This blog is a chronicle of my journey in pursuit of my goal of earning a PhD in Biology (or a masters degree in Applied Mathematics.) I have a Bachelors degree in mathematics and, before applying to the program, I plan to review basic biology, linear algebra, all three levels of calculus, and maybe learn how to value financial derivatives. I am also learning to use the freely downloadable program, Blender, to do computer animation. In addition to self-study, I work full-time as a university administrator. I have my hands full but figure that I will learn these subjects better if I write about them. Also, I am taking a class in Mandarin Chinese toward my goal of becoming fluent in Chinese but I don't know that I will include these efforts here in this blog. The best way to learn something is by teaching so the idea is that I will teach what I have learned via the blog. As you are my audience/students, feel free to ask me questions as needed.

Tuesday, October 28, 2008

Rosalind Franklin

See this site for more information on this forgotten key figure behind the discovery of the double helix. Watson and Crick stole her work, using it without asking or letting her know and never giving her recognition she very much deserved in doing the foundational work that led to their discoveries. Watson was a prick in other ways as well, he regularly made wildly racist comments about various groups. Ironically, after he made blatantly racist and inflammatory comments about the intelligence of people with african ancestry (or rather the "black race"), it was discovered that he had a strong genetic background from the continent of Africa. So much so in fact that it is likely he has a great-grandparent from Africa.

Learning Outside of the Classroom

Another way I am learning this material is by listening to podcasts and watching webcasts online from universities like UC Berkeley and MIT.

You really can't beat free lectures from highly respected universities like this. I love that they are making this knowledge available to all.

Sunday, October 26, 2008

Still Posting...Biology Lesson 6

Atoms and Molecules of Ancient Earth (and not so ancient Earth) -

The All Cells-from-Cells theory proposes that every cell developed from another cell. However, if we follow the evolutionary family tree back to its very beginnings, we must conclude that, at some point, there must have been a first cell (otherwise, cells would have to have been in existence infinitely into the past) and furthermore, since we have also stated that all biological organisms are made up of cells, then that first cell must have come from something non-biological. Chemical evolution is the theory that that first cell developed from more and more highly complex/organized chemical compositions in the chemical cocktails present in early earth.

In primordial earth, there existed a soup of basic atoms which, while sharing the same space, bonded with each other more than every now and then. These atoms then formed molecules which again reacted with each other in a multitude of ways. Eventually, these molecules formed more and more complex structures and, through a process similar to natural selection, the structures that remained were those with more protection, those that could best exist on their own. A cell is a self-containing structure that's primary focus is protecting and regenerating itself and we can imagine that a cell might have done quite well in this early primordial soup.

To further understand what Chemical Evolution proposes happened early in earth's history, we need to understand something more about chemistry and, in particular, the most basic of chemical structures and the bonds by which new structures are created from the old ones.

The most fundamental of structures is the atom. While all living organisms are made up of cells, everything in the universe (including living organisms) is made up of atoms. At this point, it might be interesting to note the similarities between cells and atoms, for example in shape. They are both self-containing (spherical?) structures and ...<--Must go back to this idea another time. Atoms consist of a central nucleus made up of neutrons and protons. Outside of this, there are extremely small particles orbiting the nucleus called electrons. Protons have a positive electric charge, neutrons are electrically neutral, and electrons (those little bitty things circling the nucleus) are negatively charged. Atoms as a whole are electrically neutral when the electrical charges of those composite particles balance. This happens when the number of protons and the number of electrons are the same. (question: Why do they balance when they have different sizes? Are their masses the same?)

All atoms of any particular element have the same number of protons. For example, all Helium atoms have two protons. All Carbon atoms have six protons. The number of neutrons, however, is variable...not consistent from one Helium atom to the next, one Carbon atom to the next, and so on. We refer to all forms of elements with the same number of neutrons as a particular isotope. For example, there is an isotope of uranium that contains 143 neutrons and there is another isotope of uranium that contains 146 neutrons.

The sum of the protons and neutrons in an atom is called its mass number.
Scientists measure the mass of atomic particles using a special unit called the atomic mass unit (amu) or dalton. From an article on

Within the context of biochemistry and microbiology, often the term dalton (abbreviated Da or D) is used. This is useful for describing the mass of large organic molecules, typically rendered in kilodaltons (kDa). The Latin prefix kilo-indicates 1,000 of something, and "kilodalton" is much less of a tongue-twister than "kilo-amu". The term "dalton" honors English chemist John Dalton (1766-1844), who, as we shall see, introduced the concept of the atom to science.

Protons and neutrons have virtually identical masses and are measured as 1 amu each. So, for example, a carbon atom that has 6 protons and 6 neutrons has a total mass of 12 amu and a mass number of 12.

Radioactive Decay -

The Current Plan

Clearly, I have not been posting frequently as I had hoped. There is just too little time in the day...I have barely had the time for my Chinese studies and I'm taking a class in that. My current hope/plan is to finish a year of Chinese in the Spring and then to take a year of Biology during the summer. I will only be able to study Biology over the summer if this is alright with my department chair and if summer studies are covered by my tuition waiver (classes are so darn expensive). I would have to be away from my office for three hours every morning throughout the summer. If I can do this then I will next take Molecular and Cellular Biology in the fall, as well as studying general Chemistry and Physics on my own and actually applying to graduate programs. I am, and have been, most fascinated by the study of genetics. If this actually works out, then I will begin what would then be an at least 5 year journey toward earning my PhD. I'll have to figure out also where I want to apply. If this all worked out, I would have a PhD in 2015 when I'm 34. Ugh...I don't want to think about that.

Sunday, October 5, 2008

Notes on Fine-Tuning My Process of Studying

I used a utility knife to cut out pages from my giant biology textbook (the one that looks like it's on steroids) and hole-punched the pages. Now I can carry just the sections I am reading at any one time with me in my binder and study on the commute to work. Hopefully, this will result in more frequent blogposts as I am able to go through material more rapidly. My next posting on Biology will the first post on the chemical foundation of life from the chapter in the text, The Atoms and Molecules of Ancient Earth.

Wednesday, October 1, 2008

Biology - Lesson 5

Hypothesis Testing involves two key steps:

  1. Stating the hypothesis as clearly as possible and listing the predictions it makes

  2. Designing an observational or experimental test for the validity of those predictions.

Prediction – Something that can be measured and that must be correct if a hypothesis is valid.

The predictions are the pegs upon which a hypothesis is hung. The predictions must be sound for the hypothesis to hold weight. When this doesn't happen, when predictions do not prove accurate, then more testing must be done to clarify and confirm the results and/or the hypothesis must be modified or completely revised.

The example the text gives for the necessity of hypothesis testing is the prior hypothesis for why giraffes have long necks. For decades, scientists have accepted the validity of the hypothesis that giraffes' long necks developed as an adaptation to living where there are abundant food sources in high locations. With long necks, giraffes can eat from high locations in the trees. However, more recently, scientists have discovered that giraffes use their long necks for a different purpose. When competing with each other during mating seasons, male giraffes use their necks to beat each other up, slamming each other with their necks by swinging their long necks at each other. The longer their necks are the harder they can swing at their opponent. Oftentimes, giraffes are injured (even seriously) during these fights where giraffes have been known to knock their opponent unconscious or even kill them. This wasn't at all taken into account by the original hypothesis about why giraffes have long necks. The original hypothesis therefore needed to be revised to reflect this new data. Scientists are now hypothesizing that competition among males may constitute part of the reason for the development of long necks and that they may also use their long necks for feeding in high places during droughts so that their long necks contribute to the fitness of individual giraffes in more than one way.

The other example given in this section is the hypothesis as to why chili peppers are hot. Connected to this hypothesis is the proposal that natural selection should favor fruits that taste bad to animal species that would destroy the seed if they ate it and should taste good to animal species that wouldn't destroy the seed but would disperse it after eating it. This is the directed dispersal hypothesis.

Further definitions from this section:

Null hypothesis – what we should observe if the hypothesis being tested doesn't prove accurate.

Sunday, September 28, 2008

Biology - Lesson 4

Linnaeus was classifying organisms based on what they looked like, what characteristics and other similarities they appeared to have in common. This made it difficult to classify organisms that seemed to share characteristics with both kingdoms that Linnaeus proposed, Plants and Animals. For example, fungi including mold and mushrooms do not move (or do they?) so they seem to be plants but, unlike plants, they do not make their own food. Fungi live off of the nutrients they absorb from dead or living plants and animals.

Instead of trying to organize organisms based on the characteristics they appeared to have in common, as the evidence for evolution mounted, the goal of taxonomy became showing how
organisms are actually related, ancestrally. This is called Phylogeny (meaning "tribe-source").

On a wall in Martin Hall, Swarthmore College Dept of Biology

Furthermore, when scientists started to study cells in more detail, they found a new and crucial difference between groups of organisms. Some organisms have cells with a nucleus and others have cells with no nucleus. The former are called eukaryotes and the latter are called prokaryotes. Most eukaryotes are multicellular ("many-celled") beings while most prokaryotes are single-celled or unicellular.

Researchers discovered that they could also organize species based on their rRNA or Ribosomal RNA, an important part of what cells use to grow and reproduce.

rRNA is similar among closely related species and differs more significantly the farther apart species are from each other ancestrally speaking. By studyingn the rRNA of organisms, biologists were able to recatagorize them into three major groups or domains: the Bacteria, another group of prokaryotic, single-celled organisms called the Archaea, and the Eukaryotes (the domain Eukarya). Domain was added then as another taxonomic level. One of the most interesting facts I read about in this chapter of my text is that, based on rRNA, fungi is much more closely related to animals than to plants.

Sidenote: Does this mean that, as a vegetarian, I shouldn't eat mushrooms? Hmmmm.