebra, but with a knotty twist. You may have noticed that the two knots on the same row as the hopf link are in fact unknots, but their polynomials are not the same! One has a positive degree while the other is negative.


The little formula at the base solves the problem. The w(K) (called a writhe) is equal to the number of positive crossing minus the number of negative crossings for a knot K.

Then Jones did another revision after Kauffman. I am not sure how recent updates work, or if there are even any.


There is something mysterious about knots. It may appear to be just a piece of string, yet it can be so spatially complex. It is a mesmerizing tangle of intraplay. True, simple, aesthetic. I like.

Damn. What will humans decide to number next?

Friday, 14 August 2015

Timbre and Overtones

Followup of Harmonic Intervals and Resonance

Prerequisites: physics, music theory

Common misconception: play an A on the violin and the frequency is 440 Hz.
Almost true.

Most sounds are actually a blend of many frequencies above the fundamental frequency. Timbre, or colour, is the difference in harmonic distribution that gives each musical instrument its own distinct sound. Timbre can also vary between each person's voice, or subtly between each violin.

Recall the formula f = n*(v/2L) where
f = frequency
n = harmonic number
v = speed of sound
l = length of string or open pipe
and the fundamental frequency is when n = 1

Here is what I mean by "a blend of many frequencies". The higher frequencies are harmonics. The fundamental is most amplified and so the most noticeable.


This reminds me of overtone singing (if you have no idea what that is: https://www.youtube.com/watch?v=7zZainT9v6Q). The funny whistling sound are overtones , or harmonics, and the lowest note is the fundamental. Frequency ratios early in the harmonic series are easier to produce than ratios further down the series. Meaning, consonant intervals have stronger resonance from constructive interference, while dissonant intervals sound fainter from destructive interference.

Not all of us regard the human body as a musical instrument. There are many hollows in the human body that allow strong vibration, which is needed for harmonics to be noticeable at all. Resonance is not only established with others, but with the self as well when you let your other harmonics ring. Maybe not necessarily to produce overtones, but to build a richer timbre.


 Consider the fact that organisms are designed according to their functions. What function does singing serve humans? Why is music even a thing? For me, music is more than an art or a recreation. There is something transcendental about the way music works. I am still figuring things out here..