Saturday, January 31, 2009

More interesting times in Oklahoma

Just wanted to share a great news article we had here in Oklahoma. A pair of conjoined twins were separated! I believe these girls are thoraco-omphalopagus conjoined twins. I got to see their heart catherization on my cardiology rotation. Fascinating!
Here's the article:
and pictures:

Wednesday, January 28, 2009

TQT Time and What is Up for Tomorrow


Again, I encourage you to post comments to the posts of the other authors. It could start interesting conversations.

Now to school - Tomorrow is TQT and you should send them as comments to this post. We will begin tomorrow with a few comments on FRQ-12 then we will see if you have questions regarding FRQ-13. After, we will take a look at the fruit flies. I will demonstrate how to anesthetize the flies and show you how to sex and distinguish the phenotypes. Finally, you will have an opportunity to work with and observe the flies. If we have time we will discuss how the experiment will be conducted.

Be reading the text. You should be through chapter 14 and beginning 15. Read, Read, Read. Trust your intelligence and keep pushing. The AP test is on May 11.

Mr. Baker

Tuesday, January 27, 2009


I'm Ken, another former Mr. Baker student. I took his AP biology class in 1999-2000, and I can honestly say that without Mr. Baker's class, there's a good chance I would not have ended up in the biosciences. You're lucky to be where you are! I remember drawing diagrams of helicase unzipping a coil of DNA, and that's still pretty much the model I have in my head.

After high school I went to the University of Washington, double-majored in Computer Science and Molecular Biology (and minored in math for good measure). At the same time, I shot pictures for UW's student newspaper, which is where I learned I needed a career where I was intimately involved with all types of people every single day. So I went to medical school! I'm in my fourth and final year at Columbia in New York, where I've confirmed that medicine is exactly the right career for me. And it opens doors to do anything from solely practicing clinical medicine, to answering the unanswered questions of life (and that's what biology is, anyway), to teaching next year's doctors.

There are many, many, many questions yet to be answered in medicine and in biology. Science gives us the tools to answer these questions. The most popular article on the New York Times' website right now is about a possible link between coffee drinking and lowered dementia risk ( The research is preliminary (they allude to why in the NYT article) and there is a lot of work to be done to either prove or disprove this hypothesis. Are you going to be the one that solves this? If you're really interested, you can dig up the actual article - an abstract, or summary, is at

Sunday, January 25, 2009

Goodbye Chapter 14


Tomorrow, we will be wrapping-up chapter 14. I will focus on reading pedigrees and you should read pages 252-258. Pay particular attention to learning the particular examples of human genetic disorders, fetal testing, and neo-natal testing. I will not discuss these directly and will rely on you to ask questions.

Later this week we will dive into chapter 15 and begin to understand the relationship between chromosomes and genes and how the chromosome theory of inheritance was first formed. To supplement this learning we will begin the Drosophila genetics lab. It is great fun seeing Mendel's ratios in action!

Be sure to ask the blog co-authors questions when they submit a post. They are an excellent information resource.

Mr. Baker

Thursday, January 22, 2009

Applied Sciences: Medicine

My name is Samara Mohamed. I'm also a former student of Mr. Baker, who took general biology in 1994, genetics in 1997, and was formally introduced to the wonderful world of genetics bench work by Mr. Baker in 1997.

I went to Seattle University, and Majored in Biology and Chemistry with a minor in Physics. I did continue to do research in college: various collegiate projects and even a 2 summer internship with the Merck pharmecutical company in their vaccine department. However, I felt a greater need for human connection which led me to medicine.

I went to Midwestern University--Arizona College of Osteopathic Medicine. Osteopathic medicine is a parallel track to allopathic medicine with a focus on holistic treatment of the patient and includes additional manipulation treatment. I graduated in 2002 and started a Pediatric Residency at the Oklahoma State University Medical Center in Tulsa, OK. I'm currently 6 months from finishing my residency and will be deployed by the US Army for general practice. Since the military paid for my medical school bills, I will repay them with 4 years of Active Duty service. I do plan on pursuing a sub-specialty in Pediatrics in the near future--possibly Adolescent medicine, palliative care, emergency medicine or interventional cardiology.

I like to think of medicine as applied science. I have been amazed at how helpful basic chemistry, genetics, and newtonian physics have contributed to my understanding of the human body. It's been invaluable to have good research background to decipher the mounds of research that comes out daily.

I don't have any cool articles to post at the moment, but I'll try to post some as I come across any.

Wednesday, January 21, 2009

Cells, Molecules, Neurons & Synapses

Hi everyone,

My name is DJ Brasier. I took Mr. Baker's freshman biology class back in 1994, and my senior year he taught an advanced class in genetics instead of the AP biology that you all are taking. In college, I majored in biology with an emphasis on cellular and molecular processes.

I went to graduate school at Univ. of California, San Diego in Neurosciences where my dissertation focused on how the synaptic connections between neurons change as your brain learns. Aside from my dissertation work, I've done molecular neurobiology research on protein structure and function. Currently, I'm working as a postdoctoral fellow at UC - San Francisco. I've had to reacquaint myself with the details of genetics that I learned in Mr. Baker's genetics class in my current research using fruit fly genetics as a tool to look at synaptic function.

The research that I do is basic science: which means that instead of working on curing a particular disease like Alzheimer's, I am working to understand the basic biological processes that go on in all of our neurons. That isn't to say that my work doesn't have relevance for diseases. In fact, problems with synaptic function are known to contribute to almost every known neurological disease from epilepsy to Parkinson's to schizophrenia. I believe that we need a much more complete understanding of the basic biological processes in order to know how healthy as well us unhealthy brains function and to provide more intelligent treatments.

I'm going to steal Jonathan's idea and post a couple of interesting articles. The first is from Scientific American and it shows how modern brain imaging equipment can be used first to watch brain activity and the coordination of different brain areas as a subject (in this case a monkey) makes a decision. Then, after the task becomes familiar, the imaging is used to see how the pattern of brain activity is different than it was when the subject was first learning the task.

The second article discusses a rare neurological phenomenon called synesthesia, when sensory input from one of the senses (such as vision) activates the area of the brain that normally processes information from a different sense. In this case visual input activates the auditory region of the brain, so people with this experience "hearing" a visual stimulus. Only in the last few years has it even become accepted that this actually happens and it's not just people speaking metaphorically. I think the most interesting thing about this is that essentially no one has the first clue how this is happening or what goes on genetically or developmentally to cause this.

Happy reading!


No TQT This Week

Hey Bios,

Because I have been getting many good questions in class this week I have cancelled TQT for this week. Please complete your FRQ-12 by Friday. On Friday I will be distributing FRQ-13. This is a genetics problem set that extends simple Mendelian genetics. Read the remainder of chapter 14 to get acquainted with this material.

Also, two more former students have accepted my invitation to join the blog. Ken Michelson is studying medicine at NYU (right Ken?)and DJ Braiser is working on a post-doc project at the University of California San Francisco. So feel free to ask these guys about life after high school and in particular studying science.

Tomorrow, the remainder of chapter 14.

Mr. Baker

Sunday, January 18, 2009

What to Read For Your FRQ This Week

The information needed to understand the FRQ for this week can be found in chapter 14 on pages 239-247. Take time to learn the vocabulary and Mendel's laws of segregation and independent assortment. Becoming familiar with terms such as P generation, true-breeding, allele, and others is essential in order to understand the genetics problems. Next week you will receive questions that cover the second part of chapter 14. I will be monitoring the blog this weekend so if you have questions be sure to write and remember that you can help each other. Finally, welcome Jonathan Richardson to the blog, read his post, and ask him questions.

Mr. Baker

Friday, January 16, 2009

An Interlude for Ecology

Hi Everyone,

I just wanted to quickly introduce myself and post links to a couple of articles that you all might be interested in. My name is Jonathan Richardson and I was a student in Mr. Baker's AP Biology class back in 1999-2000. We certainly didn't have a blog back then, so it's been interesting to see how this one has started and been used by Mr. Baker and you guys. Anyway, I'm currently a graduate student at the Yale School of Forestry and Environmental Sciences here in New Haven, Connecticut. My dissertation research deals mainly with the intersection of population ecology and evolution, both topics that you will cover soon enough (at which point I will probably be of more use to your class). Specifically, I study amphibian populations (spotted salamanders and wood frogs native to the eastern US and even into Alaska) and how landscape structure (as in intact forest habitat vs. habitats with barriers to these guys moving to other areas) can alter the long-term persistence of populations. Hopefully my own research will more interesting to you and germane to your studies once Mr. Baker starts to talk about ecology and evolution. In the meantime, I just wanted to introduce myself and I'll also attach links to 2 very interesting articles.

The first is from the Seattle Times in 2005, and discusses the reintroduction of wolves to the Greater Yellowstone ecosystem. When wolves were hunted to extinction, their prey no longer needed to worry about being killed, so they (elk, in this article) consumed more of the vegetation, which in turn led to a dramatic shift in the tree species regenerating and forest ecology. The wolves were reintroduced in 1995, so now ecologists have a fantastic opportunity to see how things change when the top predator is returned to the ecosystem. One of my good friends is currently tranquilizing wolves from a helicopter as a student at the University of Wyoming as part of this project. Ecologists get to do some amazing things in amazing places!

The second article is from this week's New York Times Science Tuesday section (a great read every week!). It discusses a phenomenon called artificial selection. This is analogous to the natural selection Charles Darwin described, however the selective force here is introduced by humans (hence the term "artificial"). A quick example of this is fishing - if you only catch and keep the large fish and throw the small one back, you are "selecting against" big fish and selecting for small fish within the population (it sounds counterintuitive at first), and the size of fish within that population will decrease. Dog breeding is also an extreme form of artificial selection (from wolves originally?).

Anyway, take a look if you have some time. Hopefully they will get you excited for the evolution and ecology sections of Mr. Bakers class - definitely my favorite! Have a great weekend.


Wednesday, January 14, 2009

Three Question Thursday for 1-15-09

It is that time again! Send me your TQTQs as a comment to this post. As before, I will try to answer as many as I can.

Mr. Baker

Tuesday, January 13, 2009

Walking Through Chapter 13

Hey Bios, tonight's post will be a walk through chapter 13. So grab your book and come along.

First of all, be sure to work on understanding the bold typed words. The bold typed words in chapter13-15 are central to your understanding genetics because they will be used freely and regularly. If you will look at my comment to Ana in the previous post you will see that I am questioning taking time to prepare vocabulary cards. I would like your opinion on this.

The chapter has three main sections; An Introduction to Heredity, The Role of Meiosis in Sexual Life Cycles, and Origins of Genetic Variation. The first section points out that understanding meiosis is really the first step in understanding genetics because genetics (heredity) is transmitted through gametes and meiosis makes gametes. It also discusses asexual and sexual reproduction in terms of the amount of variation passed to the next generation. See figure 13.1, this is a hydra budding. It is a type of asexual reproduction. A hydra is like a tiny sea anenome, notice the tentacles. Many simple animals have the ability to reproduce asexually.

Now we move to the second section, The Role of Meiosis in Sexual Life Cycles, on page 229 there is a description of how a human karyotype is made. Spend some time examining figure 13.3 and 13.4. Notice how the 2n and n stages alternate and whenever gametes come together (fuse) there is new genetic variation. Now the chapter moves on to meiosis. Study figure 13.6 and if you do not understand it, ask me questions. Notice that there is two divisions and at metaphase I the chromosome twins pair up rather than line up as in mitosis. Meiosis I is the reduction division because there is only one set of chromosomes in each cell when it is complete. Meiosis II is just about separation the chromatids and it results in four cells.

The final section is about how meiosis creates genetic variation. First, independent assortment is the "shuffling" of chromosomes at metaphase I. With 4 chromosomes there are (4) combinations and the 46 chromosomes of humans results in well, an astronomical number (see text)! Now that's variation. Second is crossing over the process in which homologous (twin) chromosomes exchange parts (See figure 13.9). This introduces additional shuffling. So with just independent assortment and crossing over there exists tens of millions if not more possible genetic variants in the gametes of one human. This leads us to the last source of variation - random fertilization. Think of it this way, if any gamete has an equal chance of meeting all the others, imagine the potential number of new genetic variants! And this does not even account for mutation! That is a lot of shuffling? Comments?

That's it for now. I will be up for just 1/2 hour more but will be looking for your comments. Gotta go get Kingston's bone ready for the morning and prep the coffee maker.

Mr. Baker

Monday, January 12, 2009

Read Ahead

Please feel free to read ahead. Read chapters 13 and 14 and do not try to understand everything. I suspect that you will understand some of it and the rest I will explain in class. But read, get in the habit. Find the time, set it aside and read an hour a day. You will know more, feel better about your effort, and biology will become interesting - really.

An unabashed lover of biology,
Mr. Baker

Sunday, January 11, 2009

Morning Cup O' Joe

Ok, here is the reminder to study for the test. The test requires you to recall the content of all six chapters so cuddle up with your book and study. Here is a brief list of topics study.

1. The difference between a prokaryote and eukaryote.
2. The parts of plant and animal cells and their functions.
3. The structure and function of the cell membrane.
4. Diffusion and osmosis.
5. Active transport mechanisms.
6. Cellular respiration - glycolysis, Krebs cycle, and electron transport chain.
7. Alcoholic fermentation.
8. Photosynthesis - light reactions and Calvin cycle.
9. C3, C4, and CAM plants - know the difference.
10. Cell signaling - G-protein-linked receptors, tyrosine-kinase, and phosphorylation cascade.
11. Cell cycle - mitosis and control of cell cycle.

This is just to get you going. Study, trust your intelligence, and I will be monitoring the blog today so if you have a question, post a comment to this post.

When you get to class, the test will be up front ready for you to pick up and start. Just put your things away and get going. There are 50 multiple-choice questions.

Mr. Baker

Saturday, January 10, 2009

Getting Ready for the Test

Be sure to read the questions posted by your classmates and the responses as you get ready for the test. Remember, you are welcome to answer each others questions. It would be a good way to prepare for the test. Also, as you re-read the chapters and chapter summaries, if questions pop up send it as a comment to this post.

Mr. Baker

Morning Cup O' Java - aka TQT Time

Ca asked -
1. What caused the decline of "maturation promoting factor" (M-phase) at the end of the mitosis cycle?
Answer - The M-phase promoting factor, the complexing of B-cyclin and Cdk-1, signals the cell to move to metaphase and initiate the anaphase-promoting complex (APC). Once activated the APC will signal the separation of sister chromatids and the destruction of B-cyclins thus "turning off" the M-phase promoting factor.

2. A protein is released by a certain body to stimulate other cells to divide. At which point would cells stop dividing?
Answer - I don't know much about this but what I know is, a cell is signaled to grow and divide when growth factors are released from other cells. When this signal is turned off cells cease growing a dividing. This is an area of active research.

3. What are the differences between density-dependent inhibition and anchorage dependence?
Answer - Both are related to the growth and division of cells but are different in that density-dependent inhibition is about the restraint of cell division and anchorage dependence is about stimulating cell division. As the number of cells increases and thus the density, a point is reached where the cells no longer divide. This is density-dependent inhibition. In anchorage dependence cells do not divide unless they are on some sort of substrate (surface). This was originally discovered when researchers notice that when cultured cells were suspended in a liquid medium they greatly slowed or stopped their division. But when placed on a solid medium the same cells freely divided (until density-dependent inhibition).

Tahira, your questions make me smile. I am not sure how to answer them but I like 'em.

Hong-An asked -
1. In many online science website, mitosis has a prometaphase. Does that mean that the distinction between prophase and metaphase stage is very broad?
Answer - Really, the entire cell cycle is a continuous process not a series of steps. We teach it as steps to aid understanding and the introduction of intermediate steps such a prometaphase introduces emphasis on what is happening. So regarding prophase, prometaphase, and metaphase; prophase is when the chromosomes are condensing and the nuclear membrane disintegrates, prometaphase is when further condensation happens and microtubules begin to attach to the kinetochore, and metaphase is when the chromosomes have lined-up at the equator of the cell.

2. In pictures they always show four chromosomes. Is this to simplify?
Answer - You bet. The mechanics of mitosis is the same no matter the number of chromosomes. It is just easier and hopefully clearer if we sketch 4 chromosomes rather than 46 (humans), 68 (coastal cutthroat trout), or 114 (lilly).

That took two cups of coffee and I am sufficiently caffinated but it is Saturday and I will have more. BTW - did you know that coffee has its origins in Ethiopia? I learned that when the family visited the Lucy exhibit at the Pacific Science Center over winter break.

More Later Ta-Ta,

Mr. Baker

Friday, January 9, 2009

Su-more TQTQ Answers

Anna asked the following three questions -
One of the chapter quizzes (11) had the following Question:
Lipid soluble signal molecules, such as testosterone, cross the plasma membranes of all cells but affect only their target cells because?
The answer:
Intracellular receptors are present only in target cells.
Could you please explain this?
Typically, lipid signal molecules such as testosterone will bind to a receptor molecule within the cytoplasm. This molecule, now activated will then turn on gene(s).

In chapter 10 there is the talk about photosystems I and II. Can a thylakoid membrane function without one of these? Well, the thylakoid membrane is where the proteins of photosystem I and II are embedded. So the membrane can be seen as scaffolding for the photosystems. They are both part of the photosynthetic structure called a chloroplast.

What exactly is Pyruvate? Recall that cellular respiration is composed of three main steps; glycolysis, Kreb's cycle, and electron transport chain. Glucose, the food molecule, is first processed in series of reactions called glycolysis which occurs in the cytoplasm. During this process glucose is transformed into two, three-carbon molecules called pyruvate. It is pyruvate with the help of a transport protein that enters the mitochondrion for further processing. The goal of glycolysis, Kreb's cycle, and electron transport chain is to harvest the energy and transfer it to form ATP. It is ATP that can be used for work in the cell.

From Keely, this is interesting -
Since genetic disorders come from mutation in chromosomes in gametes why doesn't the body find a way to destroy mutated gametes? Like how the body destroys mutated cells during mitosis. Answer - It does seem that just as defective cells are destroyed but the immune system the same should hold true for gametes. So why not? Until release, gametes are protected by cells that in effect guard them. The cells keep away the macrophages that may destroy them.

That's all for now. I see a couple of interesting questions from Ca. I will get to those tomorrow.

Mr. Baker

And More TQTQ 1-8-09 Responses

Zena asked - What is meristem? Meristem is a type of cell in plants that has not differentiated. This means that the cells have not become a specific type of cell. Because of this they can become many types of cell. So when you see that we are looking at apical meristem in the onion root tip this tells us that the tissue is likely rapidly dividing and can become vascular tissue, epidermis, root hairs, root cap, and others.

Zena also asked - Does an ameoba have cell division? Yes, they do what is called binary fission. During this process the nucleus does replicate its DNA and divides it equally. This is how you get more ameobas.

Wendy asked - Is it a conicidence that the cell cycle and one day are 24 hours in duration? The answer for the cells we were looking at, yes. Remember, there is a great range of cell cycle times. For example a nerve cell never divides, whereas a bacterial cell can divide in as few as 15 minutes. So the time for cell cycle completion depends on the type of cell you are looking at.

Going to the lab now, more later.

Mr. Baker

Some More Responses to TQTQ 1-8-09

I have a few minutes here and with my cup of coffee in hand here goes -

Inwoo asked - Without centrioles, how do plant cells split? It is interesting that though animal cells have centrioles, plant cells do not. So clearly the organization of the spindle does not require centrioles. But I read Inwoo's question as asking about chromatid splitting during anaphase. The movement of chromatids is due to the action of kinetochore motor proteins "walkimg" along a kinetochore microtubule, dragging its chromatid along.

Gotta go,


Thursday, January 8, 2009

Some Responses to TQTQ for 1-8-09

Hey thanks for the great questions. I have only enough time for a few answers now but tune in later for more.

Cintia asked why cancer cells lose their density dependent inhibition and anchorage dependence. Briefly, this is due to multiple gene mutations in the original tumor cell. Cancer likely is the result of more than one mutation and if those mutations involve genes that regulate the cell cycle, density dependent inhibition, and anchorage dependence; you have a tumor that can metastasize.

Which leads us to a question by Inwoo, what is metastasis? This is the spreading of cancer cells throughout the body. Rather than being encapsulated and a benign tumor, a metastatic tumor is malignant and spreads, this is one of the reasons they are so deadly.

Inwoo also asked why human chromosomes are purple. The answer is they are not. The chromosomes you saw in class were stained (probably with aceto orcin stain) which causes them to be purpleish-pink and easily visible.

More later,

Mr. Baker

Wednesday, January 7, 2009

Three Question Thursday Time

Write your TQTQ for 1-8-09 here. Just click on comments and submit your questions. I will respond to some of them and each week post a new TQTQ request.

Mr. Baker

Monday, January 5, 2009

Snow is Pretty - Particularly in the Mountains

As you know by now, we are two hours late today. This means a short class period and no lab. Instead, we will review mitosis and meiosis and familiarize everyone with the blog.

See you in class,
Mr. Baker

Sunday, January 4, 2009

Prepare for the Lab Monday

Monday through Thursday we will conduct the mitosis and meiosis lab. It would be best if you would review mitosis and look ahead to meiosis. Mitosis is covered in chapter 12 while meiosis is found in chapter 13.

Though chapter 13 is not included in the next exam, pairing the learning of mitosis and meiosis allows you to compare and contrast each. Meiosis is the type of cell division that reduces the chromosome complement by 1/2 and is done by gametes (sex cells / sperm and eggs).

Test is Looming

The chapter 7-12 exam will be this Friday. It will be all multiple choice with 40 to 50 questions. If you have questions about the chapters reply with a comment to this posting and I will answer as soon as I can.

Mr. Baker