on 28-Jan-2017 (Sat)

To defuse situations and maximize the illusion of respect, you need to tell people why you are asking or explain why you are telling. Giving someone a justification for your ask turns an order into a reasonable and rational request for assistance.

If you can master the arts of indirection, learning to seduce, charm, deceive, and subtly outmaneuver your opponents, you will attain the heights of power.

If you can master the arts of indirection, you will be able to make people bend to your will without their realizing what you have done. And if they do not realize what you have done, they will neither resent nor resist you.

Notice that the array is three-dimensional, with a datum in every one of the 24 cells. We would like to rearrange the data so that there is one datum per row, with each row also specifying the levels of the array from which the datum came. This is done by the melt command

In R’s basic command window, set the working directory by selecting menu items File → Change dir. In RStudio, set the working directory by selecting menu items Session → Set Working Directory.

In general, a function in R in defined by code of the form: functionName = function( arguments ) { commands } The commands inside the curly braces can extend over many lines of code.

You invoke the function by commanding R thus: functionName( arguments=argumentValues )

Notice the arrangement of curly braces across lines in the if-else structure above. In particular, the line containing “else” begins with a closing curly brace, which tells R that the “else” clause is continuing the preceding “if.” A line that begins with “else” causes an error

A simple way to measure processing time is with the proc.time function, which returns the current computer-system time. To measure the duration of a process, use proc.time at the beginning and end of the process, and compute the difference between the times

In general, for loops are slow relative to vectorized operations

Uncertainty is measured in terms of probability

Whenever we ask about how likely an outcome is, we always ask with a set of possible outcomes in mind. This set exhausts all possible outcomes, and the outcomes are all mutually exclusive. This set is called the sample space

The sample space is determined by the measurement operation we use to make an observation of the world.

Many coins minted by governments have the picture of an important person’s head on one side. This side is called “heads” or, technically, the “obverse.”

The degree of belief about a parameter can be denoted p(θ )

Both “probability” of head or tail outcome and “degree of belief ” in biases refer to sample spaces.

When we flip a given coin, we are sampling from the space of head or tail. When we grab a coin at random from a sack of coins, in which each coin may have a different bias, we are sampling from the space of possible biases

If you want values displayed in scientific notation (floating-point form) whatever their size, enter the command format short e

Use format bank for financial calculations; you get fixed point with two dec- imal digits (for cents)

Use format hex to get hexadecimal display.

Use format rat to display a number as a rational approximation (ratio of two integers)

he number of times the loop is executed may be calculated from the fol- lowing equation: floor last −first increment +1 where the MATLAB function floor(x) rounds x down toward −∞. This value is called the iteration or trip count.

A more general form of for is for index = v where v is any vector. The index moves through each element of the vector in turn, providing a neat way of processing each item in a list.

The MATLAB function clock returns a six-element vector with the current date and time in the format year, month, day, hour, minute, seconds. Thus, t0 records when the calculation starts.

The function etime returns the time in seconds elapsed between its two ar- guments, which must be vectors as returned by clock.

here is a neater way of monitoring the time taken to interpret MATLAB state- ments: the tic and toc function.

The MATLAB function rand generates a random number in the range 0–1

The simplest form of if in a single line is if condition; statements; end

In general, the elseif clause is used: if condition1 statementsA elseif condition2 statementsB

switch executes certain statements based on the value of a variable or expres- sion.

The symbol i may be used to assign complex values, for example, z=2+3*

If z is a complex number, real(z), imag(z), conj(z), and abs(z) all have the obvious meanings

A complex number may be represented in polar coordinates: z =re iθ angle(z) returns θ between −π and π ; that is, atan2(imag(z), real(z)). abs(z) returns the magnitude r

If y is complex, the statement plot(y) is equivalent to plot(real(y), imag(y)) The statement axis(’equal’) is necessary to make circles look round; it changes what is known as the aspect ratio of the monitor. axis(’normal’) gives the default aspect ratio.

For complex matrices, the operations ’ and .’ behave differently. The ’ op- erator is the complex conjugate transpose, meaning rows and columns are inter- changed and signs of imaginary parts are changed. The .’ operator, on the other hand, does a pure transpose without taking the complex conjugate.

In the simplest case of a uniform vector field ~ A and a surface S per- pendicular to the direction of the field, the flux U is defined as the product of the field magnitude and the area of the surface

If the vector field is uniform but is not perpendicular to the surface, as in Figure 1.6(b), the flux may be determined simply by finding the component of ~ A perpendicular to the surface and then multiplying that value by the surface area

A vector is the mathematical representation of a physical entity that may be characterized by size (or “magnitude”) and direction

The word “vector” comes from the Latin vehere meaning “to carry;” it was first used by eighteenth-century astronomers investigating the mechanism by which a planet is “carried” around the Sun

In text, the vector nature of an object is often indicated by placing a small arrow over the variable representing the object (such as F), or by using a bold font (such as F), or by underlining (such as F or F ∼ ).

In other words, if you were to move the vector shown in Figure 1.1(a) to a different location without varying its length or its pointing direction, would it still be the same vector? In some applications, the answer is “yes,” and those vectors are called free vectors.

You can move a free vector anywhere you’d like as long as you don’t change its length or direction, and it remains the same vector. But in many physics and engineering problems, you’ll be dealing with vectors that apply at a given location; such vectors are called “bound” or “anchored” vectors,

You may see the term “sliding” vectors used for vectors that are free to move along their length but are not free to change length or direction; such vectors are useful for problems involving torque and angular motion

You can understand the usefulness of bound vectors if you think about an application such as representing the velocity of the wind at various points in the atmosphere. To do that, you could choose to draw a bound vector at each point of interest, and each of those vectors would show the speed and direction of the wind at that location (most people draw the vector with its tail – the end without the arrow – at the point to which the vector is bound). A collection of such vectors is called a vector field

If you think about the ways in which you might represent a bound vector, you may realize that the vector can be defined simply by specifying the start and end points of the arrow. So in a three-dimensional Cartesian coordinate system, you only need to know the values of x, y, and z for each end of the vector

Now consider the special case in which the vector is anchored to the origin of the coordinate system (that is, the end without the arrowhead is at the point of intersection of the coordinate axes, as shown in Figure 1.2(b). 3 Such vectors may be completely specified simply by listing the three numbers that represent the x-, y-, and z-coordinates of the vector’s end point.

In this representation, the values that represent the vector are called the “components” of the vector, and the number of components it takes to define a vector is equal to the number of dimensions in the space in which the vector exists

A scalar is the mathematical representation of a physical entity that may be characterized by magnitude only

you might suspect that there are other entities involving magnitude and directions that are more complex than vectors (that is, requiring more numbers than the number of spatial dimensions). Indeed there are, and such entities are called “tensors.”

A tensor is the mathematical representation of a physical entity that may be characterized by magnitude and multiple directions

An example of a tensor is the inertia that relates the angular velocity of a rotating object to its angular momentum. Since the angular velocity vector has a direction and the angular momentum vector has a (potentially different) direction, the inertia tensor involves multiple directions

So in 3-dimensional space, a second-rank tensor is represented by 3 2 = 9 numbers. In N-dimensional space, scalars still require only one number, vectors require N numbers, and tensors require N R numbers

a tensor may be represented by an array of 3 R numbers in 3-dimensional space. In this expression, “R” represents the rank of the tensor.

Recognizing scalars, vectors, and tensors is easy once you realize that a scalar can be represented by a single number, a vector by an ordered set of numbers, and a tensor by an array of numbers.

Do not fool yourself into thinking that life has changed much since the days of Louis XIV and the Medicis. Those who attain high standing in life are like kings and queens: They want to feel secure in their positions, and superior to those around them in intelligence, wit, and charm.

It is a deadly but common misperception to believe that by displaying and vaunting your gifts and talents, you are winning the master’s affection. He may feign appreciation, but at his first opportunity he will replace you with someone less intelligent, less attractive, less threatening, just as Louis XIV replaced the sparkling Fouquet with the bland Colbert. And as with Louis, he will not admit the truth, but will find an excuse to rid himself of your presence.

This Law involves two rules that you must realize.

First rule:

You can inadvertently outshine a master simply by being yourself. There are masters who are more insecure than others, monstrously insecure; you may naturally outshine them by your charm and grace.

No one had more natural talents than Astorre Manfredi, prince of Faenza. The most handsome of all the young princes of Italy.

In the year 1500, Cesare Borgia invaded Faenza. When the city surrendered, Borgia simply occupied its fortress, executed none of its citizens, and allowed Prince Manfredi, eighteen at the time, to remain with his court.

A few weeks later soldiers hauled Astorre Manfredi away to a Roman prison. A year after they killed him. Borgia justified the horrible deed with some sort of trumped-up charge of treason and conspiracy.

The real problem was that he (Borgia) was notoriously vain and insecure. The young man was outshining him without even trying.

Given Manfredi’s natural talents, the prince’s mere presence made Borgia seem less attractive and charismatic.

The lesson is simple: If you cannot help being charming and superior, you must learn to avoid such monsters of vanity. Either that, or find a way to mute your good qualities when in the company of a Cesare Borgia.

If you cannot help being charming and superior, you must learn to avoid such monsters of vanity. Either that, or find a way to mute your good qualities when in the company of a Cesare Borgia.

Second Rule:

Never imagine that because the master loves you, you can do anything you want. Entire books could be written about favorites who fell out of favor by taking their status for granted, for daring to outshine.

Second Rule example:

In late-sixteenth-century Japan, the favorite of Emperor Hideyoshi was a man called Sen no Rikyu. The premier artist of the tea ceremony, which had become an obsession with the nobility, he was one of Hideyoshi’s most trusted advisers, had his own apartment in the palace, and was honored throughout Japan. Yet in 1591, Hideyoshi had him arrested and sentenced to death. Rikyu took his own life, instead. The cause for his sudden change of fortune was discovered later: It seems that Rikyu, former peasant and later court favorite, had had a wooden statue made of himself wearing sandals (a sign of nobility) and posing loftily. He had had this statue placed in the most important temple inside the palace gates, in clear sight of the royalty who often would pass by. To Hideyoshi this signified that Rikyu had no sense of limits. Presuming that he had the same rights as those of the highest nobility, he had forgotten that his position depended on the emperor, and had come to believe that he had earned it on his own. This was an unforgivable miscalculation of his own importance and he paid for it with his life. Remember the following: Never take your position for granted and never let any favors you receive go to your head.

Second Rule:

Never imagine that because the master loves you, you can do anything you want. Entire books could be written about favorites who fell out of favor by taking their status for granted, for daring to outshine.

Second Rule example:

The favorite of Emperor Hideyoshi (Master) was a man called Sen no Rikyu (Disciple).

He was an artist, which had become an obsession with the nobility (became famous), he was one of Hideyoshi’s most trusted advisers.

Yet in 1591, Hideyoshi had him arrested and sentenced to death. The cause was discovered later: It seems that Rikyu, former peasant and later court favorite, had had a wooden statue made of himself wearing sandals (a sign of nobility) and placed it in the most important temple.

To Hideyoshi this signified that Rikyu had no sense of limits.

Presuming that he had the same rights as those of the highest nobility, he had forgotten that his position depended on the emperor, and had come to believe that he had earned it on his own. This was an unforgivable miscalculation of his own importance and he paid for it with his life.

Remember the following: Never take your position for granted and never let any favors you receive go to your head.

Never take your position for granted and never let any favors you receive go to your head.

First you must flatter and puff up your master. Overt flattery can be effective but has its limits; it is too direct and obvious, and looks bad to other courtiers.

Discreet flattery is much more powerful.

If you are more intelligent than your master, for example, seem the opposite: Make him appear more intelligent than you.

Commit harmless mistakes that will not hurt you in the long run but will give you the chance to ask for his help. Masters adore such requests.

If your ideas are more creative than your master’s, ascribe them to him, in as public a manner as possible. Make it clear that your advice is merely an echo of his advice.

If you surpass your master in wit, it is okay to play the role of the court jester, but do not make him appear cold and surly by comparison. one down your humor if necessary, and find ways to make him seem the dispenser of amusement and good cheer.

If you are naturally more sociable and generous than your master, be careful not to be the cloud that blocks his radiance from others. He must appear as the sun around which everyone revolves, radiating power and brilliance, the center of attention.

If you are thrust into the position of entertaining him, a display of your limited means may win you his sympathy. Any attempt to impress him with your grace and generosity can prove fatal: Learn from Fouquet or pay the price.

it is not a weakness to disguise your strengths if in the end they lead to power.

By letting others outshine you, you remain in control, instead of being a victim of their insecurity.

This will all come in handy the day you decide to rise above your inferior status. If, like Galileo, you can make your master shine even more in the eyes of others, then you are a godsend and you will be instantly promoted.

The Stars in the
Sky. There can be only
one sun at a time. Never
obscure the sunlight, or
rival the sun’s brilliance;
rather, fade into the sky and
find ways to heighten
the master star’s
intensity.

Avoid outshining the master. This is a lesson that the stars in the sky teach us—they may be related to the sun, and just as brilliant, but they never appear in her company.

You cannot worry about upsetting every person you come across, but you must be selectively cruel. If your superior is a falling star, there is nothing to fear from outshining him. Do not be merciful—your master had no such scruples in his own cold-blooded climb to the top. Gauge his strength. If he is weak, discreetly hasten his downfall: Outdo, outcharm, outsmart him at key moments. If he is very weak and ready to fall, let nature take its course. Do not risk outshining a feeble superior—it might appear cruel or spiteful. But if your master is firm in his position, yet you know yourself to be the more capable, bide your time and be patient. It is the natural course of things that power eventually fades and weakens. Your master will fall someday, and if you play it right, you will outlive and someday outshine him.

You cannot worry about upsetting every person you come across, but you must be selectively cruel.

If your superior is a falling star, there is nothing to fear from outshining him. Do not be merciful—your master had no such scruples in his own cold-blooded climb to the top.

Gauge his strength. If he is weak, discreetly hasten his downfall: Outdo, outcharm, outsmart him at key moments.

If your master is very weak and ready to fall, let nature take its course. Do not risk outshining a feeble superior—it might appear cruel or spiteful.

It is the natural course of things that power eventually fades and weakens.

If your master is firm in his position, yet you know yourself to be the more capable, bide your time and be patient. Your master will fall someday, and if you play it right, you will outlive and someday outshine him

Your mind/body connection has such a powerful survival mechanism that your muscles react instantly to truths and non-truths, to what is good for you and what is not good for you.

R has a built-in function called plot, which we call by entering plot (x,y,type="l")

The segment of code, type="l" (that’s a letter “ l” not a numeral “1”) tells R to plot connecting lines between the points, with no distinctive symbols marking the points.

R has another function, all.equal, for testing equality up to the degree of precision for the computer being used.

The standard deviation is sometimes called a scale parameter.

One case of trying to make inferences from data without using a model is a method from NHST called resampling or bootstrapping.

the anti conformation is lower in energy and occurs more frequently

there is much better stacking of the bases in the syn con- formation, as seen in a form of DNA known as Z-DNA (see Section 2.12) and in some RNA loop structures.

n the standard Watson-Crick model of DNA, all of the sugar groups have the C2ʹ endo conformation.

the C2ʹ endo conformation. Th is results in close contact between one of the oxygen atoms of the 3ʹ phosphate group and the hydrogen atom at the 2ʹ position of the ribose ring in DNA

h e distance between the phos- phate oxygen and the hydrogen atom is 1.9 Å.

If the 2ʹ hydrogen were replaced by a hydroxyl group, as in the ribose ring of RNA, the two oxygen atoms would repel each other strongly.

in RNA, the sugar adopts a C3ʹ endo conformation (Figure 2.9), which causes a change in phosphate separation and a general modi- fi cation of the double-helical structure

To get a list of all sorts of online documentation, much of it written in readable prose instead of telegraphic lists, type help.start()