Here is the transcript of the first lecture in all its glory.

Transcript of 8/21/2006

DOYLE:

Morning folks! How’re you all doing?

[couple minutes of silence, syllabi handed out]

So, has everybody got a syllabus?

I’m Jim Doyle – I’m the instructor. Summer’s over.

[nervous laughter]

Another minute or so. I guess we’ll use that clock. They all disagree around here.

Ummm – alright! Let’s see, I’m the instructor. It’s got my work phone, home phone, and email address. Lecture is Monday, Wednesday, Friday, here. Lab – you’re either in a Wednesday lab or a Friday lab – don’t look and think, “Oh my goodness, there are two labs.” Office hours are there but other days and times – by appointment. So, I have office hours – just a short time after today and I can pretty much arrange it – well, Wednesday, of course, and Friday are tight, but after-labs always work fine. Description: We’re gonna overview organismal and higher-level – we’re gonna spend most of the time looking at the diversity of organisms – all the different organisms, characteristics, classifications, life cycles. The text is the same one as – you took 181 here – it’s the same text folks used in 181. Lab manual is the same one – most of you should have that and there is a photo atlas you definitely want to get if you did not have for 181 – that’s listed in there. Grading’s based on the number of points. I do put some extra credit on exams but other than that there is no extra credit, so if you’re struggling, don’t come and say, “Is there something I can do for extra credit?” The exam’s different than probably most of the other lab courses you’ve had in that the exams will be a combination of lab and lecture material instead of having a separate lab exam, lab material will be on the exams – each of the exams, and as we go through it, you’ll see what I mean – you’ll have an idea. Variety of types of questions: 5 exams, 100 points each – 10 lab quizzes and labs – total points possible are 600. Grading scale: approximately a standard scale. Policy for missed exams: please don’t. But if you do, notify me as soon as possible. What I do for a missed exam is – there is a comprehensive final at the end of the semester for anyone who’s missed an exam. Otherwise, our last exam is just a regular exam – not comprehensive. The only exception on a missed exam is if somebody comes to me well ahead of time and there’s – something’s going on and they have to miss an exam. Give me at least two weeks notice and they take the exam before the scheduled time – I want you to take that exam otherwise you’ll have to do the comprehensive final. Lab quizzes: no make-ups. Withdraw: if you withdraw I want you to note the deadline: October 6th – that is the deadline for student-initiated withdrawal which means you don’t need my signature – you just withdraw. After that date, you need my signature, and after that date, whether you get a W – withdraw passing or a Y – withdraw failing depends on your grade at the time. If you are struggling, be sure to check with me beforehand. I don’t give any incompletes. Attendance: you’re supposed to be here – be on time. Note: in this class, you may be dropped if you miss or are late for more than 4 lectures or more than 2 labs – that’s over one week’s worth of material. If you miss a lecture, get class notes from someone. If you miss a lab, there’s no make-up on that the way the labs are set up. Depending on the situation, and I don’t know how the numbers are gonna fall out on the labs, but if I have an extra space, say, in a Friday lab, if you miss Wednesday and check with me – Wednesday’s lab, you might be able to make it up on Friday if we do the same lab or if you were in Friday’s lab and know you have to miss that if you check with me and I have space you might be able to squeeze into the earlier lab so that’s a possibility but not preferred – normally, of course you go in your regular lab. Decorum: don’t use class period for conversation, passing notes, etc., this is college – not high school. Remember there are other students – show respect for everyone in class. Obviously, no headphones, cell-phones, beepers, pagers, anything. If you do need to leave the classroom during the class period and have to go to the bathroom or something, please leave out the back door – not the front so it doesn’t disrupt students, but if you leave, please don’t come back. I don’t want people leaving and coming back, leaving and coming back. So, if you have to leave for some reason, please do not return that period. Underneath there, you can write down names, phone numbers, email addresses – you don’t have to do this – it’s for your own benefit because if you don’t get someone’s name and maybe you miss a lab…and you if you don’t want to give out your phone number and email address, you don’t have to. Sometimes it’s helpful – you miss a lecture and then, “Gee, I wish I had a way to contact that person sitting next to me, I could probably get what I missed if there were notes” or whatever. Sometimes it’s helpful to have that. Tentative lecture schedule on the next page…is tentative…5 exams are listed there…lab schedule on the next page. On the last page, I have a student information sheet I’d like you to take a few minutes to fill out so I can learn a little bit about you.

….

[Explains how to get onto Blackboard]

….

What do we have on Blackboard? Well one of the sections is “Course Documents,” and if you click on that there will be material for “Exam 1,” “Exam 2,” “Exam 3,” and if you click on “Exam 1,” it will have all of the PowerPoint chapters and slides. You could print it out – it tends to use a lot of ink because there’s a black background, but there’s also an outline form of each chapter which has just the text. I would more than encourage you to print these out because if I put slides up, I’m not going to take time for people to write down what’s on the slides when you can print it out from Blackboard. So that’s available. For each of the exams there is also a study guide to help you – that’s worth printing out early, and as you go through each chapter, work through the questions. I think I also have sample questions for each exam either as part of the study guide or a separate file. You can access all of that. Another portion of Blackboard is the “Gradebook” and all your grades for your quizzes and all appear there. You can, at any time, check to see how you are doing or, you’ve forgotten what you got on the last exam or what you get on the quiz is all right there. Also, for the labs – later on we’ll be looking at a lot of different organisms and there are a lot of structures and general phyla (I think) you need to know – the photo atlas is a big help because there are photographs and structures identified, but also on Blackboard I put files under “Lab Review” or something that will have reviews of all the material you’re looking at as well, so that should be helpful. Any questions on that? I would encourage you to log in as soon as possible and start downloading those now. I will say that, when I went to put in all the files yesterday from previous semesters into this one, it said it did it, but when I checked it, it wasn’t there, so they’re looking into what went wrong. If you log in right now you might not find it. I’ll have that straightened out later today so don’t be concerned if you don’t see any of that right now. I should be there – it said it transferred it over, but I don’t see it. But it will be there – I would check tomorrow. I would suggest using the outline view, but some people prefer printing out all the slides – whatever your preference is. That doesn’t mean, “Don’t take notes – everything is on the PowerPoint slides.” It is not. I test on what I cover in class – there’s material in the text I will not talk about and you will not be tested on it. But, anything I cover in class is fair game, so a lot of times I’ll be talking about things – but don’t assume that just because I’m not writing on the board, “Oh, this isn’t important.” Really, everything that I’m covering is important, and it’s all fair game on the exam. You certainly want to be taking notes consistently and again, if you think, “I’ll just print out these online things – that’s all I need,” you will not do well on the exam. You’ll say, “I don’t know this stuff – there’s questions that weren’t on there,” and that’s because this is not the only material. Do you have any questions? Basically, anything that is said in class is fair game, but if you’re not sure, you can ask me.

STUDENT:

Do you give points for doing Blackboard?

DOYLE:

No.

STUDENT:

Is there information on Blackboard that you do not cover in here?

DOYLE:

In Blackboard, there are the PowerPoint slides that I made or modified, so usually we will go through everything in it. If there is a point were, “I don’t wanna talk about that,” then I’ll say it, you know, “Slide 23” or something. There are a few times where I’ll scratch out slides and that means that I will not ask you to study it. If somebody wants to tape the lecture, that’s fine. I don’t have a problem with that. Some people prefer to do that. Any other questions?

STUDENT:

Do we need to bring our book every day?

DOYLE:

I would say no. It’s extra weight. As a teacher it’s always nice, though, if someone has a book so I can show a diagram every now and again. But as a general rule, especially if you’re taking just one class then you’re leaving, you should probably bring it, but if you’d be lugging a bunch of books around all day, I’d leave it at home. But, absolutely you’ll need the lab book and photo atlas for labs. Anything else?

[STUDENT asks if he can use a completely different textbook. DOYLE responds, and then other STUDENT tells first STUDENT that he can check out the book at the learning center. Yawn]

Are we good? Let’s get started.

Starting on chapter 21: a little bit of population genetics. By the way, population refers to a group of individuals of the same species in a given area. Population does not include all the organisms – population is one species. And we’re going to be looking at gene flows and gene frequencies in a population and this photograph – this is a population of a lupine kind of flower, and you can see some of them have white flowers and some of them have purple. For a population geneticist, they were looking at this – what’s some of the questions you might ask if you were trying to make sense of this? You’ve got purple and white flowers – what might come to mind if…

STUDENT:

Hybrid… (mumbles)

DOYLE:

The genetics, right, just, basic genetics. Is it a dominant trait? Is it a recessive trait? Is it one gene? Is it more than one gene? Sometimes differences can be environmental. Maybe there’s not even a genetic component. Usually flower color, of course, is genetically based. Not always, flowers can start out at one color and as they get older and fade, their color changes. It could be simply development. What else might you think? This is a “why” question.

STUDENT:

Mutation?

DOYLE:

Yeah, if you’re looking at what caused it. Why is there both purple and white? Is there an advantage to having purple flowers? Is there an advantage to having white flowers? Why would a flower color have an advantage?

STUDENT:

Dominant and recessive.

DOYLE:

Dominant and recessive?

STUDENTS mumble.

DOYLE:

Dominant and recessive – we’re going to get to that. Let’s see, true or false: let’s say there are a lot more purple-flowered plants than white-flowered plants. Does that mean that purple is dominant?

STUDENT:

Not necessarily, it could have an advantage to the environment or predation.

DOYLE:

Think about it. Is the dominant the most abundant?

STUDENTS mumble.

DOYLE:

That’s one of the things we’re going to be talking about in this chapter. Different flower colors – what could be the advantage?

STUDENT:

Natural selection?

DOYLE:

For what…natural selection in flower color, why? Who’s selecting?

STUDENT:

Pollinators?

DOYLE:

Pollinators, right. First thing that would come to my mind in pollinators since they’re…does more than the color attract pollinators better? I might look at seed set. Do you get a lot more seeds on these that have purple flowers than those that have white? You might see a lot more bees on the purple ones than on the white or more on the white. I can look at “is there an advantage in natural selection?” I might also wonder, “Gee, if I came back in 10 years, would there be a greater percentage of white flowers or less? Are they becoming more abundant or less abundant over time?” Might be interesting following frequencies over time. Some of the things we’ve talked about are things you don’t see. That is – the genetics of it. Is there one gene, are there two alleles, which is dominant, which is recessive? Can we calculate, lets say, purple is dominant. If purple is dominant, true or false, if purple is dominant, all white-flowered forms are homozygous.

STUDENTS produce mixed guesses.

DOYLE:

Single gene. If purple flower is dominant, true or false, then all white-flowered forms are homozygous.

STUDENTS produce more mixed guesses.

DOYLE:

If purple is dominant, you can be homozygous purple or heterozygous purple. Little “p” is the recessive allele. These purple dominant would both be purple. The little “p” would be white, right? So, yeah, if purple is dominant, all white-flowered forms are homozygous recessive. I might wonder, “How many of the purple forms are heterozygous?” You can’t tell by looking at them. You can start with some questions to ponder or consider.

[talks with student]

Ah, questions to consider. What is genetic variation? What is its role in evolution? How do we measure it? We’re going to talk about the Hardy-Weinberg principle – how it’s calculated. How many of you discussed Hardy-Weinberg in 181?

STUDENTS mumble.

DOYLE:

We’re going to go into more detail in this class. What are the factors that would cause a population not to be in Hardy-Weinberg equilibrium? We’re going to explain what that means. What do we mean by survival of the fittest and how do we measure it? Different types of selection and a little bit about evolutionary potential. Genetic variation is the raw material of the evolution. Here is Darwin’s definition: evolution is descent with modification – modification of what?

STUDENTS mumble.

DOYLE:

The geneticists, population geneticists, would say that evolution is a change in allele frequencies over time. And we can see that with the change…if the little “p” allele became more abundant, you would have more white-flowered forms. White flowers…is that a phenotype or a genotype?

STUDENTS produce mixed guesses.

DOYLE:

Phenotype. Phenotype…white, purple. Genotype…pp, Pp, PP. Three genotypes, two phenotypes. Alleles are “P” and “p”. Since you have two of them you can have two bigs, two littles, or a big and a little. So geneticists would say that evolution is the change in allele frequencies over time. If we were to go back to that field in ten years, if the allele frequencies have changed, then the phenotypic frequencies would change. What percent of the individuals are purple? What percent are white? The current definition of evolution is actually pretty much the same as Charles Darwin said…change in allele frequencies over time. Important point – individuals do not evolve – populations do! Several years ago, I was hearing a report on smog in big cities and they were talking about the problems with animals in the zoo dealing with smog…difficulties and the announcer said, I don’t remember, maybe it was the New York zoo, that the gorillas were evolving longer nose hairs to deal with the smog. Is that a correct statement?

STUDENTS look at each other in silence.

DOYLE:

Let’s say they really are growing more nose hairs because of the smog. That’s adaptation. When you go out in the sun and tan, that’s adaptation. That doesn’t mean you evolved. Organisms have an amazing ability to adapt to an environment. So, individuals can adapt, and they have to have the genetics for adaptation. Right, they have to have the ability to grow more nose hairs or to tan or whatever. But that’s not evolution – evolution is the change in the allele frequencies over time – generation to generation which means that individuals can’t evolve. Your alleles – your genotype isn’t changing over time. We change over time. We grow taller…hopefully we get smarter. But that’s not evolution. But on natural selection, as we’ll see, when we raise the question of “why would these allele frequencies change over time?” oftentimes the immediate thought is “natural selection,” and natural selection is one mechanism, not the only one, for change in allele frequencies. We’ll see there are several others as well…it’s the one we tend to give a lot of attention to, but there are other reasons that you could go back to that field and find that the allele frequencies have changed. Natural selection is only one reason. Natural selection is not the same as evolution. Natural selection is a mechanism for evolution. It is a means by which allele frequencies can change. Not the only. Natural selection, I think you probably know the basics. Some individuals in a population possess certain inherited characteristics and play a role in producing more surviving offspring. If the purple-flowered form – certainly an inherited characteristic – if they produce more offspring, maybe because of pollination – pollinator preference or whatever, they produce more offspring the next generation, the next year we expect to see more purple-flowers percentage-wise. Population gradually includes more individuals with the advantageous characteristic. And although individuals don’t evolve – we don’t evolve, natural selection operates at the level of the individual. It’s not the population that is leaving more descendants, its individuals. It’s individuals with purple flowers producing more seeds – they leave more descendants. So, natural selection operates at the individual and it doesn’t operate on the genotype, it operates on the phenotype. PP, or Pp. If you have purple flowers, and there’s an advantage…more pollinators, then you’re going to have more pollinators either way whether you’re homozygous purple or heterozygous purple. The genotype isn’t what determines it, it’s the phenotype. If you have an advantageous condition – purple flowers vs. white…you can leave more offspring. So, it operates at the phenotype not the genotype. Oftentimes, we talk about one of the earlier views of evolution – Lamarck…by the way – Darwin did not come up with the idea of evolution. It’s been around really since the time of the Greeks. Darwin’s major contribution was the mechanism. He came up with the mechanism of natural selection. And there were earlier views of how evolution could have occurred. Darwin’s grandfather actually was a well-known biologist who wrote on evolution. Actually, Erasmus Darwin, his grandfather – he actually believed Lamarck’s views. Let’s compare the two of those. Classic case: how did giraffes develop long necks? Let’s start with the bottom one here which is Darwin’s theory of natural selection – the variation is inherited. What Darwin would have said is that there’s variation in neck length that went back millions of generations when giraffes had necks no different than any other mammal, but some of them had slightly longer necks than others just like people had slightly different heights than others. And, for various reasons, those that had longer necks were at an advantage. They’re out in the Serengeti Plain – there is a pronounced dry period, there are leaves on the trees but no vegetation down below. The giraffe with a slightly longer neck can get higher up; he is feeding when those with shorter necks aren’t. That giraffe is healthier. He/she is going to leave more offspring so that the next generation there are a greater proportion of giraffes with slightly longer necks and repeat that generation after generation. Over many generations, longer-necked individuals are more successful perhaps because they can feed on taller trees. And so that ability became the more fruitful, they produced more offspring and now we have long-necked giraffes. Lamarck’s view, the earlier view, was that the variation is acquired. The term we often use to associate with Lamarck is inheritance of acquired characteristics. Things that you acquire, according to Lamarck, you could pass on to your offspring. He doesn’t mean stuff. Let’s say you go to the gym and work out every day and you develop big muscles – Lamarck would say you can pass those muscles on to your offspring. You acquired that. How does this relate to the giraffe? Well there are the poor giraffes – there’s no vegetation, no food to eat and they are stretching their necks to get the last leaf they can reach and the process of stretching their necks leads to longer necks and then they pass that on to their offspring. Do you all see the difference between the two? The common view is closer to Lamarck – you develop something and then you can pass that on. By the way, cultural evolution is Lamarckian. That’s how cultures pass on – something is acquired – the ability to make air conditioners. I was reading in the paper yesterday that it was the hundredth anniversary of the air conditioner. Thank goodness for that. We acquired that knowledge and we can pass it on to the next generation. Our literature – our culture is Lamarckian. We acquire something and we can pass that down. But biological evolution is not. Cultural evolution is a lot faster than biological evolution. We can go back 50,000 years and there is very little genetic difference between you and individuals 50,000 years ago. But there is a whole lot of cultural difference. If you could resurrect someone from 50,000 years ago…if we could bring a baby born 50,000 years ago to today, there is not a lot of genetic evolution, but cultural evolution…there’s a lot. There are measuring rules of genetic variation. A number of populations would use things like blood groups. We can look at, for example, in humans, the A, B, O blood group – what percentage of the population is blood type A? What percent is B? Is that a phenotype or genotype?

STUDENTS produce mixed answers.

DOYLE:

If you have blood type A – is that your genotype of your phenotype?

STUDENTS produce mixed answers.

DOYLE:

It’s your phenotype. You might actually remember from 181 – you have 3 different alleles – not all genes have 2 alleles, this one has 3 alleles. How can we have 3 alleles if you’re diploid? You only have 2, right? How do we get 3? How do you get 3 alleles if you’re diploid?

STUDENT:

Incomplete dominance.

DOYLE:

Well it does have incomplete dominance, but why do we have 3 alleles when you only have 2?

STUDENT says something.

DOYLE:

Think of the individual and the population. In the population, there are 3 different alleles. The individual only has 2 of those alleles, but in the population, all 3 are present. What’s the blood type?

STUDENTS provide mixed responses.

DOYLE:

A. So A is a phenotype – there are 2 different genotypes that result in that. Blood types are phenotypes. Genotypes – if you’re blood type A, you could be homozygous or heterozygous. What you couldn’t be is heterozygous this way. What is that? AB. That’s co-dominance. Another thing we can look at for genetic variation is enzymes. When we start measuring genetic variation – how much genetic variation is there in humans? That’s what this question addresses – how do we put a number on the amount of genetic variation in a population? There are two measures. The first measure is polymorphism and that equals the percentage of genes for which there is more than one allele. In the population, is there more than one allele in the population? That’s polymorphism. Another way, a better measure in my opinion, is heterozygosity, and that is the average percentage of heterozygous individuals. Let’s throw some numbers in to see if we can make sense of that. It’ll take just a minute. There’s gene 1, 2, 3, 4, 5 – there’s 5 genes. When you run electrophoresis, and so we can see what percent of the individuals have 2 alleles that are the same, we’ll call ‘em Aa…how many are heterozygous? Let’s do some numbers…there are 20, 30, 60, 40, 100 individuals in all. Gene 2: we’ll say everybody is heterozygous. Gene 3, everybody is AA. Gene 4: 40, 40, 20, and 50, and 50. [STUDENT points out messed math, Doyle fixes it]. Polymorphism – is there more than one allele for gene 1? Yes or no.

STUDENTS:

Yes.

DOYLE:

Gene 2?

STUDENTS:

No.

DOYLE:

Yes, more than one allele, there are two alleles. There is a big “A and a little a”. There’s only one phenotype, but there’s more than one allele. Gene 3?

STUDENTS:

No.

DOYLE:

Gene 4?

STUDENTS:

Yes.

DOYLE:

Gene 5?

STUDENTS:

Yes.

DOYLE:

Polymorphism – 4 out of the 5…percent of the genes for which there is more than one allele…80%. That’s the polymorphism – I grabbed the population and tested 5 enzymes and found it to be 80% polymorphism. Heterozygosity: for gene 1, what is the percentage of heterozygous individuals?

STUDENTS produced mixed responses.

DOYLE:

There are 100 individuals. How many are heterozygous?

STUDENTS produce mixed responses.

DOYLE:

30 out of a hundred, 30%. Gene 2 – what’s the heterozygosity?

STUDENTS:

100%.

DOYLE:

100%, they’re all heterozygous. Gene 3?

STUDENTS:

0.

DOYLE:

0. Gene 4?

STUDENTS:

40.

DOYLE:

Gene 5?

STUDENTS:

0.

DOYLE:

0. Let’s see, if you average that, what do you get?

Let’s stop there.

 

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