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.

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 Answers.com...

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.

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.

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.

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.

Biology - Lesson 3

Linnaeus didn't stop at giving organisms just these two classifications either. He came up with a hierarchy of taxonomic groups:


At the top of this is the least specific of grouping, Kingdom, and at the bottom is the most specific grouping, Species.

Humans, for example, are within the Kingdom Animalia, the Phylum Chordata (animals having a notochord, or dorsal stiffening rod, as the chief internal skeletal support at some stage of their development), the Class Mammalia, the Order Primates, the Family Hominidae, the Genus Homo, and the Species Sapiens.

Biology - Lesson 2

That tendency over time for populations of organisms to diverge and become completely different species over time is called speciation.

Ultimately, given the assumption that life arose on Earth just once, scientists would like to be able to map out a family tree of organisms, or tree of life, that shows the origin of all species in one mother ancestor at the very top.



The labeling and classification of organisms is called taxonomy. Carolus Linnaeus was one of the first scientists who attempted to organize all the many organisms being discovered at the time into groups of organisms that had clear commonalities. He gave each type of organism a two-part name consisting of its genus and its species. A species was defined as a group of organisms that regularly breeds together or has characteristics distinct from those of other groups.



The genus was defined as a closely related group of species such as humans or Homo sapiens and other (now extinct) species of beings that walked upright and frequently used tools. So, the scientific name that Carolus Linnaeus gave organisms went from a more general classification to the more specific classification. Linnaeus also said that all types of organisms should be given a unique genus and species name. So, for example, while there are other members of the Homo genus and while there may be sapiens in other genera (plural of genus), humans are the only Homo sapiens. This system of naming organisms in two-parts is called binomial taxonomy.



Phylogeny

Biology - Lesson 1

A theory is an explanation for a very general class of phenomena or observations.

Modern Biology is founded on two key theories: The cell theory and the theory of evolution.

A cell is defined as a highly organized compartment bounded by a thin, flexible structure called a plasma membrane and that contains concentrated chemicals in an aqueous (watery) solution.

The Cell Theory says that all organisms are composed of cells and all cells come from other cells.

The Theory of Evolution by Natural Selection says that new species develop from preexisting species and that all species change through time as a whole through mutations that affect the fitness of the composite organisms.

Fitness is defined as the ability of those organisms to reproduce and to survive.

A trait that improves the fitness of an organism within a particular environment is called an adaptation.


Cell theory contradicted the prevalent previous theory (or rather hypothesis) that life develops spontaneously. In the late 1850s, scientist Louis Pasteur decided to test the Spontaneous Generation Hypothesis by setting up two beakers of 'pasteurized' broth, one open to the air and thus vulnerable to being settled in by bacteria and the other closed to the air. He left both for months during which the first beaker filled quickly with bacteria and fungi and the second beaker did not. His conclusion was that cells arise only from preexisting cells, not spontaneously from nonliving material. This convinced scientists that the All Cells-from-Cells Hypothesis was correct and not the Spontaneous Generation Hypothesis.

Recall that Cell Theory states that all cells come from pre-existing cells (this is called the process component of Cell Theory). If this is so, then in organisms that each have only one cell (Single-Celled organisms), each organism must come from another organism, who must have come from a previous organism, and so on tracing back to a single organism or mother of them all. ----note: I'm not following that last bit of logic. This does not demonstrate that all the single-celled organisms have a common ancestor. If they could all have one common ancestor that didn't come from a cell, then why could there have been two or more lines or two ancestors that developed from something other than a cell and spawned two separate lines of single celled organisms? In other words, clearly not all cells came from other cells unless you believe that there have always been cells going back infinitely into the past, but if there were ancestor cells that came about some other way, why not believe that there were more than one of these original/first ancestor cells?

It was the scientists Charles Darwin and Alfred Russel Wallace that, separately, published essays hypothesizing that all species are connected by a common ancestry. They defined species as all distinct, identifiable types of organisms.

Darwin stated that natural selection changes the characteristics of a wild population over time, just as the deliberate manipulation of "artificial selection" changes the characteristics of a domesticated population over time.