The Basics - Definitions

AS404 –Day 1

The Goals of this Class:

· Difference between scientific thought and philosophical thought

· Learn the basic definitions used in the scientific community

· Learn the basic theories of Quantum Mechanics

· Learn the basic models of chemical structure and reactions

· Understand the cycles of sugar, fat and carbohydrate metabolism

· How living organisms breakdown, create, store and retrieve energy

Grading & The Final Exam:

· All the reading is required

· 50% of your grade is the final exam

· 50% of your grade is the homework and I take the median.

· Your final exam will be 60 questions answered in 2 hours or less

· Questions will be taken from class lecture, homework and all the readings

· 30% questions on Physics, 30% of the questions on Organic Chemistry and 30% of the questions on Biochemistry.

· You will be expected to memorize chemical structures, models and cycles

Definitions

A Form – An Outline of Powers and Limits - Mathematics

A System – A decision made before the question arises – A method used to answer a question

A Principle – A basic truth or law or assumption – Natural Laws

What is science? Study of the Natural World

What is religion? A strong belief in a supernatural power or powers

Science is about Cosmic Order: Religion is about Cosmic Purpose

What is physics? The study of matter and energy.

What is chemistry? The science of matter; how is matter put together? The branch of the natural sciences dealing with the composition of substances and their properties and reactions.

What is biology? The study of living organisms. A much more complex science. It is dealing with matter that is alive!

What is mathematics? The study of patterns of structure, change, and space

Physics is the foundation of all the other sciences. An understanding of science begins with an understanding of physics.

Scientists answer questions:

Who?

What? 90% populace & media focus on these

When?

Where?

How? Engineers – Take theory and put it into practice - lubrication & adhesion

Why? Scientists – Theoretical and Experimental arenas

Just a note: most of the lecture notes that I use are drawn from other websites, textbooks, and electronic library resources. Please do not take the following lecture notes as original! I have copied, compiled and collated. Basically, I have borrowed from the work of people MUCH smarter than me to bring this information to you. I have made every effort to put links in place to send you to the original web sites where this information came from.

The Four Known Universal Forces

Strong Nuclear Force

Electromagnetism

Weak Nuclear Force

Gravity

The Strong Nuclear Force

· It is the strongest

· It has the shortest distance of influence

· Its main job is to hold together the subatomic particles of the nucleus: called nucleons.

· like charges repel (+ +, or - -), and unlike charges attract (+ -).

· why would the nuclei of these atoms stay together?

· The strong nuclear force is created between nucleons by the exchange of particles called gluons. This exchange can be likened to constantly hitting a ping-pong ball or a tennis ball back and forth between two people. As long as this gluon exchange can happen, the strong force is able to hold the participating nucleons together.

· The nucleons must be extremely close together in order for this exchange to happen. The distance required is about the diameter of a proton or a neutron

· The dotted line surrounding the nucleon being approached represents any electrostatic repulsion that might be present due to the charges of the nucleons/particles that are involved. A particle must be able to cross this barrier in order for the strong force to "glue" the particles together

· In the case of approaching protons/nuclei, the closer they get, the more they feel the repulsion from the other proton/nucleus (the electromagnetic force). As a result, in order to get two protons/nuclei close enough to begin exchanging gluons, they must be moving extremely fast (which means the temperature must be really high), and/or they must be under immense pressure so that they are forced to get close enough to allow the exchange of gluons to create the strong force.

· Now, back to the nucleus. One thing that helps reduce the repulsion between protons within a nucleus is the presence of any neutrons. Since they have no charge they don't add to the repulsion already present, and they help separate the protons from each other so they don't feel as strong a repulsive force from any other nearby protons. Also, the neutrons are a source of more strong force for the nucleus since they participate in the meson exchange. These factors, coupled with the tight packing of protons in the nucleus so that they can exchange mesons creates enough strong force to overcome their mutual repulsion and force the nucleons to stay bound together.

· The preceding explanation shows the reason why it is easier to bombard a nucleus with neutrons than with protons. Since the neutrons have no charge, as they approach a positively charged nucleus they will not feel any repulsion. They therefore can easily "break" the electrostatic repulsion barrier to being exchanging mesons with the nucleus, thus becoming incorporated into it.

Electromagnetism

One of the four fundamental forces, the electromagnetic force manifests itself through the forces between charges (Coulomb's Law) and the magnetic force, both of which are summarized in the Lorentz force law. Fundamentally, both magnetic and electric forces are manifestations of an exchange force involving the exchange of photons . The quantum approach to the electromagnetic force is called quantum electrodynamics or QED. The electromagnetic force is a force of infinite range which obeys the inverse square law, and is of the same form as the gravity force.

The electromagnetic force holds atoms and molecules together. In fact, the forces of electric attraction and repulsion of electric charges are so dominant over the other three fundamental forces that they can be considered to be negligible as determiners of atomic and molecular structure. Even magnetic effects are usually apparent only at high resolutions, and as small corrections.

Weak Nuclear Force

One of the four fundamental forces, the weak interaction involves the exchange of the intermediate vector bosons, the W and the Z. Since the mass of these particles is on the order of 80 GeV, the uncertainty principle dictates a range of about 10^-18 meters which is about 0.1% of the diameter of a proton.

The weak interaction changes one flavor of quark into another. It is crucial to the structure of the universe in that

1. The sun would not burn without it since the weak interaction causes the transmutation p -> n so that deuterium can form and deuterium fusion can take place.

2. It is necessary for the buildup of heavy nuclei.

The role of the weak force in the transmutation of quarks makes it the interaction involved in many decays of nuclear particles which require a change of a quark from one flavor to another. It was in radioactive decay such as beta decay that the existence of the weak interaction was first revealed. The weak interaction is the only process in which a quark can change to another quark, or a lepton to another lepton - the so-called "flavor changes".

The discovery of the W and Z particles in 1983 was hailed as a confirmation of the theories which connect the weak force to the electromagnetic force in electroweak unification.

The weak interaction acts between both quarks and leptons, whereas the strong force does not act between leptons. "Leptons have no color, so they do not participate in the strong interactions; neutrinos have no charge, so they experience no electromagnetic forces; but all of them join in the weak interactions."(Griffiths)

Beta Radioactivity

Beta particles are just electrons from the nucleus, the term "beta particle" being an historical term used in the early description of radioactivity. The high energy electrons have greater range of penetration than alpha particles, but still much less than gamma rays. The radiation hazard from betas is greatest if they are ingested. Beta emission is accompanied by the emission of an electron antineutrino which shares the momentum and energy of the decay.

The emission of the electron's antiparticle, the positron, is also called beta decay. Beta decay can be seen as the decay of one of the neutrons to a proton via the weak interaction. The use of a weak interaction Feynman diagram can clarify the process.

Gravity

Gravity is the weakest of the four fundamental forces, yet it is the dominant force in the universe for shaping the large scale structure of galaxies, stars, etc. The gravitational force between two masses m₁ and m₂ is given by the relationship:

This is often called the "universal law of gravitation" and G the universal gravitation constant. It is an example of an inverse square law force. The force is always attractive and acts along the line joining the centers of mass of the two masses. The forces on the two masses are equal in size but opposite in direction, obeying Newton's third law. Viewed as an exchange force, the massless exchange particle is called the graviton.

The gravity force has the same form as Coulomb's law for the forces between electric charges, i.e., it is an inverse square law force which depends upon the product of the two interacting sources. This led Einstein to start with the electromagnetic force and gravity as the first attempt to demonstrate the unification of the fundamental forces. It turns out that this was the wrong place to start, and that gravity will be the last of the forces to unify with the other three forces. Electroweak unification (unification of the electromagnetic and weak forces) was demonstrated in 1983, a result which could not be anticipated in the time of Einstein's search. It now appears that the common form of the gravity and electromagnetic forces arises from the fact that each of them involves an exchange particle of zero mass, not because of an inherent symmetry which would make them easy to unify.

Examples of Trajectories

Common misconceptions about guns:

A dropped bullet will hit the ground before one which is fired from a gun.

As shown in the illustration of a horizontal launch, gravity acts the same way on both bullets, giving them the same downward acceleration and making them strike the ground at the same time if the bullet is fired horizontally over level ground.

Bullets fired from high-powered rifles drop only a few inches in hundreds of yards.

Fired at twice the speed of sound, a bullet will drop over 3 inches in 100 yards, and at 300 yards downrange will have dropped about 30 inches. Plug in numbers into the bullet drop calculation to see for yourself. Ammunition manufacturers contribute to this misconception by stating the drop of their projectiles as just the extra drop caused by frictional drag compared to an ideal frictionless projectile.

Drop of a Bullet

If air friction is neglected, then the drop of a bullet fired horizontally can be treated as an ordinary horizontal trajectory. The air friction is significant, so this is an idealization.

Inverse Square Law, General

Any point source which spreads its influence equally in all directions without a limit to its range will obey the inverse square law. This comes from strictly geometrical considerations. The intensity of the influence at any given radius r is the source strength divided by the area of the sphere. Being strictly geometric in its origin, the inverse square law applies to diverse phenomena. Point sources of gravitational force, electric field, light, sound or radiation obey the inverse square law. It is a subject of continuing debate with a source such as a skunk on top of a flag pole; will it's smell drop off according to the inverse square law?

Inverse Square Law, Gravity

As one of the fields which obey the general inverse square law, the gravity field can be put in the form shown below, showing that the acceleration of gravity, g, is an expression of the intensity of the gravity field.

Inverse Square Law, Electric

As one of the fields which obey the general inverse square law, the electric field of a point charge can be put in the form shown below where point charge Q is the source of the field. The electric force in Coulomb's law follows the inverse square law.

Inverse Square Law, Radiation

As one of the fields which obey the general inverse square law, a point radiation source can be characterized by the relationship below whether you are talking about Roentgens , rads, or rems . All measures of exposure will drop off by inverse square law.

The source is described by a general "source strength" S because there are many ways to characterize a radiation source - by grams of a radioactive isotope, source strength in Curies, etc. For any such description of the source, if you have determined the amount of radiation per unit area reaching 1 meter, then it will be one fourth as much at 2 meters.

Homework Day 1 -Quantum Mechanics

1. Define the differences and similarities of a Confederation, a Democracy, a Republic and how they interact with the populations of people under them.

2. Define Science and Religion. Explain the different methods used by each to obtain knowledge. Are there any similarities?

3. Define Physics, Chemistry, Biology, Biochemistry and Mathematics. How do these disciplines build upon one another?

4. Define Classical Physics and Quantum Mechanics. Explain the challenges that Einstein had with Newton’s work and what he had to do to overcome preexisting paradigms.

5. What was the Copenhagen Interpretation and who was involved? Why was Einstein so upset by this?

6. What are the four known forces in our Universe? Give examples of what they do and how they interact with matter.

7. What is the difference between Average, Mean, Median and Mode?

8. What is a positive charge? A negative charge? Why was Benjamin Franklin’s assignments “unfortunate”?

Periodic Table of Desserts

I have to thank a geek girlfriend of mine, Alison from North Carolina who submitted this "did-you-know" link. A place of posters that you can order which present the Periodic table of desserts, vegetables, fruits and endangered species. A super cool place to wander for Christmas presents. This is just an FYI when you're having a hard time finding that just-right gift for your scientific friend (or is that fiend?)

Enjoy!

Geek Think: How Scientists Approach the World

Almost there, aren’t we? Congratulations. Now, at last, it is time to consider why you have been taking this class.

A few facts about chemistry is one good reason. Learning how to think like a scientist is the other.

Today we will be addressing the second point, the fine art of honing the geek mind. We will approach this subject by example, by going through the experiment that was assigned a couple of sessions ago. The following little piece constitutes my own effort at completing the task, with a few editorial comments thrown into spice the stew. Naturally in the normal order of things all of this would be recorded in a laboratory notebook so that you could sign and date the entries, to protect your important insights from competitors in the Alka-Seltzer analysis field. You will just have to settle for reading about it on line.

Let’s start with HYPOTHESES. I came up with two:

Two-tailed: Altering the reaction temperature will alter the reaction rate.

One-Tailed: The reaction will increase as the reaction temperature rises.

A two-tailed hypothesis is one that makes no assumption about what outcome will occur (i.e., a rising reaction temperature will alter the rate either up or down), while a one-tailed hypothesis picks a specific way in which you think the outcome may trend.

The next thing a good experiment needs is a list of MATERIALS. I include separate headings for reagents (the stuff that participates in and/or is consumed during the chemical reaction – in this case Alka-Seltzer and water) and equipment to perform the experiment (clear glass, 1-cup measuring cup, watch with second hand, thermometer). The materials list is followed by a really detailed, step-by-step set of METHODS. One must pay great attention to detail in this section so that (1) you can catch any mistakes you have made in running the experiment and (2) so that other people can replicate your work. In science, if it can’t be repeated is not considered reputable. The methods I used for this experiment were, in order, the following:

1. Alka-Seltzer tablets were unwrapped two at a time.

2. Water was prepared as follows:

a. Cold (~0°C): Four 1-in³ ice cubes were added to four cups of water and left for 15 minutes

b. Normal (~20°C) Four cups of water were decanted from a receptacle after sitting for 24 hours at room temperature

c. Hot (~100°C) Four cups of tap water were heated to boiling in a teapot

3. The glass was equilibrated to the desired water temperature by pre-filling with either ice water or hot water.

4. One cup of water at the appropriate temperature was placed in the glass. A 1-in³ ice cube was added to the “cold trials” to keep the water cold.

5. A single tablet was dropped from a 2-inch height into the vessel.

6. Time (in seconds) to complete dissolution of the primary tablet (i.e., the end of violent fizzing) was recorded.

7. Ancillary (“other”) measurements included observations on tablet motility and gas evolution.

Of course, the point of an experiment is to get some RESULTS. These are the ones I got. I put them into a table so that the raw data (the values measured during all the trials) would be available for inspection. Then I calculated the mean (the average) of the results for each temperature so that someone wanting to quickly see the outcome would be able to do so at a glance.

	Temperature
Trial	0°C	20°C	100°C
1	87 s	47 s	34 s
2	100 s	45 s	33 s
3	80 s	49 s	32 s
4	66 s	49 s	32 s
Mean	**83	48	**33
SD	14	2	1

The double asterisks (**) denote that the mean values for these two groups are significantly different from the mean value for the 20°C group, p < style=""> (Normally, statistical significance is assigned to an outcome if p <>

I made a few additional observations on characteristics of Alka-Seltzer. These traits were not the focus of my hypotheses, so I did not measure them exactly. However, I made some reasonable “guesstimates” regarding their repeatability so that I could investigate them in more detail.

1. Tablet motility varied by temperature. Tablet orientation became:

a. Cold (~0°C): Vertical at 45 to 50 s

Floated at 55 to 60 s

b. Normal (~20°C) Vertical at 15 to 20 s

Floated at 20 to 25 s

c. Hot (~100°C) Vertical orientation not seen

Floated immediately

2. Tablet character upon cessation of fizzing.

a. Cold (~0°C): Many small particles and much foam cover most of the surface

b. Normal (~20°C) A few fine particles and some foam line the rim of the glass

c. Hot (~100°C) No particles or foam remain

3. Gas evolution varied by temperature.

a. Cold (~0°C): Fine bubbles made from top of tablet, large ones from beneath

b. Normal (~20°C) Fine bubbles made from top and bottom of tablet

c. Hot (~100°C) Myriad fine bubbles from entire surface of tablet, as well as elaboration of steam from upper surface

Finally, you use the results to make an INTERPRETATION. This step is also called drawing conclusions or making inferences. In this case, my results confirmed the hypotheses I made: the rate of a chemical reaction is significantly increased as the reaction temperature is raised.

A word on STATISTICS. Mark Twain popularized the Benjamin Disraeli proverb, “There are three kinds of lies: lies, damned lies, and statistics.” This statement is knocking statistics, but those who would use a mass of poorly understand numbers – even if correctly calculated – to support an inaccurate conclusion. Scientists rely on statistics to avoid false positive and false negative conclusions. A false positive or Type I error occurs when the statistical calculation suggests that something is of significance but in reality it is not, while a false negative or Type II error occurs when something significant in the real world is not identified as such using the statistical analysis. In general, scientists tend to try to avoid the Type I error more vigorously. A detailed consideration of statistics s way, way, way beyond the scope of this blog. Just keep in mind that statistical calculations can be used by different scientists working on the same problem to bolster totally opposite points of view. Just because a number is thrown at you, don’t believe that the “answer” it is trying to reinforce is true. The concept caveat emptor – “Let the buyer beware” – is particularly true in science. Be open to new ideas, but be skeptical about adopting them without a thorough review of the data for yourself.

Sleep tight. It all ends tomorrow. The class, I mean….

The Universe Within: Quantum Chemistry

Halfway there after today, folks. Hang in there.

The topic for this morning is a continuation of the periodic table, particularly the chemical properties of the major elements and the subatomic structure of the atomic nucleus.

The main topic to consider in mastering the modern periodic table in its relationship to quantum mechanics is how to describe electrons in the nucleus. Each electron has a unique address in the electron cloud, a position in an orbital. Each orbital, or shell, is a wave function describing the likely location of electrons based on the lowest possible energy state of the nucleus. We cannot know precisely where any given electron is in an orbital as stated in the Heisenberg uncertainty principle, but we can still describe it numerically. Modern quantum theory holds that each electron orbits the nucleus in a specific shell and sub-shell with a given orientation. Thus, each electron has a unique “address” composed of four quantum numbers.

The principal quantum number, n, defines the shell in which the electron resides. Values of n are positive, non-zero integers. The shells with n = 1, n = 2, and n = 3 are called the first shell (also called the K shell, for no particular reason), second shell (L shell), and third shell (M shell). The secondary quantum number, l, divides each shell into sub-shells of slightly different energies. For a given orbital n, the l values can range from 0 to (n – 1). Thus, for the first shell (n = 1), the only value of l is 0, and only one sub-shell exists; for the second shell (n = 2), values of l can be 0 or 1, and two sub-shells are present; and so on. The sub-shells are designated by a letter code, where the first (l = 0) is labeled “s”, the second (l = 1) is “p”, the third (l = 2) is d, the fourth (l = 3) is “f”. To designate a particular sub-shell, we write the principal quantum number followed by the letter code for the sub-shell. The lower the sub-shell number, the lower the energy. The third quantum number is known as the magnetic quantum number and is designated m_l. It divides each shell into individual orbitals. Values for m_l can range from +l to –l. Thus, the s sub-shell (l = 0) has a single orbital since +0 and -0 are still just 0, while the p sub-shell (l = 1) has three orbitals (+1, 0, -1). All the orbitals of a given sub-shell have the same energy. The fourth quantum number is the spin quantum number, m_s, which is either + ½ or - ½. The Pauli exclusion principle states that no two electrons in the same atom can have identical values for all four quantum numbers.

Atoms are built from the inside out, by adding electrons to the lowest possible orbital because this is the lowest and therefore most favored energy state. This concept is termed the aufbau principle (German for “building up”). When added to a specific orbital, Hund’s rule states that electrons will spread out as much as possible, avoiding pairing within an orbital for as long as possible.

The interaction of atoms in chemical reactions is dictated by the electron configuration in the outer (or valence) shell. Elements in the same group (column) of the periodic table have similar arrangements of electrons in their valence shell. The valence shells fill as one progresses from left to right in the periodic table, until all positions are occupied in the VIIIA group (noble gases) located farthest to the right. The completely filled valence shell of the noble gases renders them quite unreactive. Many other elements undergo chemical reactions in such a way that their electron configuration tends to assume the same configuration as the nearest noble gas.

Rest well until tomorrow – in body, if not in mind.

The Big Picture: Chemistry Gets Organized

One day down, four to go. Let’s rock on.

The major topic for the next couple of days is MODERN ATOMIC THEORY. Chemistry did not begin until this principle had gained general acceptance in the early 1800s . The first recorded hypothesis regarding the basic unit of material things is attributed to the pre-Socratic Greek philosopher, Democritus (c. 460–c. 370 B.C.). After his teacher Leucippus had noted that a beach looks smooth from afar but really consists of individual sand grains, Democritus said that the concept could be extended to all matter because material things were made of indivisible particles. Democritus called his particles atomos, meaning "cannot be cut." His ideas were largely ignored until the scientific revolution of the western Enlightenment (16^th to 18^th centuries) due to widespread acceptance of Aristotle’s (c. 384–c. 322 B.C.) view that all matter was comprised of earth, air, water, and fire in varying proportions, and that matter could be transmuted into gold by adjusting the ratios of these four elements. (Aristotle also limited matter to four essential properties: hot, cold, dry, and wet!)

In modern times, atomic theory was rediscovered by John Dalton (1766-1844), an English physical scientist. In the early 1800s he was a professor of mathematics and natural philosophy, and he dedicated his research efforts to standardizing then known chemical knowledge. The result was a series of principles to explain the structure of matter:

1. Matter consists of tiny particles (atoms).
2. Atoms are indestructible. In chemical reactions they can rearrange but not break apart.
3. All atoms of a given element are identical in mass and other properties (true then, as isotopes had not been discovered).
4. Atoms of different elements differ in mass and other properties.
5. Elements combined into a given compound always react in a fixed ratio.

The atomic theory provided the impetus for later attempts to develop a unifying principle for all chemistry (and physics!) knowledge, the PERIODIC TABLE. Many scientists in the late 1700s and early 1800s contributed to its theoretical underpinnings, but the laurel for the first modern version goes to Dmitri Mendeleev – to give the most common of the spellings for his name). This Russian chemist is accorded the honor because his array not only attempted to systematize existing chemical knowledge but because he used his model to make predictions about the existence and properties of then unknown elements. Mendeleev arranged his table into columns (groups) and rows (periods) according to elemental atomic weights (representing the mass of protons and neutrons), while modern tables use atomic number (proton number). Entities in a given group or period share certain chemical properties based on their atomic structure, and particularly the number and arrangement of electrons in the outer (or valence) orbital. But more on that tomorrow….

Chemistry Experiment

Chemistry AS403 – Experiment

Chemical reactions proceed at a set rate, but the rate varies depending on many factors. Environmental conditions in particular have a major impact on the rate at which reactions may proceed.

Undertake the following experiment at home to test this principle.

Buy a box of Alka-Seltzer anti-indigestion medication. This product combines acetylsalicylic acid (aspirin), sodium bicarbonate (baking soda) and citric acid.

You will be conducting an experiment with 3 tablets. Place one tablet in a glass of hot (but not boiling) water, another in a glass of ice-cold water, and a third in a glass filled with water that is at room temperature. Measure how long the fizzing continues in each glass after dropping the tablet.

Prior to the experiment, construct hypotheses about (1) the likely outcome and (2) the mechanism by which the fizzing is produced. After gathering data, interpret your results, design any follow-up experiments that might be needed to refine the data, and make a list of factors that might have impacted the accuracy of your experiment.

Feel free to use the left-over Alka-Seltzer to sooth your heartburn....

Simulation on Public Policy

Chemistry AS403 – Simulation

Washington, D.C.

Spring, 2019. The one bright spot in the usual atmosphere of political infighting and intrigue is public contentment with the austere homeland security policies that finally succeeded in interdicting illegal immigration across the nation’s 2000-mile southern border beginning in 2013. This success was achieved through the combined use of multiple electrified fences backed by solid concrete walls, with regular defoliation of the intervening no-man’s-land between the barriers using biodegradable herbicides.

In 2014, the United States had suffered a severe bout of inflation due to the rise in wages associated with the loss of several million “guest” workers, while Mexico underwent a major recession due to many factory closures stemming from the loss of major American markets. Mexico responded by suspending diplomatic relations with the United States. Relations were restored in 2017 thanks to the efforts of the newly elected Administration, which moved rapidly to restore free trade (but not immigration). Mexican factories in border towns were reopened, and the adjacent border became the main route for transporting Mexican goods to the eager American consumer. The entire free trade zone along the Texas – Mexican border developed almost overnight into an economic powerhouse to rival the success of South Korea and Taiwan. Communities on both sides of the border are benefiting by the rapid increase in employment, income levels, and public services. The flagship accomplishments touted by governmental officials in both nations are ample schools and libraries, low-cost medical clinics, and careful environmental stewardship.

Despite the promise, a concern for the region’s population is the rising number of birth defects in infants and cancers in people of all ages. The problem has been smoldering for nearly three decades, but in the last five years the incidence has accelerated rapidly. The local economies are in danger of collapse as potential workers avoid relocation to the region while the incumbent population seeks to leave.

You are a member of a bilateral public policy commission tasked with identifying likely cause of the epidemic and pinpointing means by which the threat may be ended. Develop one or more hypotheses regarding the cause of the problem. Design the necessary tests to verify or negate the hypotheses, keeping in mind both scientific considerations and ancillary concerns (e.g., cost and international relations). Prepare a brief for delivery to the President outlining your hypotheses, proposed experiments (both initial and follow-up), and likely recommendations for dealing with the scenario.