Lecture 8 (6/5/09): A Biology Bedtime Story...Chapter II

Look at these 3 words: fuliginosa, magnirostris, fortis.

If you have absolutely no idea what these words means, then you need to go back and begin our story from the beginning ("A Biology Bedtime Story...Chapter I").

For the rest of you, read on...

A Recap of Where We've Been

When we last left our story we said that we were going to follow the population of Forts on Daphne Major in the years leading up to, during, and immediately after the severe drought of 1977-78. In particular, we said that we were going to track the Forts' beak size, which we know varies quite widely throughout the population. This is to say that there are Forts with larger beaks, Forts with smaller ones, and Forts with every beak size in between. In other words, Forts are highly variable with respect to their beak size.

Now, the fortis population numbers that I'm about to use in the rest of this story are completely made up to make certain things more clear. Please know that I didn't take them straight out of The Beak of the Finch by J. Weiner, I took them instead (and adapted them) from an activity created by Presada Calrabi called "Evolution: A Natural Experiment," which was in a book that I can no longer find.

Daphne Major Census: 1976

Lets pretend that at the beginning of the wet season in 1976 there was an easy way to classify the population of Forts on Daphne Major according to a particular body part: Their beaks. Rather than use actual quantitative measurements for things like beak length, beak depth, and beak width, lets just lump all of these measurements into single category and call it "Beak size/strength." Imagine that we can then capture all of the Forts on Daphne Major and classify their beak size/strength as Average, Below Average, or Above Average. Simple, right?

As we learned in Chapter 1, 1976 was a a fairly normal year in terms of rainfall and food availability. If we were performing a census on Daphne Major at the beginning of 1976, here's what our census might look like (click on it to enlarge it):

A census is just an official count or survey of a population, typically recording various details of individuals. In this case, lets walk through the numbers...

• The table says there are 50 adults breeding pairs for each beak phenotype. Remember, these are all Forts with phenotypes for either average, below average, or above average beak size/strength. So, 50 breeding pairs of each phenotype means a total of 300 adult Forts.

• The table also says that these breeding pairs produce a total of 300 offspring (100 offspring produced by each of the different beak phenotypes).

• Of the 100 below average phenotype chicks born this year, 60 survive. Of the 100 average phenotype chicks born this year, 80 survive. Of the 100 above average phenotype chicks born this year, 55 survive. This means that a total of 195 Fort chicks survive.

Let's assume that about 10% of the adults typically die every year (old age, predation, accidents, etc.). So by the end of 1976, how many Forts make up the population of Forts on Daphne Major? The table at right summarizes the numbers.

As you can see, a total of 465 Forts survive 1976.

Lets also assume that chicks become become adults and breed the year after they are born. This means that there are 465 adult Forts that survive 1976: 150 below average beak size/strength, 170 average beak size/strength, 145 above average beak size/strength.

How do we talk about what happened in 1976 in terms of ideas in BS110?

Well, it's clear that the Forts demonstrate phenotypic variation within their population. We should also say that beak size/strength is heritable, which simply means that Forts' beak size/strength is passed on from parents to their offspring through certain alleles of genes. To see this fact you have to put on your "In There..." glasses. You need to be able to 'see' things like alleles, chromosomes, base pairs, and DNA when looking at a table of data like this. You also need to be able to see that things like Punnett Squares, meiosis, crossing over, independent assortment, and gametes are lying just beneath the surface of this table. Can you see them?

Is there genetic variation in this population? Yes. There are alleles present in the Fort population that actually code for three beak phenotypes (average, below average, and above average size/strength). How do we talk about the frequencies of alleles (or allele frequencies) in this population? Well, frequency basically means "how often." So how often do the alleles for average, below average, and above average size/strength beaks occur? We can calculate this as follows: 150 out of surviving 465 birds have the allele combination that gives them below average beaks (32.3% of the surviving Fort population); 170 out of 465 surviving birds have the allele combination that gives them average beaks (36.6% of the surviving Fort population); 145 out of 465 surviving birdshave the allele combination that gives them above average beaks (31.2% of the surviving Fort population). When we put it in percentages, it seems that no one allele combination is too much more frequent than the others, right?

What about the fitness of this population? According to Prof S, the fitness of this population of Forts is determined by measuring the number of Fort chicks produced that can then produce offspring themselves. In 1976, these Forts seemed pretty 'fit,' don't you agree? 195 Fort chicks survived who we assume all have the potential to develop into adults by 1977, where they can then start reproducing themselves.

Daphne Major Census: 1977, the Drought

At the start of the 1977 the Fort population seemed to be in a relatively decent state: only 10% of the adults were dying and lots of chicks were born. Not only that, but the many chicks that survived 1976 and entered the 1977 wet season as adults were ready to breed themselves. If we took another census of the Fort population on Daphne Major at the start of 1977, we could imagine that it might look something like this:
Lets briefly walk through the numbers in this table, which lists mostly data about "pairs" of birds instead of individuals.

• The table shows that there was a 10% mortality rate among the adults from the year before. You can see this because 50 adult pairs from the year before has dropped slightly down to 45 adult pairs. Remember, these are all Forts with phenotypes for either average, below average, or above average beak size/strength. So, 45 breeding pairs of each beak phenotype means a total of 270 adult Forts (45 pairs x 2 individuals x 3 beak phenotypes).

• The table also shows that there are "new adult pairs." These are the chicks who survived 1976 and are now adults themselves! They pair up and add even more adults to the total Fort population, 184 new adults to be exact (30 pairs + 40 pairs + 22 pairs x 2 individuals).

• The last line of the table shows the total number of adult breeding pairs of each phenotype at the beginning of 1977. There are 75 total breeding pairs of birds with the below average beak phenotype (150 individuals). There are 85 total breeding pairs of birds with the average beak phenotype (170 individuals). There are 67 total breeding pairs of birds with the above average beak phenotype (134 individuals).

Had 1977 been anything like 1976, we would expect all of these of breeding pairs of Forts to have lots of chicks throughout the wet season. However, I've already told you that 1977 was the beginning of an 18 month drought on Daphne Major. Take a look at this census data from the end of 1977:


Stunning...isn't it? Now, I told you that I've invented these numbers to illustrate some important ideas. However, in the Grant's actually finch data from 1977 a similar drama unfolds in term of the plummeting numbers of each of the three Fort beak phenotypes. The table above does not show pairs--it shows the number of individuals still found on Daphne Major by the end of the dry season in 1977. NO CHICKS HATCHED that year. Only 2 below average beak Forts survived (98.7% mortality rate). Only 3 average beak Forts survived (98.3% mortality rate). Only 27 above average beak Forts survived (80% mortality rate). Compare that to the 10% mortality rate that we saw in adult Forts during 1976!

How do we talk about what happened in 1977 in terms of ideas in BS110?

[The following discussion about genetic drift was modified/corrected/revised on 6/8/09]

Is genetic drift occurring here? The short answer is, "NO." But there has been some confusion about this term as it was presented in class. In Lecture 8, Prof S presented genetic drift as "a change in allele frequencies in response to...unpredictable events [that often] happen to populations."

Unfortunately, many of us are tempted to look at the drought of 1977 and think to ourselves, "The drought was definitely an unpredictable event...and the drought definitely led to a change in the allele frequencies of the Fort population...therefore, this must be a case of genetic drift!" At least that's the logic I used when I went back over my own notes from Lecture 8 and initially wrote this Blog. As I said above, this is unfortunate. Why is it unfortunate?

This is unfortunate because--at least when it comes to thinking about the concept of genetic drift--this is the wrong way to think about unpredictability. Before we tease this idea apart any further, lets first establish one thing that we should all agree on at this point: The drought led to a change in the allele frequencies in the Fort population. Why am I so confident that we can accurately make this statement? Because of the following data:

• Before the drought 150 out of 465 Forts had the allele combination for below average beaks (32.2%). After the drought, 2 out of 32 surviving Forts had this same allele combination (6.25%).

• Before the drought 170 out of 465 Forts had the allele combination for average beaks (36.6%). After the drought, 3 out of 32 surviving Forts had this same allele combination (9.375%).

• Before the drought 145 out of 465 Forts had the allele combination for below average beaks (31.2%). After the drought, 27 out of 32 surviving Forts had this same allele combination (84.375%).
  

When we put this story in 'before/after' drought percentages like this, it should be clear that one particular allele combination--the one coding for above average beak size/strength--occurs in the Fort population much more frequently AFTER the drought compared to before the drought. Therefore, the drought has in fact led to a "change in the frequencies of the alleles" in the Fort population. Can you see this too? Unfortunately, this is only one part of the complete definition of genetic drift. In order for this instance to be a case of genetic drift, Prof S also said that this had to be an "unpredictable" (or "random") event that led to this change in allele frequency.

I know what you're thinking...you're still thinking that the drought was an "unpredictable" or "random" event! This is a classic case in science where finding the right words to use (and the right order to put them in!) makes all the difference. Sure, from a certain perspective, the drought could be seen as an random or unpredictable event. However, what about the phenotypic response of the Forts to this event? Is their phenotypic response random? Is their phenotypic response unpredictable? In other words, as a scientist, if you knew a drought was coming to Daphne in 1977, would you predict that the allele combinations for beak size/strength would change in response to a severe drought? SURE YOU WOULD! Thus, in our drought episode, biologists don't see the changes in the frequencies of the allele combinations for beak phenotype as random or unpredictable. They see these changes in the allele frequencies as entirely non-random and predictable!

So what would a case of genetic drift look like with our Fort population? To see that we have to use our imagination and go back a short ways in time...

Imagine that Daphne Major from 1972-1976 is an incredibly stable place. Imagine that it receives the same amount of rainfall each year, has no new introduction or loss of predators, has no major changes in the plant communities, etc. In other words, imagine that there are no significant changes in the selective forces that might choose certain beak size/strength phenotypes over others. Imagine also that there are, say, 150 Forts on the island: 50 below average (with aa alleles), 50 average (with Aa alleles), and 50 above average (with AA alleles).

Now here's an important question for you: With no new significant changes in selection pressures acting on this population of 150 Forts, is it possible that in 1976 we could find the following distribution of Fort individuals: 100 below average (aa), 25 average (Aa), and 25 above average (AA)? Is this type of allele distribution possible without some major selective pressure on the Forts? What do you think?

The answer, at least in theory, is: "YES, it's entirely possible." How is this possible?

This hypothetical change in allele frequencies between 1972-1976--in our case, the small "a"'s appear in the Fort population in 1976 more frequently than they do in 1972--we said is not due to a drought or any other major selection pressure. In our example (again, a hypothetical one), this change can be viewed as due to the unpredictable or random event which is best summarized by a few (closely related) questions: (1) Which male phenotypes happened to mate with which female phenotypes? (2) Which male gametes randomly came forth from meiosis? (3) Which female gametes randomly came forth from meiosis?

Take an Aa male and an Aa female (imagine that both show the average beak phenotype because of incomplete dominance). During a straightforward episode of meiosis, the male can produce two types of gametes: A and a. Similarly, the female can produce two types of gametes: A and a. If these two Forts mate according to a Mendillian model of genetics, they have a 25% chance of having a baby Fort with AA (above average beak), a 50% chance of having a baby Fort with Aa (average beak), and a 25% chance of having a baby Fort with aa (below average beak). And you thought Punnett Squares wouldn't be useful to you any more!!! What's to stop the Aa parents in this population from producing a bunch of aa offspring? They have a 25% chance of producing this kind of chick every time they mate, right? The answer to the questions is, "Nothing, can stop them." Nothing, that is, except for some generally accepted 'laws' of chance/probability, but if you've ever flipped a coin those are easy to break!

Have you ever flipped a coin and gotten 4 heads in a row? If you did, you temporarily violated the laws of chance/probability (theoretically speaking you should have gotten 2 heads and 2 tails in your 4 flips of the coin). Why should the gametes of finches be any different than a quarter or, say, a pair of dice multi-sided dice? Why couldn't there be four aa babies born in a row--one each year for four years--to a pair of Aa parents? If this type of random or unpredictable event happens without any type of selection pressure for a particular phenotype, and it results in changes in the frequencies of allele combinations present in a particular population, we say that it is an example of genetic drift.

Because of this random pairing of gametes from parent birds, in the example above we can say that the allele combinations for the average (Aa) and above average (AA) beak phenotypes have 'drifted' from the Fort gene pool on Daphne Major (in other words, it's harder to come by the A allele in the Fort population in 1976). We can also talk about this in terms of the Fort genome, which is a collection of all of the different alleles in the Fort population. In this case, we can say that the Fort genome is "less diverse" following our hypothetical example of genetic drift between 1972-1976. Or, following the draught of 1977, we could also say that the Fort genome has "lost" some of its diversity following the natural selection event (i.e., the drought).

[The above discussion about genetic drift was modified/corrected/revised on 6/8/09]

Has there been immigration in this episode of drought? In other words, have any new Forts arrived at the island from other islands? Not that we can see in the data tables, so we have to assume that no new Forts have found their way to Daphne Major from neighboring Galapagos islands.

Has there been emigration? In other words, have any new Forts departed the island for other islands? Well, only that 'Big Island' in the sky :) Again, our data tables don't report any emigrants so we have to assume that the Daphne Major Forts died on the island instead of flying off to a nearby island. Has there been gene flow? Prof S said that gene flow was when "individuals move between populations," and we just said there was no immigration or emigration to or from Daphne Major (which holds the entire Fort population), so there must have been no gene flow!

What is this population of Fort's relative fitness? In other words, what is this Fort population's fitness relative to the Fort population of 1976? Can you say, abysmal? That should be easy to see. If fitness is determined by measuring the number of Fort chicks produced that can then produce offspring themselves, then the fitness of the 1977 Forts is practically zero since no chicks were born that year. Fortunately, at least two birds of each phenotype survived. So, assuming that there is a surviving male and female in each of the beak phenotypes, there is still a chance that the relative fitness of the population could increase in 1978 if the rains return.

Are we seeing founder and/or bottleneck effects? As you saw in lecture (see slide below left), Prof S defined the founder effect as events where there is a "loss of allelic (genetic) diversity because of small numbers of individuals starting a new population elsewhere."

Did our Forts lose allelic diversity in 1977? YES. Was it because a small number of individuals started a new population elsewhere? NO. So, did we see a founder effect in this population? NO, we did not.

What about a bottleneck event? Prof S defined these as events that result in a "decrease in genetic [or allelic] diversity after catastrophe." Did our Forts lose allelic diversity in 1977? YES. Was it because of a catastrophy? YES. Need I say more?

Daphne Major Census: 1978

One last year's worth of data and then we can wrap up our biological bedtime story. By now, you can read tables like this and keep track of things like individuals, pairs, chicks hatched vs. chicks surviving, etc.

Lets briefly walk through the numbers in this table...

• The table says that at the beginning of 1978 there is now only 1 adult breeding pair of the below average and average beak phenotypes. However, there are 13 breeding pairs of the above average beak phenotype. Remember, these are all Forts! These are all member of the same species who can interbreed anytime they desire. So, 15 total breeding pairs means a total of 30 adult Forts (in 1976 there were 300).

• The table also says that these breeding pairs produce a total of 35 offspring (2 below average chicks + 3 average chicks + 30 above average chicks).

• Of the 2 below average phenotype chicks born this year, 2 survive. Of the 3 average phenotype chicks born this year, 3 survive. Of the 30 above average phenotype chicks born this year, 27 survive. This means that a total of 32 Fort chicks survive.

Lets take the census data from 1976-1978 and combine it in a single frequency histogram (bar graph) to show the TOTAL NUMBER OF BIRDS alive with each beak phenotype at the end of each year. By this time in your school career you should be able to see three stories within this one graph: The story of 1976 is bold in BLUE; the story of 1977 is told in RED; and the story of 1978 is told in GREEN.

If you concentrate on the stories told by each of the colored bars you will see that we've clearly seen a natural selection event between 1976 and 1978.

• If you connected the very tops of the three blue bars with a single line, you could see that the line would be rather 'flat,' with only a small hump in the middle (due to the average beak phenotype). The story behind this line would be this: In 1976 the three different allele combinations for beak size/strength could be found with (nearly) equal frequency in the Daphne Major Fort population.
  

• If you connected the very tops of the three red bars with a single line, you could see that the line would be rather 'skewed' to the right. This time the hump would be more prominent and to the right (due to the above average beak phenotype). The story behind this line would be this: In 1977 the three different allele combinations for beak size/strength could not be found with equal frequency in the Daphne Major Fort population; as a percentage of the total Fort population, you could find more individuals with above average beak size/strength.
  

• If you connected the very tops of the three green bars with a single line, you could see that the line would be quite 'skewed' to the right. This time the hump would be even more prominent and to the right (due to the even greater number of birds with the above average beak phenotype). The story behind this line would be this: In 1978 the three different allele combinations for beak size/strength could not be found with equal frequency in the Daphne Major Fort population; as a percentage of the total Fort population, you could find even more individuals with above average beak size/strength.

I now want to make one last connection with a slide that Prof S used in class (see below). This was the slide that he used to talk with you about 3 types of selection: directional, disruptive, and stabilizing selection. Given the story of the Forts from 1976-1978, the histogram I created above, and the bullets that talk about 'lines' and 'humps' and 'skews,' you tell me: What type(s) of selection did we see occurring with the Fort population on Daphne Major?


I sure hope you answered: Directional selection.

Well, that's the end of Chapter II of our Biology Bedtime Story. Between Chapters I & II, we've seen a story unfold that has asked you to put all three pairs of your Darwinian glasses (In There..., Out There..., and During There...). I've held up my end of the bargain by telling you a story about a single species of finch in the Galapagos Islands and I've mapped nearly all of the important terms from Lectures 7 & 8 onto this story (I guess I forgot inbreeding, but maybe you can insert that one yourself). You've now got your own work to do by continuing to integrate this story with your lecture notes, your experiences in lab, and your textbook.

In future Chapters (e.g. Chapter IV), we will take a look at how the other species on Daphne Major--like the Mags and the Fulis--dealt with drought of 1977.

Lecture 8 (6/5/09): A Biology Bedtime Story...Chapter I

Every now and then we all need a good story told to us. I was told a story by author Jonathan Weiner sometime around 1995 when I got a hold of his Pulitzer Prize-winning book, The Beak of the Finch. What I would like to do over the next couple of Blogs is use this story--which follows a husband and wife team on their yearly research trips from Princeton University to the Galapagos Islands--to map the language of the BS110 lectures onto some images and a narrative that I hope you'll enjoy (not to mention find useful!). Here goes:

Once upon a time...

Peter and Rosemary Grant (at right, inset) have been traveling to the Galapagos Islands since the 1970s. During that time, they've spent most of their time on a single island called Daphne Major (also at right).

Daphne Major, as Weiner describes it, is "small and lonely," and there is only one way onto it. At low tide, the Grants have to leap from a rowboat onto a small ledge as most of the island's 'shore' consists of concave 3-story cliffs all the way down to the water of the Pacific Ocean.

What might live on such an isolated tip of an old volcano 600 miles (1000 km) from mainland South America? Well, birds, for one. There are iguanas too, but in this story I want to talk mostly about a group of birds, a group of "finches," in fact, and also organisms such as the plants on which the Daphne Major finches regularly feed. Since Prof S has been talking about individuals, species, and populations in lecture, I want to introduce these terms into today's story in the hope that you will slowly (but surely) become more comfortable with them. More importantly, I want you to learn to use them how biologists use them when they speak 'biologese.'

If you travel, as the Grants have, throughout most of the islands and islets in the Galapagos archipelago, you will likely run across 13 different species of finches spread throughout them. Well, at least this is the number of species that most taxonomists currently agree on.

What does it mean to say that there are "13 different species of finches" in the Galapagos Islands?

It means that while these different 'groups' of birds share many common characteristics (e.g. behaviors and physiology), they either (1) CAN'T produce fertile offspring even if they tried, or they (2) COULD produce fertile offspring IF they tried, but they DON'T usually try!

An important point! Reason "(1)" above is my own simplified version of the Biological Species Concept, which Prof S discussed in Lecture 7 this past Wednesday. Reason "(2)" above is my own known simplified version of the Ecological Species Concept, which Prof S has not discussed (at least so far) in our course. I'll say more about this in a minute...

Lots of bird taxonomists currently lump these 13 species of finches into four "groups of species" or genera according to the species's behavior & diet. Click HERE to see a high-quality image with pictures of individuals from 11 of the 13 species--you'll probably get some sense of how four main groups are possible just by looking at their beak and head similarities/differences.

• Group A: The finches that live in trees and eat fruits and bugs.
  
• Group B: The finches that live in trees, but are strict vegetarians (i.e., no bugs!).
  
• Group C: The finches that live in trees, but they don't look and act like the other groups of tree finches...they actually look and act more like a different genera of birds (like the "warblers").
• Group D: The finches that spend most of their time hopping on the ground.
  

The Grants have spent most of their 30+ years of research on Daphne Major looking specifically at Group D, which consists of 6 different species. Because all six of these species are most frequently observed hopping on the ground, it won't surprise you to know that scientists use the Latin term Geospiza as they genus name for all six species (Geo- is Greek for "earth" or "of the ground"). Here's a list of the Genus/species names for this group of six species of ground finches:

• Geospiza difficilis: the sharp-beaked ground finch.
• Geospiza scandens: the cactus finch.
• Geospiza conirostris: the large cactus finch.
• Geospiza magnirostris: the large ground finch.
  
• Geospiza fortis: the medium ground finch.
  
• Geospiza fuliginosa: the small ground finch.
  

To connect once again to ideas in the past two BS110 lectures: Why do scientists consider these groups of ground finches as six different species?

What IS a species?
IF, we define species according to the Biological Species Concept (which Prof S talked about in Lecture 7), we would say, for example, that when a female Geospiza fortis tries to mate with a male Geospiza fuliginosa, they might produce an baby bird BUT it would be sterile. In other words, it would be impossible for the baby bird they produce to then go and mate (with either a G. fuliginosa or a G. fortis, it doesn't matter) and produce "viable offspring" (i.e., babies that can have babies).

Funny thing is, on Daphne Major, if a female G. fortis tries to mate with a male G. fuliginosa they can actually produce viable offspring, yet scientists still consider them as two different species. How is this possible? Well, that's because many biologist define species not by the Biological Species Concept (which I'll call BSC), but instead by the Ecological Species Concept (which I'll call ESC). The ESC looks at species a little bit differently. The ESC calls a group of finches a "species" when that group of finches could but--for any number of different reasons--choose not to reproduce on somewhat of a regular basis. So, you see, biologists actually have a number of different ways of talking about species, of which I have shared just two. And yes, they have more ways to talk about species--in fact, I know of at least two additional ways, but they're not really that important for our story, which we need to get back to...

Looking closely at Geospiza fortis on Daphne Major...

Glance back up at the top of the page and look again at the picture of Daphne Major. Can you imagine all of the individual Geospiza fortis--the medium ground finches--on the entire island (who from now on I'll simply call the "Forts"). In Lecture 7, Prof S introduced the the term "population" like this:

• Population: All of the individuals of a single species in a defined area or "habitat" that will potentially interbreed.
  

I now ask you: Do you think there's a single population of Forts on Daphne Major or multiple populations?

Considering Prof S's definition above, one way to ask this same question is this: Do you think all of the individuals of a single species found in this habitat can interbreed? Here's another--albeit less-scientific!--way to ask this same question: Do you think it's possible (or likely) that all of the male and female Forts found on Daphne Major can find each other and have sex with one other if they want to?

To be honest with you--but I can't say for sure--I think the Grants would answer this question as, 'Yes, we consider all of the Forts on this Daphne Major to be a single population.' (I should have asked them this when I called them at Princeton in 1996--the day after they got back from their most recent trip to Daphne Major--and talked at length with both of them on the phone!)

Lets just say for the sake of own our BS110 story that there is only one population of Forts on Daphne Major. It doesn't matter if the Forts sleep on one side of the island or the other, near the ocean, or up inside of the dormant crater. When they want to reproduce, they can (and do) find each other.

So do you feel like you're getting a good sense of a what a species is and what a population is so far? Good, I thought so. But before we see how Mother nature can mess with these birds in some mind-bending ways, lets look at this single population of Forts on Daphne Major in even greater detail...

Variation in a single population

I've written extensively about variation in my Blogs this semester, so you should be getting quite confident in your ability to talk about variation across different scales. Do the Forts in this population show variation? In other words, do the Forts look different on the outside? (And in the words of Prof S, do the Forts show "phenotypic variation?")

DURING THERE: If you read one of my earlier Blogs ("Learning the Language of Variation"), then you know how to talk about variation at the molecular and the cellular scales (you use terms like base pairs, DNA, gene/allele, chromosomes, etc.). If you read the Lecture 7 Blog ("Hey, Four Eyes!"), you know that Prof S has been recently trying to teach you how to talk about variation on larger scales, like in individuals and in groups of similar individuals or populations.

In the Lecture 7 Blog, I told you that I like to talk about individual variation as "DURING THERE." That is, during an individual organism's time on earth, why/how does the individual show phenotypic variation? This is an easy question to answer when we think about a single Fort finch...

Like humans, Forts go through a number of stages from sperm/egg to death. We often call this their "life cycle." Young Forts are often called "juveniles," and they are called "adults" as soon as they develop the ability to reproduce (that is, when they reach "sexual maturity"). This is different than with humans, isn't it? Biologically speaking, many male and female humans develop the capability to reproduce sometime in their early teen years. Legally speaking, however, in the U.S. we don't usually consider humans to be "adults," until they're 18...well past when they could be considered a biological 'adult.' Not so in the bird world.

Imagine the beak of a single Fort...

Does the beak size of a single Fort change during its life cycle? Absolutely, Forts have smaller beaks when they are young "fledglings" than when they are adults (fledglings are even younger than the juvenile stage). Therefore, we say that a single Fort's beak size shows variation during or over the course of its life span.

Believe it or not, the Grants and their graduate students have spent 30+ years measuring the beaks of every Fort on the island multiple times over the course of each Fort's life span. If you click on the image to the right, you can get a good idea as to the types of data that the Grants collect for each of the Forts found on Daphne Major. If they want to try to answer the all-important--at least in the sciences--why and how questions, biologists have to do A LOT of this type of "During there..." or descriptive work.

Is there phenotypic variation in the Daphne Major Forts population?

Thanks to work of the Grants, we can actually answer that question: 'Yes, across the population on the island, the beaks of the Forts are variable.' How variable are they? That's a good question, and one the author of The Beak of the Finch describes like this:

"...the medium ground finch, fortis, sometimes shades into the species above it, magnirostris, or the species below it, fuliginosa. The very biggest specimens of fortis are just as big as the very smallest specimens of magnirostris, and so are their beaks. At the same time the very smallest specimens of fortis are just as small as the biggest fuliginosa, and so are their beaks. Within each of these three species, the beak of individual birds are variable...You can't distinguish these three species by their plummage, and usually not by their build or body size either. You have to tell them apart by their beaks." (p. 42-43)

Can you imagine? What a logistical research nightmare for biologists hoping to study any one of three species of ground finches on a single island!

Well, this is actually the case on Daphne Major where all 3 species of ground finches can be found hopping around on the soil, looking for food, reproducing, and trying to avoid predators. Oddly enough, the finches do these things under the watchful eyes of Peter and Rosemary Grant and the rest of their "Finch Unit" crew. After 30+ years of practice watching and measuring the ground finches, the staff at the Charles Darwin Research Station on a nearby island have an unsurprising saying which goes something like this: Only God and the Grants can recognize the difference between species of Galapagos finches.

Looking ahead...

In the Grants' first four years doing research on Daphne Major, between 1972-1976, all of the ground finch species on the island had it pretty good. There was enough rain so that the plants on the island produced lots of food (mainly in the form of seeds) for all of the ground finches to eat (seeds are the preferred food of magnirostris, fortis, and fuliginosa). In the language of BS110, there was very little "competition" for "resources" (like seeds) within and between the different "species" of ground finches. In the language of economics: When it came to the ground finches favorites foods, supply outstripped demand.

Just how good were things between 1972-1976?

Well, when the Grants first arrived on Daphne Major during the wet season (there are only 2 seasons in the Galapagos: wet and dry), they began collecting finch data and they estimated about 1500 Forts to be living on the island (i.e., the total population of the species on Daphne Major). At the end of the dry season, just before the next wet season began, the Grants estimated that about 9 out of every 10 of those Forts survived the dry season (about 1350 of them). That's a 90% survival rate following the dry season, when food is typically harder to find than in the wet season. This logic makes sense, right? Less rain = Less plant growth = Less seed production by plants = Less food for the ground finches = Less raw 'materials' for cell processes like cellular respiration. Can you see in this last sentence how "Out There..." is coming into this survival equation? Changes in the environment (Out There...) lead to some interesting changes inside of the cells of an organism (In there...)...

In 1977, however, what nature had been accustomed to giving Daphne Major somewhat regularly between 1972-1976, i.e., rainfall, it decided to take away...rather abruptly. Begining sometime in 1977, no rain fell on Daphne Major for about 18 consecutive months. The Mags, Forts, and the Fulis were forced to deal with the fact that sometime in 1977 the island's plants stopped producing seeds. All 3 species of ground finches had to rely on finding and cracking open seeds that had fallen to the ground and been ignored or overlooked in previous years. In other words, the only food that existed on Daphne Major in late 1977 were the seeds left lying in the dirt and under small rocks from years like 1976 and 1975.

In the language of BS110, the ground finches of Daphne Major experienced a severe "selection pressure" or a "selective force" starting in 1977. Finding enough food to eat and survive each day was a "struggle" for survival. In the next Blog, we'll look specifically at how the Forts dealt with this selection pressure or 'force.' We will look things like the Forts overall birth & death rates, as well as the measurements--thanks to the Grants!--of the beaks of those Forts that died (and survived) the 18 month drought of 1977-78.

By doing this, we can then map onto our story those terms that Prof S used extensively in Lecture 8, terms like:

• genetic variation (including phenotypic & genotypic variation)
  
• heritability
• allele frequencies
• genetic drift
• founder effects & bottleneck effects
• genetic diversity
• fitness & relative fitness
  
• immigration/emigration
• gene 'flows' & gene 'pools'
  
• inbreeding
• selection (including stabilizing, directional, and destabilizing selection)

I have a feeling that the above terms will become less confusing and more 'natural' for you when set firmly in the context of the Grants' swashbuckling adventures on Daphne Major. If you don't want to wait for my next Blogs, you can go find The Beak of The Finch at the library or likely at any of the bigger local book stores and start reading about them for yourself. Although I didn't know this until today, I understand that the Grants' have finally written a book themselves called, How and Why Species Multiply: The Radiation of Darwin's Finches.

Looks like my summer reading list just got a little bit longer...

Lecture 7 (6/3/09): "Hey, Four Eyes!"

On Tuesday afternoon, I got myself over to the NCG cinemas with a couple of good friends to see the new Pixar movie, "UP" (I'm a big fan of all the Pixar animated films). The thing is, it was in 3D and we all had to wear the new 3D glasses (shown at top right) during the show.

I must say, the new animated 3D movie experience is quite impressive and nothing like the lame attempts at 3D films when I was growing up in the 70s & 80s (I was 13 yrs. old when Jaws 3-D was released-you can do the math). At least in the hands of the skilled animators at Pixar studios, the use of this new 3D technology in UP truly offer viewers an entirely new type of visual experience. There was a certain 'texture' to the film that I hadn't seen in any of the previous Pixar films (or, for that matter, any animated film). At least for the 96 minutes it was playing on the screen, I saw the world--both literally and figuratively--through a new pair of glasses.

OK, so why am I telling you this and what does it have to do with Lectures 6 & 7 in BS110?

Well, late last night I was thinking that my experience watching "UP" through the 3D glasses is not unlike how Professor S has been asking you to see the natural world...that is, through a pair of Darwinian glasses.

I've been telling you that this was coming for at least a week in my previous Blogs (in particular, see "When Darwin Meets Madonna" & "Learning the Language of Variation"). On Monday, however, Professor S plunged us fully into the world of Darwinism and our time here in this Blog will be time well spent if we re-walked through some of the slides he shared with you in Lecture 7 (in a future post, I will come back to the "Critters" that he presented to you in the last 20 minutes of Lecture 6...after the exam).

In many ways, the old picture at left is a perfect image representing what you and your classmates were supposed to look like by the end of yesterday's lecture: You all were supposed to walk out of lecture with the ability to look at events in occurring in the natural world through a new pair of glasses. Lets now take a look at some of the interesting ways that Professor S crafted these new Darwinian lenses...

Translating a VERY IMPORTANT slide...

I'm not sure if you realized it at the time, but the slide at right is an extremely important slide...maybe as important as a single slide I drew your attention to in the Lecture 1 Blog ("Concepts, Principles & Models Oh My!").

I don't know about you, but I thought many of the slides Professor S used in Lecture 7 were very nicely sequenced. He tackled difficult ideas but managed to choose graphics and a sequence for his slides in such a way that I felt I could easily follow his ideas. I know I walked away from class with a better understanding of things that I thought I already understood!

The slide at right, however, is the one exception: For a slide that contains such important ideas, I thought it could have been presented a little differently...so as to maybe bring the important ideas in it more forward, and into a different light. Here's one way that you and I might translate this slide...

As you can see, in the slide below at right, Prof S's text is still there (in light gray) and I have translated each of his phrases or words into my own (in black). At the top, you can see that I think he was asking you a question: What makes organisms appear different? If you have a brother or a sister, for example, what could possibly make you taller than him or her? And this is where your Darwinian glasses come in, so please find them and put them on...I'll wait.

In a Darwinian world, there are at least 3 likely explanations as to what could make you taller than your brother or sister, (1) You might appear different because of something 'IN' there, (2) You might appear different because of something 'OUT' there, or (3) You might appear different because of something 'DURING' there.

Is there a "(4)" i.e., some combination of 1, 2, and/or 3 above? There is!!! Which is why Prof S had all of the red arrows between the different words and phrases on his original slide. This is one of the reasons why biology research might be considered 'hard' or difficult: Every time you want to figure out what makes one living thing (or a group of living things) is different from another, you have take 3 different individual 'factors' into consideration--IN there, OUT there, and DURING there (or some combination of the three!).

Here's a question for you: Why did I make a dotted red square around the "Genetics (Genotype)" (or "IN there") term?

I did this because I want to draw special attention to the fact that this is where you have been spending lecture time with Prof S during Lectures 1-5. For the past two weeks, you've been exploring terms like base pairs, nucleotides, DNA, genes, alleles, chromosomes, meiosis, etc. Why?

Because Prof S wants you to be able to talk more fluently about what's IN THERE. In where? INside of organisms! Which means INside of cells! Which means INside of chromosomes! Which means INside of genes/alleles! Which means INside of DNA! Which means INside of nucleotides and base pairs! (By the way, can you see that I've just walked you 'down' in scale with each of my "Which means..." phrases? Each successive phrase walks you down a size scale--from larger things to smaller things.)

OUT THERE and DURING THERE..

In this course, have we spent much time in lectures talking about what is OUT there that might make organisms appear different? (In other words, what is OUTside of an organisms cells or body.) Have we spent much time talking about what is DURING there that might make organisms appear different? (In other words, DURING an organism's time living on the Earth.) The answer to both questions is, "No, not really." Why do you think this is?

I have a possible explanation I'd like to share with you. I think that biology professors make an assumption: they often assume that you already know about what's OUT there (and what's DURING there) that might make organisms appear different. Why do they assume this? They assume this because the OUT THERE (i.e., the "environment") and the DURING THERE (e.g., the different stages of an organisms "life cycle") are things that they assume you have seen or experienced in your time on Earth. They assume that you already know about some things in the environment (OUT THERE) and they assume that you already know some things about different phases, states or "stages" in which organisms can be found between birth and death (DURING THERE). They don't, however, assume that you know much about what's IN there because, optically speaking, what's IN THERE (i.e., in your cells, in your chromosomes, in your DNA, etc.) is really difficult to see without technological supports like microscopes and gel electrophoresis contraptions.

Now, where was I...how did I get on that tangent?

Oh yeah...

Prof S has just spent the first 5 lectures devloping the part of your Darwinian glasses that allow you to see how what's IN THERE can make organisms appear different. One way to think about the exam you took last Friday was as a test to see how your IN THERE glasses 'fit.' In other words, Prof S was testing how well you could use your IN THERE glasses when needed. For the time being, think of your IN THERE glasses as the yellow pair of glasses in the image at right.

I don't know if you realized it or not, but in Lecture 7 Prof S started teaching you how to use the OUT THERE glasses (the blue ones) and the DURING THERE glasses (the red ones).

Do you remember the oak tree slide at left? Which pair of glasses do you think Prof S was teaching you how to use when he showed you this slide?

I hope you said the DURING THERE glasses. This was a slide in which he talk about how an oak tree displays "phenotypic variation" depending upon the stage the oak tree is in its life cycle. This is the lanaguage of DURING THERE glasses.

Do you remember the spruce tree slide at left? Which pair of glasses do you think Prof S was teaching you how to use when he showed you this slide?

I hope you said the OUT THERE glasses. This was a slide in which he talk about how a spruce tree shows "phenotypic variation" depending on the environmental conditions in which it has to grow. This is the language of OUT THERE glasses.

These weren't the only two slides in which Prof S was practicing going back and forth between the yellow, blue and red glasses! Do you remember the thought exercises he had you do with your lab partners regarding the population of bald eagles on the Manistee River, the population of E. coli in the petri dishes, and the population of white-footed mice in the MSU woodlots? Each of these scenarios was designed to teach you how to use the 3 pairs of glasses at the same time. Pretty cool, huh?

Over the next few weeks (and for much of the rest of the semester), I have a hunch you will be learning much more about how to use the OUT THERE, DURING THERE, and the IN THERE glasses. Some of you may get really good at using one of them, however, a word of caution: My guess is that your exam performance will largely depend on how well you can coordinate wearing all three glasses at the same time.

Wrapping up today's Blog...

Why did I put the term "population" in bold blue italic text above? I did this because I wanted to draw your attention to the fact that in Lecture 7 Prof S was starting to take a step 'up' from where we've been in the course in terms of scale. In Lecture 7 you didn't really hear that much about molecules and cells did you? (Although, if you've been following my Blog you know that they were there! You just needed to put your IN THERE glasses on to see them.)

Instead of cells and molecules, Prof S talked more about individual organisms and populations of organisms. This is a step 'up' in terms of scale from something smaller (a single organism) to something bigger (a group or population of organisms). Given this new step up scale, I have a suggestion. Last week, a BS110 student asked me to end my Blogs with a question or an exercise that would help prepare her for future exams. So here goes...

In Lecture 7, Prof S showed a slide that I will talk about in much more detail in my next Blog. The slide is at right. Here's what I think you should do:

• Carefully craft a paragraph to describe the ideas found within this slide (recall that Prof S referred to it as a "model"). Here's a suggestion of terms to be sure to include: DNA, cell(s), individual(s), organism(s), population(s), species, genes, alleles, variation, environment, life cycle.

If you want you can send the paragraph to me by email and I'll choose a paragraph or two to talk/walk through in a future Blog (we can make them anonymous if you want).

Looking ahead...

Given the end of Prof S's lecture on Monday, it may seem strange to you that I didn't say anything in today's Blog about "natural selection" or "evolution." I want to emphasize right now that there were some very important moments (HUGE, important moments, actually) near the end of Lecture 7. No doubt I will get to these item in the next couple of Blogs, but I felt it was more important to put forth some basic language that I will try to use consistently for the next couple of weeks. I will continue to use phrases like "IN THERE," "OUT THERE," and "DURING THERE" until you can comfortably go back and forth between these phrases and their more scientific/technical equivalents.

In the meantime, I highly recommend you take a break from your studying, go to the movies, and get to know something that requires a different type of glasses...some non-Darwinian glasses...in other words, a pair of (3D) glasses that can help you see what is "UP" there.

Meiosis & Variability

If you're preparing for BS110 Exam 1, then you should NOT start your preparation tonight with this Blog entry...instead, you should head straight to the Lecture 5 Blog ("Why Can't We Be Friends?...Meiosis & Punnett Squares finally shake hands"), which will eventually bring you back to this (more recent) post--by way of a link in the text--at precisely the right moment. So go there now...

If you're reading on, then you're right in the middle of reading the Lecture 5 Blog and you followed the proper link. Congratulations, either I haven't bored you to death or you'll do just about anything to do well on Exam 1! In that case...the text below is a short diversion from the Lecture 5 Blog designed especially for you...

You have been told in that post, and also in a previous post ("Learning the Language of Variation") that meiosis and variation have some intimate connections. Given all the time I've put into the Lecture 5 Blog today, I can't afford to go in much detail about meiosis and variation above and beyond what I've already included in the aforementioned posts. However, I do think it is worthwhile to point out a couple of things to help you better prepare for the exam when it comes to meiosis and variation. I will do this mainly through a couple of images presented to you in class by Professor S.

A Blend of Images Lectures 4 & 5...

On the left is one of the main images that I built my Lecture 5 Blog around. It was also used by Professor S in Lecture 3. Let me be clear about this: This image shows one version of meiosis.

Brett, what do you mean it shows "one version of meiosis?"

Well, it turns out that in Lecture 4 Professor S showed you another version of meiosis. The slide that he used to show you another version of meiosis is shown below on the right. I hope you are able to see it in the image, but take special care to notice that the bottom row of gametes in both of the images are similar and different.

On the one hand, they both show 4 gametes each with a single chromosome inside each gamete--this makes sense because they are both representations of meiosis. On the other hand, look specifically at the colors of the chromosomes in each of the gametes. In the first image (above left), there are 2 gametes with entirely blue chromosomes and 2 gametes with entirely red ones. In the second image (below right), there is 1 gamete with an entirely blue chromosome, 1 gamete with an entirely red chromosome, and then 2 gametes (the middle two gametes) with chromosomes that have both red and blue color in them!

If we could put this in more scientific terms, we could say that the gametes produced by the first version of meiosis (above left) have less genetic variation than the gametes produced by the second version of meiosis (at right). How many types of gametes are produced by the first version of meiosis (answer = two types, red and blue). How many types of gametes are produced by the second version of meiosis (answer = three types! red, blue, red/blue mix #1, and red/blue mix #2).

How is this different combination of colored chromosomes (i.e., this genetic variation) possible given the fact that the original parent cell was exactly the same? (If the image on the right showed the original parent cell it would be the same as the one shown in the image on the left--trust me on this one.)

The answer to that perplexing question was presented to you mainly in Lecture 4 by Professor S. That day, he showed you some slides that had terms such as synapsis, chiasmata, crossing over, meiosis I, metaphase I, and independent assortment. Do you remember these slides? I hope so, but if not you can look up these terms/concepts in your textbook. These are the terms that Professor S used to explain to you how there can be increased variation in gametes as a result of meiosis.

Look closely at the right-hand slide up above. Do you see how down the right-hand side of that slide Professor's S was writing the names of the different phases of meiosis I and meiosis II? These are indications of the exact stages in which increased genetic variation is occurring. Another slide he used that day (shown below at left) illustrates something called independent assortment.

There are no stages or phases or meiosis written on this slide, but maybe that is something that you can do now that you know that this process can also lead to increased genetic variation in gametes.

Anyhow, this little diversion from the Lecture 5 Blog ("Why Can't We Be Friends?...Meiosis & Punnett Squares finally shake hands") was necessary to try to tie together some additional images that will be important for exam 1. Now, you should go back to the Lecture 5 Blog and continue seeing if and how Punnett Squares & meiosis will finally shake hands...