A JOB BEHIND THE CURTAIN?

I've been asked to serve on the board of the Central California chapter of the Interfaith Alliance, which works on common causes with other interest groups, among them Americans United for Separation of Church and State.

IACC is interested in promoting certain things in the public schools, among them a commitment to the First Amendment, minority rights and an appreciation for religious diversity. My qualifications for this are murky, but I suspect writing letters to the editor, publicly debating creationists, and working to promote free thought on my particular campus are things that might've commended me. That, and I'm halfway decent as a speaker---though you'd never know that from this.

Well, shoot, if I'm not effective, at least they're not paying me.

BARRIER TO UNDER-STAN-DING?

Stan and I have been bouncing back-and-forth, and I suppose a quick gloss of our perorations would be 'examining the philosophical basis of scientific practice.' It's that gray area, one supposes, between epistemology per se and the philosophy of science.

But Stan, we seem to have a problem as far as fostering a dialogue that's easy for others to follow, and that is that I can't seem to link to new specific posts on your blog. It seems as if any links I offer automatically take me to this site, which is Stan's web site, rather than to a specific blog post. What a hassle!

Now, Stan has obviously spent a lot of time organizing the above site to articulate his views, and it would be unreasonable to expect him to alter its entire structure simply to facilitate our discussion, so I am going to suggest that perhaps we should just do all the blogging here. With that in mind, I'm going to post a list of some (not all) of the things that Stan described as First Principles now, and respond (in part) in my next post

1. The Intuitive Principles

These principles, while not provable, are known to be valid intuitively

a. Identity. If it is true, then it is true; if it exists, then it exists.
b. Non-Contradiction. If it is true, then it cannot be false; if it exists, it cannot NOT exist.
c. Excluded Middle.A (singular, unity) concept cannot be somewhat true and somewhat false; a (singular, unity) thing cannot somewhat exist and somewhat not exist.
d. Cause and effect. Every effect has a cause that is both necessary and sufficient.
e. Cogito (Descartes). Because I doubt my own doubt, it is true that I think; because I think (truth), I must exist (fact).

2. The Probabilistic Principles.
These Principles seem to encompass both truth and existence

a. The Immutability of math throughout the universe.
b. The Immutability of physical law throughout the universe
c.The mutability of all levels of verifiability (Godel's laws).

3. The Presuppositional Principles
These principles are declared either as empirical constraints, or as part of a worldview.

a. No form of reality exists that cannot be either observed and measured directly or by the use of instrumentation.
b. No Singularities (temporary violations) exist in the physical laws of the universe.

REVIEWING THE FALL SEMESTER (GULP)

"What are they teaching kids these days?" People really have no idea, in general, what exactly is being covered in a high school biology course. Reading the state standards would help, but laypeople will struggle to convert the standards (which are 'wish lists' of understanding) into the sort of factoids deemed essential. Recognizing that vocabulary and concepts are not in themselves an education, I present for your consideration the following handout totalling 2,400 + words given my Biology students which summarizes the highlights of the fall semester:

THE ‘NATURE’ OF SCIENCE

Science investigates the natural world. Science assumes, but never proves, that the Universe follows Laws of Nature. Based on that assumption, scientists attempt to explain the phenomena they see in terms of natural causes alone. Science attempts to answer questions about Cosmic Order. Other aspects of human experience (like art, music and religion) ask and attempt to answer different kinds of questions, often having to do with Cosmic Purpose.

SCIENTISTS TEST THEIR IDEAS

Scientists try to build theories, which are powerful, well-tested models that explain many different phenomena. For example, physicists have developed the idea of gravity, and that idea can be used to explain different things: why rain falls, why there are moons, why planets go around the sun. In fact, (so far) everywhere scientists have looked for it, they’ve found a force they call gravity.

Does this prove that gravity is found everywhere else in the Universe? Probably not, but it does show that gravity is a powerful model that has (so far!) survived attempts to disprove, or falsify it! The important thing to a scientist is not whether an idea is true or false, but whether or not it can be tested. Ideas that can’t be tested (even if we think they are true!) are non-falsifiable and they can’t be used in science.

THE SCIENTIFIC METHOD

Scientists do more than test their ideas, however. They use what is called scientific method to develop ideas, carefully test them, and share their results and conclusions with the rest of the scientific community. Just as there is no one way to make a cake, there is no single ‘recipe’ for doing science. Your teacher has described scientific method with the acronym O.H.E.C.K., which stands for Observations, Hypothesis, Experiment, Conclusions and Knowledge-Sharing.

EXPERIMENT AND THE HYPOTHESIS

Experiments are designed to test a specific idea called a hypothesis. A hypothesis is often described as an ‘educated guess’, but you can actually get a hypothesis from any source, as long as the idea is falsifiable (can be tested). If we can’t test the idea by observation and experiment, we can’t use it in science! And, when we do experiments, the results are only valid if there are controls for variables, which are things which can change during the experiment, or which vary from one trial to the next. Some variables are deliberately changed, while others change regardless of what the experiments do, but in any case well-designed experiments always account for these changes.

BIOLOGY’S RELATIONSHIP TO OTHER SCIENCES

Since the scientific method requires scientists to share their results and conclusions with other scientists, the results of one experiment leads naturally to other experiments, and so scientific knowledge grows over time. In fact, as science has grown, one field of study has led to another. The ancient Greeks, for example, developed many concepts in Mathematics, like geometry. These math concepts were useful in the development of Physics, which studies basic things like matter, motion and energy. Chemistry is based on physics and studies the ways that matter and energy can be arranged. In turn, Biology can be thought of as a special branch of chemistry, one that studies a particular way that matter and energy can be arranged, which is to say organisms (living things).

So biology is based on chemistry, and chemistry is based on physics! Because of this, it’s helpful to review a little physics (atomic theory) and chemistry (chemical bonding, organic compounds) in order to help us ‘do’ biology!

A LITTLE PHYSICS (ATOMIC STRUCTURE)

Matter comes in units called atoms, which are the smallest pieces of matter that retain unique chemical properties. Atoms appear as elements in the periodic table. There are 92 different naturally-occurring elements listed in that table, and they are arranged on the basis of common properties. Atoms are formed from three kinds of sub-atomic particles: protons, which are massive, positively-charged particles in the atom’s nucleus; neutrons, which are like protons but have no charge, and electrons, which are nearly massless, have a negative charge, and occupy energy levels called shells outside the atom’s nucleus.

A LITTLE MORE PHYSICS (ISOTOPES AND IONS)

The atomic number of a given element is equal to the number of protons. Atoms which have the same number of protons and neutrons in the nucleus tend to be stable, but there are versions of atoms with extra mass in the form of neutrons which are extra-heavy, unstable and likely to fall apart. These extra-heavy atoms, called isotopes, are radioactive, because they radiate energy when they fall apart!

Atoms which have an equal number of protons and electrons are electrically-neutral, because they have an equal number of positive and negative charges. Atoms or molecules in which the number of protons and electrons are not equal will have an overall charge, and these are called ions.

Many elements exist in nature as ions, and ions with opposite charges (such as Na+ and Cl-) often form neutral compounds held together by ionic bonds, like NaCl (table salt). Solutions with excess positive charge are called acids, and solutions with excess negative charge are bases.

A LITTLE CHEMISTRY (COVALENT BONDING AND MACROMOLECULES)

The bond that holds ions together is a weak bond in which an electron is transferred, but there are much stronger bonds, called covalent bonds, in which one or more electrons are shared by two atoms. These bonds are strong enough to build large compounds called macromolecules. Organic chemistry studies macromolecules based upon chains of carbon atoms. There are four important classes of organic macromolecules: lipids, carbohydrates, proteins and nucleic acids. In each class, long chains called polymers are formed from carbon-based subunits called monomers to build the macromolecules.

Lipids (mostly C and H) are constructed from monomers called fatty acids. The monomers of Carbohydrates (largely C, H and O) are known as simple sugars, or monosaccharides. The most common monosaccharide in living things is glucose. Carbohydrate monomers are used to build complex polysaccharide chains such as starch, cellulose and glycogen. Proteins (mainly C, H, O and N) are built from monomers called amino acids.

Most living things use the same set of 20 amino acids to build the proteins that they need. The sequence of amino acids in the chain determines the final folded shape of the desired protein. The protein’s shape, in turn, determines its function. Many proteins are enzymes, which are reusable molecules not directly involved in a chemical reaction which nevertheless have a special shape which makes a particular reaction more likely to occur. The information needed to sequence the amino acids properly to build the right protein is encoded in the final class of macromolecules, Nucleic Acids.

FINALLY, SOME BIOLOGY (BOUNDARY OF THE CELL)

All living things today are made of cells and come from pre-existing cells. All cells are defined by a double-layered boundary called the cell membrane, which is made of molecules called phospholipids. Cell membrane is dynamic and constantly-changing, and is said to be selectively-permeable due to its ability to partially control what goes in and out of the cell. Small molecules (such as water) can move through the membrane automatically in a passive process called diffusion. (The diffusion of water is known as osmosis).

Larger molecules will often require active transport, in which energy is expended to move the item in or out, often through special protein channels embedded in the membrane. Many cells can also transport larger chunks of material or fluid by folding membrane around specific targets, capturing (endocytosis) or releasing (exocytosis) their desired targets.

THE INTERIOR OF THE CELL

All cells have certain features in common, among them DNA, a cell membrane and miniature protein-building machines called ribosomes. Many of these cells tend to have a simple internal organization without much folding of cell membrane. These cells, known as prokaryotes, do not have a nucleus or any membrane-bound organelles, but conduct all their business in the fluid-filled interior of the cell known as the cytoplasm. This includes the ‘naked’ DNA of bacteria, which is often found as a single circular chromosome floating in the cytoplasm. For this reason, many parasites and viruses prefer to attack prokaryotes. Scientists working in the field of biotechnology often ‘hijack’ the genetic equipment of prokaryotes for the same reason.

Cells with a nucleus and membrane-bound organelles are called eukaryotes (‘true nucleus’). These cells contain a network of structures based upon the folding of cell membrane. Eukaryotes can be either single-celled or (as in the case of humans, animals, plants and fungi) multicellular. Organelles of interest include chloroplasts, mitochondria, the nucleus, the ER (endoplasmic reticulum) and the Golgi complex. Chloroplasts (found in plants, protists and some bacteria) capture solar energy and convert it into chemical energy. Mitochondria liberate stored chemical energy for the function of the cell. The nucleus stores the information-carrying chromosomes made of DNA and protein. Proteins are built in ribosomes in the cytoplasm and the surface of the rough ER. Many of these proteins are further modified and ‘packaged’ for transport in the Golgi complex.

CELLULAR ENERGETICS

As mentioned before, plants and other organisms capture sunlight and convert it into chemical energy. To put it another way, they are autotrophs that make their own food. Animals, on the other hand, are heterotrophs: they either eat autotrophs or other organisms in the food chain to get the energy they need to survive. When organisms die, the energy stored in the covalent bonds of the molecules in their body eventually becomes available for plants and other autotrophs. Since this is true, most of the organisms on Earth participate in a ‘Great Circle’ that recycles different atoms and promotes the flow of energy through the environment.

Most organisms on Earth, therefore, depend on autotrophs to create sugars for short-term energy usage, but they and heterotrophs will often convert those sugars to lipids (fats, waxes and oils) for long-term energy storage. For convenience, stored energy is used to synthesize smaller, energy-carrying molecules like ATP. In a sense, sugars and fats are like $100 bills, while a single ATP is like a small coin.

More energy is liberated by chemical reactions which use oxygen (aerobic respiration) than by those that don’t (anaerobic respiration), so large organisms which require lots of energy don’t have a choice: they must employ oxygen in respiration, even though free oxygen is dangerous and can easily damage cells. For this reason, animals produce many enzymes to control the flow of oxygen, and the reactions themselves are kept inside the ‘combustion chamber’ of the mitochondria.

CELL DIVISION (MITOSIS):

Most of the life of the cell is spent growing: doing chemical reactions, building structures, and capturing, storing, and releasing the energy needed for all that activity. This period in between acts of cell division is called interphase. During this period, the DNA is replicated, so that there are two copies of each DNA molecule. During mitosis in eukaryotes, the chromosomes of DNA and protein condense, the nucleus dissolves, and the centrioles (tiny barrel-shaped structures) migrate to opposite poles of the cell. There, a network of microtubule fibers will first align the chromosomes, and then pull them apart to opposite poles of the cell. There, a pair of nuclei will form and then the cell divides (cytokinesis), producing two identical daughter cells.

DNA: THE MOLECULE OF HEREDITY

The information needed to do all these chemical reactions, and build all these structures, is encoded in DNA (deoxyribonucleic acid). DNA is a double-stranded chain constructed from monomers called nucleotides. Each nucleotide has three parts to its structure: a sugar (deoxyribose), a phosphate group, and one of four nitrogen bases (adenine, cytosine, guanine and thymine).

The two strands of DNA move in opposite directions and are held together by bonds between the bases in the middle, like the rungs of a ladder. The bonding follows the base-pairing rule ‘GCAT’: guanine always binds with cytosine, and adenine always binds with thymine. It follows that all the information needed to copy one strand of DNA is always found on the opposite strand!

THE CENTRAL DOGMA: DNA TO RNA TO PROTEIN

In eukaryotes, DNA remains in the nucleus except during cell division. This helps protect it from viruses, free oxygen and other things that might damage the DNA and cause mutations. The DNA strands are only opened either to copy the entire molecule (DNA replication) or to ‘read out’ a set of instructions to build a protein. Enzymes cause sections of the DNA strand to open and separate; another enzyme (RNA polymerase) will ‘read’ the DNA strand and copy its message onto a similar molecule, RNA (ribonucleic acid).

RNA is simpler than DNA: it is single-stranded, it uses the sugar ribose rather than deoxyribose, comes in many forms and substitutes the base uracil for thymine, following the base pair rule ‘GCAU.’ Since the message is basically in the same ‘language’, that of nucleic acids, this process of DNA to RNA is called transcription.

Once it is transcribed, this messenger RNA (mRNA) will be transported outside the nucleus and captured in large enzyme complexes, also made of RNA, called ribosomes. The ribosomes will ‘read’ the mRNA sequence and use it to attach complementary nucleotides of transfer RNA (tRNA). Each tRNA has an amino acid attached to it, so as the chain of tRNA grows, the amino acids are brought close together. As the message is read, the amino acids will break away from the ribosome, forming peptide bonds with each other.

Eventually, the RNA message will end, and the new chain of amino acids, or polypeptide chain, will fold up to form a completed protein. The shape of the folded protein is determined by the sequence of amino acids in the chain, and that amino acid sequence is specified by the mRNA sequence. This process (RNA to protein) is called translation, since it converts a nucleic acid ‘message’ into the ‘language’ of proteins.

Anyway, that's a thumbnail sketch of the fall. You will begin to appreciate the enormity of the task before me when you understand that this only addresses less than half of the state standards in Biology.