Rebecca Irwin (rirwin@utm.edu) from 206.240.201.242 at 01/10/99 04:18PM
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Welcome to the archive of Organic Evolution (Biology 391) lab 53's discussions.
Rebecca Irwin (no email) from 206.240.201.242 at 01/22/99 02:49PM
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Welcome to lab. REMEMBER: CLICK YOUR RELOAD BUTTON frequently to see new comments. When you arrive, submit a comment; include your name and say hello -- otherwise you will be counted as absent. Once you've done that, to get the discussion started, submit a comment in which you either: 1. ask a question about something that wasn't clear in the paper by Gould on Nonoverlapping Magesteria or 2. explain what one of the following means: magisterium of science, magesterium of religion, NOMA.
Greg Tester (no email) from 192.239.150.77 at 01/22/99 02:51PM
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Hello
Rebecca I (no email) from 206.240.201.242 at 01/22/99 02:52PM
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Hi Greg. What did you think of the Gould paper?
Greg Tester (no email) from 192.239.150.77 at 01/22/99 02:53PM
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I had a question about number 4 in chapter 4 of the lab manual. I'm not real clear about what the question is asking. An example of what you are looking for would be very helpful.
kristi (no email) from paydial11.utm.edu at 01/22/99 02:53PM
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Hello, this is Kristi Wenz logging in.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 02:55PM
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Well, you know I never answer anything straight out, so
let's start from basics. First, this is the question you
mean, right? 4. Write a question about the origin of humans that, according to Gould and Pope John Paul II, would be appropriately answered in the magisterium of science, but not the magisterium of religion. Now write a question about the origin of humans that, according to Gould and Pope John Paul II, would be appropriately answered in the magisterium of religion, but not the magisterium of science.
So first, what's the magisterium of religion and what's the magisterium of science?
Greg (no email) from 192.239.150.77 at 01/22/99 02:55PM
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The Gould paper was very insightful. I had never before heard of the NOMA principle. I was raised in a christian home and often have questions how the two magesteria can exist together. The paper answered many of the questions about that aspect.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 02:56PM
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Hi Kristi. You can take a look at chapter 4, question 4, too.
It's a good place to start.
Greg (no email) from 192.239.150.77 at 01/22/99 02:56PM
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Yes, that is the question I had questions about.
kristi (no email) from paydial11.utm.edu at 01/22/99 02:58PM
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Kristi: This is my answer to what I think NOMA means: NOMA is the principle that
science and religion teachings don not overlap. It is the principle of teaching
authority that the net of science covers the empirical universe:
its origins and theories of how it works and that the net of religion extends over questions of moral
meaning and value does not overlap.
Rebecca i (no email) from 206.240.201.242 at 01/22/99 02:58PM
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I hadn't heard of NOMA before I read that paper either. I
had heard people discuss, rather vaguely, that evolution and
religion looked at two different aspects of life, or were
different ways of understanding life, but this seems to spell
it out better. Given that, how DOES it spell it out better?
What is appropriate to study in the magisterium of religion? What is appropriate
to study in the magisterium of science? This is what question 4 is getting at.
Greg (no email) from 192.239.150.77 at 01/22/99 02:59PM
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The magesteria of science is the teachings which involve the empirical universe, what it is made of and why does it work this way.
the magisterium of religion extends over questions of moral meaning and value.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:00PM
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OK, so if the magisterium of science extends over the empirical universe,
what can be answered about the origin of humans empirically?
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:02PM
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Kristi: good description of NOMA. When we say they don't
"overlap" just what does that mean? This is getting at
question 4 again -- what can we appropriately study within
science, and what can we appropriately study within religion?
Greg (no email) from 192.239.150.77 at 01/22/99 03:03PM
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Is the question getting at that in the magisterium of science the question would include evolution from a single type of organism into what we see today and that the earth began approximately 4.6 billion years ago.
In the magisterium of religion the question would involve creationism (in the beginning there was nothing and God created everything)
kristi (no email) from paydial11.utm.edu at 01/22/99 03:05PM
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could this be an example of a question of humans that could be appropriately
answered by the magisterium of science and not religion?
Since there is fossil evidence of evolution, is it not scientific proof
of the origins of human,etc.?
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:06PM
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Greg: certainly the scientific explanation is evolution. I
think Pope John Paul and certainly Gould would argue that the
mechanism of physical creation is more appropriately studied
with science, at least for the parts of it where we can make
observations. However, questions about morals or about aspects
of humans that must be taken on faith (a soul, an afterlife, for
example) would be addressed within the magesterium of religion.
Greg (no email) from 192.239.150.77 at 01/22/99 03:08PM
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So, a question answered by science would be the evolution of humans, where we come from and what we are made of. A question answered by religion would be what happens to our soul when we die, is there an afterlife, etc.
Rebecca i (no email) from 206.240.201.242 at 01/22/99 03:08PM
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Kristi: looks like you made the point I was trying to make
before I saw your comment :-) The one point I'd make on your
comment (since I'm picky about this -- take note, all) -- is that you use
the word "proof" and it's never possible to prove anything. Now, you
do say "scientific proof" which is a phrase used to mean "supported as
well as possible, scientifically" so really you're OK, as long as we all
know that "scientific proof" doesn't really mean that something is proven
beyond any doubt.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:12PM
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Greg: yes, those are appropriate questions for the two
magesteria -- again, the idea is it isn't appropriate to use
religion for the empirical realm and isn't appropriate to use
science for the realm of morals and faith. Since question 4
asked for questions about the ORIGIN of humans, within the
magesterium of religion you might ask where did the human soul
come from? I bring this up also because it's a point the popes make --
that it is appropriate to study the origin of the human body by studying
evolution as long as one has faith in a divine origin of the human soul.
The soul is of course something one can't study with science.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:14PM
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is question 4 OK now? If not, yell (via computer.) If so, let's look at
some of the other questions. Consider chapter 4 of the lab
manual questions 5 and 6 (pick whichever you like to start with): 5. In what major way does Pope John Paul II's 1996 statement with regard to evolution differ from Pope Pius XII's statement with regard to evolution?
6. What does Pope John Paul II (as cited by Gould) regard as a significant argument supporting the theory of evolution; how does this affect the main point he makes in his statement.
Greg (no email) from 192.239.150.77 at 01/22/99 03:15PM
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My next question comes from chapter 5 in the lab manual. Question number 12 which deals with salmon spawning. I understand what you are asking but do not fully understand the situation I'm trying to explain which come from the first two sentences in the question.
Greg (no email) from 192.239.150.77 at 01/22/99 03:17PM
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Let's come back to chapter 5. Chapter 4 question 5: Paul II's statement says additional data and theory have placed the factuality of evolution beyong reasonable doube while Pius XII says its possible but is potentially untrue.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:18PM
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OK Greg, so here's the question (just so I know we've all got it): 12. Salmon return from the ocean to the streams where they were spawned in order to reproduce. Suppose someone tells you that to ensure that salmon find each other so that the species will not die out. Clearly explain to this person why this argument does not make evolutionary sense. Give an argument based on natural selection that does make evolutionary sense.
The key to understanding why it doesn't make sense is in the phrase "to ensure that ... the species does not die out" Think
about how natural selection works. Is it working to ensure that the species does not die out?
Greg (no email) from 192.239.150.77 at 01/22/99 03:19PM
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I now understand what chapter 5 question 12 is asking.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:19PM
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As you're discovering, in this format we tend to get into several discussions at
the same time. It's OK to pick either one and go with it, or wait and get back to
one later. So, Greg, good explanation of the difference between Pope John Paul and
Pope Pius. Kristi, are you still there?
kristi (no email) from paydial11.utm.edu at 01/22/99 03:20PM
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Question 5: Pope Pius permits Catholics to entertain the evolution
of the human body, so long as they accept the divine Creation and
infusion of the soul. Pius proclaimed that evolution may be legitimate in theory,but had not been proven and could be wrong.
Pope John Paul defends the evidence of evolution and the theory's consistency
with Catholic teachings. Pope John Paul says that there has been too much growth of data
to doubt evolution.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:22PM
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Good Kristi, you've got the main distinction between what the
two popes said. OK, now how about question 6? Or, if you like,
look at the salmon question -- Greg, you say you now see what it's
asking. Can you answer it?
Greg (no email) from 192.239.150.77 at 01/22/99 03:24PM
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Natural selection is backward looking, not forward looking. The salmon do not have an insight into the future and do not act to ensure the continuation of the species.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:26PM
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Greg: right, natural selection is "backward looking" in that
the traits we see are what has evolved based on what had highest fitness
in past environments -- it can't look into the future. Can anyone think
of how based on past environments the rather strange reproductive behavior
of salmon could have evolved through natural selection?
Greg (no email) from 192.239.150.77 at 01/22/99 03:26PM
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Chapter 4 Question 6:
The theory has been progressively accepted by researchers, following a series of discoveries in various fields of knowledge. the convergence of the results of work that was conducted independently is in itself a significant argument in favor of the theory of evolution.
kristi (no email) from paydial11.utm.edu at 01/22/99 03:26PM
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I have a question in Chapter 5 ,As you can already tell I get confused with the way
some words and phrases in evolution ought to be said. Can you help with question
9?
Greg (no email) from 192.239.150.77 at 01/22/99 03:28PM
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If they were originally freshwater species, they may have evolved progressively towards being able to have a higher fitness in the marine environment. Due to the plethora of foraging opportunities in the marine environment the salmon were able to grow bigger and stronger quicker and therefore have a higher fitness but still had to return to freshwater to spawn.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:30PM
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Kristi: everyone has a hard time getting the wording right in
evolution -- even people who study it; I've been at conferences where
evolutionary biologists start to pick on each other for imprecise wording.
The problem is if you get the words a little off what you say can be interpreted
as meaning something totally wrong. So question nine is: 9. Why is it incorrect to say that a trait has evolved "for the good of a species" or "to help a species survive?"
and this is related to the question Greg asked (#12, on salmon.) Take a look at his answer
to that, see if that helps. Then see if you can explain or ask more about it in your own words.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:31PM
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Greg: good, this makes sense in terms of individual fitness and doesn't imply
anything that is forward looking or "for the good of the species."
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:33PM
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With regard to question 9, and question 12, it might also help to remember
explicitly how natural selection works -- the four conditions that must be
true (Darwin's four postulates) as you discussed in last week's homework.
Is there anything in there about "the good of the species?" For what (species, population, individual...)
ARE the traits that tend to evolve through natural selection "good"?
kristi (no email) from paydial11.utm.edu at 01/22/99 03:36PM
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Is it true that evolution does not help a species survive, but
a trait can help individual survival. Through natural selection,
evolution will occur on how well an individual reproduces and survives but not
on how a group does.
Greg (no email) from 192.239.150.77 at 01/22/99 03:36PM
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The traits that tend to evolve are good for the individual. They are usually a result of the environment which the parent lived in. A parent which had good traits for a certain environment would have a higher fitness and would have a higher fitness for that environment. It would be more likely to pass on those traits to its offspring and so long as that trait provided a higher fitness, it would tend to increase in occurence throughout the population over time.
Rebecca i (no email) from 206.240.201.242 at 01/22/99 03:38PM
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Right Kristi, natural selection occurs BECAUSE some individuals,
with some traits, survive and reproduce better than others, so those
traits get reproduced more and become common. So that traits that evolve
are, as you say, those that increase individuals survival and reproduction.
They may or may not help the group (population, species.) So we can't say
natural selection occurs "for the good of the species."
kristi (no email) from paydial11.utm.edu at 01/22/99 03:40PM
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No, traits that evolve through natural selection are not necessarily always good.
For example in the book it mentions about the cubs in the lion pride
being killed by another pride leader. It is "good" for the individual that did the killing but not for the species as a whole.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:40PM
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OK, it looks like we all got it at the same time (good explanation Greg; Kristi, read
Greg's explanation it may be clearer than mine.) Any other questions? If so, ask -- if not,
look at and try to answer Chapter V Question 2. Many biologists refer to amphibians as primitive vertebrates and mammals as advanced vertebrates. From an evolutionary point of view, what are problems with referring to these species as "primitive" and "advanced"? What differences between amphibians and mammals are they trying to describe with these terms, and what would be a more evolutionary accurate way of describing these differences?
Greg (no email) from 192.239.150.77 at 01/22/99 03:43PM
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The two groups are alive today so they are equally advanced. Neither is primitive as a species. They are trying to describe traits which evolved earlier in the time line and a more accurate way of stating it would be that amphibians evolved earlier in evolutionary history than did mammals and some of the amphibian's traits are more primitive but not the group as a whole.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:44PM
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Good example about lions, Kristi. Note that this would answer Chapter V Question 10
in the lab manual. I like the way you put quotes around "good." Evolutionarily (in
terms of natural selection) "good" means "increases survival and reproduction." It doesn't
have any moral value associated with it (we don't really like to think of killing cubs as
good) but then as we've discussed moral values fall within the magesterium of religion, not
science.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:45PM
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Good Greg. Kristi -- Greg had already asked a question regarding "primitive" and "advanced"
traits versus species; does the distinction make sense to you?
kristi (no email) from paydial11.utm.edu at 01/22/99 03:48PM
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Mammals and amphibians have both evolved form a common ancestor.
Both contain primitive and modern traits since they have been evolving for the same length of time.
Do you want examples of primitive and modern traits?
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:48PM
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Since we're just about out of time here let me also note that
the last lab section got into a long discussion of religion versus
evolution -- whether they conflict, whether the NOMA argument resolves
them -- we got through the basic points to the paper pretty quickly, but
do either of you have any other comments on this? Also, once I get them
archived (which I will do right after we're done) you might want to
look at lab 52's previous discussion of this, it was interesting.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:51PM
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Kristi: you don't have to give examples but we might consider some just to
illustrate the point. Mammals have some advanced traits -- skin specializations
such as fur, reproductive specializations to bear live young at an advanced stage
(this may be evolutionarily advanced but i can tell you it's really uncomfortable)
but have fairly primitive structure of the hind legs compared to frogs, one amphibian
group, that has advanced adaptations of the pelvic girdle and hind legs for jumping
even though it has primitive skin structure and reproduction.
Greg (no email) from 192.239.150.77 at 01/22/99 03:52PM
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To me NOMA is not a final solution to the problem which has been plaguing religion and science ever since the first evidence of evolution emerged but it does help clear up many misconceptions and the paper makes a good distinction between the magesteria of science and religion.
Rebecca I (no email) from 206.240.201.242 at 01/22/99 03:52PM
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Hey, the bell just rang so you're officially excused. I'll be here for a while
so if you have more questions feel free to ask.
kristi (no email) from paydial11.utm.edu at 01/22/99 03:55PM
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The paper is clear about defining NOMA to me. I also found it reassuring that
Pope John Paul even agrees with the factuality of evolution beyond
reasonable doubt.
Greg (no email) from 192.239.150.77 at 01/22/99 03:56PM
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Signing off.
Bye.
Rebecca Irwin (rirwin@utm.edu) from paydial09.utm.edu at 01/29/99 02:46PM
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Welcome to lab for week 3. REMEMBER to click RELOAD regularly to see what comments other people have. When you arrive, send a comment that says "hello" so we know you're here (otherwise you'll be marked absent.) If you've got questions to ask, you can start asking them now or at any time through the lab. To get the discussion started, I'd like everyone to take a look at Lab Manual Chapter VI Question 8. Start thinking about how to work this problem, what kind of problem it is, what the first steps are -- read through it carefully. Once I see people have arrived, I'm going to start asking the kinds of questions about this question that you should get into the habit of asking yourself whenever you see one of these problems.
Greg (no email) from 206.240.201.227 at 01/29/99 02:53PM
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Hello
Renee (no email) from crockett200.iswt.com at 01/29/99 02:54PM
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hello! Can anyone hear me? My comments are not showing up on my computer!!!!
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 02:55PM
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Hello Greg
Greg (no email) from 206.240.201.227 at 01/29/99 02:55PM
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Renee- I hear you
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 02:55PM
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Hi Renee. Your comment showed up on mine. Are you
getting this?
kristi (no email) from paydial12.utm.edu at 01/29/99 02:55PM
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Hello, everyone!
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 02:56PM
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Hi Kristi
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 02:59PM
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OK, here's a question, since no one's asking (but feel free to
ask other questions, too.) Look at the question I suggested,
question 8 in chapter VI. We're looking at two basic kinds
of models: Hardy-Weinberg Equilibrium and natural selection,
so these questions have to be about one of the other. Is this a natural selection or a Hardy-Weinberg Equilibrium problem; how can you tell? And what do natural selection and Hardy-Weinberg Equilibrium mean, anyway?
Renee (no email) from crockett200.iswt.com at 01/29/99 02:59PM
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Yes I can read your comments!!! Good! I was starting to get worried!
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:00PM
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Renee -- good, I was starting to get worried too!
Greg (no email) from 206.240.201.227 at 01/29/99 03:02PM
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This is a natural selection model because selection is occurring. dd is being selected against because the crayfish with this gene do not function as well in cold environments. In natural selection evolution is occurring and in the Hardy-Weinberg equilibrium there is no change in the population over time so evolution is not occurring.
Renee (no email) from crockett200.iswt.com at 01/29/99 03:02PM
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HW- you assume the pop is infinitely large
there is random mating
no mutations, no movement of individuals amoung pops, and no nat sel.
kristi (no email) from paydial12.utm.edu at 01/29/99 03:03PM
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This is a natural selection problem since individuals survive better and higher fitness than others.
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:03PM
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OK, Greg has the key thing to look for to tell if the
question is natural selection or H-W Eq. If you see differences
in fitness (survival, reproduction) as in this case in which dd
individuals do not survive as well, it's natural selection. H-W
Eq. assumes (among other things) equal survival and reproduction
of individuals of all gentoypes.
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:06PM
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Kristi -- good, you got the main point too. Renee: you've
got all the assumptions of H-W Eq. listed, that's good.
Note that our natural selection model assumes 4 of the same
things (the pop is infinitely large there is random mating no mutations, no
movement of individuals amoung pops) but there are differences in survival
for natural selection and that's what we've got here. OK, next question,
everyone: in all these questions there has to be information to get the
FREQUENCY of something -- alleles or genotypes. What information in this question allows you to determine the FREQUENCY of something at the outset? And what does frequency mean, anyway?
Greg (no email) from 206.240.201.227 at 01/29/99 03:10PM
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Frequency is the occurrence of something, how many times it happens or occurs. The question states that there are 10000 individuals 2000 of which are dd. This gives you a genotype frequency of .2, take the square root of that and you get the allele frequency. 1-allele frequency gives the frequency of the other allele
kristi (no email) from paydial12.utm.edu at 01/29/99 03:11PM
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First you must find the genotype freq of the zygote with the given information:
2000/10000 so the freq of dd=o.2 Take the square root to find the allele freq.:
which will be q^2=0.45
and 1-.45 gives you the allele freq of D=0.55
Since I have the allele frequencies of the zygotes I can solve the rest of the problems!
Renee (no email) from crockett200.iswt.com at 01/29/99 03:12PM
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My computer is slow and it is not printing some of my comments!!!
Is it absolute fitness?
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:13PM
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Greg -- good. Any other comments on frequency? Next question:
taking the square root of the frequency of dd to get the
frequency of d is applying the formula that the frequency of
dd is q^2 so to get the frequency of d, which is q, you take
the square root. This formula usually applies to HW Eq. In
THIS case it also applies to this problem, which is a natural
selection problem. This formula won't always apply to a natural
selection problem. How come it applies here? (it does, Greg
has the correct answer.)
kristi (no email) from paydial12.utm.edu at 01/29/99 03:15PM
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It is applied here because zygotes are in Hardy-Weinberg
proportions.
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:16PM
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Kristi -- great! To solve the rest you'll also need one
other thing, though -- relative fitnesses. Renee -- resubmit
your comments if they don't show up (it won't matter if we get them
twice.) Absolute fitness tells you the expected survival, reproduction,
of the different genotypes, not the amount of them (frequency) that there
are. Can you see Greg's and Kristi's comments on frequency?
Everyone -- how come we can take the square root here when we're not
in HW Eq?
Greg (no email) from 206.240.201.227 at 01/29/99 03:18PM
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At this point selection is not yet occurring so they are in equilibrium but once fitness takes place they will no longer be in equilibrium
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:19PM
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Kristi -- great. When natural selection is occurring, zygotes
are in the same proportions as for HW Eq (these are called the
Hardy-Weinberg proportions.) This is because the gametes,
with allele frequencies p and q, unite at random and this
random mating results in these proportions (p^2, 2pq, and q^2.)
This won't last through life, though, because some (in this case
DD and Dd) survive better than others. So to continue we'll need
relative fitness values, which measure how well they survive. Anyone
have these yet (I guess I'd better submit this comment and find out!)
kristi (no email) from paydial12.utm.edu at 01/29/99 03:19PM
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You have to take the square root to get the allele freq.that was present at the start of the next generation?
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:20PM
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Good Greg, you said it much more concisely than I did. Renee --
note Greg's comment on why zygotes are in HW proportions.
Now, what are the relative fitnesses of the three genotypes?
How do we get this information from what's given?
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:23PM
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Kristi -- you've already taken the square root and you
have the allele frequencies that are present in the zygotes;
these are the same as the allele frequencies that were
present in the gametes since there has been, so far, no
selection to change them. So these are your values for p and q (you
calculated them in one of your previous responses; they are correct, .55 and .45)
What information are you given
about fitness (how well DD, Dd, and dd survive)?
kristi (no email) from paydial12.utm.edu at 01/29/99 03:23PM
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relative fitness values are found by dividing each absolute fitness by the largest
absolute fitness of 3 so: wDD=1 and wDd is also 3/3=1 and
wdd- 2/3=.22
Greg (no email) from 206.240.201.227 at 01/29/99 03:23PM
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The relative fitnesses are DD=1, Dd=1, and dd=.22
the max is 3 and for DD and Dd which both have an absolute fitness of 3, 3/3=1. The absolute fitness of dd=.67, that divided by the max (3)=.67/3=.22
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:24PM
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Renee -- are you still there? Is your computer OK?
Renee (no email) from crockett200.iswt.com at 01/29/99 03:24PM
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Would it be DD=1 Dd=1 and dd= 2/3???
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:26PM
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Kristi and Greg -- good, you have the relative fitnesses now.
To get to the adult stage, what is the next step? There's something
we always have to calculate for these natural selection questions --
what is it? NOTE also that now that you have relative fitnesses
(wDD, wDd, and wdd) and allele frequencies (p and q) that you have
the same basic information that you had for the natural selection problem you worked
for homework. So you can do the same basic steps.
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:28PM
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Renee -- you are right for DD and Dd -- wDD= 1 and wDd=1.
To get wdd you take the absolute fitness (2/3) and divide by
the highest absolute fitness for any genotype, which in this
case is 3 since both DD and Dd have an absolute fitness of 3.
So you divide (2/3)/3 which gives you 2/9, or 0.22
Renee (no email) from crockett200.iswt.com at 01/29/99 03:28PM
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Would we calculate wbar?
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:30PM
comment
Renee: YES, we would calculate wbar. That's always the
next step to get beyond the gamete or zygote stage of a
generation. How do we calculate that?
kristi (no email) from paydial12.utm.edu at 01/29/99 03:31PM
comment
Now you must find the average fitness of the population
wbar=p^2wDD+2pqwDd+Q^2(wdd)
Greg (no email) from 206.240.201.227 at 01/29/99 03:32PM
comment
To get to the adult stage you take allele frequencies and plug them into p2 2pq and q2. which will give DD, Dd and dd respectively. these would be .3, .5, and .2. Then relative fitness takes effect, DD and Dd will not change but there will be fewer proportion of dd. This is gotten by multiplying relative fitness and genotype frequency.
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:32PM
comment
Kristi -- good, that's the formula. Now, can you plug
in the numbers? Everyone -- what value do you get for
wbar?
Renee (no email) from crockett200.iswt.com at 01/29/99 03:32PM
comment
wbar=p^2wDD+2pqwDd+q^2wdd
kristi (no email) from paydial12.utm.edu at 01/29/99 03:33PM
comment
the value for wbar is 0.84
Greg (no email) from 206.240.201.227 at 01/29/99 03:34PM
comment
I get .84 for wbar
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:34PM
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Greg -- to combine your information with Kristi and Renee's:
you need to multiply the values of p^2, 2pq, and q^2 (.3, .5, and .2,
respectively) by the fitness values, as you say, AND you need to
divide each by wbar, the average population fitness which indicates
how well the whole population has survived.
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:35PM
comment
I get .84 for wbar, too. Now, to continue through the
generation, how do we get adult genotype frequencies, and
what are the values?
Renee (no email) from crockett200.iswt.com at 01/29/99 03:35PM
comment
wbar=.84
Renee (no email) from crockett200.iswt.com at 01/29/99 03:38PM
comment
fitness/wbar
Greg (no email) from 206.240.201.227 at 01/29/99 03:39PM
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Adult genotype frequencies are gotten by by multiplying the relative fitness and gamete frequency, DD=.3, Dd=.5 and dd=.04
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:41PM
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Renee: not just fitness/wbar, but fitness*initial frequency/wbar.
That is, for ex, the adult genotype frequency of DD=wDD*p^2/wbar
kristi (no email) from paydial12.utm.edu at 01/29/99 03:41PM
comment
To get adult genotype frequencies take the part of the average fitness that represents each
genotype and divide by the average fitness
Freq(D)= p'=(p^2wDD + pqwDd/wbar
so plug those in and the answer should be 0.65
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:43PM
comment
Greg: you're forgetting to divide by wbar. Note that
the three numbers you have, .3, .5. and .04, do NOT add up
to 1. But genotype frequencies have to add up to 1. If you
add them up, you'll discover that they add up to .84, which
remember is wbar. By dividing by .84 (wbar) you will get
the genotype frequencies, and they'll add up to 1.
Greg (no email) from 206.240.201.227 at 01/29/99 03:44PM
comment
I forgot to divide by wbar so the answer should be DD=.36, Dd=.60 and dd=.05
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:46PM
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Kristi: the first part of your answer is a good explanation
for how to get the adult genotype frequencies. In the
second part you're skipping ahead to the actual answer to
part (c) of the question, the frequency of D in the gametes
that start the next generation. That's fine. To show
an intermediate step, I'd also like people to calculate the
adult genotype frequencies. Then we'll use those to get
the allele frequency and show you get the same thing using
the method you did.
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:48PM
comment
Greg: good, those are the adult genotype frequencies. Kristi
has used one formula for getting to the allele frequency of
D that starts the next generation. Can you (all of you) use
the adult genotype frequencies as calculated by Greg and get
to the frequency of D that starts the next generation? This is what
you would have to do if I gave you a question in which I gave you
adult genotype frequencies (there ARE questions like this -- question 6 in
the lab manual ch. VI is an example -- so it's something you
need to be able to do.)
Greg (no email) from 206.240.201.227 at 01/29/99 03:50PM
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Once you have genotype frequencies you can find allele frequency by adding DD+1/2Dd to get D, then 1-D to get d, D=.65, and d=.35
kristi (no email) from paydial12.utm.edu at 01/29/99 03:50PM
comment
Okay, here are my frequencies for DD=.36 Dd=.59 dd=.05
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:51PM
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Some final comments since we're almost out of time: NOTE that
these natural selection problems can start in any of three different
stages of the life -- gametes, zygotes, or adults. Your homework
question started with gametes, the question we've been working started
with zygotes, question 6 (which you should try at some point to
make sure you can do that kind) starts with adults. So that's an
important thing to look at. Also note that you're going to be starting
a computer assignment next week that continues with these models but
looks at them long term. The information to get started is on the web
and in the lab manual -- I recommend you start looking at it.
I'll stick around for a while if you have further questions but I suspect the
bell is ringing as I type. See you -- thanks for working these
well!
Renee (no email) from crockett200.iswt.com at 01/29/99 03:51PM
comment
Is it .35???
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:53PM
comment
Greg and Kristi -- good. Note that Greg's answer for
the frequency of D is the same as what Kristi got earlier using
the other formula (it had better be, since the formula Kristi used
is what you get when you apply the formula Greg used to the general
case.) Good job, you made it through the question.
Greg (no email) from 206.240.201.227 at 01/29/99 03:53PM
comment
Bye, see you next week.
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:53PM
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Renee: the frequency of d is .35, the frequency of D is .65.
kristi (no email) from paydial12.utm.edu at 01/29/99 03:54PM
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Goodbye,everyone!!
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:55PM
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Oh, Renee, the genotype frequency of DD also comes out to
about .35. Which were you asking?
Renee (no email) from crockett200.iswt.com at 01/29/99 03:56PM
comment
OK, I see, you got that by using p+q=1. Right?
In regards to my homework, I took the sq rt when I had adults in nat sel. could i have done that for HW Eq or would it still be the same?
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 03:58PM
comment
Renee: when you have a natural selection problem and have
adults, it does NOT work to take the square root -- you
have to do what Greg did: Freq(D)=Freq(DD)+(1/2)Freq(Dd).
This is because you're not in HW Eq. If you WERE in HW
Eq. then you COULD take the square root (does this make
sense?)
Renee (no email) from crockett200.iswt.com at 01/29/99 04:01PM
comment
Yes it does. That is how i got the final answer, except I was not specific in saying D=something and d=something else.
Rebecca I (no email) from paydial09.utm.edu at 01/29/99 04:03PM
comment
Renee: Good job.
Renee (no email) from crockett200.iswt.com at 01/29/99 04:05PM
comment
Thanks for your help. I am going to have to do some extra work this week end. I am afraid i am getting confused on some things. I will probably meet w/ you on one of your office hours.
Have a nice weekend!!!!
Renee (no email) from crockett200.iswt.com at 01/29/99 04:05PM
comment
Thanks for your help. I am going to have to do some extra work this week end. I am afraid i am getting confused on some things. I will probably meet w/ you on one of your office hours.
Have a nice weekend!!!!
Rebecca I (rirwin@utm.edu) from paydial10.utm.edu at 02/05/99 02:50PM
comment
Welcome to lab, 5 February 1999. SOME IMPORTANT ANNOUNCEMENTS:
REMINDER: you should be working on Computer Assignment 1; it is due
Weds. 8 Feb (next weds) to the Biology Dept. Office by 5:00 p.m.
Instructions are linked to the lecture web page under this week's
lectures; more complete instructions are in your lab manual.
REMEMBER that the first exam is a week from Monday. I will
not be available much (if any) next week (if I don't go into labor
on my own this weekend the doctor's going to induce me on Monday.)
If you have questions please talk to Dr. Buschhaus. Her office hours
are posted outside her office in Brehm Hall; in addition, she is available
during the official lecture times for this course, MW 2-3. FOR TODAY'S
LAB: First, in your "hello" message, send me a defintion of gene flow,
genetic drift, or local adaptation -- these are the three main concepts
for today. Next, I asked (on the web) people to prepare one of three
questions for discussion today: Chapter VIII 4, 12, or 13. Start looking
at those. Once I see you're here, and have good definitions, I'll start
asking questions about them.
James Tolene (no email) from 206.240.200.156 at 02/05/99 02:55PM
comment
Gene flow - the movement of alleles from one population to another population, typically via the movement of individuals or via the transport of gametes by wind water or pollenators.
Greg Tester (no email) from 206.240.201.227 at 02/05/99 02:55PM
comment
Hello, gene flow is the random loss in variation of genes over time, genetic drift if individuals from one population, migrating and breeding in another population, and local adaptation is when a population adapts, through natural selection, to have a higher fitness under the current conditions.
Greg (no email) from 206.240.201.227 at 02/05/99 02:55PM
comment
Sorry, I switched gene flow and genetic drift.
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 02:56PM
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James, nice definition of gene flow -- good inclusion of
the ways alleles can get moved from population to population.
James T (no email) from 206.240.200.156 at 02/05/99 02:56PM
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I can't take personal credit for it or that would be plagerism
Greg (no email) from 206.240.201.227 at 02/05/99 02:57PM
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You're a funny guy James!
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 02:57PM
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Greg: good definitions (once you un-switched gene flow
and genetic drift.) Everyone: accidentally switching gene
flow and genetic drift is one of the most commonly made
mistakes; take note and be careful.
kristi (no email) from paydial02.utm.edu at 02/05/99 02:58PM
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Hello, here are my definitions:
gene flow is evolution that occurs because individuals move among populations.
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 02:59PM
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I did notice a certain familiar ring to James' definition.
Fortunately, it's generally acceptable to memorize and
repeat definitions in this context -- otherwise we'd all
be arrested for plagiarism.
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:00PM
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Hi Kristi, good definition
Renee (no email) from 199.78.37.226 at 02/05/99 03:00PM
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I'm here!!
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:04PM
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Now, everyone, I can't remember what groups you're all in.
I assigned groups 1 and 4 to look at question 4, groups 2 and 5
to look at question 12, and group 3 to look at question 13 (all
from lab manual Chapter VIII.) We'll try to look at
these today and, if we have time, we'll also look at Ch. VIII
question 10. NOTE if we DON'T get to qu. 10 (the other sections
didn't) that you should look it over and ask about it if you have
questions (I'll post answers after lab, too.) So, take a look at
your assigned question (4, 12, or 13.) Each of these is about a study
that looks at genetic drift and/or gene flow (and also in some natural
selection.) For your assigned study, what is the hypothesis being
tested? (identify which study you're talking about when you answer.)
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:05PM
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Hi Renee
Greg (no email) from 206.240.201.227 at 02/05/99 03:06PM
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Question 4
Buri was testing whether eye color in the fruit fly (Drosophila melanogaster) was related to natural selection or genetic drift. In natural selection the same eye color would likely become fixed in all populations while if genetic drift was occurring a certain eye color would become fixed in about half the populations and lost in about half the populations
James (no email) from 206.240.200.156 at 02/05/99 03:09PM
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I did the banded water snakes in Lake Erie. The hypothesis that they had was that migration tended to homogenize populations.
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:09PM
comment
Greg has a nice summary of Buri's experiment. Note that
what Buri did was to look at a lot of lab populations of
fruit fly; in each he started with half with one allele for
eye color and half with a different allele for eye color.
So the two hypotheses he tested, as indicated in Greg's
explanation, are:(1) eye color evolves through natural selection, or
(2) eye color evolves through genetic drift. Greg's got the predictions
of each of these. Now, WHY would natural selection predict the same
allele fixed in all popualtions, and WHY would genetic drift predict
half the pops to have one allele fixed and half the other allele?
kristi (no email) from paydial02.utm.edu at 02/05/99 03:11PM
comment
Here is my answer to #12 - The island would consist of unbanded and banded snakes even if natural selection favors the unbanded snakes on the island. This is because in every generation several
banded snakes move from the mainland to the islands and interbreed with the island snakes;
and the ratio of unbanded and banded snakes would be the same on the island and the mainland.
Here is the answer to the rest of the question but i'm not too sure about it:
If gene flow was the only type of evolution occurring then the populations will become more similar to each other. Since most of the mainland's snakes
are banded,gene flow occurring from the mainland to the island
will cause the populations to become more genetically similar. The more gene flow occurs, over time the two populations will become genetically just
like each other,having the banded pattern as opposed to the unbanded.
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:11PM
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James -- since Greg's message got in just before yours,
let's look at qu 4 first, just to maintain a sort of coherent
discussion (hard in this format!). Then we'll get to the banded
water snakes next (you've got a good place to start from.)
Renee (no email) from 199.78.37.226 at 02/05/99 03:11PM
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Buri is performing and exp. on eye color in fruit flies. He is checking to see if the eye color occurs through genetic drift. He is also checking on the evolution of the eye color through nat. sel.
Greg (no email) from 206.240.201.227 at 02/05/99 03:12PM
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If natural selection was occurring the individuals with a certain eye color would have a higher fitness and would more likely survive and reproduce, thus increasing the chance that the next generation would have more of the eye color with the higher fitness. If genetic drift were occurring the allele would be lost at random. This randomness would cause one eye color to become fixed about half the time and lost the other half.
James (no email) from 206.240.200.156 at 02/05/99 03:14PM
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Doesn't natural selection make the trait with the greatest fitness survive while genetic drift just loses genes randomly. Meaning that natural selection is directional (toward the one with the greatest fitness)in what genes are selected while gene flow one is random. This only works in small pops. and when there isn't gene flow right?
kristi (no email) from paydial02.utm.edu at 02/05/99 03:14PM
comment
sorry about putting my answer in too soon!!
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:14PM
comment
Kristi, that's generally very good. We'll come back to it --
for now let's all look at qu 4, then we'll get back to you and James
on question 12. Greg and Renee have both identified the hypotheses
being tested in question 4. Greg has the predictions. What I want to
know now (and probably someone's writing the answer as I type here)
is why the different forms of evolution predict different things.
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:15PM
comment
Kristi -- that's no problem! I know while you're typing an
answer you can't see what the rest of us are saying! We
all have this problem with this format, don't worry about
it. I'm just trying to see what I can do to make these a
LITTLE more coherent.
Renee (no email) from 199.78.37.226 at 02/05/99 03:18PM
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In nat sel, the gene with the greatest fitness will survive and be passed on to the offspring. I have a hard time understanding genetic drift. I am unsure on it.
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:19PM
comment
James and Greg -- you've got the basic idea. Natural selection
would results in the same allele becoming fixed in all populations because
one allele has highest fitness so it becomes most common; genetic drift
is random. James, I think you said gene flow for genetic drift (I guess
everyone's making that mistake today.) In response to your last question,
we'd only expect to see strong effects of genetic drift in small populations,
so that's where we'd look for it; it occurs in large populations but the
effect is really small. We do see less impact of genetic drift if gene flow
is also occurring since gene flow tends to add genetic variation back into
populations, while through drift it is lost.
James (no email) from 206.240.200.156 at 02/05/99 03:20PM
comment
oops my bad.
Renee (no email) from 199.78.37.226 at 02/05/99 03:21PM
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Am I understanding you when you say genetic drift is random. Does that mean no specific allele is dominant over another?
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:22PM
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Renee -- good explanation for natural selection. For genetic drift,
changes are occurring at random. Sometimes an allele happens by chance
to get reproduced more, other times an allele happens to get reproduced
a little less. It's hard to understand because there's no obvious cause,
unlike the other forms of evolution. It's something that just occurs at
random. Because it's random, we'd expect sometimes one eye color allele
would happen to be fixed and other times the other would; on average, if
we look at a lot of populations (as Buri did) we'd see that half the time
by chance one allele would be fixed and the other half the time by chance
the other allele would be fixed.
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:24PM
comment
Renee -- random here means alleles are changing by chance
not because one has higher fitness than the other. Be
careful of the word "dominant" -- that, genetically, means
expressed in the heterozygote (as opposed to recessive) --
and genetically whether alleles are dominant or recessive
doesn't affect how they evolve through genetic drift. That
is an allele could become more common by chance (through drift)
whether it is dominant or recessive.
kristi (no email) from paydial02.utm.edu at 02/05/99 03:26PM
comment
is it true that when we talk about any form of evolution that we
should not mention dominant or recessive alleles?
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:31PM
comment
Buri's experiment is a nice example of the scientific method--
there are two clear hypotheses (genetic drift vs. natural selection),
different predictions for each, and his results clearly support genetic drift
since the populations had pretty close to half of them with one eye color
allele fixed and half with the other color. If there are further questions on
this, keep asking, but let's take a look now at Question 12 and what Kristi and
James said a while back. First, note the situation: there are populations of water snakes
on the mainland and on islands. Snakes can be banded or unbanded in color. On the
islands, they found that unbanded snakes survive better than banded snakes. Now look at
what James and Kristi wrote, and at the question. James -- what form of evolution
(natural selection, gene flow, or genetic drift) are you using in your hypothesis? Kristi,
clarify what is different if both natural selection and gene flow are occurring versus if
just gene flow is occurring. You're on the right track in your answer, just make it
a little clearer what the difference is between the two outcomes you discuss.
James (no email) from 206.240.200.156 at 02/05/99 03:32PM
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Gene Flow
James (no email) from 206.240.200.156 at 02/05/99 03:33PM
comment
And Natural Selection (got alittle quick on the enter button)
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:35PM
comment
Kristi -- we can talk about dominant and recessive alleles;
in fact, in the computer assignment that's due WEDNESDAY (another
reminder!) you will look explicitly at how natural selection occurs
when dominant alleles are favored vs. recessive alleles. The problem
is that a common mistake is to say "dominant" when we mean either "more
common" or "higher fitness." So the point is to keep the three concepts
separate. "Dominant" is a genetic term that means that if this allele
is present in an individual it will be expressed (for ex. even though I know
I have an allele for blue eye color because my father has blue eyes it does
not show because I also have the allele for brown eye color and that is
dominant.) "More common" or "in higher frequency" means in a populations, there
are more of this allele than of other alleles. "Higher fitness" means individuals
with this allele, or genotype, survive and reproduce better. Probably
mixing up the use of these words is the other most common mistake (in addition to
mixing up gene flow and genetic drift.) So if we discuss all the mistakes today none
of you will make them on the test, right?
James (no email) from 206.240.200.156 at 02/05/99 03:36PM
comment
Natural selections works toward the two pops. diffrent, gene flow is working toward making them homogenous.
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:37PM
comment
James -- gene flow is what you're talking about when you
talk about migration having a homogenizing effect. Natural
selection is the other form of evolution they discuss -- the
other hypothesis. How does natural selection affect these
snakes?
Greg (no email) from 206.240.201.227 at 02/05/99 03:37PM
comment
Of course we won't make them on the test, we were just testing you anyway.
James (no email) from 206.240.200.156 at 02/05/99 03:38PM
comment
Natural selection works toward making. Disregard the first part.
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:38PM
comment
Good James, you're answering my questions before I ask them.
Everyone -- why does natural selection make populations different
and gene flow make them like each other?
kristi (no email) from paydial02.utm.edu at 02/05/99 03:39PM
comment
thankyou for clearing that up for me!!!
James (no email) from 206.240.200.156 at 02/05/99 03:40PM
comment
Natural selection favors the unbanded snake on the island, banded on the mainland.
Greg (no email) from 206.240.201.227 at 02/05/99 03:40PM
comment
Natural selection tends to make populations adapt to their local environments so populations which were spread would adapt and become less like the other populations. Gene flow makes them more similar because individuals from other populations are breeding in populations other than the ones in which they were born which adds variation in that population but decreases variation among different populations.
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:41PM
comment
Greg -- I'm glad to hear it. I'm not sure I'm passing any
tests today though (I will quite happily blame this on my
current peculiar physiological condition, and on associated
sleep deprivation, but I'm told I have to learn to function
with serious sleep deprivation very soon anyway so I have to stop
using that as an excuse.)
James (no email) from 206.240.200.156 at 02/05/99 03:44PM
comment
Having Animal Ecology makes this alot easier to get, doesn't it Greg?
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:44PM
comment
Greg -- good explanation (everyone, read Greg's explanation.)
James, right, natural selection favors unbanded snakes on the
island, banded on the mainland, and that's why the populations
are predicted to become different through natural selection in this
example. Now, what was actually observed in these snakes? Were the
populations different? Were all island snakes unbanded? How is it
explained in terms of gene flow and natural selection?
Renee (no email) from 199.78.37.226 at 02/05/99 03:45PM
comment
Nat sel would be different because the pop would eventually express a trait that has been passed through offspring that may not be present in the same species in a different area.
Greg (no email) from 206.240.201.227 at 02/05/99 03:46PM
comment
James-Yes having animal ecology makes this class much easier.
kristi (no email) from paydial02.utm.edu at 02/05/99 03:47PM
comment
gene flow makes populations genetically similar to each other because alleles that occur in one population
will also occur in the other population once they are introduced. over time as more gene flow occurs the populations become more similar.
natural selction makes populations genetically different from each other because different populations
are occurring in different environments, so traits having the highest fitness in one population
will be different from the traits that have highest fitness in the other population, both populations having evolved through natural selection.
James (no email) from 206.240.200.156 at 02/05/99 03:48PM
comment
The populations were diffrent, however because of gene flow there were some banded snakes on the island. However the were virtually no unbanded oon the mainland. Gene flow from the mainland pop. was much greater to the island than vice-versa because of relitive pop. size explaining the difference.
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:48PM
comment
Renee -- and the reason it would be different in different
populations, as noted by James and Greg (who have, as noted
heard all this from me in Animal Ecology -- I HOPE it helps)
is that in some populations one trait would have high fitness
(survive, reproduce better) and in other populations a different
trait would have high fitness (survive, reproduce better.) in
this case, as noted, it turns out that unbanded snakes survive better
on islands, banded snakes survive better on the mainland (this is
probably because of something to do with how their color matches the
different backgrounds in the different areas -- predators may see one
form more easily on islands and the other on mainlands.)
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 03:51PM
comment
Kristi -- good explanation. James -- good explanation of
the results. It looks like we've made it through these
two experiments, and through the hour. I think the bells
must be ringing. I'll stay around to take questions, comments,
if you have them, but you're excused (do be sure to look at question
10 and other questions in this chapter over the lecture material at some point before the EXAM A WEEK FROM MONDAY though.)
Greg (no email) from 206.240.201.227 at 02/05/99 03:52PM
comment
James-if you would like to work on the computer assignment this weekend call me at 587-0595.
kristi (no email) from paydial02.utm.edu at 02/05/99 03:55PM
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Goodbye and Take care!!!!
Renee (no email) from 199.78.37.226 at 02/05/99 03:55PM
comment
You had told us if we had any questions we could contact Nancy B. I can't remember the last name. Is she answering questions over e-mail, if so, what is her address. You will probably be busy this weekend, and I am having some problems with genetic drift. Also, I was going to run over to the library to get the copies of test on file. You said you would put some new ones on file, have you done that yet?
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 04:01PM
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Renee -- Nancy B. is Nancy Buschhaus and her e-mail is
nbuschha@utm.edu you can e-mail her or go by her office during
the week. I'm afraid I didn't get the last set of exams into
the library but there are still a bunch there that will have the
basic format. I don't think I'm going to make it to my office or
the library this weekend (this is based on how I'm feeling now;
it could be another false alarm in which case I'll try to get them
there.)
Renee (no email) from 199.78.37.226 at 02/05/99 04:03PM
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Thanks! Good luck this weekend. Maybe we will find out on monday you have finally had this new addition to the family!!
Rebecca I (no email) from paydial10.utm.edu at 02/05/99 04:05PM
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Have a good weekend everyone! Bye.
Greg (no email) from 206.240.201.227 at 02/12/99 02:54PM
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Hello, it's me again!
James Tolene (no email) from 206.240.200.156 at 02/12/99 02:54PM
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Hello. I'm here.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 02:55PM
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Hello all, welcome to lab Friday, 12 February. This is Nancy Buschhaus. I'm "standing" in for Dr. Irwin while she takes some time off with her new baby. While I'm typing in all of the announcements that I have for today, please indicate that you are present in lab by saying "hello".
Renee (HeyImherealso) from 199.78.37.229 at 02/12/99 02:55PM
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Greg (no email) from 206.240.201.227 at 02/12/99 02:55PM
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Hey James, don't you love having a class this late on Friday afternoon!!!
Dr_ B (no email) from 192.239.150.197 at 02/12/99 02:55PM
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Hi James and Greg--you both are faster than I am. I'll start typing the announcements now.
James (no email) from 206.240.200.156 at 02/12/99 02:56PM
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I'm suppose to have this on Thursday, but it has worked out that this is alittle more convienent
Renee (no email) from 199.78.37.229 at 02/12/99 02:56PM
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Ok, I'm starting off real great!! That's not my e-mail. Now, I'm here!!
Greg (no email) from 206.240.201.227 at 02/12/99 02:57PM
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Lucky for you, since I'm in here you're guaranteed to have a good time.
James (no email) from 206.240.200.156 at 02/12/99 02:57PM
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Besides I'd rather be one the computer in my room than in a classroom
Dr_ B (no email) from 192.239.150.197 at 02/12/99 02:57PM
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Announcement 1: Your FIRST EXAM is MONDAY, Feb 15. You should attend either 1-3pm or 5-7:30 pm to take the exam. The exam will be held in Brehm B208. Information for the exam is posted on the website under next week.
Greg (no email) from 206.240.201.227 at 02/12/99 02:58PM
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That's true I just wish the time was different.
James (no email) from 206.240.200.156 at 02/12/99 02:58PM
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We're feeling saucy this afternoon aren't we?
Greg (no email) from 206.240.201.227 at 02/12/99 02:59PM
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You'd better believe it.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 02:59PM
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Keep "talking" and entertaining yourselves while I get through these billion announcements!
Announcement2: I will hold a review session on Sunday, 2-4pm, for anyone interested. We can go over the answers to the lab questions for previous weeks, clarify any topics you are having trouble with, etc. The review will be in Brehm 211.
James (no email) from 206.240.200.156 at 02/12/99 03:00PM
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I hope we have more people in here today than just three.
Greg (no email) from 206.240.201.227 at 02/12/99 03:01PM
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Yeah, three's not quite a crowd in this situation. Although, with only three, if you have questions about something you can get them answered more quickly.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:01PM
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Announcement 3: Your computer assignments are graded (except for the paragraph...Dr. Irwin will be grading that and returning it at a later time). Yes, I know it's surprising for those of you who know me, but they ARE GRADED. Currently, your assignments are residing in the Biology office, but after 4:15pm I will post them outside of my office. Please pick them up. James and Renee, make sure you read the comments on the front page
Renee (no email) from 199.78.37.229 at 02/12/99 03:02PM
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I hope there is more than 3 also, because I am not that great at answering some of these questions!!!
James (no email) from 206.240.200.156 at 02/12/99 03:02PM
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Plus, I guess it's not as hard to follow.
kristi (no email) from paydial11.utm.edu at 02/12/99 03:03PM
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Hello! sorry I'm late!
Greg (no email) from 206.240.201.227 at 02/12/99 03:03PM
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Precisely, the conversation tends to stay more focused on one thing instead of several things all at once. Plus, you've got me, what more could you need!
James (no email) from 206.240.200.156 at 02/12/99 03:04PM
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Saucy indeed.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:04PM
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Announcement 4: I'll try to get the answers to this week's lab questions posted as soon as possible. However, notice that one of the questions at the end of this chapter is guaranteed to be on the exam. Therefore, I will not be posting the entire answer (someone suggested that Dr. Irwin often posts outlines, I'll check with her). If you would like to try one of the essays at the end of the assigned lab and get feedback on it, Dr. Irwin said that she would be checking her email this weekend. AS for the answers for your homework from this week, I will grade them and notify you via email sometime on Sunday.
Renee (no email) from 199.78.37.229 at 02/12/99 03:05PM
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I hate to ask this, but by saying front page, are you talking about the announcement section on the web page? I am lost???
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:09PM
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Well, well, we are saucy today...hmmm. Anyway, now I am done with the announcements and ready to move on to the questions. I know that each of you were assigned a "what to know" section from the lab, but let's hold off on those for now. Rather, let's go over each graph and discuss the important points from each. Graph 1 (to remind you) had the comparison between dominant with highest fitness vs. recessive with highest fitness. The situation was that the peppered moth dark form was dominant (C allele=dark) over the recessive phenotype of the light form (T allele=light). If you happened to notice, in the case where the dominant phenotype had the highest fitness (line C), when the frequency of the allele C started out low (.01), it quickly increased but never became fixed. Why do you suppose it never became fixed?
Greg (no email) from 206.240.201.227 at 02/12/99 03:11PM
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It never became fixed because the dominant homozygote and heterozygote both had equal fitness. The equal fitness allows the heterozygote to carry on the recessive allele.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:11PM
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Renee--sorry for the confusion. I meant for you to check the comment that I put on the front page of your assignment.
James (no email) from 206.240.200.156 at 02/12/99 03:12PM
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Just a guess, but does it have anything to do with the phenotype showing the dominate trait but still carring a recessive allele.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:14PM
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Greg--yes, because both the CC and CT have the dominant phenotype, they have equal fitness (both are =1). Therefore, the heterozygote "carries" the recessive allele even in cases where the recessive phenotype (genotype = TT) is constantly lost from the population due to lower fitness.
Okay, given that answer, why is it that when the recessive phenotype has the highest fitness, the recessive allele becomes fixed?
kristi (no email) from paydial11.utm.edu at 02/12/99 03:14PM
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could it have anything with population size or is that just important in genetic drift?
Greg (no email) from 206.240.201.227 at 02/12/99 03:15PM
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The recessive becomes fixed because the dominant homozygote and the heterozygote both express the dominant allele so both have a lower fitness than the recessive homozygote which has the highest fitness.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:15PM
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Good job, James. Does everyone see how the heterozygotes can maintain the recessive allele even when many of the recessives do not survive to reproduce (due to lower fitness)?
James (no email) from 206.240.200.156 at 02/12/99 03:16PM
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In order to show the recessive phenotype, both allels have to be the same. If they have a higher fitness than the dominate allele (and phenotype) the it will work itself out of the population.
Renee (no email) from 199.78.37.229 at 02/12/99 03:16PM
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Because it is the one that is reproduced the most therefore it is passed on to offspring more often. Then the majority of the pop will have this allele.
James (no email) from 206.240.200.156 at 02/12/99 03:16PM
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"It" being the dominate allele
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:18PM
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Krisit--population size does affect genetic drift. However, generally the total population size does not have an effect on selection because a phenotype has an advantage or not regardless of how many individuals have it in the pop.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:21PM
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Wow, you people are quick. Yes, in cases where the recessive phenotype has higher fitness it eventually becomes fixed because the homozygous dominant and heterozygote both have (the same) lower fitness and eventually the dominant allele disappears. Any comment about why it took so many generations in the situation from Graph 1?
kristi (no email) from paydial11.utm.edu at 02/12/99 03:21PM
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okay thankyou, i justed wanted to make sure
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:22PM
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The first "it" in my previous comment referred to the recessive allele
Greg (no email) from 206.240.201.227 at 02/12/99 03:23PM
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It took so long because natural selection is the only thing occurring and natural selection implies the assumption of an infinitely large population. The large population would prevent one genotype to fix quickly.
kristi (no email) from paydial11.utm.edu at 02/12/99 03:24PM
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is the reason it took so long because the heterozygote and the dominant homozygote had equal fitness?
James (no email) from 206.240.200.156 at 02/12/99 03:24PM
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Again, just a guess, I was under the impression that the dominate wasn't a complete bust as far as reproductive sucess is concerned, just not as good as the recessive. I assumed that it just took alittle while for the recessive to out compete the dominate.
renee (no email) from 199.78.37.229 at 02/12/99 03:25PM
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Would it take so long because the pop size is infinite?
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:26PM
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Greg--yes, but I want you to explain the difference in the "speed" of evolution (in generation time) between the situation where the dominant allele quickly increased when the dom. phenotype had the highest fitness to the case where the recessive phenotype had the greatest fitness. Why was the "speed" different if both started at .01 frequency
Greg (no email) from 206.240.201.227 at 02/12/99 03:28PM
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The speed was different because in the first situation, both the dominant and the heterozygote had the highest fitness, there was two possibilities of a genotype having a higher fitness whereas where the recessive had the highest fitness, only the recessive genotype (TT) had the high fitness and therefore it took longer for the population to show the higher fitness of the recessive genotype.
James (no email) from 206.240.200.156 at 02/12/99 03:28PM
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The dominate will show itself with only one allele, recessive with both only. To get one is easy (statistically (sp?)) to get both and pass them bith along is alittle more difficult.
James (no email) from 206.240.200.156 at 02/12/99 03:29PM
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Bith=both. Speech impedament, sorry.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:30PM
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All of you are getting close! The infinite population size has an effect. Given the frequency of the dominant allele at the beginning of this situation, even with their lower fitness, which type of offspring was more likely in generation 1, 10, 25, etc? Think back to general phenotype ratios and the potential types of offspring from different combinations of gametes.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:31PM
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Again, you all are much quicker than I am. You had the answer posted before I could clarify the question. Good job!
kristi (no email) from paydial11.utm.edu at 02/12/99 03:32PM
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I think I made a comment about the wrong graph!!
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:32PM
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Does anyone have any questions about graph 1? I think we summed it up well. Let's go on to Graph 2. Discuss the effect of population size on the speed of fixation, the likelihood that any one allele will be fixed, and the point where "infinite" population size likely begins.
Greg (no email) from 206.240.201.227 at 02/12/99 03:33PM
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I understood your first question but when you clarified it I became real confused, I'm glad we answered it the first time.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:34PM
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Kristi--from your previous comment, I think that you were looking at the right graph (the homozygous dominant and heterozygote had equal fitness).
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:35PM
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Hey, Greg, who ever said that you were allowed to critique the stand in? Just kidding, for those of you that are shocked by that interaction, Greg was a previous student of mine and, therefore, open to intructor evaluations
James (no email) from 206.240.200.156 at 02/12/99 03:36PM
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I'd say that population size is directly proportional to speed of allele fixation. The larger that population the slower the fix. I'd also say that and infinate number as far as population is concerned would differ in different species. The faster a species goes through a life cycle the larger the population would have to be to be considered infinite.
Greg (no email) from 206.240.201.227 at 02/12/99 03:36PM
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It seems that somewhere around a population size of around 200, it acts as an infinite population and can maintain both alleles infinitely whereas anything less than that, one allele will likely become fixed in the population. The smaller the population size, the quicker an allele will become fixed.
James (no email) from 206.240.200.156 at 02/12/99 03:37PM
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What about current students?
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:38PM
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Greg, to clarify the clarification, I meant that a cross between two heterozygotes would have a 3:1 phenotype ratio (3 dominant phenotype to 1 recessive phenotype) and the genotype ratio would be 1 homozyg dom, 2 heterozy, 1 homozy recessive (and that's just a cross between two heterozygotes). Essentially, given the intial frequency of the dominant allele, most individuals would be either homoz dominant or heterozygous. Therefore, even if they don't reproduce as quickly there are fewer potential crosses that would result in a recessive phenotype. Sorry for the confusion.
Greg (no email) from 206.240.201.227 at 02/12/99 03:39PM
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Yes, James, go ahead, she doesn't mind, in fact she thinks it makes her a better instructor. Teacher evaluations are much welcomed, especially if they concern Dr. B.
kristi (no email) from paydial11.utm.edu at 02/12/99 03:39PM
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In my graph, the small population took the longest to become fixed
and the Yellostone population never became fixed at all?
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:42PM
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Good, an infinite population probably starts somewhere around 200 or so, but James had an important point that I'd like him to clarify "it probably depends onthe species". Do you have any thoughts as to why it might depend on the species? For now we are assuming that the species we examine are freely interbreeding. Is that always the case? (yes, James, current students should also beware of "instructor evaluation"...have I graded your exam yet?)
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:44PM
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Kristi--yes, that is the graph. The small population became fixed, the Yellowstone population never became fixed, and the Alaska population? Does anyone remember? What would you call the situation with the Alaska population?
kristi (no email) from paydial11.utm.edu at 02/12/99 03:44PM
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James, did you mean that when it depended on the species that the species may have different rates
of reproduction time,gestation,etc?I'm confused.
Greg (no email) from 206.240.201.227 at 02/12/99 03:45PM
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It definitely depends on the species. Distribution depends on the species and a species which doesn't distribute freely is less likely to have the infinite population size but instead would be smaller sub-population. Selective mating would also play a role, if the females were selective in choosing their mate, a particular genotype may be selected for more often than another.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:45PM
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Greg is right. I always welcome CONSTRUCTIVE critism from students...it makes all of us better instructors.
Renee (no email) from 199.78.37.229 at 02/12/99 03:45PM
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The Alaska pop stayed the same at .50. it never changed.
James (no email) from 206.240.200.156 at 02/12/99 03:45PM
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I suppose we should consider demes in this. It seems to me that there is a mighty big difference in 200 e-coli strands and 200 elephants. OR maybe it should have something to do with the possible number of alleles?
Greg (no email) from 206.240.201.227 at 02/12/99 03:46PM
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The situation in the Alaska population would probably have a high enough population to be considered infinite and since natural selection was not occurring it would be in the Hardy-Weinberg equilibrium.
James (no email) from 206.240.200.156 at 02/12/99 03:46PM
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Alaska population was experencing genitic drift.
James (no email) from 206.240.200.156 at 02/12/99 03:48PM
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I'm smoking crack, it wasn't the alaska pop, it was the smaller one, which ever that was. Alsaka was big enough that drift would mess with it.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:49PM
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Kristi--I'm sort of jumping ahead in topics, I'm sorry. What I wanted James to address, and what Greg mentioned, was that depending on the species our assumptions of freely-interbreeding infinite populations may not be realistic. As Greg mentioned, distributions and mating systems can affect the actual (in terms of breeding individuals) number of individuals in a population. Essentially, if individuals do not have equal opportunities to mate (and, hence, unequal fitness), then larger populations become essentially much smaller. But that is not extremely important for right now.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:50PM
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Good Renee! It did stay at .5. Isn't it interesting that even random chance doesn't change the allele frequency?
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:52PM
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Can you believe that the bell rang? And here I was having a great time! I guess I will let you go now :( But, I'll stick around for a few minutes to continue comments (I haven't made it through all of them). By the way, James it is not recommended to use mind-altering substances...your fitness becomes extremely low.
Greg (no email) from 206.240.201.227 at 02/12/99 03:52PM
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The bell rang, if you don't need any more answers from me I've gotta got :)
James (no email) from 206.240.200.156 at 02/12/99 03:53PM
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It makes my hands work faster than my brain. (or my mind slower than my hands) I've got to hand out keys so until next time, adious.
Dr_ B (no email) from 192.239.150.197 at 02/12/99 03:54PM
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James, yes the size of the species could be a factor. Greg, yes the population was in Hardy-Weinberg equilibrium.
Renee (no email) from 199.78.37.229 at 02/12/99 03:58PM
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I have a question. I hope I have not got myself in a mess. I did not turn in a paragraph. Was I suppose. I did the assignment like I did it the last time I took this class. If I only made a 50 on it there is no way I will ever recover!! Can you tell me if I messed up?
kristi (no email) from paydial11.utm.edu at 02/12/99 03:59PM
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Goodbye everyone!!! Happy studying, see you on Sunday!!
Dr_ B (no email) from 192.239.150.197 at 02/12/99 04:02PM
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Renee, I'm confused. You did not turn in the paragraph that described one of the graphs with your own hypothetical species? If so, that paragraph is worth 5pts of the total 30pts for the computer assignment. I would suggest that you go ahead and turn one in. Perhaps, Dr. Irwin will accept it late (minus a few points, of course)
Rebecca Irwin (rirwin@utm.edu) from paydial08.utm.edu at 02/19/99 02:39PM
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Welcome to lab, 19 February, 1999. ANNOUNCEMENTS: 1. You should start working
on the next computer assignment (on phylogenetic analysis) by next week. Information
for this, including next week's lectures and an introduction to the assignment,
is now
available on the web linked to the lecture index. Be SURE to read this AND the
more complete
introduction in your lab manual; e-mail me if you have questions. 2. For lab next week,
WE WILL MEET IN PERSON, in the assigned lab room, instead of on the internet. We'll do this
for three main reasons: first, the material for next week's lab is graphical and
a lot of us
have had a hard time with discussions of graphical/mathematical material over the internet. Second,
it will give you a chance to ask questions about the computer assignment, which
is related to next
week's lab material, so BE SURE TO READ OVER THE ASSIGNMENT CAREFULLY BEFORE LAB
NEXT WEEK! Third,
we can discuss whether we want to continue to have labs over the internet or whether you would rather
meet in person (you can see how the lab goes in person and decide which you prefer.) 3. Before you ask -- no, the exams are not done yet. I plan to do them over the weekend; check with the bioloy dept. office on monday,
FOR THIS WEEK'S DISCUSSION, we'll be talking about the reading you have done from the textbook
chapter on the origin of life. In your "hello" message, please list one of the
three main steps
in the Oparin-Haldane model of the origin of life. Then start looking at the question your group
was assigned; I'll be asking about it soon. Remember, you were assigned to prepare to discuss the following from lab manual chapter XVI: group 1: 2, group 2: 3, group 3: 4, group 4: 5, group 5: 6
James Tolene (no email) from 206.240.200.156 at 02/19/99 02:46PM
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Hello, just got back to the room and I'm alittle early. 1.Nonbiological processes synthesized organic molecules that would later server as the building blocks of life.
Renee (no email) from 199.78.37.230 at 02/19/99 02:46PM
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hello....
#2 The organic building blocks in the pre-biotic soup were assembled into biological polymers, such as protens and nculeic acids.
For lab next week, do we meet at this time, or is everyone meeting at one specific time. Also, it is is this time, can I meet with the 1:00 session???
Greg (no email) from 206.240.201.226 at 02/19/99 02:48PM
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#3 some combination of biological polymers were assembled into a self-replicating organism that fed off the organic molecules in the pre-biotic soup.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 02:50PM
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Hello James and Renee, good steps 1 and 2. Renee, we'll meet at the usual lab times and you (or anyone)
can go to whichever you like, I can't remember any more which labs people were
officially in anyway!
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 02:51PM
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Hello Greg, good #3.
James (no email) from 206.240.200.156 at 02/19/99 02:51PM
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Wow a bunch of us are here early!
Greg (no email) from 206.240.201.226 at 02/19/99 02:52PM
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If we're here early, maybe we can be excused early?
James (no email) from 206.240.200.156 at 02/19/99 02:52PM
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There's a thought...
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 02:54PM
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So to summarize the Oparin-Haldane Model, the first step is to get the small subunit molecules (like amino acids) that living things are made of from inorganic molecules, the next step is to get those small subunits put together into large molecules like proteins, and the third step is to get some kind of genetic system -- a molecule that will replicate itself. Those are the basic things that have to happen to get life.
We'll consider the questions now. Since this is a small group ther may be some that no one has prepared but we should be able to work through them anyway. Note that all the questions (2-6) are related to one of the steps in the Oparin-Haldane model. As we discuss the questions, consider what step they're related to. First, everyone look at XVI question 2 now. Answer one part of it first -- What conditions did Miller create?
kim renfroe (no email) from 170.143.229.159 at 02/19/99 02:56PM
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hello. I am going to join this lab today to see if seems alittle less hectic than the 1:00 lab on fridays!
Greg (no email) from 206.240.201.226 at 02/19/99 02:56PM
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He created an atmosphere of ammonia, methane, and hydrogen, he though this was possibly the atmosphere of the young Earth.
James (no email) from 206.240.200.156 at 02/19/99 02:56PM
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The way I understood it, he tried to recreate the conditions of early earth-simalar atmospheric conditions and temp.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 02:57PM
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If you early birds can get through the questions early then
sure, you can be excused early. But we've got to make sure
this origin of life stuff makes sense first. Now yoou should be
inspired to really work at it, right?
James (no email) from 206.240.200.156 at 02/19/99 02:57PM
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You got it.
Greg (no email) from 206.240.201.226 at 02/19/99 02:58PM
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Let's get the lead out, what are we waiting for?
Renee (no email) from 199.78.37.230 at 02/19/99 02:58PM
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He tried to recreate the environment of the young earth???
James (no email) from 206.240.200.156 at 02/19/99 02:59PM
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That's what I'm saying.
kim (no email) from 170.143.229.159 at 02/19/99 02:59PM
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one of the three main steps in the oparin-haldane model was that the orgainc building blocks in the pre-biotic soup were assemebled into biological polmerws, such as proteins and nucleic acids.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:00PM
comment
Hi Kim, welcome! James and Greg, good statement of what he created and why. So
he wanted to see if, in the conditions he thought were those of early
earth, organic molecules would form from the non-living stuff in the atmosphere.
Did they? What formed?
James (no email) from 206.240.200.156 at 02/19/99 03:00PM
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Could I get a list of the people in my lab group, in case I need to get a second opinion on stuff that we're assigned?
James (no email) from 206.240.200.156 at 02/19/99 03:01PM
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He got some ammino acids some nucleotides and sugars.
Greg (no email) from 206.240.201.226 at 02/19/99 03:01PM
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After running the apparatus, he obtained a reddish colored cloudy mixture. He used paper chromatography to identify the contents which consisted of organic molecules such as amino acids (glycine, alpha alanine, beta alanine.)
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:02PM
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Renee -- yes, what James is saying is correct. He wanted to know if organic molecules could
form in that environment since that would be a necessary first step for life to
form. Did they?
Renee (no email) from 199.78.37.230 at 02/19/99 03:03PM
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he created a red cloudy liquid
kim (no email) from 170.143.229.159 at 02/19/99 03:04PM
comment
In miller's experiment organic material were produced, probably amino acids glycine, alpha-alanine, and beta alanine. And in similiar experiments chemists documented the formation of amino acids, nucleotides, and sugars.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:05PM
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OK, good, he did get organic stuff like amino acids. Which step in
the
Oparin-Haldane model did he simulate? (James, I'll have to e-mail you your group
members, I don't have the list right here. Good idea, though.)
James (no email) from 206.240.200.156 at 02/19/99 03:05PM
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He got step one.
kristi (no email) from pmm105.aeneas.net at 02/19/99 03:06PM
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Sorry, I am late. I'm using a friend's computer off campus and it is taking forever to do anything!
kim (no email) from 170.143.229.159 at 02/19/99 03:06PM
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He provided evidence for the first step in the oparin-haldane theory.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:06PM
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Good, Kim. Renee, the molecules Kim and others have listed are what made the liquid red and cloudy.
Greg (no email) from 206.240.201.226 at 02/19/99 03:06PM
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He simulated the first step, synthesis of organic molecules, such as amino acids and nucleotides, that would later serve as the building blocks of life.
Renee (no email) from 199.78.37.230 at 02/19/99 03:07PM
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He did #1.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:09PM
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Greg's right, it's the first step. Look at qu. 3 now, it's also on the first step. Miller's experiment was to see
if organic molecules could have formed in the atmosphere. What are other possible sources of these molecules?
Once you answer that, consider, and comment on, the arguments for and against both the atmosphere as a source and these other possible sources.
kim (no email) from 170.143.229.159 at 02/19/99 03:12PM
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These molecules could have came from other palnets in our solar system by way of a meterite.
Greg (no email) from 206.240.201.226 at 02/19/99 03:12PM
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Meteors and comets which contained organic molecules could also have been a source. If the atmosphere was as Miller suggested, the organic molecules would have burned up befor ehitting the ground. However, if the atmosphere was predominantly CO2, as volcanoes suggest, then it may have cushioned the fall enough to allow some organic molecules not to combust before hitting the ground. some could have survived, this is shown as evidence from the Sudbury Crater however the organic molecules may have been created during the crash as a result of the heat.
Renee (no email) from 199.78.37.230 at 02/19/99 03:13PM
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microbes could have reach earth from meteorites. These meteorites may have come from other planets that were bombarded by meteorites and they traveled through space to the earth.
James (no email) from 206.240.200.156 at 02/19/99 03:13PM
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It could have traveled here from some extra-terestrial source. Cool Idea. Hard to live through atmosphereic entery plus inpact I would think, but still cool.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:15PM
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Kim, good source for these molecules. Greg's got the
explanation for how this would work. So if Miller was
right about the atmosphere, the meteroite/comet idea
probably won't work, but if he was wrong and there was
more CO2 in the atmosphere then the meteorite/comet idea
would work. If the atmosphere had a lot of CO2 would
Miller's idea that the organic molecules formed in the
atmosphere work? Why/why not?
kristi (no email) from pmm105.aeneas.net at 02/19/99 03:15PM
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Other soursces could have been from meteors and comets in the atmosphere but the organic molecules were probably destroyed by the heat of the collisions.
Greg (no email) from 206.240.201.226 at 02/19/99 03:17PM
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No, because an atmosphere dominated by carbon dioxide and molecular nitrogen appears to be much less conductive to the formation of organic molecules.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:17PM
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James -- I think the extra-terrestrial source ideas are
pretty cool, too. As noted by Renee, some people have argued
that actual microbes (organisms) arrived on comets or
meteorites; others have argued as noted by Greg that
it was the organic molecules (not actual organisms) that
arrived via meteorite or comet.
kristi (no email) from pmm105.aeneas.net at 02/19/99 03:18PM
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if there was a dense Co2 atmosphere then there may have been a soft enough landing for the meteors and comets so some of their organic materials could have survived.
James (no email) from 206.240.200.156 at 02/19/99 03:19PM
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It just says that it's less conducive to organic syntheseis, with more CO2 and molecular nitro.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:19PM
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Hi Kristi, good. Greg's got the answer to my other question -- if the
atmosphere had a lot of CO2 then organic molecules don't form well in
the atmosphere so that idea wouldn't work. But the comet/meteorite idea
would work better with a CO2 atmosphere so one way or the other it looks
like there's a plausible way for organic molecules to have built up on earth.
So step 1 in the model is plausible. Now let's consider step 2, the formation of
biological polymers. Question 4 is relevant to this one so look at qu. 4. Consider
the first parts first: What is a biological polymer? What is the major problem that could have prevented formation of biological polymers in the "pre-biotic soup." How did Ferris et al. simulate a situation that could overcome this problem?
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:21PM
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James and Kristi -- good. Putting your answers together, a CO2 atmosphere would be less
conducive to synthesis of organic molecules but would make it more likely for
organic molecules in comets/meteorites to survive the crash to earth.
Greg (no email) from 206.240.201.226 at 02/19/99 03:23PM
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Biologic polymers are proteins and/or nucleic acids, made of organic building blocks which may have been in the pre-biotic soup. They can readily be synthesized but also break down quickly by hydrolysis even as they are being build. They may not have lasted long enough to serve as a basis of a self-replicating primordial organism out of a simple organic soup. Ferris et al. added a common clay mineral montmorillonite which organic molecules readily adhere to. When they adhere to the montmorillonite they are much less vulnerable to hydrolysis and remain able to grow in length by addition of new bases to the end of the chain.
Renee (no email) from 199.78.37.230 at 02/19/99 03:24PM
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there are doubts that polymers would serve as the basis of a self-replicating primordial organism would everh formed in the simple organic soup.
kim (no email) from 170.143.229.159 at 02/19/99 03:24PM
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in the textbook it also discusses how a dense co2 atmosphere could have provided a soft enough landing, even for large meteors and comets, for some of the organic materail to survive. In this casse would a dense atmosphere help in the survival of organic materail?
kristi (no email) from pmm105.aeneas.net at 02/19/99 03:24PM
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Ferris suggested thatthe first organic polymers may have formed on clay crystals so simulated a pre-biotic soup in the lab and added clay mineral montmorillonite, when the polynucleotides stick to this clay they are less likely to go through hydrolysis.
James (no email) from 206.240.200.156 at 02/19/99 03:25PM
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I assumed that a Biological polymer was along the line of a DNA or RNA. Apparently the polymers have a hard time surviving to replicate themselves because of hydrolysis. The reseaches stuck the "soup" on some clay that make them less vunerable to hydrolysis
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:26PM
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Note Greg's answer to qu. 4, all. I must say one advantage
to this internet format is we don't have to try to pronounce
"montmorillonite" -- that always seems to be the big problem
discussing this question out loud. Now consider the last
part to question 4: Is this situation (the situation simulated by Ferris's experiment) likely to have existed during the time that life was developing from non-life on earth?
kristi (no email) from pmm105.aeneas.net at 02/19/99 03:26PM
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How can you write so fast ,Greg?
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:27PM
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Kim -- yes, a dense CO2 atmosphere would make meteorites/comets
come to earth more slowly/gently so they'd be less likely to crash
and burn and any organic molecules in them would be more likely to
survive and build up on earth.
Greg (no email) from 206.240.201.226 at 02/19/99 03:27PM
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Yes, minerals in sediments were continuously bathed in the prebiotic soup and could have nursed the formation of polymers that were long enough to form a self-replicating primordial form.
james (no email) from 206.240.200.156 at 02/19/99 03:28PM
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They started with a 10 nucleotide chain. Kinda long for the origin of life. I wonder why the didn't try to run the experement with something alittle smaller
Greg (no email) from 206.240.201.226 at 02/19/99 03:28PM
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Kristi--practice, practice, and more practice!
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:29PM
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James and Kristi -- yes, the polymers are things like DNA,RNA, proteins.
Remember all these macromolecules are made up of a bunch of smaller subunits
in a chain -- a polymer is a molecule made up of a bunch of small subunits.
Hydrolysis (breaking bonds by adding water) tends to break them up but in
the presence of clay they can form attached to the clay as you've noted
and don't get broken down by hydrolysis. I've wondered how Greg can
type so fast, too. I'm usually in a panic typing as fast as I can and
making a bunch of typos at this point.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:32PM
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Greg -- good, the conditions of prebiotic soup washing over
sediments (rocks) with clay should have been common on early
earth. James, interesting point that they started with
chains of 10. Makes you wonder if they tried with smaller
chains but didn't get it to work? This would cast some doubt on
whether the clay can really overcome the hydrolysis problem, wouldn't it?
I don't know the answers to that, but it's interesting to think about.
I think we're OK on question 4 now but ask if you've got more questions.
Look at questions 5 and 6 now; both are about something called the RNA world
hypothesis. What is the RNA world hypothesis?
James (no email) from 206.240.200.156 at 02/19/99 03:34PM
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In a nutshell, life orinated with self replicating RNA.
Greg (no email) from 206.240.201.226 at 02/19/99 03:34PM
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The RNA world hypothesis is that an important early self-replicator was made largely or entirely of RNA. Early versions of this envisioned a self-replicating RNA as the primordial form itself.
James (no email) from 206.240.200.156 at 02/19/99 03:34PM
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Hah! I beat Greg finally :)
kim (no email) from 170.143.229.159 at 02/19/99 03:35PM
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The RNA - wolrd hypothesis came from the idea that an important early self-replicator was made largely or entirley of RNA.
James (no email) from 206.240.200.156 at 02/19/99 03:35PM
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However my spelling needs work.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:35PM
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James, good nutshell version of the hypothesis. Now, what's
the rationale for this? Why do people think the first replicating
molecule was RNA rather than DNA or protein? Also, what step of the
Oparin-Haldane model are we looking at here?
Greg (no email) from 206.240.201.226 at 02/19/99 03:35PM
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James- orinated???
kim (no email) from 170.143.229.159 at 02/19/99 03:36PM
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We are looking at the Third step in the Oparin - Haldane theory.
kristi (no email) from pmm105.aeneas.net at 02/19/99 03:37PM
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it is the hypothesis that RNA replicates itself serving as a proto-organism
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:37PM
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Kim and Greg -- good statements of RNA world hypothesis.
James -- hey who can type fast and not leave out, add, or mix up
letters anyway? After I typed "yoou" for you somewhere I
decided I'd better not comment on spelling...
Renee (no email) from 199.78.37.230 at 02/19/99 03:37PM
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The 3rd step.
Greg (no email) from 206.240.201.226 at 02/19/99 03:38PM
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The rationale for this is that when using the universal phylogeny the clues found seem to point to RNA. RNA molecules can both store genetic information and, like proteins, act as catalysts.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:38PM
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Kim -- good, we're at the third step. Now, all, why
RNA? Why not DNA or protein?
James (no email) from 206.240.200.156 at 02/19/99 03:39PM
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Step 3
The reasons they think it's RNA is because it can act as a catalyst and because it seems to suggest that it's RNA when you look at a universal phylogiany
Renee (no email) from 199.78.37.230 at 02/19/99 03:39PM
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Because RNA's would be able to evolve.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:40PM
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Greg's got the two main reasons people think RNA was the
first self-replicator. First, the universal phylogeny --
can you explain more about that? Second, the properties
of RNA -- it can both be a catalyst AND store genetic material.
Can either DNA or protein do BOTH of these? Which can DNA do? Which
can protein do?
kristi (no email) from pmm105.aeneas.net at 02/19/99 03:41PM
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RNA can both store genetic information and act as catalysts much like proteins,so it is more likely for RNA to catalyze its own replication while functioning as a ribozyme.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:41PM
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Renee -- Think about what it means to say the RNA is able to evolve. This is
getting at what others are saying -- it can replicate itself
potentially, so it can reproduce -- that is necessary for
anything to evolve.
James (no email) from 206.240.200.156 at 02/19/99 03:42PM
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I assumed that the Universal phylogeny as a very big phylogeny that had eveything on it, people to bacteria.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:43PM
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James, yes, that's the universal phylogeny. How does RNA
function in ALL the life in this universal phylog.?
Greg (no email) from 206.240.201.226 at 02/19/99 03:44PM
comment
The most highly conserved and universal component of the information processing machinery in cells is the apparatus for translation, this is build on a frame made of
RNA. This points to RNA using the universal phylogeny. I'm not sure about DNA and proteins but I think DNA his involved with replication and transcription and proteins are involved with translation.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:45PM
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Everyone -- we've made it past where the other labs did so I
should also honor your early request -- you're officially excused but feel free to stick
around and discuss.ask moer if youd like. sorry about the typos!
James (no email) from 206.240.200.156 at 02/19/99 03:46PM
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RNA is the template for DNA or, in those pesky retro-viruses, its the real deal.
kim (no email) from 170.143.229.159 at 02/19/99 03:46PM
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I thought that the reason they considered rna to be the first replicator was because it was the most highly conserved and universal component of the inforamtion processing machinary in cells. For example it is the apparatus for translation.
Greg (no email) from 206.240.201.226 at 02/19/99 03:46PM
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Bye, see you next week, this time it'll actually be in person.
James (no email) from 206.240.200.156 at 02/19/99 03:47PM
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Hey, what can we say. The best lab is us.
Renee (no email) from 199.78.37.230 at 02/19/99 03:47PM
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I would like to know how RNA functions in all of life, I don't know!!
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:48PM
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Greg's got the point on the universal phylogeny. In general,
DNA stores genetic material but can't catalyze reactions so it can't replicate itself. Proteins can catalyze but
don't store genetic material. Only RNA does both.
kim (no email) from 170.143.229.159 at 02/19/99 03:48PM
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Dr. Irwin, i really like this lab alot better than the 1:00 on friday because i can follow it much easier. I may start coming to this lab if we continue to do things over the internet.
kristi (no email) from pmm105.aeneas.net at 02/19/99 03:49PM
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I am going to try to send some e-mail to you now-
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:51PM
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Kim, good, that's the main point. Renee -- as noted by Kim,
RNA functions in translation -- that is, protein synthesis.
It consists of a sting of nucleotides like DNA so it has the
genetic information but it is RNA, not DNA, that is used
directle as the template for making proteins. This is
true in all life.
renee (no email) from 199.78.37.230 at 02/19/99 03:52PM
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thanks... see ya next week.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:52PM
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Kim, you're welcome in this lab. Kristi, I'll watch for your e-mail.
Rebecca I (no email) from paydial08.utm.edu at 02/19/99 03:53PM
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Everyone have a good weekend!
Rebecca Irwin (rirwin@utm.edu) from paydial13.utm.edu at 03/05/99 02:53PM
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Welcome to lab, 5 March 1999. ANNOUNCEMENTS: I have checked your phylogenies; you can pick them up from the Biology Dept. Office. Be sure to pick them up. If it says "good" in the upper right hand corner it means there are no problems and you can start writing your paper. If you have any corrections that need to be made they are described on the paper, and I have also e-mailed you about them. REMEMBER that if you want me to read a rough draft of the written part of the assignment I need to receive it by 5:00 p.m. on Monday; you can leave it in the Biol. Dept. Office for me. If you hand in a rough draft (and with your final paper) BE SURE TO HAND IN THE PHYLOGENY AND CHARACTERS again -- whether your written part is correct or not depends on your phylogeny and your characters, I can not correct the written part without those. FOR TODAY'S LAB we will be discussing the molecular clock hypothesis. In your "hello" message please tell me something about the molecular clock -- define it or ask a question about it.
Greg (no email) from 206.240.201.226 at 03/05/99 02:54PM
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Hello!
Greg (no email) from 206.240.201.226 at 03/05/99 02:55PM
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The molecular clock hypothesis states that the same gene in different species evolves at the same rate over time.
James (no email) from 206.240.200.156 at 03/05/99 02:56PM
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Hello.
Molecular clock hypothesis
assuming the same genes evolve at the same rate in diffrent species, differences amoung species directly reflect the time of seperation. However, personally, I really don't see why this would be the case.
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 02:57PM
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Hello Greg. That's the basic molecular clock hypoth.
definition. Any other mol. clock definitions/ comments from
anyone?
Renee (no email) from crockett227.iswt.com at 03/05/99 02:57PM
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Hi! MCH-DNA may evolve at a constant rate. Working in a clock like fashion.
James (no email) from 206.240.200.156 at 03/05/99 02:57PM
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What do you say we get out early again this week?
Greg (no email) from 206.240.201.226 at 03/05/99 02:58PM
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James-that is a super-terrific idea, so what do you say Dr. Irwin??
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 02:58PM
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James, good definition. And excellent comment. Everyone
take note -- can anyone explain why we might expect the
same gene in different species to evolve at the same rate?
If you're not sure you might consider, and comment on or ask
about, what affects the rate at which a gene evolves.
Greg (no email) from 206.240.201.226 at 03/05/99 03:00PM
comment
Gene evolution is random because mutation and genetic drift are the main causes of it both of which are random. Over time random things tend to happen at the same rate. It may take long periods of time to show the general rate at which things happen but over time random things happen at a constant rate.
kristi (no email) from paydial05.utm.edu at 03/05/99 03:00PM
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Hello! Molecular clock hypothesis states that the number of molecular differences between species indicates the time since they have speciated, therfore the phylogeny
is drawn from the number of molecular differences.
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:00PM
comment
When you get through as much as the last lab sections did,
on the molec. clock hypoth., I'll let you know and after
that you can leave if you want to. In the mean time, why
would we expect the same gene to evolve at the same rate
in different species? (that's the first point we've considered
in all the labs.)
James (no email) from 206.240.200.156 at 03/05/99 03:02PM
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The only reason I could think of for the clock thing to work would be if the same variation in a gene occured in the two unrealted individuals and the genes were both under simalar directional selection. I'm not seeing how the same gene in a rat in south africa can evolve simalarly in a sheep in south america.
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:02PM
comment
Greg has noted that the rate may be the same because the
things that cause gene evolution are random (mutation and
drift) so they'll average out to occur at the same rate
over time. That's correct. Why is so much of gene evolution
expected to be caused by these random forms of evolution --
why not by natural selection (which is NOT random and would
NOT be expected to result in a constant rate of evolution)?
Greg (no email) from 206.240.201.226 at 03/05/99 03:06PM
comment
Many of the mutations are lethal. If a mutation occurs which is lethal the organism will not reproduce. Many of the changes which are not lethal are neutral with respect to phenotype or affect on the organism and have no relation to fitness otherwise the organism would have a higher or lower fitness depending on which gene it had. Therefore randomness is the key to gene evolution.
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:07PM
comment
With regard to James' comment: suppose you looked at the
gene for, say, insulin in a rat species in S. Africa and at
the same gene in a sheep species in S. America. The same
portions of this gene in both species should be crucial for
insulin function; mutations in such areas would be subject to
natural selection and would typically mess up insulin function and be
quickly selected against. Then there would be areas of the gene
that are not subject to natural selection (why not???) and these
areas would evolve through genetic drift and mutation. It turns out
that it is primarily the rate of mutation that affects the rate at which
these areas will evolve -- mathematically, the population size effects
of genetic drift end up cancelling out and it is the mutation rate that
determines how fast these areas can evolve. Mutations are not predictable
in that we can't say whether a particular rat or sheep will have a mutation,
but there is an average rate of mutation (often about one in a million.)
So the rat and the sheep have about the same amount of area, in their genes
for insulin, where the evolution will depend primarily on the mutation rate.
The mutation rate is on average constant, so the rate of evolution should on
average be constant. Does this make any more sense?
Greg (no email) from 206.240.201.226 at 03/05/99 03:09PM
comment
That makes much more sense to me!
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:10PM
comment
Note that Greg has made the same points I was trying to,
without the rat/sheep/insulin example. If this makes sense,
the next thing to consider about the molecular clock hypothesis
is what is it good for? That is, what can we learn about evolution
if the molecular clock hypothesis is correct -- how can we use it to
study evolution? You can ask more about the constant rate thing -- it's
kind of a tricky point -- or you can comment on what the molecular clock
hypoth is good for. (or you can comment on/ ask about anything else...ideally
something about the molecular clock or molecules and phylogeny.)
kristi (no email) from paydial05.utm.edu at 03/05/99 03:11PM
comment
Yes, I understand it better, but why are there certain areas of the gene not subject
to natural selection?
Renee (no email) from crockett227.iswt.com at 03/05/99 03:12PM
comment
Is the MCH good for determining speciation?
James (no email) from 206.240.200.156 at 03/05/99 03:13PM
comment
Ok one in a million sound cool, but shouldn't actual pop. size and reproductive rates figure in here?
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:14PM
comment
Renee -- yes, MCH is good for determining the dates of
speciation -- when, in the past, did two species separate
from each other? To use the MCH for this you need to know
the rate at which a gene evolves. The next thing to consider is
how do we determine the rate of DNA evolution?
Greg (no email) from 206.240.201.226 at 03/05/99 03:14PM
comment
Using the molecular clock hypothesis you can find out how related species are by using their DNA. If you have a good fossil record then you use radiometric dating to find the age of the fossils and thus time since speciation you can then find two modern species, test them for differences. The number of differences divided by the time since separation which equals the rate at which a gene evolves. Then you can take any two modern species, count number of differences in this gene between them and divide by the rate of DNA evolution and that tells you the time since speciation.
kristi (no email) from paydial05.utm.edu at 03/05/99 03:17PM
comment
I agree with what Greg just said!!
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:17PM
comment
Kristi -- some areas of DNA are not subject to natural
selection because they don't affect the protein that is
coded by the gene so they don't affect the phenotype. For
examples the mutations called "silent substitutions" change
the DNA but do not change the amino acid that is coded by
that part of the DNA because there is often more than one
3-base sequence that codes for the same amino acid so changing
among these does not affect the protein or phenotype, so
individuals with these mutations are just like individuals without
them and therefore have the same fitness so there's no natural
selection on this kind of change. This is called being "neutral with
respect to selection." Now I'll get to James' question...
kristi (no email) from paydial05.utm.edu at 03/05/99 03:23PM
comment
I know we are not discussing this quite yet but on question 16B, where it
asks about the base pairs in the third codon positions of a gene coding for a peptide(protein hormone) and how quick
ly it evolves does natural selection change the phenotypes so it effects fitness and how fast it evolves?
I think I confused myself on this one!
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:24PM
comment
James -- generation length affect the clock; it should
be constant over generations not absolute time. For many
organisms generations are close enough to the same so that
this turns out not to have a major effect, but if you
compared bacteria and elephants you'd want to look at the
length of generations not the absolute amount of time. For
your rat versus sheep example generations turn out to be probably
similar enough so it doesn't have a big effect. Population size
turns out not to affect how fast we'd expect the clock to run. There
is an argument showing this on page 230 of your text; roughly,
it says that since there are 2N copies of an allele present in
a diploid population, the chance of any mutation being fixed is
1/2N if mutations are neutral and the result is that the
rate of evolution is (mutation rate)(alleles in population)(chance of being fixed) =
(mutation rate)(2N)(1/2N) = mutation rate; the population size effects cancel
out. Uh oh, we're doing math on the internet again.
James (no email) from 206.240.200.156 at 03/05/99 03:27PM
comment
Ok, could you use bacteria as an evoultionary model for for elephant (or Humans for that matter) if it is similar? ie - how many generations will it be before elephants evolve trait X?
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:28PM
comment
Kristi -- 16B is relevant to the whole rate of evolution
discussion so let's look at it. Third position mutations often
result in silent substitutions -- the way the genetic code works, it
is often the first two positions that determine the amino acid and
any base in the third position gives the same amino acid. So these
are neutral with respect to selection. Areas that are neutral are
generally expected to evolve more rapidly because as Greg noted earlier
mutations in areas subject to selection are often lethal -- if they occur,
the individual with the mutation dies, and the mutation doesn't evolve. So
there are only a few, if any, mutations that can evolve in areas subject to
selection and evolution is slow. But in areas where the mutation does not affect
the phenotype, any mutation can survive -- there are more possible mutations in
these areas, so there is more variation and evolution can occur faster. Does this
make sense? So third position changes are typically NOT subejct to natural selection
and they evolve rapidly.
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:30PM
comment
Now, everyone has noted I hope that Greg has a nice description
of how to calibrate the molecular clock (how to find the
rate at which a gene evolves.) Note that a key point
in what he said is "if you have a good fossil record" --
do we always have a good fossil record? Can we always determine
speciation dates from the fossil record?
James (no email) from 206.240.200.156 at 03/05/99 03:31PM
comment
plus, if you remember "wobble" from genetics (for 16b)then that would make sense.
James (no email) from 206.240.200.156 at 03/05/99 03:32PM
comment
Nope - our fossil record is pretty shoddy, but it's getting better all the time. I would think that we can, however, get a pretty good fix on the age of the fossils we do have.
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:33PM
comment
James -- you could use bacteria, potentially, as a model
for how fast you would expect traits to evolve in humans
or elephants but you couldn't say when trait X would evolve
because we can't predict here which traits will evolve --
that is random, depends on mutations -- only how fast
these genes will change. They may change in quite different
ways but changes will occur at the same rate. This, again,
is because we're only looking at areas that are neutral
with respect to selection -- there's no higher fitness form,
all forms have equal fitness so we can't tell which one will
evolve.
kristi (no email) from paydial05.utm.edu at 03/05/99 03:33PM
comment
Thanks, that helps alot! Now, I understand .
Greg (no email) from 206.240.201.226 at 03/05/99 03:33PM
comment
We do not always have a good fossil record, it is much more probable that a very limited if any fossil record exists. You need a very good fossil record to tell time since speciation because you have to know at about what time the species speciated. You may start with one species then a couple thousand years later have two species which will show a lot of error in your calculations because of the vast time period between the fossil record.
James (no email) from 206.240.200.156 at 03/05/99 03:35PM
comment
so it's not specific change (ie how fast elephants develop green skin) but just change itself (ie genetic change of any sort in elephants)?
kristi (no email) from paydial05.utm.edu at 03/05/99 03:35PM
comment
Hey, what is "wobble"? I haven't had genetics in like 3 years!!
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:37PM
comment
James -- wobble is an explanation for the 3rd position thing,
good. And you're right, we've got a shoddy fossil record.
This is relevant to the mol. clock hypoth. because if we
had a great fossil record we could determine all the speciation
dates from fossils and wouldn't need to mess around with
molecules. Since we've got a shoddy record (which IS getting better,
but which will probably never be great for some groups because some
groups just don't have parts that fossilize well) we can use what
fossils we have to determine rates of evolution of molecules, and
then use the rate of evolution of the molecules to try to determine
speciation dates for groups for which we DON'T have good fossils.
Now, this brings me to the final main point we've got to consider --
is the molecular clock hypoth. generally true? And, specifically, how
do we test it? Note
that question 13 in ch. XII is relevant to this.
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:39PM
comment
James -- right, we can't say elephants will evolve green skin
(and in fact skin color is usually subject to natural selection
so this hypothesis wouldn't apply to it at all) we can just look
at the rate of change in these areas of DNA that do NOT affect the
phenotype and aren't subject to natural selection. And you'd better
explain wobble to Kristi!
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:40PM
comment
So, how do we test the molecular clock hypothesis?
kristi (no email) from paydial05.utm.edu at 03/05/99 03:41PM
comment
It is true if we compare the differences between each member of an ingroup to the outgroup and
and if each member of the ingroup has the same number of differences from the outgroup.
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:44PM
comment
Greg, by the way, if you've only got error of a couple of
thousand years in the fossil record you're pretty lucky.
There are always pretty large ranges on the dates we determine
for speciation -- we can't get terribly exact but maybe figure the
date falls within 10 thousand years, or within a million years,
or something like that -- depending on how old the fossils are
(we can often be more sure of more recent dates, less sure of earlier
dates.)
James (no email) from 206.240.200.156 at 03/05/99 03:44PM
comment
Ok wobble (without the aid of my genetics notes) refers to the order of base pairs in DNA. The first two base pairs are critical in making of protiens. If either oon changes what is coded for changes. However in that third base pair wobble can occur. In some of the codes the first two base pairs are the same but the last one can be diffrent and they will still code for the same protien. Therefor if the is a point mutation in the third base pair it may not change the protien it's coded for. But it may, just depends on the base pair. Whew!
Greg (no email) from 206.240.201.226 at 03/05/99 03:44PM
comment
The molecular clock hypothesis is tested by the relative rates test which, given a phylogeny for a group, the individuals which have been evolving separately for the same amount of time will have the same number of differences, if they do, then it passes the relative rates test, if they do not have the same number of differences, then the relative rates test is not supported.
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:46PM
comment
Kristi has the answer to how we test the molecular clock
hypothesis -- it is supported (not necessarily true, but
at least there is evidence supporting it) in the conditions
she states. So if you look in your lab manual at question
13, can you tell which pairs of species should have the
same number of DNA differences between them to support the
molec. clock?
James (no email) from 206.240.200.156 at 03/05/99 03:47PM
comment
A) has the same number of differences between the differing species.
Greg (no email) from 206.240.201.226 at 03/05/99 03:47PM
comment
Number 13. D is an outgroup so D-C, D-B, and D-A will all have the same number of differences. C-B and C-A will also have the same number of differences and then B-A will have the same number of differences.
kristi (no email) from paydial05.utm.edu at 03/05/99 03:48PM
comment
Thanks James, so you still have your genetic notes? I may need to look those over sometime!!
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:48PM
comment
Good job, James, without the aid of your genetics notes.
As I recall, without the aid of mine, the word "wobble"
has something to do with how the tRNA and mRNA line up on
the ribosome -- the third position is less crucial to
how they pair or something. Greg, you also got the
relative rates test.
James (no email) from 206.240.200.156 at 03/05/99 03:48PM
comment
Getting enter happy again. A and B should have the same number of diffrences.
James (no email) from 206.240.200.156 at 03/05/99 03:51PM
comment
Yeah still got my notes, I keep them from all my classes. Makes for a heck of a test file for my friends who need help classes I've aleady taken.
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:51PM
comment
Note all that Greg has mostly the correct answer to 13.
The only problem he has is the last statement that B-A
has the same num. difs -- there's nothing to compare
B-A to so we can't use it. But the rest is good.
I'm afraid you didn't get out early but you have made it
through the main points: the reason for the constant rate,
what we can learn with the molec. clock, how to calibrate
the clock, and how to test the clock. Good discussion, all.
Lab's officially over, I'll stay around for a while to
see if there are questions.
Greg (no email) from 206.240.201.226 at 03/05/99 03:52PM
comment
Bye- until next week!!
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:53PM
comment
James -- you have the same problem as Greg did at the
end of his statement. You have to compare at least two
pairs of species to each other (D and A compared to D and B for example
-- there should be the same number of differences between D and A as
there are between D and B.) Does this make sense -- it's awkward
to type (or say.)
James (no email) from 206.240.200.156 at 03/05/99 03:53PM
comment
Adious amigos, trabajador todos los dias.
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:54PM
comment
Have a good weekend everyone but don't forget to work on
your phylogeny papers.
kristi (no email) from paydial05.utm.edu at 03/05/99 03:55PM
comment
Dr.Irwin, I e-mailed you right before class because I couldn't get into the lab
-so just disregard it I guess-
James (no email) from 206.240.200.156 at 03/05/99 03:55PM
comment
I think I got it - I really not competely buying into MCH though. Call me cynical.
Renee (no email) from crockett227.iswt.com at 03/05/99 03:56PM
comment
You said at the beginning of lab you would e-mail us about our papers. I checked my e-mail before coming to lab and i have not received anything?
kristi (no email) from paydial05.utm.edu at 03/05/99 03:57PM
comment
Ciao everyone!!
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:57PM
comment
James -- OK I confess I don't really buy into it either.
There's a lot of disagreement on how often it's likely
to be true. I'm TRYING to present it in an unbiased way
but really I'm cynical, too...
Rebecca I (no email) from paydial13.utm.edu at 03/05/99 03:58PM
comment
Renee -- I only e-mailed people who had problems. You
had no problems with your phylogeny :) so you didn't get
an e-mail -- you're all set to write your paper!
James (no email) from 206.240.200.156 at 03/05/99 03:10PM
comment
I really think that's it's strange to base a timing hypothesis on something that it random. It way avg. out overall that someting evoloves at a simalar rate but I really have to wonder about avgs. too. I've been in many classes where there are ten A's and ten F's. Class avgs. a C but nobody got one.
Greg (no email) from 206.240.201.226 at 03/05/99 03:41PM
comment
Studies indicate that sometimes, for some species and some genes, the molecular clock hypothesis is supported. It is supported by passing the relative rates test. To perform the relative rates test you need a phylogeny for a group of species. If the DNA is evolving at a constant rate then species which have evolving separately for the same amount of time will have the same number of differences. If the individuals are tested and have the same number of differences then it passes the relative rates test, if not then it is not supported by the relative rates test.
James (no email) from 206.240.200.156 at 03/05/99 03:55PM
comment
I think I got it - I really not competely buying into MCH though. Call me cynical.
Renee (no email) from crockett227.iswt.com at 03/05/99 03:59PM
comment
Thanks. Bye and everyone have a great weekend.
Rebecca Irwin (rirwin@utm.edu) from paydial13.utm.edu at 03/12/99 02:49PM
comment
Welcome to lab, 12 March 1999. ANNOUNCEMENTS: Don't forget to turn in your toucan phylogeny paper by 5:00 on Friday to the Biology Department Office. If you handed in a rough draft and haven't picked it up yet, please do pick it up from the Bio. Dept. Office. FOR TODAY'S LAB: one of the reasons it's hard to define species (as indicated by the different species concepts you wrote about in your homework this week) is that there is variation within species so that it's hard to tell where species boundaries are. In your "hello" message today please define one of the forms of variation: define either polymorphism, clinal variation, or a hybrid zone. Once we've got these forms of variation defined, we'll start looking at speciation so start looking at Lab Manual Chapter XIII Qu. 5, or ask questions about speciation.
Greg (no email) from 192.239.150.156 at 03/12/99 02:53PM
comment
Polymorphism is variation within a population where the individuals are different but are in the same population since they reproduce with one another. ex. screech owl or snow goose. Clinal variation refers to variation over geography ex. mammal size from north to south. Hydrid zones are geographic areas where different forms of organisms contact and interbreed but outside the zones are different from each other ex. flickers.
kim (no email) from DIALUP50.tnhun.usit.net at 03/12/99 02:53PM
comment
Hello. Polymorphism refers to variation within a population where different individuals in the population have distinctly different structures, colors, biochemistry, etc. but clearly belong to the same population since they reproduce with each other.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 02:57PM
comment
Hello Kim and Greg. Good definitions. Can you elaborate
on some of the examples while we're waiting for other
arrivals? And others, as you arrive -- please define allopatric,
sympatric, or parapatric speciation.
Renee (no email) from crockett228.iswt.com at 03/12/99 02:57PM
comment
Hello! A hybrid zone occurs in geographic areas where 2 distinctly dif forms of organism contact each other and interbreed. Outside the zone the 2 forms have distinct diff from each other.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 02:58PM
comment
Hello Renee. Good definition of hybrid zone. Can you
give an example?
kristi (no email) from paydial02.utm.edu at 03/12/99 02:59PM
comment
Hello!Polymorphism is a variation within the populations where some individuals will have different
characteristics traits such as color,structures,etc. but since they can all reproduce with each
other then they belong in the same population.
james (no email) from 206.240.200.156 at 03/12/99 03:00PM
comment
hello- polymorphism variation within a population where dif individuals in the same pop have disticly diffrent features
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:00PM
comment
Hello Kristi! Good definition of polymorphism. Can you give
an example?
Greg (no email) from 192.239.150.156 at 03/12/99 03:00PM
comment
Screech owls and Snow geese come in different color phases (colors) but can and do reproduce with each other. The phases are not related to sex, age, or environmental factors. They are different yet can be part of the same population. Mammals in the south tend to be smaller than mammals in the north. Flickers are separated into red-shafted flickers and yellow-shafted flicker. In the hybrid zone they can and do reproduce with one another. Outside the zone each is fixed with a different DNA form and only in the hybrid zone does both forms occur.
Renee (no email) from crockett228.iswt.com at 03/12/99 03:00PM
comment
allopatric spec occurs when groups that evolve to be seperate species are in different locations and are isolated from each other so they cannot move between the locations.
James (no email) from 206.240.200.156 at 03/12/99 03:01PM
comment
Polymorhism ex. UTM students from dif ethinic groups.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:02PM
comment
Hello James. OK, I think we've seen how variation can
be present in species. Now let's look at speciation. There
are three categories of speciation -- allopatric, parapatric,
and sympatric. Pick one of these and define it.
Greg (no email) from 192.239.150.156 at 03/12/99 03:02PM
comment
note-screech owls and snow geese do not reproduce with each other, I meant that within each species the different color phases reproduce with each other.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:02PM
comment
Good definition of allopatric, Renee. Now the rest of you,
do parapatric or sympatric.
Renee (no email) from crockett228.iswt.com at 03/12/99 03:03PM
comment
An example of a hybrid zone would be the red shafted flickers and the yellow shafter flickers that breed with each other in a specific area, but outside of that area they do not breed with each other.
Greg (no email) from 192.239.150.156 at 03/12/99 03:03PM
comment
Sympatric speciation is speciation that occurs when the groups that evolve to be separate species occur together in the same geographic area.
James (no email) from 206.240.200.156 at 03/12/99 03:04PM
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Sympatric speciation-speciation that occurs when the groups that evolve to be sperate species occur together in the same geoographic area.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:04PM
comment
Good examples, Greg and James. Thanks for the clarification
on the owls and geese, Greg.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:05PM
comment
Good definitions of allopatric and sympatric. So in allopatric the
groups that evolve to be dif. species are in totally dif. geog. areas;
in symp. they're in the same area. How about parapatric?
Greg (no email) from 192.239.150.156 at 03/12/99 03:06PM
comment
Parapatric speciation occurs when the groups that evolve to be separate species are geographic neighbors, individuals can move between the areas.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:07PM
comment
Thanks for the definition of parapatric, Greg. OK now we've
got the definitions we can start looking at question 5. The
first sentence says "discuss the role of gene flow, genetic drift, and natural selection in speciation." So which
of these forms of evolution makes speciation unlikely? Which make it likely? And why? (you
can answer all or part of this.)
James (no email) from 206.240.200.156 at 03/12/99 03:08PM
comment
Gene flow make speciation not possible I would think.
Greg (no email) from 192.239.150.156 at 03/12/99 03:09PM
comment
Gene flow tends to make populations similar to each other, this tends to prevent speciation from occurring. Genetic drift and natural selection tend to make populations different from each other. This can result in evolution of differences among populations and therefore can cause speciation to occur.
kristi (no email) from paydial02.utm.edu at 03/12/99 03:10PM
comment
Parapatric speciation occurs if populations that evolve into new species are geographic neighbors and individuals can move between the areas since they are next to each other.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:11PM
comment
James, gene flow certainly makes speciation much less
likely. As to whether it makes it impossible, that's something
that evolutionary biologists are still not sure of and arguing about.
If parapatric speciation occurs, then speciation can occur with some
gene flow; some models of sympatric speciation suggest speciation can
occur with some gene flow. Why does gene flow make speciation unlikely
or impossible? And in these forms of speciation that suggest speciation
can occur with some gene flow, what counteracts the effect of gene flow?
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:12PM
comment
Greg has noted the reason gene flow makes speciation unlikely,
and explained the roles of genetic drift and natural selection.
If gene flow makes speciation unlikely, how can speciation occur
in parapatric speciation in which, as just noted by Kristi, individuals
CAN move between populations so gene flow does occur?
Greg (no email) from 192.239.150.156 at 03/12/99 03:13PM
comment
Gene flow tends to make populations similar. If a species remains similar it cannot speciate to become totally separate species. If parapatric speciation is occurring there must be a strong selection to counteract the effect of gene flow. A form must have a high fitness in one area and a low fitness in the neighboring area, and hybrids between these forms do not have a high fitness in either area.
James (no email) from 206.240.200.156 at 03/12/99 03:14PM
comment
It seems with sympatric speciation that there must either be some sort ofecological isolation or some strong disruptive sectionthat produces selection for the extremes and aginst the intermediates
James (no email) from 206.240.200.156 at 03/12/99 03:16PM
comment
It still seems that gene flow cannot occur for speciation to happen, even with the examples. The only way I can concieve of this happening would be if they migrated to mate and some group migrated to another place to mate and not a signifigant amount of the two groups ever got in contact.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:17PM
comment
Good, Greg and James have noted strong disruptive selection
as the process that can (possibly) counteract the effect
of gene flow in parapatric and some forms of sympatric
speciation. So with regard to the rest of question 5, you've
pretty much answered it -- in parapatric and some forms of sympatric'
speciation, there has to be strong disruptive selection or speciation
won't occur. In allopatric speciation, or sympatric speciation with
ecological isolation, gene flow between the groups can't occur and
weaker natural selection or genetic drift can result in groups becoming
different, evolving into different species.
Renee (no email) from crockett228.iswt.com at 03/12/99 03:18PM
comment
For speciation to occur, there must be stong selection to counter act the effects of gene flow.
James (no email) from 206.240.200.156 at 03/12/99 03:19PM
comment
Hey Renee, is crockett228.iswt. in crockett county?
kristi (no email) from paydial02.utm.edu at 03/12/99 03:19PM
comment
Natural selection and genetic drift make speciation possible because they can make populations different from each other.If parapatric speciation occurs then gene flow is possible to occur, so there are
effects of natural selection that can cause evolution of differences within the different populations.
If allopatric speciation occurs there are few effects of natural selection
and genetic drift,because of the gene flow not present,but theses effects could result in the species having different enough characteristics to become different species.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:22PM
comment
James, many evolutionary biologists would agree with you! Let me
give you a proposed example, though, of parapatric speciation. There
are areas where there are abrupt changes in soil type so in some areas
there are heavy metal ions in the soils and in neighboring areas there
aren't (this can be from pollution but also occurs because of abrupt
changes in the underlying rock.) Some forms of plant can tolerate the
heavy metals -- they have adapted to detoxify them -- but do very poorly
in normal soils (apparently it takes a lot of energy to produce the
detoxification system so they don't compete well on normal soils.) Other
plants are killed by the heavy metal ions but do fine in normal soil.
It is possible for pollen and/or seeds to move from one area to the next,
but the forms do so badly in the "wrong" area for them that they mostly die
out. The result of this (strong disruptive selection) is that most individuals
resulting from gene flow die. So there's really very little gene transfer between
areas and these different plant forms have evolved other differences and are
considered different species at least by the phylogenetic concept.
James (no email) from 206.240.200.156 at 03/12/99 03:22PM
comment
Dr. Irwin, what's the attendance policy for lab?
Renee (no email) from crockett228.iswt.com at 03/12/99 03:22PM
comment
Yes it is from Crockett Co. How bout alamo.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:23PM
comment
Kristi, good expanation of qu. 5
Now, everyone, James brought up this idea of "ecological isolation"
at some point. What IS ecological isolation?
James (no email) from 206.240.200.156 at 03/12/99 03:23PM
comment
Been there- went to high school in Halls.
James (no email) from 206.240.200.156 at 03/12/99 03:24PM
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Ecological Isolation - some ecological diffrence that prevents the motion of genes between populations.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:24PM
comment
James: attendance policy: you're supposed to be there. You
get a point each time you're present and contributing (you
need to contribute something beyone "hello" for the full
point.) If you miss three labs your grade automatically
drops one level (ex. from B to C). If you miss three more,
your grade would drop another level. Etc.
Greg (no email) from 192.239.150.156 at 03/12/99 03:25PM
comment
Ecological isolation is when different groups occur in the same geographic area but do not contact each other because of some ecological difference that prevents gene flow between the groups. An example would be flowers that attract different pollinators and are only pollinated by certain specialist pollinators and the pollinators will not have gene flow between them.
kim (no email) from DIALUP5.tnhun.usit.net at 03/12/99 03:25PM
comment
ecological isolation is in which different groups occur in the same geographic area but do not contact each other because of some ecological difference that prevent gene flow between the groups.
James (no email) from 206.240.200.156 at 03/12/99 03:26PM
comment
Greg, you probably got about a thousand lab points.
Renee (no email) from crockett228.iswt.com at 03/12/99 03:27PM
comment
eco isolation occurs in the same geo area but a species does not does not come in contact with others because of the goe diff. It prevents gene flow.
Greg (no email) from 192.239.150.156 at 03/12/99 03:27PM
comment
James-I wish it worked that way, I would only have to come to every other lab or so to get the full credit.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:27PM
comment
OK, with James' definition of ecological isolation, I'd
like you all to take a look at question 10. It asks about
whether sympatric speciation would be likely or not in certain
situations. The idea is that sympatric speciation will be likely
if there's something that causes ecological isolation; otherwise
it is less likely (or James might argue that it's impossible. I'm
not sure if it's possible or not.) So what you want to do for
this question is see if there's something that would make ecological
isolation likely or not. Start with 10a and 10b. In which of these
would sympatric speciation be more likely? Why?
kristi (no email) from paydial02.utm.edu at 03/12/99 03:28PM
comment
Ecological isolation is when different groups occur in the same geographic are but do not have contact with each other because of an ecological difference
that prevents gene flow between them.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:30PM
comment
But, alas, Greg, if you only came to every other lab you
would automatically drop too many grade levels. And
unfortunately there are only about 15 total points for lab
participation so you can't actually accumulate a thousand.
James (no email) from 206.240.200.156 at 03/12/99 03:30PM
comment
I think with b) that it would be very difficult to have ecological isolation, only geographic isoltion would apply easily.
Greg (no email) from 192.239.150.156 at 03/12/99 03:30PM
comment
10A would be most likely to speciate through sympatric speciation. Due to the specificity of the host requirement, the different populations may never come in contact with each other.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:31PM
comment
Good definitions of ecol. isol., all of you. Now, how
about 10a and 10b. Let's see if someone has answered
while I've been typing...
Renee (no email) from crockett228.iswt.com at 03/12/99 03:31PM
comment
for a it would be possible because there is a potential for different groups to be geographically isolated from each other.
kim (no email) from DIALUP5.tnhun.usit.net at 03/12/99 03:31PM
comment
it would be more likely in 10a part. it is more likely because different groups of parasites could have different host organisms.
kristi (no email) from paydial02.utm.edu at 03/12/99 03:33PM
comment
For A) it is likely because different groups could be ecologically isolated on different hosts, so that a parasitic breeds on a
specific host.
For B)It is unlikely because there would be alot of gene flow if there is mating in the air so speciation would be unlikely.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:33PM
comment
I suspected as much -- Greg and James answered a and b
while I was typing. The rest of you (Renee, Kim, Kristi) can you
do 10c and d? In which of THOSE situations would sympatric
speciation be more likely?
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:34PM
comment
Good it looks like everyone got 10 a and/or 10b. So you
see the basic idea. So can you apply it to 10c and d now?
James (no email) from 206.240.200.156 at 03/12/99 03:34PM
comment
I would guess that there is a direct proption between moblity of a species and the chance that it can be isolated reproductively.
Greg (no email) from 192.239.150.156 at 03/12/99 03:35PM
comment
10D is more likely to speciate through sympatric speciation because the specific kind of pollinator would be attracted to a specific flower and the pollinators would probably not have gene flow between them.
kim (no email) from DIALUP5.tnhun.usit.net at 03/12/99 03:36PM
comment
it would be more likely in 10d. Because groups could become ecologically isolated if they attratcted different types of pollinators. This would prevent gene flow.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:36PM
comment
James -- seems likely that there would be at least a strong
relationship between mobility of a species and reproductive
isolation. However for 10c and 10d it could be that pollen
from either species could move as far (depending on how
far the winds in the region blow the pollen and how far the
pollinators fly) but sympatric speciation would be more
likely in one situation than in the other.
James (no email) from 206.240.200.156 at 03/12/99 03:36PM
comment
Depends on the polenator. If that joker is a rat or an ant I'd say that the chances are pretty great. If it some migating or long ranging bird the I'd say that the chaces are kinda slim.
Renee (no email) from crockett228.iswt.com at 03/12/99 03:36PM
comment
For C, if the pollen is dispersed by wind, it can go anywhere so it is not isolated. but for D, there is one pollinator, so it would be isloated.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:37PM
comment
Kim and Greg -- good explanations of 10D. So note, James,
that mobility isn't necessarily the whole explanation for
ecological isolation.
James (no email) from 206.240.200.156 at 03/12/99 03:38PM
comment
If one is more likely than the other it's got to be c) more likely than d).
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:38PM
comment
James -- most long ranging species do spend time within local
areas so within an area could result in ecol. isol.
kristi (no email) from paydial02.utm.edu at 03/12/99 03:39PM
comment
10c) is unlikely because there would be al large amount of gene flow since the wind will disperse pollen and speciation would be unlikely.
!0d)It is likely because groups can become ecologically isolated since the attract different
kinds of pollinators.This prevents gene flow and makes speciation likely.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:40PM
comment
James, everyone else argued that D was more likely; note
Renee's explanation, she said it concisely. Do you disagree?
James (no email) from 206.240.200.156 at 03/12/99 03:41PM
comment
Okay so let me get this strait, pollenators are generally not non-longranging (is that a word or somethig I created?)
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:42PM
comment
Incidentally, we have now reached the point that the other
labs reached. Would you like to leave early? If so, you
can -- have a great spring break and don't forget to
hand in your paper before you leave (so I have to work over
break.) If not, you're welcome to stay and continue the
discussion/ ask questions.
James (no email) from 206.240.200.156 at 03/12/99 03:43PM
comment
I not totally following here....
kim (no email) from DIALUP5.tnhun.usit.net at 03/12/99 03:43PM
comment
see ya later! Everyone have a great and safe spring break!
Greg (no email) from 192.239.150.156 at 03/12/99 03:43PM
comment
I would very much enjoy and appreciate being excused early. I'll see you in two weeks. Have fun over spring break everyone.
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:44PM
comment
James, if pollinators were really quickly long ranging they
wouldn't effectively pollinate the plants within an area, would
they? I mean, they'd fly off somewhere and maybe never find another
member of that plant species. So I think you'd expect plants to evolve traits
that attract non-longranging (to use your newly created word.)
kristi (no email) from paydial02.utm.edu at 03/12/99 03:44PM
comment
Goodbye everyone,have a great spring break!
James (no email) from 206.240.200.156 at 03/12/99 03:45PM
comment
Okay that makes sense. I'm outta here.
Renee (no email) from crockett228.iswt.com at 03/12/99 03:46PM
comment
Bye! Dr, Irwin...Don't work too hard over break! See ya!
Rebecca I (no email) from paydial13.utm.edu at 03/12/99 03:46PM
comment
oops I left a word off the last one. they'd evolve
to use non-longranging pollinators. And then the idea is
that if a species has a trait that attracts one specific pollinator,
but there's a mutation so some members now have a trait that would
attract a different specific pollinator (say it now has a longer flower and attracts a pollinator with a longer
tongue), this is a situation in which
sympatric speciation could occur -- the original flower would be pollinated by
short-tongued pollinators, the new form by long-tongued, and so there would be little/no gene
flow between them because they attract different pollinators. Does this make more sense (are you
still there)?
Rebecca Irwin (rirwin@utm.edu) from paydial08.utm.edu at 03/26/99 02:48PM
comment
Welcome to lab, 26 March, 1999. ANNOUNCEMENTS: DON'T FORGET the exam on Monday! Remember you can take an hour and a half for the exam either between 1 and 3 or between 5 and 7:30. I will lead a REVIEW SESSION Sunday at 2:00, Brehm Hall 211. NEXT WEEK labs will not meet (because of the Good Friday Holiday on Friday); you will have two homework questions to answer and they will be due on Thursday by 5:00. FOR TODAY'S LAB: any time during lab feel free to ask questions about any of the material to help prepare for the exam. To start the discussion, I noted some confusion in the homeworks I got from you yesterday about chromosomes and speciation. In your hello message, please answer one of the following questions about a situation in which an individual in a population is produced with a chromosomal duplication (all the chromosomes are duplicated so it has twice as many chromosome sets as did the original individuals in the population). Try to answer the question that has your group number: (1) Is this individual likely to be healthy? (2) Is this individual likely to be fertile? (3) Could this individual reproduce with members of the original population? (4) If this individual could reproduce with a member of the original population, would their offspring be healthy and/or fertile? (5) If this individual could reproduce with another individual like itself (also with a duplicated number of chromosomes) would their offspring be healthy and/or fertile?
Greg (no email) from 206.240.201.226 at 03/26/99 02:50PM
comment
#4) If the individual with duplicated chromosoes reproduced with a member of the original population, their offspring would be healthy AND sterile.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 02:51PM
comment
Hello Greg. Good answer. While we're waiting for the others to arrive,
can you explain why the offspring would be sterile?
Greg (no email) from 206.240.201.226 at 03/26/99 02:51PM
comment
The individual would be sterile because during meiosis the chromosomes have to pair, the offspring would have an odd number of chromosomes which means the chromosomes will not be able to pair evenly and the daughter cells end up with an unbalanced number of chromosomes and are not functional and don't produce functional gametes.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 02:53PM
comment
Greg, you can't possibly type that fast! Good answer.
Greg (no email) from 206.240.201.226 at 03/26/99 02:53PM
comment
Thanks, I guess I have a gift. I just wish organic evolution was as easy as typing.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 02:55PM
comment
When I took my first organic evolution course I would type
up my class notes to try to understand them and I used
to wish understanding was as easy as typing, too.
Greg (no email) from 206.240.201.226 at 03/26/99 02:55PM
comment
Should I answer some of the other questions to keep things moving?
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 02:57PM
comment
Greg -- why don't you answer #5 and explain any differences
between your answer to #5 and the answer you just gave to
#4.
Renee (no email) from crockett225.iswt.com at 03/26/99 02:57PM
comment
hello
kim (no email) from DIALUP52.tnhun.usit.net at 03/26/99 02:58PM
comment
i'm here.
Greg (no email) from 206.240.201.226 at 03/26/99 02:59PM
comment
If the individual with duplicated chromosomes mated with an individual like itself their offspring would be healthy AND fertile. This is because the offspring would have an even number of chromosomes and the pairing processs during meiosis would not leave any unmatched chromosomes.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 02:59PM
comment
Hello Renee. Read over my first announcement and answer
1, 2, or 3.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 02:59PM
comment
Hi Kim, you can also answer 1, 2, or 3.
Renee (no email) from crockett225.iswt.com at 03/26/99 03:00PM
comment
The individuals would be healthy, but their offspring would be sterile.
Renee (no email) from crockett225.iswt.com at 03/26/99 03:01PM
comment
let me change that, the offspring would be healthy, but they would be sterile.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:01PM
comment
Renee-- you are correct that the individuals would be
healthy. Whether or not their offspring would be sterile
depends on who they reproduce with, a member of the original
population or another individual with duplicated chromosomes.
Greg should be writing about this now, I think.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:02PM
comment
Renee -- my last comment still holds. They would be healthy and their
offspring would be healthy but might or might not be sterile depending
on who the other parent is.
Greg (no email) from 206.240.201.226 at 03/26/99 03:02PM
comment
I've already answered the questions concerning the offspring of similar and dissimilar matings.
kim (no email) from DIALUP52.tnhun.usit.net at 03/26/99 03:04PM
comment
#11 the offspring would be healthy but the would be sterile.
Renee (no email) from crockett225.iswt.com at 03/26/99 03:05PM
comment
The offspring would be sterile if a 4N mated with a 2N because you would get a 3N individual. You cant get pairs to match up in 3N.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:06PM
comment
Greg -- right, I just found your explanation. Renee, read
Greg's explanations, they're good and clear, I think. Note that
whether these individuals offspring are fertile or not depends on whether they
have odd or even numbers of chromosome sets -- if even, which they
get if they mate with other individuals like themselves, then chromosomes can
pair with homologous chromosomes during meiosis so they can make gametes and they're
fertile. If they have odd chromosome set numbers then the chromosomes can't
pair right in meiosis and they can't produce functional gametes.
kim (no email) from DIALUP52.tnhun.usit.net at 03/26/99 03:07PM
comment
#11 The offspring would not be able to reproduce with the orginal population.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:09PM
comment
Kim by #11 do you mean 1 (did you type an extra 1)? Anyway,
the individual with duplicated chromosomes is healthy and
fertile (it has an even number of chromosome sets) and if it
reproduces with the original type in the population it has
an offspring with an odd number of chromosome sets which is sterile
but if it reproduces with another like itself then the offspring has
the same even number of chromosome sets that it does and is fertile.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:10PM
comment
Kim: the duplicated individual could reproduce with the original
but their offspring would be sterile.
kim (no email) from DIALUP52.tnhun.usit.net at 03/26/99 03:11PM
comment
Sorry. i just get so mixed up when thinking about this.
Renee (no email) from crockett225.iswt.com at 03/26/99 03:12PM
comment
Is this the result of 2 different individuals breeding w/ each other or 2 of the same individuals breeding w/ one another and it ends up 2N and 4N?
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:12PM
comment
So, everyone, the points here are: first, be careful and think
whether any individual you're talking about has odd or even numbers
of chromosome sets -- if odd, it's sterile, if even, it's fertile.
Second: chromosomal duplication produces a new species because if the indiv. with the duplication
reproduces with the original type the offspring are sterile. But the individual
with the duplication is not, itself, sterile so it can be part of a new sexually
reproducing species, IF it has another individual like itself to reproduce with. So
HERE'S THE NEXT QUESTION: Where would another individual with duplicated chromosomes come
from, most likely?
Greg (no email) from 206.240.201.226 at 03/26/99 03:13PM
comment
Another individiual with duplicated chromosomes would most likely come from asexual reproduction.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:14PM
comment
Kim -- you don't have to apologize; everyone gets confused
thinking about this, that's why we're discussing it. Can
you ask about what's confusing?
bj (no email) from 170.143.229.165 at 03/26/99 03:14PM
comment
couldn't get logged on, Sorry i'm late
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:17PM
comment
Renee -- I'm not sure exactly what you're asking. If a 2N and a 4N reproduce the
offspring is 3N. If a 4N and a 4N reproduce with each other the offspring is
also 4N. Does this answer your question or were you asking something else?
kim (no email) from DIALUP52.tnhun.usit.net at 03/26/99 03:18PM
comment
I guess what gets me confused is trying to understand when the offspring are capable of reproducing and when they are not.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:18PM
comment
Note, all, that Greg has the answer to where other individuals
with chromosomal duplications come from. The individual with the duplication
reproduces asexually; the result is more individuals like it. Then they can
reproduce sexually with each other and their offspring will be fertile (like
them.)
Renee (no email) from crockett225.iswt.com at 03/26/99 03:19PM
comment
I guess what I am asking is if you have a 2N and a 4N, are they both the same species. For example, they are both German shepard dogs? But one is 2N and the other is 4N.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:20PM
comment
Kim: it depends on the number of chromosome sets. If it's even (say, 4N)
then they can reproduce, if it's odd (say, 3N) then they can't. If the
original population is 2N (like us, diploid, 2 copies of each chrom.) then
the duplicated individual is 4N (so it can reproduce sexually) but when the 4N
reproduces with the 2N the offspring are 3N (so they can't reproduce sexually.)
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:21PM
comment
Renee -- your question gets to the point of this, good (others, take note of this!)
The 2N and 4N are different species because their offspring are sterile -- they can't
reproduce with each other to produce fertile offspring, so they're different species
by the biological species concept, and having the new trait of being 4N makes the 4N
individual a new species by the phylogenetic species concept.
BJ (no email) from 170.143.229.165 at 03/26/99 03:22PM
comment
In response to Renee's question wouldn't they be the same species according to the phylogenetic concept and not the biological species concept
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:22PM
comment
BJ -- hi, you came in in the middle of a discussion, sorry
I couldn't say hi faster!
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:23PM
comment
BJ -- different by the phylogenetic, too; in general, if
two forms can't reproduce to produce fertile offspring they're
different species by any concept.
Renee (no email) from crockett225.iswt.com at 03/26/99 03:24PM
comment
Thanks!! That answers my confusion!
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:24PM
comment
OK everyone, we have another topic to cover. You can keep
asking about this one, too, but if you're ready to move
on here's the next topic: founder effect speciation. So
to start, what IS founder effect speciation?
Greg (no email) from 206.240.201.226 at 03/26/99 03:25PM
comment
Founder effect speciation is when a small number of individuals disperse to a new location which was previously unoccupied by that species. A new small population is formed and genetic drift occurs.
kim (no email) from DIALUP52.tnhun.usit.net at 03/26/99 03:28PM
comment
Founder effect speciation is when a small number of individuals move out into a new location which has previously been unoccupied by that species.
Renee (no email) from crockett225.iswt.com at 03/26/99 03:28PM
comment
It is where a small number of indificuals disperse to a new location previously umoccupied by that species.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:29PM
comment
Greg has given a good complete def. of founder effect speciation. Now, consider qu. 8 in ch xiii of your manual.
It asks for an argument that founder effect speciation is likely and an argument that it is unlikely. These arguments are
based on effects of drift, so what ARE the effects of drift?
Greg (no email) from 206.240.201.226 at 03/26/99 03:30PM
comment
Genetic drift causes a decrease in genetic variation.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:30PM
comment
Kim and Renee you have good definitions too.
BJ (no email) from 170.143.229.165 at 03/26/99 03:31PM
comment
with gen.drift there would be a loss of variation so new pop. unlikely to evolve much, not expected to become a new species
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:31PM
comment
Does the decrease in genetic variation caused by drift make it more or less likely that the new pop. will evolve to be a new species?
Greg (no email) from 206.240.201.226 at 03/26/99 03:33PM
comment
The loss of genetic variation means that the population will be less likely to evolve to a new species.
Renee (no email) from crockett225.iswt.com at 03/26/99 03:33PM
comment
They will not evolve into new populations.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:33PM
comment
note everyone -- BJ answered my question before I asked it (good job, BJ) So that's an
argument that founder effect speciation is UNLIKELY. There's also an arguement that it's
likely; it's based in part on other possible effects of drift. Before variation is lost,
how do traits evolve through drift?
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:34PM
comment
Greg and Renee good (but Renee, I think you mean they won't evolve into new species, not populations.)
Renee (no email) from crockett225.iswt.com at 03/26/99 03:35PM
comment
the traits will evolve at random in the pop.
BJ (no email) from 170.143.229.165 at 03/26/99 03:35PM
comment
the changes in the allele frequencies are random and may move the pop. to a near new adaptive peak. As the pop. grows larger you see less drift. through nat. sel. pop. evolves to a new adaptive peak
Greg (no email) from 206.240.201.226 at 03/26/99 03:36PM
comment
Genetic drift changes populations randomly but it may not occur for very long since the population is probably growing exponentially at first. The larger population will no longer show big effects from genetic drift. The new, large population may be closer to a different adaptive peak from the original poopulation and through natural selection they will evolve to a new peak, different from the original, and therefore become a new species.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:37PM
comment
BJ and Renee, good. BJ has introduced the important concept of adaptive peaks and explained
that drift will randomly change traits so they will end up near new adaptive peaks. This
is basically the answer -- the reason that founder effect speciation is likely. To make
sure it makes sense, can someone explain what adaptive peaks are?
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:38PM
comment
Greg, you've got it explained well, too. Everyone -- what's an adaptive peak?
Greg (no email) from 206.240.201.226 at 03/26/99 03:39PM
comment
An adaptive peak is the peak of an adaptive landscape. An adaptive landscape is a discription of the fitness of all possible combinations of different traits in a population. Adaptive landscapes are frequently represented graphically.
Renee (no email) from crockett225.iswt.com at 03/26/99 03:40PM
comment
Adaptive peaks are where combinations of traits have high fittness and they appear as peaks on a graph.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:40PM
comment
So an adaptive peak is a combination of traits with high fitness.
Do populations always evolve to the highest adaptive peak (the combination
of traits that, together, give the highest fitness?)
BJ (no email) from 170.143.229.165 at 03/26/99 03:41PM
comment
they don't always evolve to the peak with the best traits for the pop.
Greg (no email) from 206.240.201.226 at 03/26/99 03:41PM
comment
Populations tend to evolve to towards the closest adaptive peak and not the highest. This is because peaks are separated by a valley which has a combination of traits which have a very low fitness and the individuals cannot evolve across a valley and therefore evolve towards the closest adaptive peak.
Renee (no email) from crockett225.iswt.com at 03/26/99 03:42PM
comment
No, they tend to evolve toward the closest peak not the one with the highest fitness.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:45PM
comment
BJ's right, they don't always evolve to the highest fitness peak. They
evolve to the peak that's closest to the combination of traits a population
starts with. So if genetic drift in the small, newly founded populations of
a founder event changes the frequencies of traits randomly, then the population
is likely to end up with a trait combination near a different adaptive peak,
and evolve to that new peak. It would thus be very different from the original
population -- likely to be a new species or on its way to becoming one. OK, you've
reached the point I wanted to get to in the labs. If you have more questions (there
is, after all, an exam on Monday -- don't forget! And if you're interested, a review
session Sunday at 2) you can stay around but if you'd like to leave early (now) you
may do so. Have a good weekend, but study!
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:45PM
comment
Note that Greg has a good explanation of why populations don't evolve to the highest peak,
but rather to the closest one.
Greg (no email) from 206.240.201.226 at 03/26/99 03:46PM
comment
Bye, see you on Monday when we have a wonderful opportunity for expressing our knowledge of organic evolution for grading purposes.
Renee (no email) from crockett225.iswt.com at 03/26/99 03:47PM
comment
Will you be conducting the review session, and will there be time before or after the session to ask questions one on one?
kim (no email) from DIALUP52.tnhun.usit.net at 03/26/99 03:47PM
comment
bye.
Rebecca I (no email) from paydial08.utm.edu at 03/26/99 03:49PM
comment
I will be conducting the review session; I'll be busy before the session but
should have time afterwards to answer questions one on one (I might have to
take a bit of a break to take care of Camille but will have time after that.)
renee (no email) from crockett225.iswt.com at 03/26/99 03:50PM
comment
Thanks ByE
Rebecca Irwin (rirwin@utm.edu) from paydial10.utm.edu at 04/16/99 02:48PM
comment
Welcome to lab, 16 April 1999. ANNOUNCEMENTS: DON'T FORGET: if you want to give me a rough draft of your critique assignment I must receive it by 5:00 Wednesday. After that time, you can still ask questions but I will not read over papers. If you have questions on the paper you are critiquing, be sure to ask me. FOR TODAY: to prepare for the critique we will be evaluating the brief paper that you've read on the web. Note that if you don't have a copy of it in front of you, you should open a second window in your web browser so you can easily refer to the paper during lab today. The address of the paper is: http://www.utm.edu/~rirwin/391CritiqueWarmUp.htm The reason we're doing this exercise is that in your critique you will have to evaluate the methods used in making and interpreting the phylogeny presented in the paper you're reading about aphids. . The points we discuss today about this small, made-up paper will also apply to your real critique assignment. TO GET STARTED: I've asked you to learn what some terms mean. Below, I'm asking you to define some of them -- find the question after your name, and answer it (if you're not sure you can also ask questions.) I've assigned the questions based on who I think will be here today -- if anyone else is here let me know and I'll assign you a question. Once you've answered your question, look at the other questions and the answers other people are giving. We will use these a place to start a discussion of the good and bad aspects of the methods used in this paper (these will also apply to your real critique).
Renee: What does it mean to say that different traits in a phylogenetic analysis were equally weighted?
Kristi: What is bootstrap analysis, and for what does such an analysis provide support (bootstrap support)?
Greg: What does it mean to do a heuristic search?
Kim R: What does it mean when it says, in the paper, "Sequences were aligned by visual examination."
RENEE (no email) from crockett227.iswt.com at 04/16/99 02:53PM
comment
Hello: When traits are equally weighted that meants they are taken into consideration equally and the numbers that are studied were considered equally. One is not studied more than another.
kimr (no email) from DIALUP27.tnhun.usit.net at 04/16/99 02:53PM
comment
Hello. In this paper aligned means to figure out which sites are homologous.
Greg (no email) from 206.240.201.225 at 04/16/99 02:55PM
comment
Heuristic searches are effective with large datasets and branch-and-bound algorithms become impractical. One way to do a heuristic search is stepwise addition. As each taxon is added, only the best or few best trees are saved before adding an additional taxon. The final output is sensitive to which taxa are chosen to start the search and may not be the best ones.
kim (no email) from DIALUP27.tnhun.usit.net at 04/16/99 02:55PM
comment
Dr. Irwin; I need to leave a little early today. Do you mind?
kristi (no email) from dialup03.utm.edu at 04/16/99 02:58PM
comment
Bootstrap analysis is a statistical technique where a computer creates a new dataset from
the existing one by repeated sample. After repeating the process
many times particular branches occur in 50%,80%,100% of the trees estimated
The more times a branch occurs then it is supported that the brach actually exists.
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 02:59PM
comment
Hello Renee and Kim, good definitions. So now I'll ask
some further questions on these topics. With regard to
equal weighting, in this paper (the one on the web that we're looking at today) it says they weighted transitions
and transversions equally. What are transitions and transversions?
Do you think it is a good thing or a bad thing to weight them equally?
With regard to alignment, in this paper it says sequences were aligned
visually. Why is alignment important in a study of phylogeny? Is aligning
the sequences visually likely to be reliable?
Greg (no email) from 206.240.201.225 at 04/16/99 03:01PM
comment
Transition is when, in DNA, a mutation substitutes a purine for a purine or a pyrimidine for a pyrimidine.
Transversion is a mutation that substitutes a purine for a pyrimidine or a pyrimidine for a purine.
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:02PM
comment
Kim, we'll probably finish a little early so it should be OK. If we're not done when you
leave be sure to read the end of the discussion sometime. Hello Kristi and Greg. Good
definitions so now I'll ask more questions about them. With regard to a heuristic search,
as Greg noted, it doesn't always find the best phylogeny for a set of species and characters.
What can be done to make it more reliable -- more likely to find the best phylogeny? Did they
take steps to make it more reliable in the paper we're looking at on the web? With regard to
bootstrapping, what does bootstrapping indicate about the reliability of the phylogeny shown
in the paper we're looking at on the web? (Based on the numbers in the figure.)
kim (no email) from DIALUP27.tnhun.usit.net at 04/16/99 03:03PM
comment
Transition is a mutation that substitues a purine for a purine or a pyrimidine for a pyrimidine. Transversion is a mutation that substitutes a purine for a pyrimidine or a pyrimidine for a purine.
Renee (no email) from crockett227.iswt.com at 04/16/99 03:03PM
comment
Transitions are in DNA when a mutation changes a purine for a purine or a pryimidine for a pryimidine. Transversios changes a purine for a pryimidine and vise versa.
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:03PM
comment
Greg has a good definition of transitions and transversions.
Which kind of mutation is more likely (occurs more often)?
How would this affect the chance of convergent evolution
in transitions versus transversions?
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:05PM
comment
Well it looks like everyone has definitions of transitions and
transversions. To be picky, I guess I should ask what purines
and pyrimidines are (just to make sure you remember.)
Greg (no email) from 206.240.201.225 at 04/16/99 03:05PM
comment
The problem of heuristic searches not finding the best possible tree can be dealt with by doing a large number of searches, starting with different taxa and adding subsequent groups randomly or in various prespecified orders. The paper dealt with this by doing three different searches using randomly chosen initial trees.
renee (no email) from crockett227.iswt.com at 04/16/99 03:06PM
comment
bootstrapping would say it is reliable since the numbers are 88 90 and 100. You do have one 52 though.
kim (no email) from DIALUP27.tnhun.usit.net at 04/16/99 03:06PM
comment
Based on the numbers it indicates good reliability.
kristi (no email) from dialup03.utm.edu at 04/16/99 03:08PM
comment
All of the numbers on the phylogeny of the paper are above 50 so it would seem that the tree is well supported.
Renee (no email) from crockett227.iswt.com at 04/16/99 03:08PM
comment
Purines are the nitrogen bases guanine and adenine and pry are thymine and cytosine.
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:11PM
comment
Greg and Renee, good comments. Note, everyone, that Greg
and Renee's comments are starting to evaluate the methods and
interpretation of the paper. This is really what we're trying
to learn to do today. The reason for doing this is that you are
reading a real paper (the paper by Stern on aphids) that you have to
critique -- in your critique you will have to identify two points to
evaluate, either two ways in which the study was well done, two ways
in which it was poorly done, or one of each. And you'll have to explain
why these ways were good or bad. And you'll have to relate them to the
conclusions of the paper. So I've given you this little made-up paper that uses
some of the same methods; the goal is to give you ideas for things to look for in
the real paper. So, Greg has noted how a heuristic search can be a problem and
a way to correct the problem, and noted that they did do this way of correcting the
problem in the little paper. So that should make the phylogeny in the little paper more
likely to be the best phylogeny based on the data, and that will make conclusions
drawn from the phylogeny more reliable. Renee has noted that most branches are
well supported based on bootstrapping, so they are reliable. But she has noted that
there is a 52. How does that 52 (not good support) affect our confidence in relationships
in the phylogeny shown?
Greg (no email) from 206.240.201.225 at 04/16/99 03:11PM
comment
Transitions are more likely because transitions are easier mistakes for polymerase to make and cause much less disruption in the DNA helix during synthesis.
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:12PM
comment
Renee thank you for the pur, pyr identifications.
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:13PM
comment
Greg has correctly noted that transitions are more likely,
and explained why. So would transitions or transversions
be more subject to convergent evolution -- what causes most
convergent evolution in DNA anyway?
Greg (no email) from 206.240.201.225 at 04/16/99 03:15PM
comment
Transitions are more likely to be subject to convergent evolution because they are more likely to occur in general and therefore are more likely to evolve independently in different distantly related groups.
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:17PM
comment
Now we get back to the part about equal weighting. Given
that convergent evolution is more likely in transitions,
as noted by Greg, is it appropriate to weight transitions
and transversions equally as they did in this paper? What
is the point to equal versus unequal weighting?
kristi (no email) from dialup03.utm.edu at 04/16/99 03:19PM
comment
It doesn't seem like trasition and the tranversions should be equally weighted but I'm not quite sure of the point of equally an nonequally weighted?
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:21PM
comment
Kristi is right that there may be a problem with equal weighting. Can anyone clarify the point to unequal weighting?
kim (no email) from DIALUP27.tnhun.usit.net at 04/16/99 03:24PM
comment
In equally weighing, the transitions and transversions have the same and equal consideration throughout this study.
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:24PM
comment
To help with the weighting question -- if you weight the
characters equally it means that every one contributes the
same amount to determining what the best phylogeny is. If
some characters are more reliable and others less reliable,
do we want them to contribute the same amount to determining
the phylogeny?
Greg (no email) from 206.240.201.225 at 04/16/99 03:25PM
comment
When they are unequally weighted, one is studied more than the other and they are not considered equally. Transitions are more likely to occur and show convergent evolution, therefore transversions are more likely to show true relationships between species and should be considered more as compared to transitions.
kim (no email) from DIALUP27.tnhun.usit.net at 04/16/99 03:25PM
comment
Unequal weighing would mean that transitions and transversions were not considered equally. One of these two were relied on more heavily than the other.
Renee (no email) from crockett227.iswt.com at 04/16/99 03:25PM
comment
If it is less reliable, then you would not want it to pull the same weight as a trait that is reliable. If it is not reliable, would it cause errors?
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:27PM
comment
Renee -- If one form (transitions) is not reliable, then weighting
it too much COULD cause errors, yes. So you'd want to
weight transversions more.
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:29PM
comment
OK let's look back at that question of bootstrap support for
the tree. The conclusions in this study (that monoecy is
primitive) depend on the tree. Most branches in the tree
have very good support but one, with the 52, has kind of
weak support. Which relationships among yellowleaf plants
are we unsure of (look at the figure -- which branch has
the 52 on it)? Does this affect the conclusions?
Renee (no email) from crockett227.iswt.com at 04/16/99 03:30PM
comment
Am I understanding you, transversions ARE more reliable than transitions. ALWAYS?
kristi (no email) from dialup03.utm.edu at 04/16/99 03:33PM
comment
We would probably be unsure of the ancestor to the dioecious
plants(red,blue,and spotted yellowleaf)
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:33PM
comment
Renee -- well there's never an ALWAYS in biology, but we
predict transversions to be generally more reliable because
they are less likely to occur and therefore will not show
convergent evolution as quickly. People have found exceptions
to this -- situations where transversions and transitions are
equally common, we're not sure why -- but as a general rule transitions
are less likely to happen, less likely to show convergent evolution, and
therefore more reliable in studying phylogenies.
Greg (no email) from 206.240.201.225 at 04/16/99 03:33PM
comment
The relationship we are unsure of is between the pink yellowleaf and the rest of the in-group. This definitely affects the conclusion because it makes that relationship less reliable and in reality the pink yellowleaf may be more closely related to one or more of the ingroup rather than equally related to all of the ingroup.
Renee (no email) from crockett227.iswt.com at 04/16/99 03:36PM
comment
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:36PM
comment
Kristi has a good comment on the relationships. We would
be unsure whether the ancestor to the dioecious yelloleaves
is really most related to the orange and white yellowleaves --
it could be more related to the pink. Or, the pink, orange, and
white could be more related to each other than to the dioecious
yellowleaves. So it looks like we're unsure about the ancestor to
the species that have the trait (dioecy) that we're trying to study.
Is this a good or bad place to be unsure about the phylogeny given
that we want to draw conclusions about the origin of monoecy and diecy?
renee (no email) from crockett227.iswt.com at 04/16/99 03:40PM
comment
Would this be a bad place to be unsure since it is in one of the earliest ancestors? Would it place doubt on the rest of the bootstrap values?
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:40PM
comment
Greg's making the same kind of point and noting it DOES
affect the conclusions. If the pink is really more related
to the orange and white, then there would be one group in
the ingroup that is monoecious (pink, orange, white) and
another group that is dioecious (red, blue, spotted) and in this case
we could not tell which is primitive. So I set this tree up so
that the place where we're not as sure of relationships IS one that
affects th conclusions. In critiquing the real (aphid) paper this
is another thing you can look for -- if there are areas where we're
not as sure of the phylogeny, are they areas that affect the hypotheses
about the evolution of horned soldier aphids that are being made in the
paper? In general, when you evaluate the paper, you will first consider
whether the methods are good or bad and then you will consider how
that might affect the reliability of the phylogeny and then, based on
the reliability of the phylogeny, how it affects the conclusions that'
are based on the phylogeny.
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:42PM
comment
Renee -- it doesn't affect the other bootstrap values. That
is, since the bootstrap value for, for example, the red, blue,
and spotted ancestor is 88, we're still very sure that these three
species are closely related to each other. The question is just at
the point where there is a 52.
Renee (no email) from crockett227.iswt.com at 04/16/99 03:47PM
comment
It would be an ok place to be unsure since we are sure of the rest of the bootstrap values???
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:48PM
comment
I just made a comment that isn't showing up on my screen so I'll
make it again -- I may be repeating myself if it turns up. You
should have a basis from this lab for discussing, in the Stern paper,
the use of bootstrapping, heuristic searches, weighting of transitions
versus transversions, and perhaps alignment. you only need two points
so I hope this gives you a good start -- I'd recommend you READ THIS
DISCUSSION AGAIN to help you discuss the Stern paper -- and do read
the Stern paper carefully (it's a hard paper to read.) Have a good weekend --
I'll stay for a few minutes to see if you have more questions.
Greg (no email) from 206.240.201.225 at 04/16/99 03:50PM
comment
Bye!
Renee (no email) from crockett227.iswt.com at 04/16/99 03:50PM
comment
Is it a good or bad place? does it matter since the other values are not affected by the 52? I don't understand?
Kristi (no email) from dialup03.utm.edu at 04/16/99 03:50PM
comment
Goodbye!Have a good weekend everyone!
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:51PM
comment
Renee -- in this case it's NOT an OK place to be unsure because
the relationships at the point where the 52 is determine whether
the pink species is the outgroup to the rest of the yellowleaves,
as shown in the tree, which is what shows that dioecy is derived,
or if the pink is really more related to the orange and white, in
which case no yellow-leaf is an outgroup to the rest and, since
the outgroup we used has both monoecious and dioecious species, we
couldn't tell whether monoecy or dioecy is derived. So whether or
not it's an OK place to be unsure depends on what other relationships
might be likely if the one we're unsure of isn't correct, and whether
that affects the conclusions we're making from the tree.
Renee (no email) from crockett227.iswt.com at 04/16/99 03:54PM
comment
Ok, I think. Have a nice weekend!
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:55PM
comment
Renee, let me illustrate with an example. On the tree in
the figure you're given, the bootstrap value for the ancestor
to the red and blue is 100. Suppose that that was the point
where we had a low value, but that the value for the ancestor to
the red,blue, and spotted was still high (88). In that case what
we would be unsure about is whether the red and blue were really closely
related, or if one of them was more related to the spotted, but we
would still be sure that all three of these species were close relatives.
In that case, we would still be sure that all three dioecious species (red,
blue, spotted) were close relatives, and this would NOT affect our conclusions
about the evolution of dioecy -- however those three are related within the group,
as long as the three are closest relatives then it appears that dioecy evolved in
their ancestor.
Rebecca I (no email) from paydial10.utm.edu at 04/16/99 03:55PM
comment
have a nice weekend all!
Rebecca Irwin (rirwin@utm.edu) from paydial15.utm.edu at 04/23/99 02:44PM
comment
Welcome to Lab, 23 April 1999. ANNOUNCEMENTS: Don't forget the exam on Monday (you can take it, as usual, during a 1.5 hour period between 1 and 3 or 5 and 7:30.) I'll have a review session on Sunday at 2:00 in Brehm 211 (or if it's in use, I'll put a sign on the door to 211 saying where the review is.) FOR TODAY: we're going to talk about sex. Well, about the evolution of sexual reproduction, anyway. This topic relates to several other topics we've seen. To start out, we need to define some of the things to do with sexual reproduction and these other topics, so choose one of the following questions (choose one that no one has answered yet when you start answering the question, if possible) and answer it -- when you've finished that, read other answers, and if questions remain unanswered keep answering more! Here are the questions: 1. What's the differenence, genetically, between sexual and asexual reproduction? 2. What is meant by the two-fold cost to sex? 3. What is group selection. 4. Does group selection usually occur or not -- why or why not? 5. What is species selection?
Greg (no email) from 206.240.201.225 at 04/23/99 02:51PM
comment
The two-fold cost to sex is that in sexual reproduction, each reproducing individual passes on just one of the two alleles it has for each trait, but when asexual reproduction occurs, each reproducing individual passes on both alleles it has for that trait. The allele for sex gets passed on at half the rate of an allele for asexual reproduction.
Renee (no email) from crockett231.iswt.com at 04/23/99 02:52PM
comment
hello Two fold cost to sex refers to the fact that when sexual reproduction occurs, each reproducing individual passes on just one of the 2 alleles it has for each trait, but when asexual reproduction occurs, each reproducing indiv. passes on both alleles it has for each trait.
kristi (no email) from paydial07.utm.edu at 04/23/99 02:54PM
comment
The two-fold cost refers to when sexual reproduction occurs only one of the
two alleles for a trait from each parent is passed on, but when asexual reproduction occurs both alleles of the trait being passed on is present.
Asexual reproduction pass on two alleles for every one allele passed by sexual reproduction as it occurs so really asexual reproduction has the advantage and sexual reproduction only has half the fitness of asexual reproduction.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 02:54PM
comment
Greg has a good definition of the two-fold cost to sex. Note that based on
this we would NOT expect sexual reproduction to evolve since it should have
only half the fitness of asexual reproduction. We'll consider why it does
evolve later -- first, let me see if there are any more questions answered...
Greg (no email) from 206.240.201.225 at 04/23/99 02:55PM
comment
Species selection refers tot he process through which traits become common throughout all of life because species that have them have a high rate of speciation or a low rate of extinction.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 02:55PM
comment
I guess everyone liked the 2-fold cost to sex. Now try answering some of the
other questions.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 02:56PM
comment
Good definition of species selection Greg. Now, how is species selection
relevant to sex?
James T_ (no email) from student-e76.at.utm.edu at 04/23/99 02:56PM
comment
hello,
Sexual reproduction has to do with reproduction between two diffrent sexes- male and female. Where as asexual reproduction has to do with one sex reproducing itself.
Renee (no email) from crockett231.iswt.com at 04/23/99 02:57PM
comment
Group selection ws when sexual reproduction causes recombination of genes and therefore creates more combinations of genetic traits in a pop. more genetic variation.
James (no email) from student-e76.at.utm.edu at 04/23/99 02:57PM
comment
My bad missed the geneticly speaking part of that question.
kristi (no email) from paydial07.utm.edu at 04/23/99 02:58PM
comment
Group selection states that since sexual reproduction causes recombination of genes and creates more variation then a population that reproduces sexually should go through more natural selection
than an asexual population.
Greg (no email) from 206.240.201.225 at 04/23/99 02:58PM
comment
The trait for sexual reproduction would be passed on if its benefits outweighed the costs therefore becoming common throughout life. The individuals produced as a result of sexual reproduction would have a higher variability which could give them the cominations which have a higher fitness and therefore a high rate of speciation or a low rate of extinction.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 02:59PM
comment
Renee, you have given an example of a situation which might
lead to group selection, if it occurs, but you have not
defined group selection. Before we relate it to sexual reproduction,
we need a definition of what group selection is. Can you (or anyone) define
it?
Greg (no email) from 206.240.201.225 at 04/23/99 03:00PM
comment
Group selection is based on differences in extinction rates between populations of individuals with different traits and occurs more slowly than individual level natural selection.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:01PM
comment
Kristi, like Renee you need to state what group selection
is (see the lecture notes on levels of selection) before you
apply it to sexual reproduction.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:03PM
comment
Greg, in your comment on the benefits of sex outweighing the
costs, it is correct that for some reason producing variable
offspring must give higher fitness if sex is to evolve. Your
statement about speciation and extinction, which relates to
species selection, is something that may be true but does
NOT explain why sex evolves -- if sex DOES evolve it may have
this effect, but that's not why it evolved. I'm not sure from your
answer if you meant to say that's why it evolves or not, I just want
to make sure you (all of you) know that's not why it evolves.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:04PM
comment
Greg has a definition of group selection. Does group selection
typically occur?
James (no email) from student-e76.at.utm.edu at 04/23/99 03:05PM
comment
No group selection does not typically occur.
Greg (no email) from 206.240.201.225 at 04/23/99 03:06PM
comment
Group selection usually does not occur because it is slower than individual selection.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:07PM
comment
OK I think we've got basic definitions for everything. Now,
based on the two-fold cost to sex, we would argue that sex
should not evolve -- but it has. So, why has it evolved? What benefits
to sex outweigh the costs?
kristi (no email) from paydial07.utm.edu at 04/23/99 03:07PM
comment
It does not occur because there are individual level costs to sexual reproduction.
Greg (no email) from 206.240.201.225 at 04/23/99 03:09PM
comment
Sexual reproduction evolved so there must be an advantage for parents to produce genetically variable offspring. This could happen in a changing environment. The offspring may be in a different environment than the parent in which case the variability increases the chance the offspring will have a variation which will have a higher fitness.
Renee (no email) from crockett231.iswt.com at 04/23/99 03:10PM
comment
A benefit would be genetically varibility in offspring.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:11PM
comment
With regard to group selection -- James, you're right, it
doesn't occur; Greg and Kristi if we put your answers together
we'll have a nice complete answer for how this applies to sexual reproduction;
generally, group selection does not occur because it is slower than individual level
natural selection, and there are individual level costs to sexual reproduction so
group selection would not result in the evolution of sexual reproduction -- because
individual level natural selection occurs more quickly, asexual reproduction would evolve
through individual level natural selection before we ever saw any benefits to sex at the
group level causing group selection (since group selection occurs more slowly.)
kristi (no email) from paydial07.utm.edu at 04/23/99 03:12PM
comment
A benefit would be that it increases speciation.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:13PM
comment
Renee, you're correct that it produces genetically variable
offspring; to see when this would be an advantage see Greg's
answer. Now, what would cause the environment to change, so
that sexual reproduction would result in higher fitness because
of more surviving offspring?
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:14PM
comment
Kristi -- increased speciation is not a benefit to the individuals
who are reproducing sexually; it's something that happens in a species
once sex has evolved, but it can't explain why it would evolve. What we
need for benefits are reasons that sexual indivdiuals would have more
suriving offspring than asexual individuals.
Greg (no email) from 206.240.201.225 at 04/23/99 03:16PM
comment
In species with short life spans, seasonal changes could change the environment quickly enough. For some species, it is thought that change in species around them, especially in parasites and pathogens that infect them, may be what causes sexual reproduction to have a high fitness.
James (no email) from student-e76.at.utm.edu at 04/23/99 03:17PM
comment
The changing of seasons might be enough to give the sexual species a fitness advantage.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:18PM
comment
Good Greg. Now let's elaborate on this idea about parasites/pathogens.
Why would we look specifically at parasites/pathogens as something changing in
the environment (as opposed to anything else in the environment) to explain why
sex would be an advantage?
renee (no email) from crockett231.iswt.com at 04/23/99 03:18PM
comment
Changes from one season to the other for example water fleas which reproduce asexually until near winter then they reproduce sexually.
James (no email) from student-e76.at.utm.edu at 04/23/99 03:20PM
comment
I suppose that if the parisites that prey on a species continue to change then that would make for an environment that was changing, making species reproducing sexually advantagous.
Greg (no email) from 206.240.201.225 at 04/23/99 03:20PM
comment
Parasites evolve quickly to overcome host defenses so individuals with variable gene combinations for parasite resistance are likely to have a higher fitness than individuals with gene combinations that are common in a population. Asexual reproduction results in offspring exactly like the parent and are susceptible to parasites while sexual reproduction could produce an unusual gene combination that resists parasites. Sexual individuals are more likely to have offspring which can survive parasites than individuals which reproduce through asexual reproduction.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:21PM
comment
With regard to the changing of seasons -- this is a kind of environmental
change that, as Greg noted, might result in a fitness advantage in species
with short life spans. That is, species where some individuals will be born and
die within a season may have offspring that are born into a very different season,
so it could be an advantage to produce offspring sexually -- if you are adapted to
summer and your offspring are going to emerge next spring producing variable offspring
through sexual reproduction might give increased chance of offspring survival. Note
though that for species with longer lifespans where individuals live through all the seasons
this argument doesn't really work. That's why we're looking at parasites now as something
else that might change in the environment.
Renee (no email) from crockett231.iswt.com at 04/23/99 03:21PM
comment
Parasites are constantly evolving to overcome their host.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:23PM
comment
Greg and James both have the right idea on parasites. They're
something that we can predict will keep changing -- they keep adapting
to overcome host defenses (this, remember, causes negative frequency dependent
selection in the hosts.) So that's why it's thought that a main reason we
have sex (in the evolutionary sense I mean) is that it is an adaptation to parasites.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:24PM
comment
Good Renee -- short and right to the point.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:25PM
comment
Based on this discussion you should be able to answer the
lab manual questions on the evolution of sex -- to be sure
let's look at the first one in the chapter on the evolution
of sex. So please answer the following (from the lab manual): 1. Sexual reproduction results in much more genetic variation, because of recombination, than does asexual reproduction. As a result, a species with sexual reproduction is likely to have a higher ability to adapt to changing conditions than is a species with only asexual reproduction. Why do these facts NOT explain the evolution of sexual reproduction?
kristi (no email) from paydial07.utm.edu at 04/23/99 03:27PM
comment
because it is based on group selection
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:28PM
comment
Good job Kristi! Short and to the point!
Greg (no email) from 206.240.201.225 at 04/23/99 03:29PM
comment
Increased variation is something that happens in a species once sexual reproduction has evolved but does not explain why it evolved.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:29PM
comment
OK here's another one. Question 6, which is:
6. How might sexual and asexual species be expected to differ in speciation rate? Why? How could this difference help to explain why so many species have sexual reproduction?
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:30PM
comment
Greg, also good; the reason it doesn't explain why it
evolved is, as Kristi said, that it is based on group selection.
Greg (no email) from 206.240.201.225 at 04/23/99 03:31PM
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Species who reproduce through sexual reproduction are likely to have much higher variation within the species. The variability may cause some populations to become so different that they can no longer reproduce with each other and therefore are considered another species. Asexual reproduction does not result in variation and the lack of variation decreases the chances of speciation
James (no email) from student-e76.at.utm.edu at 04/23/99 03:31PM
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Asexual with have less specieation than sexual because there is less variablity among them. If it is more likely that they are to speciate it is more likely that there will be more species.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:34PM
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Greg, good. One point to note though is that it is not
the variability that directly causes populations to become
different, and therefore different species, but evolution
that can occur based on the variability that is present. The
idea is that mutation initially produces the new alleles,
sexual reproduction mixes alleles from different individuals and
creates new combinations of genes, then evolution occurs based
on those new combinations that are produced. More new combinations from
sex means more variation, more potential for evolution, more speciation
is possible. So there are lots of sexually reproducing species. Note
all of you (again) that this doesn't explain why sex evolved, but is a possible
consequence once sex has evolved.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:36PM
comment
James, also good. Well we've made it past where the other
groups did; I think you've got the basic points. Would you
like to leave early so you can go study for the exam that's
coming up on Monday? Or would you like to stay here and
ask questions relevent to the exam that's coming up on
Monday? You may do either one (of course, if you leave
early and don't go study for the exam, I won't know that...
until I see your exam, of course.)
Greg (no email) from 206.240.201.225 at 04/23/99 03:37PM
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See you Monday!!
James (no email) from student-e76.at.utm.edu at 04/23/99 03:37PM
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I know I need the time to study. I'll see you later.
Rebecca I (no email) from paydial15.utm.edu at 04/23/99 03:38PM
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Have a good weekend (have fun studying :) )
renee (no email) from crockett231.iswt.com at 04/23/99 03:39PM
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Bye see you Sunday
Kristi (no email) from paydial07.utm.edu at 04/23/99 03:40PM
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Bye!!!
Rebecca Irwin (rirwin@utm.edu) from paydial07.utm.edu at 04/30/99 02:47PM
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Welcome to the last lab, 30April 1999. ANNOUNCEMENTS: REMINDERS: Critique Due Monday, 3 May, by 5:00 p.m. Either e-mail it to me (either as an attachment to a message if you know how to do that OR you can just paste it into an e-mail message. If you do the latter it probably won't come out double spaced but I don't mind IF it's in an e-mail message since I can very easily make it double spaced on my computer) or turn it into the Biology Dept. by 5:00 p.m. Last homework due by 5:00 Tuesday 4 May. FINAL EXAM FRIDAY 7 May 12:45-2:45. If you can't make this exam time because of a class conflict you must arrange an alternative time by 30 April (that's today!) -- no exams will be rescheduled after that. I have posted IMPORTANT INFORMATION ABOUT THE FINAL on the web -- be SURE to read it since it tells you what the long essay question on the final will be, and it is something you must prepare from the textbook! I will hold a REVIEW SESSION on Weds. 5 May at 2:00 in Brehm 211 (if possible -- if it's occupied I'll put a note on the door.) Exam 3 should be graded and available on Monday 3 May from the Bio. Dept Office. I will be checking e-mail over the weekend so if you have questions on the critique do e-mail me. FOR TODAY'S LAB: we're going to discuss questions from Chapter XXIII of the lab manual -- these review areas we've studied with reference to humans. To get started reviewing these areas, in your first message, define one of the following: heritability, local adaptation, altruism, heterosis.
James (no email) from 206.240.200.156 at 04/30/99 02:51PM
comment
Local adaptation: where through gentic drift the was a loss of variablity in the gene making it fixed in a population.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 02:53PM
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Sorry, James, genetic drift does not lead to local adaptation -- loss of
genetic variation in a population is one of the things that PREVENTS local
adaptation. Try again (or someone else can help out)
James (no email) from 206.240.200.156 at 04/30/99 02:53PM
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Heritablity: the fraction of the total phenotypic variation in a population that is caused by genitic diffrences amoung indiviaduals. Thanks to the textbook.
Greg (no email) from 206.240.201.226 at 04/30/99 02:55PM
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Heterosis is when the heterozygote has a higher fitness than either homozygote, heterosis tends to maintain genetic variation.
Greg (no email) from 206.240.201.226 at 04/30/99 02:56PM
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Altruism is a behavior which decreases the fitness of the altruist and increases the fitness of the recipient.
Greg (no email) from 206.240.201.226 at 04/30/99 02:56PM
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Local adaptation is evolution through natural selection of traits that have high fitness in the environmental conditions specific to a population.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 02:59PM
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Thank you for finding the textbook definition of heritability for us, James.
Now, everyone, what we're going to do today is to use these definitions we
start with and discuss ways in which these concepts apply to humans. We may
end up having several conversations at the same time (the other labs did).
So, with regard to heritability, one area that is controversial is whether or
not human behavioral traits show heritability -- that is, are there genetic differences
among individuals in human behavior. This turns out to be difficult to study. Here are
the questions: how do we typically study heritability? Why does this method not
work well for human behavior?
Renee (no email) from crockett228.iswt.com at 04/30/99 03:01PM
comment
Hello, I'm here, I could not get a connection!
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:02PM
comment
Thank you Greg for the definitions. Now here are things for everyone to
consider based on Greg's definitions. With regard to heterosis: what
human traits are examples of heterosis? With regard to local adaptation: describe a human trait
that shows local adaptation. With regard to altruism, do you think there are human behaviors
that are examples of altruism? If so, what forms of behavior?
Greg (no email) from 206.240.201.226 at 04/30/99 03:02PM
comment
One way to study heritability is to study twins who were adopted by different parents at birth. Genetic similarities should be shown if the twins show similarities in different environments. The problem is that similarities between the twins in different environments, whether skin color or some other reason, and prenatal care may tend to make them seem more similar when they are really not.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:03PM
comment
Hello Renee I'm glad you made it on. Note there are lots of
questions to answer in the comment I just posted (just after
your last post.)
James (no email) from 206.240.200.156 at 04/30/99 03:03PM
comment
I would guess that human behavoir is mainly learned and not genitic, making it hard to study seeing as children grow up with there parents learning stuff. You couldn't very well tske away a kid from thier parents to determine if something was genitic plus they would have to be twins.
Greg (no email) from 206.240.201.226 at 04/30/99 03:04PM
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Sickle cell and cystic fibrosis may show heterosis because the heterozygote is resistant to a particular infectious disease. Malaria in the case of sickle cell and cholera in the case of cystic fibrosis. Heterosis maintains alleles that have low fitness when homozygote in high proportion because the individuals that survive and reproduce best are heterozygotes which contain both alleles and produce all genotypes when they reproduce.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:05PM
comment
Greg has given one of the main ways to study heritability of human traits.
And noted problems with it. Based on these problems would we tend to
overestimate or underestimate the heritability of traits? Also, what is the
way we looked at earlier in this course for estimating heritability, and why
doesn't it work for human behavior?
James (no email) from 206.240.200.156 at 04/30/99 03:05PM
comment
Kinda stinks if your not hetro, with that stuff.
Greg (no email) from 206.240.201.226 at 04/30/99 03:06PM
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Local adaptation is shown in relation to skin color. Light skin has a higher fitness in northern climates where UV radiation is less intense so less potentially harmful since light skin allows better vitamin D absorption. Dark skin has higher fitness in tropical climates where UV radiation is intense because skin cancer is a threat and there's so much light vitamin D will not be a problem.
Kristi (no email) from paydial11.utm.edu at 04/30/99 03:07PM
comment
Hello, sorry I'm so late- Skin color show local adaptation?
Greg (no email) from 206.240.201.226 at 04/30/99 03:07PM
comment
Earlier in the semester, with regard to heritibility, we used mid-parent offspring regression which is done by graphing the average of two parents' traits on the x-axis, and graphing the offspring's traits on the y-axis.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:08PM
comment
Right, James, that's why the studies of heritability of human
behavior have been done on identical twins that have been adopted by different
families -- the goal is to see if genetically identical individuals come out
the same even if raised in different environments. Studies of some traits,
such as IQ, done this way suggest it has a heritability of about 0.5 which
would mean half the variation we observe is genetic, half environmental, but
as Greg noted these studies also have problems. Based on the problems would you
think the value of 0.5 is too high or too low?
James (no email) from 206.240.200.156 at 04/30/99 03:09PM
comment
They could be treated simalarly because of their simalar apperance.
kristi (no email) from paydial11.utm.edu at 04/30/99 03:09PM
comment
To estimate heritability earlier we used mid-offspring parent regression
but this may not be useful because many factors offspring may be similar to their parents are due to environmental factors rather than genetic
Greg (no email) from 206.240.201.227 at 04/30/99 03:11PM
comment
Based on the problems with studies of twins, I think the estimate of 0.5 would be too high.
James (no email) from 206.240.200.156 at 04/30/99 03:11PM
comment
I'm thinking that 0.5 it way be alittle low for behavior.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:12PM
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James has noted the problem we have because of heterosis in these genetic diseases --
yes, it does kinda stink if you're not heterozygous -- and because the heterozygotes
are the ones that survive and reproduce the best and keep producing homozygotes as
well as heterozygotes there are always individuals being produced who are homozygous
and either susceptible to a nasty infectious disease (at least these are now often preventable
or treatable now) or have a serious genetic disease (sickle-cell and especially cystic fibrosis tend
to kill people at ages well below the average lifespan.) These genetic diseases are more common than
most other nasty genetic diseases, presumably because of heterosis.
James (no email) from 206.240.200.156 at 04/30/99 03:13PM
comment
I'm thinking I might have said that wrong, .5 is a little low for the amount that is learned behavior.
Renee (no email) from crockett228.iswt.com at 04/30/99 03:15PM
comment
.5 would be low because they learn what they are around and and what they see.
kim (no email) from DIALUP34.tnhun.usit.net at 04/30/99 03:16PM
comment
Hi, sorry i'm running late! Altruism means behavior that increases the survival and reproductio of other individuals, at a cost to one's own survival and reproduction.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:17PM
comment
Several comments -- first, Kristi, yes, skin color is a trait that
shows local adaptation; Greg has explained how it shows this. Then
with regard to the heritability estimates -- the problems with the twin
studies (common prenatal envrironment and possibly similar treatment because
of similar appearance) would tend to make the twins similar for environmental
reasons so I think Greg is right that based on these problems the estimate of
0.5 may be too high. Now, I think I asked a question at some point about altruism
and I don't think I've seen an answer yet (I'll check again when I post this.) Also
I have another question about local adaptation -- based on the patterns of genetic
variation that we see within and among human populations do we expect most traits to
show local adaptation? To answer this, first describe what the patterns of genetic
variation are, then what they suggest about things like drift and gene flow that might
affect the possibility that natural selection can lead to local adaptation, then what you'd expect about local adaptation.
James (no email) from 206.240.200.156 at 04/30/99 03:17PM
comment
I saw a show on Discovery that said that human babies have a less orginzed nural (sp?) structure than most animals. Presumably so that they could have the ompasity for more learned behaviors and less innate ones.
James (no email) from 206.240.200.156 at 04/30/99 03:18PM
comment
ompasity=capasity, lousy typer :)
kristi (no email) from paydial11.utm.edu at 04/30/99 03:19PM
comment
I'm not really sure,if it is too high or low but with what some children learn from behavior it is hoped that most things will be inherited genetically than from learned behavior.
Greg (no email) from 206.240.201.227 at 04/30/99 03:20PM
comment
There is high genetic variation within human populations and low variation between populations. High gene flow must be present to make populations similar, people are moving to new populations and reproducing so alleles from one population will be moved into other populations and populations will become similar. Gene flow inhibits genes to evolve in one environment. Local adaptation is less likely because the genes are being passed from population to population in different environments.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:21PM
comment
Renee and James, I'm not sure what you mean with .5 being low. Remember
that heritability=0.5 means that half of the variation in human behavior
is genetic, half environmental. Based on your arguments about learning,
neural development, it seems that more variation should be learned. This
means that you'd think the heritability should be lower than 0.5. So the
estimate of 0.5 is too high. I don't know if it's really too high or not (I
don't think anyone knows this for sure because of difficulties studying it) but
based on the arguments we've made that's what we'd expect.
kristi (no email) from paydial11.utm.edu at 04/30/99 03:22PM
comment
Maybe since there would be so much gene flow among human populations that it is not that likely that most traits are locally adapted.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:23PM
comment
Actually James it's capacity not capasity -- I made a brief detour to a spell checker to
be sure of this :)
Greg (no email) from 206.240.201.227 at 04/30/99 03:23PM
comment
There are some human behaviors which may show a form of altruism but aren't exactly altruism. A nanny who nurses and takes care of another individuals baby for pay could be considered a form of altruism but it isn't genetically based. Also, taking care of a relatives baby if they become incapable or adopting a relatives baby is also sort of altruism, and adopting a relatives baby is genetic although it may not be for the purpose of giving the biological parents higher fitness.
James (no email) from 206.240.200.156 at 04/30/99 03:23PM
comment
Well for ltruism to work you'd need to have the fitness from the alteristic trait to be greater than the trait that wasn't altristic. Mabye the fact that humans live in social groups has a higher fitness that if we we solitary.
Renee (no email) from crockett228.iswt.com at 04/30/99 03:23PM
comment
to maintain genetic variation there must be at least one individual per generation to disperse, but not so much gene flow that there are no diff. among the pop.
James (no email) from 206.240.200.156 at 04/30/99 03:24PM
comment
not a speller either.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:25PM
comment
Kristi and Greg have both explained why we wouldn't expect much local adaptation in many
human traits -- there has apparently been a lot of gene flow among human populations,
so we wouldn't expect a lot of genetic differences among populations (that is, the various
genetic traits that occur in one population will be spread to other populations.)
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:30PM
comment
With regard to Greg and James' comment on altruism -- Greg, how do you know
there isn't a genetic tendency to become a nanny? OK, I don't think there is
either, but do we know for sure? James, the idea would be that if we live in social
groups and overall in social groups more offspring are produced and some individuals
are social AND (at least historically) individuals in social groups would be relatives,
then if there are alleles for altruism in humans they would have been passed on from
generation to generation more than non-social, non-altruistic alleles. Then altruism
would have evolved through kin selection. Greg has noted that caring for/adopting the
baby of a relative would be altruism, and I think when he says "is genetic" he means that
this behavior is directed toward genetic relatives (that's what he should mean anyway)
which would be what is predicted through kin selection.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:32PM
comment
Everyone might also take note of Renee's comment on genetic
variation -- for there to be local adaptation you need some genetic
variation but not too much and she has given the conditions under which
you'd expect local adaptation. Since you've seen questions about local
adaptation on a couple of previous exams it would be a good thing to take
note of for the final (hint, hint.)
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:33PM
comment
Now getting back to altruism -- the question people studying the evolution
of human behavior ask or try to answer is, are there human behavioral traits
that have evolved (so they must be genetic) that are examples of altruism and
that may have evolved through kin selection? Do you think there are? Why/why not?
Greg (no email) from 206.240.201.227 at 04/30/99 03:37PM
comment
I can't think of any examples of altruism which would be evolved, and therefore must be genetic. I would tend to think that altruism would not evolve in humans because it would be more beneficial to have your own offspring and because of the long lifespan and long gestation period, it would require much more energy to be a true altruist. In the energy expended in being an altruist, one could have their own offspring. Being an altruist would not benefit the recipient enough to be beneficial to either individual in the long run.
Renee (no email) from crockett228.iswt.com at 04/30/99 03:38PM
comment
If altruism was present, then it would have to passed on to the next generation right? Just because a person is a nanny doesn't necesarrily mean it is found in the family. Also, the nanny would not have any offspring of her own correct?
James (no email) from 206.240.200.156 at 04/30/99 03:40PM
comment
If there was some sort of recirprocal (sp?) altruism them it could work. I'll help raise your kid while I'm young if your kid helps me raise mine. That could work if we're related.
kristi (no email) from paydial11.utm.edu at 04/30/99 03:40PM
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I don;t understand how altruism could be evolved in humans.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:42PM
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Greg and everyone -- and yet we do have these tendencies to do things like
care for children of relatives if the relatives can't care for them;
someone in a previous section noted that fighting in a war would decrease
your own survival but might help your country (which contains your family).
But are these evolved or learned? Beats me! Now, I want to thank everyone
for great discussions both today and throughout the term. We've made it through
the major points for the lecture so since I know you all have critiques to write I
will let you go, if you'd like (you can also stay and ask questions if you'd like.)
I will be checking my e-mail over the weekend so feel free to ask questions about the
critique and don't forget it's due Monday by 5:00 p.m. either to the biology dept.
office or, if you want to save paper, you can e-mail it to me by 5:00. Well try to
have a good weekend despite the fact that I'm making you do this critique thing.
kim (no email) from DIALUP34.tnhun.usit.net at 04/30/99 03:44PM
comment
Yes i don't really know why i think this but i do think that there are proably some human behavior traits that might be exampls of altruism and may have evolved through kin selection we just know them yet.
kristi (no email) from paydial11.utm.edu at 04/30/99 03:44PM
comment
Okay,prepare for many e-mail questions!!!
Goodbye!!
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:45PM
comment
Renee -- yes, if altruism is present it would have to be passed to the
next generation (typically it evolves because it is passed to the next
generation by a relative of the person who is altruistic.) If there is
heritability in altruism now then being a nanny should run in families (as
far as I know it doesn't) On the other hand maybe the fact that we have
nannies now is because in the distant past we evolved to have some level of
altruistic alleles and we all have tendencies toward this kind of behavior now.
No one really knows.
James (no email) from 206.240.200.156 at 04/30/99 03:45PM
comment
I think that because we are SO social that altrism is something that has profoundly shaped our evolution. I look for the lion while you eat the fruit. Later you walk out in front of the zebra to get it to run to me. I give your kid some zebra quarters while mibe gets some apples. If we're related we do better together than any of the solitary humans in the bush. Our clan outcompetes the the individuals in the bush (maybe together driving them out of our territory, more zebra's for our clan) and our traits prevail. Sorry had a little story for you there.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:46PM
comment
Interesting, Kim. Maybe we don't recognize them in ourselves?
Greg (no email) from 206.240.201.227 at 04/30/99 03:47PM
comment
I recently finished my Critique and had two questions, one of which I asked Dr. Buschaus about and want to make sure you are in agreement. First, Stern (1998) said the transition/transversion ratio was 1.45. Does this mean that transitions were weighted more than transversions? (That's the conclusion I came to). Second, I am not sure I did the citation of the book correctly, Freeman, Scott and Jon C. Herron. 1998. Evolutionary Analysis. (New Jersey: Prentice Hall).
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:47PM
comment
James, your story nicely illustrates what a lot of people who study human
behavioral evolution think about how our sociality/altruistic tendencies
have evolved. Thanks!
Renee (no email) from crockett228.iswt.com at 04/30/99 03:47PM
comment
Bye!
James (no email) from 206.240.200.156 at 04/30/99 03:48PM
comment
Hold on is that good or bad?
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:49PM
comment
I don't know if it's good or bad, James. From the point of
view of understanding evolution, it's good. From any other
perspective, it's outside the magisterium of science and I may
not be qualified to answer. You could ask your philosophy professors.
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:52PM
comment
Greg, on the critique -- Stern's not overwhelmingly clear
but he says that the transit/transvert ratio is 1.45 and that
they were weighted based on their probability of occurrance which
typically means that the one that's LESS likely to occur (transversions)
would be weighted more heavily. The citation's fine.
Greg (no email) from 206.240.201.227 at 04/30/99 03:53PM
comment
Thanks, have fun and study hard everyone!!
Rebecca I (no email) from paydial07.utm.edu at 04/30/99 03:54PM
comment
Bye!