Lecture 3 (4/22/09): When Darwin meets Madonna

I think I know what you're thinking: 'Brett is going to help me sort out all of this "-osis" stuff, i.e., mitosis, meiosis, and all of the other terms and ideas that go with these two confusing concepts.'

Well, this is true. I will do my very best this week to find some ways that can hopefully help you untangle the important concepts that Professor S focused his lecture on this past Friday. However, (1) it's going to take more than a single Blog to accomplish this, (2) Professor S has some more work to do with you on these concepts in future lectures, (3) you have an onion lab coming up in your lab sections that may further help untangle some things, and (4) we need to first take a step back, zoom out, and do some big-picture work. So, I want to spend some time today talking about genes, sex, scale, and Madonna...

If Madonna were a scientist...

I know that pop icon Madonna has told us repeatedly in song that we are living in a material world. Had Madonna had a few more college biology courses, however, she might have considered tweaking her infamous song lyrics. At least through the eyes of highly trained biologists, we are living in a Darwinian world. What on Earth does this mean and, perhaps more importantly, what does it have to do with what Professor S talked about in Lecture 3?

If you choose to see the world through the eyes of a biologist (and you need to in order to do well in this course), then you choose to see all of the events occurring in nature as part of one giant struggle for the right to survive. In a Darwinian world, living things are seen as always engaged in a battle for certain resources: Plants are said to fight for things like water and light, and animals are said to compete for things like water, food, and mates. In all this fighting and competition, there is also the equivalent of biological 'winners' and 'losers.' Biological winners are not only those organisms that manage to get what they need to survive, but they are also those organisms that manage to find a way--at least once during their lifetime--to make new living things! In other words, a biological victory is NOT just succeeding in finding ways to do thing like find water, food, or light; to be a biological winner you ALSO have to find a way to successfully reproduce.

Biologists: Are they obsessed with 'sex?'

OK, so we've established the fact that when biologists look at the world through Darwinian glasses, they are obsessed with two things: survival and reproduction (I don't use the term "sex" here because not every organism performs what we humans call "sexual reproduction"). I now want to introduce you to some of the different ways biologists talk about the reproduction of different things.

The reproduction of DNA...

Lets start small. When biologists talk about the reproduction of DNA, they don't normally use the term reproduction. Instead, they use the term replication (or sometimes even duplication), which basically means making an exact copy of an existing 'strand' DNA. In order to make an exact copy of existing DNA, you need to have the 'raw' materials for the new strand. If DNA were a recipe, it would go something like this: Bond together some sugars (preferably deoxyriboses), some phosphate groups, and some nucleotides (which go by the common abbreviations A, T, G, and C). The image at right is one Professor S used during Lecture 3; it shows a single strand of DNA in terms of the different parts fitting together.

Now, I know that things like nucleotides, phosphate groups and deoxyribose sugars are all fancy chemical names, but consider the fact that if you were to 'distill' them down into their basic elements, you would end up with mostly carbon (C), nitrogen (N), oxygen (O), hydrogen (H), phosophorous (P), as well as a few other common elements. When Madonna's body want to make exact copies of her own DNA, where does she get the elements needed to make these copies? Well, just think of the old saying, 'You are what you eat.' With every bite of food she puts in her mouth, she is providing her body with the elements (i.e., the matter) needed to make new replicate strands of her DNA.

The reproduction of genes...

Lets now go a step 'up' in scale and talk about the reproduction of genes. Since genes are not all that different than DNA (in fact in many respects genes are DNA), biologists talk about the reproduction of genes in much the same was as they talk about the reproduction of DNA: it's about gene replication. To see a nice pictorial relationship between genes and DNA study the image at left for a few minutes...go ahead. I'll wait.

If you're reading the image like I am, you can see that genes simply consist of regions of DNA (i.e., sequences of nucleotides) that we give names to like "exons" and "introns." When you copy DNA, and if you replicate a long-enough portion of the DNA, you basically are replicating the gene too! Do me a favor: go back up the page, look at the image of the DNA in the last section, and notice the ladder-like structure. Can you also see the same ladder-like structure in the image included in this section? I hope so...you need to train yourself to be able go back-and-forth between images presented to you in the class.

Before we talk about the reproduction of other things, lets talk quickly about one other term that is closely related to the idea of a gene. Lets pretend for a minute that the gene in the picture just above contains a 'code' for a certain observable trait, say, "hair color." How would we know if the gene is for black or blond hair color? The answer is that it depends on the arrangement of the sequence of nucleotides in that particular region of the DNA. In one arrangement, say, GCG...TAT, we might see an individual with BLACK hair. In another arrangement, say, GCG...TCT, we might see an individual with BLONDE hair. Each of these arrangements are called alleles for the gene that controls hair color. So, knowing that Madonna got one allele for the hair color gene from her mother and one allele for the hair color gene from her father, what two alleles do you think Madonna possesses?

The reproduction of chromosomes...

I also want to stick with the same image that I used above to talk about the reproduction of chromosomes, because with this image you can continue to develop a better sense of how terms like DNA, genes, and chromosomes are related despite the fact that they are terms used to talk about concepts at different scales (so far we've been moving from smaller scales--DNA--to bigger scales--genes).

When biologist talk about the reproduction of chromosomes, as was the case with both DNA and genes, they usually use the term duplication or replication. And this is why I love this particular image: Because you can see that the duplication of a chromosome is actually a duplication of the DNA and at the same time a duplication of the all of the genes encoded within that long strand of DNA.

The chromosome depicted in the red circle in this image has been "condensed," but as you unwind or uncondense it, as the diagram shows, you can see that the condensed chromosome is at the same time simply a long chain of genes (i.e., groups of exons and introns). At the same time is it also a long strand of DNA (i.e., long chains of nucleotides, sugars, and phosphate groups!). From now on, I'm not going to keep saying "at the same time" whenever I talk about chromosomes/genes/DNA. In place of all of these "nested" terms (nested, that is, in terms of scale), I'm simply going to write, the "genetic material."

The reproduction of cells...

So, here's where things get a little tricky. When biologists talk about the reproduction of cells, they don't usually use terms like cell duplication or cell replication. Instead, they prefer the term cell division. You and I need to start learning how to talk about two processes that can occur when cells are dividing: mitosis and meiosis. Lets take these one at a time...but eventually, in future postings, I want you and I to consider them together (i.e., side-by-side for a comparison).

Mitosis
If an entire cell is going to make a copy of itself (that is, if a cell is going to divide), it is also going to need to make a copy of its most important 'parts.' In eukaryotic cells, one important part is the nucleus. What's inside of a nucleus? Well, lots of things, but for our discussion today we need to remember from our previous science courses that the nucleus is where most of the genetic material is located (it's where the DNA can be found!).

PAY ATTENTION HERE: Mitosis is NOT the replication/duplication of the genetic material in the nucleus--mitosis IS the separation of already replicated/duplicated genetic material in the nucleus into two identical 'daughter' nuclei (nuclei = the plural of nucleus). ONLY when other important parts of the cell divide--later during cytokinesis--can we then form two new 'daughter' cells from the original 'mother' cell. Professor S illustrated this process in Lecture 3 with slides like the ones shown below...


You can see from the pictures above that I've left you lots of language-work to do on your own. You've got to start untangling terms like chromotids (and sister chromotids), haploid/diploid, as well as all of the different phases of mitosis. What I want to emphasize here is this:

• Mitosis is NOT the duplication/replication of the genetic material inside the nucleus; it IS the separation of the existing genetic material into two new nuclei.
  

Here are two mathematical forms to ponder that builds on the idea in the previous bullet point...

• 1 mother cell + mitosis = 1 mother cell with 2 identical nuclei

HOWEVER...

• 1 mother cell + mitosis + cytokinesis = 2 daughter cells with identical nuclei
  

Here is a narrative form to ponder that builds on the ideas in the previous bullet points...

• If you want to produce (two) daughter cells that are identical copies of (one) mother cell...FIRST you need to duplicate/replicate the genetic material (i.e., DNA replication)...SECOND, you need to separate the genetic material to form two identical nuclei (i.e., mitosis)...THIRD, you then need to duplicate/replicate AND separate the other important parts of the cell (i.e., cytokinesis).
  

• Along with a couple of other stages or "phases" not listed here, another name for this entire process of duplication/replication, mitosis, and cytokinesis is the "cell cycle."
  

Meiosis
Meiosis is a term that we can think about as another type of cell division. Whereas mitosis was an important step--along with DNA replication and cytokinesis--involved in the production of TWO identical daughter cells from ONE mother cell, meiosis is an important step involved in the (eventual) production of FOUR new daughter cells. However, EACH of the FOUR new daughter cells--sometimes called gametes--contain only HALF of the genetic material found in the ONE original mother cell!

Rather than go into any further details about meiosis tonight, however, I think I'll let you fully digest today's Blog. We'll save a more in-depth discussion of meiosis for tomorrow's post. I think today's posting will need to be read multiple times in order for it to start sinking in properly, so don't expect instant enlightenment from just a single read-through...make this a long, slow, repetitive digestion of ideas.

In the meantime, sit down, kick up your feet, put on some Madonna--new or old, it doesn't matter--and remind yourself that: Although Madonna might live in a material world, biologists live in a Darwinian world...and in this version of the world, survival and reproduction are seen as the most important orders of the day.

Lecture 2 (5/20/09): Getting ready for the quiz (Part II)

Don't forget, the Lecture 2 Blog has been divided into two posts: this one, and yesterday's Blog ("Getting ready for the quiz (Part I)"). Yesterday, I talked mostly about how/why we can think of genes as principles. This was a change from the previous Blog, in which I talked about genes as concepts. Today, the main topic is models. We're going to explore what Professor S means when he talks about "scientific models." The hope is that this discussion helps get you ready for Friday's quiz, on which you can probably expect a few questions about models. Lets get started...


Developing a concept of scientific models...

There are lots of ways that we use the term "model" in everyday language: people can be models in magazines or on billboards; kids can play with model trains and airplanes; sometimes people who do good deeds are called "model citizens." But we need to start developing a finely-tuned idea of scientific models, which I think Professor S was doing when he showed you the following slide (below left).

Just like I did in yesterday's blog with genes, I also tracked the statements that Professor S made when talking about models. Using the same form that I did with genes, take a look at the statements that I cataloged about models and the other 3 terms--theories, hypothesis, experiments--that were used in the slide:

• A theory (is a broad) model.
• A model (is a specific) theory.
• Hypotheses (inform/guide) experiments.
• It takes many hypotheses (to make a) theory.
• Hypotheses (generate) theories.
• Experiments (can inform) a model.

Practice: Connectivity work...just connect the 'dots'

With only the bulleted statements listed above, you can begin to do some of your own connectivity work. For example, the last bullet says, "Experiments (can inform) a model." The first bullet says, "A theory (is a broad) model." If you connect the ideas in these two statements, on your own you can create a new statement: Experiments (can inform) a theory (because a theory is a broad model). Congratulations...you've just practiced using formal logic.

There's nothing like an example...

If you're like me, I crave concrete examples. Let me offer you an example of the use of the four terms discussed above. Let's start with an observation...

• I planted seeds of a flowering plant in my front yard. The seeds were for the same species of plant, but they were seeds that were supposed to yield two different colors of flowers: red and white. The first year, plants with either red OR white flowers appeared. After a couple of years, I noticed that there were also plants with pink flowers.

As soon as I start asking questions like, "How did this happen?" or "Why are pink flowers appearing when I only planted red and white ones?" I am moving in the general direction of seeking a explanation. In other words, I am taking a stab at making some statements that could explain what I observed. Here's me imagining a few possible explanations for the appearance of the pink flowers...

• Explanation #1, aka. The Night Neighbor: My neighbor is sneaking into my yard at night and planting seeds of pink flowers in my flower beds.

• Explanation #2, aka. The Pooper: A non-human creature, say, a bird or a mouse, is depositing poop in my flower beds which has the seeds of pink flowers in it.
  

• Explanation #3, aka. Flower Power: The red and white flowers are somehow making pink flowers. I'm not sure how, but they're responsible for the appearance of the pink flowers.
  

Believe it or not, each of these explanations could be considered models. Why? Well, each of the 3 explanations suggest some type of explanatory "mechanism" (a human plants, a bird poops, flowers have 'flower sex') of an observed pattern (i.e., pink flowers appear when only red and white flowers are planted). Can each of these models explain the appearance of the pattern that we're observing in our flower beds? Absolutely. Can each of these models be used to predict the results of certain types of tests or experiments that we could design? Absolutely. Let me do these two things for Explanation #1:

• The Night Neighbor Model explains the appearance of the pink flowers (the pattern) by the actions of my stealthy, night-gardening neighbor (the cause).

• Can I generate a hypothesis from this model? Sure, and it might go something like this: IF I can figure out some way to keep my neighbor (the cause) out of my yard, THEN I should never observe any pink flowers in my flower beds (the pattern).

• Can I use this hypothesis to inform/guide the design of an experiment? Sure, here's one possible experiment: Send the suspected neighbor on a 3-year vacation (prevent the cause from acting!). Do you see any pink flowers (the pattern) while he's gone?
  

What if you DO see pink flowers while he's gone? Well, then maybe you have to consider other neighbors, or maybe you have to start considering The Flower Power Model or The Poop Model. I'm sure you can imagine some kind of IF/THEN hypothesis generated from The Poop Model ('If I can just figure out a way to keep the birds and mice from pooping in my flower bed, then...'). I'm also pretty sure that by now you can imagine how to use that hypothesis to design an experiment (I'm thinking about something cool like a diaper for birds and mice...) and make predictions for an experiment involving animals and diapers (e.g., The flower beds being attended by the diapered animals will not grow pink flowers, but the flower beds being attended by the diaper-less animals will grow pink flowers).

Moving towards a theory...

The big question is, after all these models have been tested, hypotheses generated, experiments designed, and predictions made...have we generated any kind of theory? In this short example, the answer is, "Well, sort of..."

Each time we test these different models we're getting closer to a 'proper' scientific theory of how to explain the pattern (the appearance of the pink flowers). However, in order to achieve scientific theory-like status the model MUST be able to explain MORE than just the appearance of pink flowers in MY flower beds...(and here's the important point)...

In other words, it must be able to explain the general appearance of the 'mixed' flower color phenomenon BEYOND the confines of my front yard! It must explain the mixed flower color phenomenon in places where there are flowers, but maybe no people; it must explain the mixed flower color phenomenon in places like greenhouses, where there are likely no birds or mice. See what I'm getting at here? Remember our statements from earlier: Theories are broad models; models are more specific theories. At this point, we're finally ready to summarize models with a few basic statements that may have more meaning to you at this point.

Scientific models....

• Explain patterns identified in data/observations/phenomena.
• Correctly predict the results of new experiments or observations.
• Are consistent with other ideas (e.g., other scientific models, beliefs, etc.)
  

Wrapping things up...

Interestingly enough, a big part of BS110 this semester will be loosely related to my Flower Power Model mentioned above. In fact, Professor S even started telling you about my Flower Power Model when he started talking about "meiosis" in Lecture 2 (see slide at left). Now, you can be sure that he probably won't use phrases like "flowers having flower sex," but nevertheless you'll be talking about certain models and theories that explain how pink flowers can result from, say, red and white colored ones.

As you talk more about meiosis in Lecture 3 and beyond, however, you could do yourself a huge favor by thinking of "meiosis" as The Meiosis Model (which is part of a broader Theory of Inheritance). Most scientists talk about concepts like meiosis SO often that they usually drop the "Model" or "Theory of" parts of their speech. A great example of this is "evolution." Yes, you still sometimes hear people say the "Theory or Evolution" or maybe even the "Theory of Evolution by means of Natural Selection," but for the most part scientists nowadays usually just say, "evolution." When scientists do this, you know that it's a concept/idea that has been or is currently pushing for consideration of being called a principle or scientific 'truth.'

I suspect we'll talk more about all of these things, and more, in future Blogs...