Wednesday, January 30, 2013

How Did I Know What the Exponential Growth Curve Looked Like?

In class I showed you the shape of the exponential growth curve.  Now I would like to explain to you how I knew to draw that particular shape for that graph.

The exponential growth curve is produced anytime

dN/dt = rN and r is constant.

Remember, that making r a constant makes this equation the simplest that it can be.

If you want to know how to draw the graph then we can simply plug some numbers in to the equation and plot the results.

We will have to make up some value for r.  The simplest value  is to assume

r = 1 individual/year/individual.

All I need to do now is to calculate dN/dt for different values of N.  The simplest values of N that I can imagine are 1, 2, 3, 4, etc.  Let's start by assuming that in Year 1 N = 1 and plugging that into dN/dt = rN.

dN/dt = (1 individual/year/individual)(1 individual) = 1 individual/year

We can now add this value to the table below.


Year        N  (individual)                            dN/dt (individuals/year)
1              1                                                 1
2
3
4
5

If we started with a population size of one individual and the population increased in size by one individual during the first year then at the start of the second year the population should contain 2 individuals.  We can add that value to the table.


Year        N  (individual)                            dN/dt (individuals/year)
1              1                                                 1
2              2
3
4
5

Following the same logic that we used above you should be able to calculate N and dN/dt for both years 1 through 6.  (make sure you can do this yourself before looking at my calculations).


Year        N  (individual)                            dN/dt (individuals/year)
1              1                                                 1
2              2                                                 2
3              4                                                 4
4              8                                                 8
5             16                                                16
6             32                                                32

You should now be able to plot the following graphs using the information held in this table.

1.  How does the population size vary over time?

2.  How does the population growth rate vary over time?

3.  How does the population growth rate depend on the population size?

Tuesday, January 29, 2013

Clarifying Natural Selection: Individual and Inclusive Fitness


There are so many more things to talk about in BIOL 1404 then we possibly have time to discuss.  Thus, every semester I have to decide what to mention and what to leave out of lectures.  This year I decided not to discuss a couple of terms during lecture and after talking to a couple of students I see that it might have been helpful to talk about these terms.

When we talked about natural selection we concluded that natural selection should produce selfish traits (those that maximize the survival and reproduction of individuals).  Thus, natural selection should maximize an organism's "individual fitness" (the number of genes that an individual passes on by reproducing itself).

Kin selection suggests that sometimes we can pass on genes by helping our close relative to reproduce more than they would have without out help.  Genes that are passed on by helping your close relatives to reproduce are known as "inclusive fitness".

Thus, "total fitness" (the total number of genes passed on by an individual) is he sum of "individual fitness" and "inclusive fitness".

Total fitness = individual fitness + inclusive fitness.

When we reexamine the process of natural selection we see that natural selection maximizes total fitness.  Thus, sometimes an organism can pass on more genes by increasing its inclusive fitness at the expense of its individual fitness.

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- define and distinguish between individual fitness, inclusive fitness, and total fitness
- discuss the role of inclusive fitness in the selection of altruistic acts via kin selection.

More Cool Info about Sexual Selection

Hello Everyone,

I am pleased that I have received some feedback that some of you found the info on sexual selection and mate choice to be interesting.  I wish we had more time to talk about this fascinating topic, but I know that you are so excited about learning the math and graphs related to population biology that we need to move on.

Some of your classmates have sent me links to some interesting online info about the topic that you might like to take a look at.  Thanks for sending them to me.

1.  The spider that loses its penis during sex to make it more fierce in battle against love rivals.

http://www.dailymail.co.uk/sciencetech/article-2158818/Nephilengys-malabarensis-spider-loses-penis-sex-make-fierce-battle-love-rivals.html

2.  The Science of Sex Appeal

http://dsc.discovery.com/tv-shows/other-shows/videos/other-shows-science-of-sex-appeal-videos.htm

This site contains several short videos that discuss some of the topics that we were only able to touch on that relate sexual selection and mate choice in humans.  These videos are pretty interesting so take a look when you get a chance.

Male-male Competition in Species With External Fertilization

I didn't have time to talk about male-male competition in species with external fertilization in class, but I have decided that this is an interesting enough topic to deserve its own post (and the subject is addressed in the Expected Learning Outcomes for Sexual Selection).


Most of the animals that we are used to thinking about have internal fertilization which means that the male mates with the female and then deposits sperm into the body of the female.  Other species, including many marine and aquatic species have external fertilization.  For example, in most fishes females deposit eggs either in a nest or in the open water column and then males swim by and deposit sperm in the water which will find the eggs and fertilize them.

Because it is possible for many males to attempt to fertilize the same eggs, in many cases the male that fertilizes the most eggs is simply the one that produces the most sperm. Thus, male-male competition in many species of fishes has led to the production of large amounts of sperm. In some cases the testes can make up almost half of the body mass of a male fish.

The Amazing Sex Life of Fish!!

Fish have some of the craziest and most interesting sex lives of all of the species on earth!  One of the interesting aspects of the sex lives of some of the coral reef fishes is that they change sex during their lives. Usually, individuals will start their lives as females and then change sex to males when they are older and larger (sequential hermaphroditism).

In some species, such as the blue-head wrasse, males defend territories that can contain several several females that he mates with.  In some populations there are fish with an interesting strategy.  There are fish that look and act just like females, but are actually males (these fish are known as "sneakers" - now the ridiculous photo at the top of the post should make sense).  The territorial male accepts the sneakers in his territory because he thinks that they are females.  When a female lays eggs in the territory the sneaker males sneak in, deposit a cloud of sperm, and fertilize some eggs! Pretty cool!!

Monday, January 28, 2013

Fun With Graphs. Exponential Growth




How do I know which graph to draw?

1) In the population ecology portion of this course we will be discussing two models of population growth- exponential growth and logistic growth. Thus, you need to know which growth model you are describing before you know which graph to draw.

2) You can't draw a graph until you know what the axes are.

Hopefully, this is a review, but it is probably worth talking about. The x-axis (the horizontal axis) is known as the independent variable. The y-axis (the vertical axis) is the dependent variable. Changing the value of the independent variable results in a change in the dependent variable. Id DOES matter which variable goes on which axis so try to get it right.

In population ecology there will be two main independent variables that we are interested in studying. Because we are interested in patterns of population growth, we will often want to observe how variables change over time. Time is always the independent variable, so it always goes on the x-axis. Sometimes we are interested in how parameters depend on population size. In this case, population size is always the independent variable.

Powerpoint Presentation

This powerpoint presentation "Fun With Graphs: Exponential Growth" reviews the graphs you are expected to be able to draw, understand, and interpret that relate to exponential growth.

http://www.slideshare.net/secret/mavlOD8flFs67G

NOTE:
Any graphs that contain the incorrect axes will be considered to be completely wrong on all exams and assignments!!

Population Biology 2. Exponential Growth



Lecture Video- http://mediacast.ttu.edu/Mediasite/Play/b8c64d66f62a4747b7983398113f0b391d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b


From the first lesson on Population Ecology we learned that the population growth rate (dN/dt) can be calculated as the product of the per capita growth rate (r) and the population size (N).

dN/dt = rN

This is the fundamental equation describing population growth and this equation is always true.

If we want to use this equation to analyze how population sizes change over time, then it makes sense to start by examining the simplest formulation of this equation which occurs when the per capita growth rate is constant. The equation dN/dt = rN when r is constant is known as the exponential growth equation and this equation describes a patter on growth known as exponential growth.

The graph plotting how population size changes over time is shown in the Exponential Growth article. This graph shows an exponential growth curve (sometimes known as the "j-curve"). If you have questions about why the graph has this shape then take a look at the blog post entitled "How Did I Know What the Exponential Growth Curve Looked Like?".

It is important that you are able to look at this graph and determine all of the information held in the graph. The exponential growth curve allows us to discuss how two parameters change over time- 1) the population size (shown by the x-axis) and 2) the population growth rate (shown by the slope of the line). I find that it is easier to discuss only one parameter at a time so let's start with the population size.

1) Over time, the population size increases (we know this because the line has a positive slope).

Now let's think about the population growth rate.

2) Over time, the population growth rate increases (we know this becasue the line gets steeper over time.

3) Over time, the rate at which the population growth rate increases over time, increases over time (we know this because the slope increases faster and faster over time).

Thus, if populations are growing exponentially then they keep increasing in size at an ever faster rate forever and ever.

Now try this-

Can you draw the following graphs?

1) plot how the population growth rate varies over time.
(hint- we have alredy described what this pattern will look like using words- just turn these words into pictures).

2) plot how the population growth rate depends on population size.
(hint- this graph is a little trickier, but we do have an equation that relates the two variables)

3) plot how the per capita growth rate varies over time.
(hint- think about what the basic assumption we made aboiut exponential growth)

4) plot how the per capita growth rate
(see the hint from number 3)

Exponential Growth is Unrealistic
Because population sizes keep increasing at ever faster rates for ever, exponential growth does not seem to be an accurate description of population growth in most animals, plants, and microbes. If this is an unrealistic model then why did I teach it to you? I started with exponential growth becasue it is the simplest model of population growth and scientists always like to describe the world using the simplest models that they can.

Obviously, in this case we have started with a model that is too simple to realistically describe the world. What is wrong with the exponential growth model? The fundamental assumption we made about exponential growth is that the per capita growth rate is constant. This must not be a realistic assumtpion.

It is important that you understand, and are able to explain, both the mathematical reasons and biological reasons that exponential growth is an unreasonable model of population growth. I tried to explain biologically why exponential growth is unrealistic in the "Exponential Growth" article and the attached Powerpoint presentation so take a look at those.

Suggested Readings

Here are some articles you should look at from the Encyclopedia of the Earth. I wrote these so they are brilliant!!!

Population Ecology http://www.eoearth.org/article/Population_ecology

Exponential Growth http://www.eoearth.org/article/Exponential_growth

Logistic Growth http://www.eoearth.org/article/Logistic_growth

Carrying Capacity http://www.eoearth.org/article/Carrying_capacity

Intraspecific Competition http://www.eoearth.org/article/Intraspecific_competition

Powerpoint Presentation

Click here for the Powerpoint presentation "Why is Exponential Growth Unrealistic?"
http://www.slideshare.net/secret/IDPugQtl2wvONv

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- draw and interpret the following graphs associate with exponential growth

a) how population size change over time in exponential growth

b) how population growth rate varies over time in exponential growth

c) how the population growth rate depends on the population size

d) how per capita growth rate changes over time in exponential growth

e) how per capita growth rate depends on population size

- explain why exponential growth is an unrealistic pattern of growth for most species

- define and explain the carrying capacity

Population Biology 1. Basic Parameters




Lecture Video: http://mediacast.ttu.edu/Mediasite/Play/20ade8c97b0b40af8eaab29ae07eee6f1d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b


IMPORTANT NOTE!!!
For the next several lectures we will be using math and graphs to help us explore population ecology. From my experience teaching this topic in the past, many of you will experience some difficulties with this material because you are not confident when dealing with math and graphs.

Rather than introducing the concepts to you in lecture and then having you work on activities to help you master the material out of class, this year I would like to "flip the class". This year I would like for you to study the material before coming to class so that we can use the class time to answer your questions and to help you master the material.

Assignment- Before Wed December 30th, I expect that you will have read the following post and are able to meet all of the expected learning outcomes listed below. If you have not mastered the material in this blog, then you will find that you will be hopelessly lost in the lectures that follow!!

Expected Learning Outcomes

By the end of this course, a fully engaged student should be able to

- define b, d, r, B, D, dN/dt.

- identify and use the proper units associated with each parameter

- use the correct algebraic equations to calculate each of these parameters

- be equally comfortable referring to these concepts verbally or via their algebraic symbols.

Basic Parameters of Population Ecology

Here is a brief introduction to some of the important parameters that we will need to understand to be able to study population ecology. For each of the parameters it is important that you know (1) the name of the parameter, (2) the algebraic symbol used to represent the parameter, (3) the units of measurement for the parameter, (4) how to calculate the parameter, and (5) how to describe (in words) what a particular value of that parameter means.

It is probably easiest for me to introduce these concepts using an example.
Imagine that in a population of 100 elephants that in one year 10 elephants are born and 5 elephants die.

1) Population Size (N) units- individuals. Measures the number of individuals in a population.

N = 100 individuals

In this population of elephants, there are 100 individuals.

2) Population Birth Rate (B) units- number of births per time. Measures the number of births per time that occur in a population.

B = 10 births/year

In this population, each year there are 10 births.

3) Population Death Rate (D) units- number of deaths per time. Measures the number of deaths per time that occur in a population.

D = 5 deaths/year

In this population, each year there are 5 deaths.

4) Population Growth Rate (dN/dt) units- number of idividuals per time. Measures the rate of change of the population size.

dN/dt = B - D

dN/dt = 10 births/year - 5 deaths/year = 5 individuals/year

In this population, the population size increases by 5 individuals each year.

5) Per Capita Birth Rate (b) units- births per time per individual. Measures the number of births per time averaged across all members of the population.

b = B/N

b = (10 births/year)/100 individuals = 0.10 births/year/individual

In this population, each year 0.10 babies are born for each individual in the population.

6) Per Capita Death Rate (d) units - deaths per time per individual. Measures the number of deaths per time averaged across all members of the population.

d = D/N

d = (5 deaths/year)/100 individuals = 0.05 deaths/year/individual

In this population, each year 0.005 individuals die for each individual in the population.

7) Per Capita Growth Rate (r) units = individuals/time/individual. Measure the rate of change in population size averaged across all individuals. The per capita growth rate can be calcuated two ways.

a) r = b - d

r = 0.10 births/year/individual - 0.05 deaths/year/individual = 0.05 ind/year/ind

b) r = (dN/dt)/N

r = (5 individuals/year)/100 individuals = 0.05 individuals/year/individual

In this population, each year 0.05 individuals are added for each individual in the population.

Practice Problem

1. In a population of 50 tigers, in one year 10 tigers are born and 20 tigers die. What is B, D, dN/dt, b, d, r?

2. List the equation/equations for calculating the following parameters
a) b
b) the population growth rate
c) r

Sunday, January 27, 2013

Copy of Old Midterm 1



Hello Everyone,

Here is a link to a copy of the First Midterm from 2010. The purpose of posting a copy of this exam is to give you an idea of the form of questions that I will ask. You can find the answers to these questions at the bottom of this post.

http://www.slideshare.net/MarkMcGinley/biol-1404-midterm-1-2010

Warning #1. Invariably, I will manage to post at least one incorrect answer on the answer key (that's right, it is hard for me to get 100% on my own exam!). So if one of my posted answers appears to make no sense, then it is probably a mistake. I hope that I have gotten all of the answers posted correctly, and I apologize in advance for any errors. Please don't come and bitch at me if there are any problems!

Warning #2. In the past, I have seen lots of students who study by focusing far too much on the past exams. If you understand the material related to the questions on the past exams then that suggests that you will be able to perform well on your exam. However, if you have only learned the answers to those 30 questions, then it is unlikely that you will perform well on your midterm.

Remember that this year the midterm will contain 50 multiple choice questions and no essays!

Answers.

1 b
2 c
3 d
4 d
5 e
6 d
7 d
8 d
9 e
10 c
11 c
12 b
13 c
14 c
15 e
16 a
17 a
18 c
19 d
20 c
21 d
22 d
23 a
24 b
25 b
26 d
27 a
28 d
29 e
30 a (note this answer was incorrectly listed as "e" until Feb 10th)

Recent Article About Antibiotic Resistant Microbes


Here is an article about antibiotic resistant microbes that was published on Sunday morning.

Superbugs: A Ticking Time Bonb

http://www.cbsnews.com/8301-3445_162-57566049/superbugs-a-ticking-time-bomb/

Friday, January 25, 2013

Sexual Selection






I think that sexual selection is one of the most interesting topics in all of biology. First, studying this topic helps to illustrate that natural selection is much more than "survival of the fittest". Second, many of the traits produced by sexual selection are particularly weird and wonderful. Finally, I think that it is fun to use what we have learned about mate choice in animals to helping us to understand human behavior.

Expected Learning Outcomes


By the end of this course a fully engaged student should be able to


- discuss the critical difference between males and females and discuss how this difference influences differences in behavior and morphology between species.

- discuss why sexual selection is just a subset of natural selection

- discus why females should be choosier about who they mate with than males

- discuss why males often compete with other males to fertilize eggs of females

- compare and contrast male-male competition in species with internal fertilization and species with external fertilization

- describe the studies used by scientists to see if females are capable of choosing the best males

- discuss how females can determine which is the best male

- discuss why the variation in female reproductive success is much less than the variation in male reproductive success

- discuss how you would use sexual selection to help you understand human behavior



Past Exam Questions (answers at the bottom of the post)


1. Why are females choosier than males about who they mate with?
(a) female gametes are much more expensive than male gametes
(b) male gametes are much more expensive than female gametes
(c) in some species, males are larger than females
(d) in some species, males compete to mate with the female
(e) c and d


2. Why should females prefer to mate with the oldest males?
(a) because they can pass on good mating genes to their daughters
(b) because they can pass on good survival genes to their sons
(c) because the can pass on good survival genes to their daughters
(d) a and c
(e) b and c


3. Why might females sometimes cause male-male competition to occur?
(a) to assure that she mates with the oldest male
(b) to assure that she mates with the most symmetric male
(c) the male who wins the fight is likely to have “good genes”
(d) a and c
(e) a, b, and c


Further Reading


Here is a link to a website that a student sent to me  called "The 30 Strangest Animal Mating Habits" http://www.neatorama.com/2007/04/30/30-strangest-animal-mating-habits/

Take a look at this and see if you can relate what the animals are doing to some of the theories that we have talked about in class.


Here is a link to a youtube video showing the mating display of lyrebirds. I was lucky enough to see a lyrebird doing its mating display when I was a kid living in Australia. There was a professional nature photographer who had been hiking around the bush for a couple of weeks waiting to see the display and he was pissed that my Dad and I were able to see the display after spending only about an hour in the woods. What do you think is going on with the lyrebirds?






Here is a link to the Powerpoint Presentation I prepared for this topic.

http://www.slideshare.net/secret/CG2HHvtrLA1KwL

Answers. 1. a, 2. e, 3. c

Here is a link to an interesting article that I  discovered on an ex-student's Facebook page. Biology is Cool!!!!!

Male spider snaps off own genitals inside female to fertilise her remotely, while being eaten.

http://blogs.discovermagazine.com/notrocketscience/2012/02/01/male-spider-snaps-off-own-genitals-inside-female-to-fertilise-her-remotely-while-being-eaten/

Thursday, January 24, 2013

Friendship in Animals Besides Humans


Here is a link to an interesting article one of your classmates sent me.  It discusses "friendship" in species other than humans.  Enjoy!

http://www.time.com/time/magazine/article/0,9171,2106488,00.html

Course Syllabus


Syllabus
BIOLOGY II (for Life Science Majors)
BIOL 1404, SPRING 2013

Class Information
Section 001: MWF 9:00 a.m. in Biology LH100; Section 002: MWF 10:00 a.m. in Biology LH100.
Test period: Tu, 6:00-7:30 p.m.
Prerequisite: BIOL 1403.
1st half: Dr. Mark McGinley                                           2nd half: Ms. Carrie Monje,
Office: 215 McClellan,                                                   Of. Hrs: M-R, 1-1:30
                                                                                      Biology rm. 606C             
Of. Hrs: MWF. 11:00, or by appt.                                  
Group Of. Hrs: Monday 6:30 Room TBA                                              
e-mail: mark.mcginley@ttu.edu                                    e-mail: carrie.monje@ttu.edu
blog: http://biol14042013/blogspot.com/

Required materials:
1. Class Text: Campbell’s Biology, 9th ed., by Reece et al. or customized version for TTU, 2nd ed
2. Lab Text: Lab Manual for Biology II, by M. Dini
3. dissecting kit and 5-6 prs of examining gloves
Item 1 is available from area textbook stores.  Items 2 & 3 are available from TTUAB near room 025 in the Biology Bldg ‘til Jan. 30.
5. Homework Website: http://www.masteringbiology.com    ID#: MB14042013

1. COURSE OVERVIEW & GOALS

BIOL 1404 is the second semester of a rigorous, writing-intensive, two-semester course.  It is offered only during the spring, and designed to prepare life science majors for upper-level courses in the life sciences.  Whereas BIOL 1403 focuses on the particulars of cell biology, biochemistry, molecular biology, classical genetics, reproductive/developmental biology and evolutionary theory, BIOL 1404 focuses on organisms as they relate to other organisms and to their physical environments (ecology), biodiversity, as well as on plant and animal anatomy and physiology.  Overall, the course aims to give you a strong foundation in the principles of biology, many of which you may not encounter again in future courses.  The course is meant to introduce you to the way that scientists approach and solve problems leading to the construction of new knowledge.  It is also our hope that the course will continue to give you an important handle in your attempt to understand the place and role of humans in the world and, perhaps, your particular place in it.  Students enrolled in this course must have passed BIOL 1403, or its equivalent at another institution.  Students on academic probation, or who received a "W" or an "F" the last time they took BIOL 1403 should immediately drop this course.  This course partially satisfies the Natural Sciences Core Curriculum requirement.

2. EXPECTED LEARNING OUTCOMES AND METHODS FOR ASSESSING LEARNING OUTCOMES

A. Explain basic concepts of evolutionary ecology, general ecology, cellular energetics, plant water potential, biodiversity, animal anatomy & physiology.  ASSESSED BY: scores earned on expository essays on each of the four unit tests, and by in-class discussions.
B. Demonstrate skills in scientific reasoning and experimental design.  ASSESSED BY: group discussion and subsequent reporting via “clickers,” by scores earned on a mid-semester laboratory science process skills test, and by scores earned on written lab reports.
C. Demonstrate ability to write research reports including: abstract, introduction, materials and methods, results, discussion, acknowledgments, and literature cited.  ASSESSED BY:  scores on draft & final versions of written lab reports.
D. Students graduating from Texas Tech University should be able to explain some of the major concepts in the Natural Sciences and demonstrate an understanding of scientific approaches to problem solving, including ethics.  ASSESSED BY: scores on expository essays on each of the four unit tests, and by end-of-semester performance on laboratory science process skills test.

3. ENROLLMENT & ATTENDANCE

You should be enrolled separately in a lecture section (001 or 002) and in a laboratory section (501-521).  See Dr. McGinley immediately if you have doubts about your enrollment.  Regular attendance is critical for the success of BIOL 1404 students.  Success in this course will require a good set of notes, hopefully written by yourself, and the critical reading of all assigned pages in the textbook, for there will be test questions on material that has not been covered in lecture.  Class will often begin with verbal announcements that are not formally duplicated anywhere else.  You are responsible for getting missed announcements from classmates.  We consider more than two absences during the semester to be excessive.  It does not matter why you are not present in lecture.  The simple fact is that if you are not present, you will not learn the material as well as you otherwise would.  During the 2nd half of the semester, class participation will be monitored using the H-iTT devices.  Particularly important is your regular attendance in lab.  You must attend the lab section in which you are enrolled.  More than two unexcused absences from lab will result in the loss of ALL points connected with the laboratory portion of this course.  Not only should you be in class at every class meeting, but you should be attentive as well.  Chatting, texting, dozing, reading newspapers, or listening to music during class are totally uncool and are not tolerated.  Access to the Worldwide Web is important for success in this course.  Firefox is the preferred browser for the MasteringBiology homework website.

4. EVALUATION

Your semester letter grade will be determined from the scores you earn on four unit tests (45%), on your laboratory work (32%), on the cumulative final exam (14%), and on on-line homework (9%).   The scores for this course are not curved.  Letter grades will be determined by the number of raw points you earn (NOT the percentage), according to the following scale:

A = 979-1100                 B = 858-978                  C = 737-857                  D = 616-736                  F < 616

The four unit tests are worth 100 points each.  If you take all four units tests, your highest score on these four tests will be doubled at semester’s end, thereby making these tests worth 500 out of the 1100 points possible by semester’s end.  The cumulative final exam is worth 150 points.  On-line homework will consist of 14 assignments of varying point value.  Late homework is not accepted.  The distribution of the 350 points connected with your laboratory work will be explained at the first lab meeting.  Computer-graded portions of tests will be composed of multiple-choice and/or matching questions.  Tests 1-3 may also contain essays.  No test scores will be dropped. 

Most of the points for each test (90-95%) will be drawn from material covered in class.  Thus, a good set of notes will be of much assistance in learning the material.  Roughly 5-10% of each test will be drawn from material in the textbook or other assigned readings, but not covered in class.  Videotapes of our lectures will be available online at http://mediacast.ttu.edu but you should be aware that equipment is subject to failure and to inexperience; thus, videotapes for all lectures are not guaranteed.  You may record the audio portions of lectures (NO video recordings or photographs), but recordings may be used only to study biology unless you have our permission to use them for other purposes.  Cellular phones, palm pilots, pagers, and beepers may not be used during tests, labs, or lectures, unless directed by the instructor.  Computers may not be used during tests.  You may be asked to leave if your devices disturb the class.

We will make an effort to design tests that challenge you to do more than regurgitate facts.  Repetitious reading of textbook and notes as a sole means of studying will get you no better than a grade of "C" because tests will ask you to apply, integrate, and evaluate information in situations which may be different from those covered in class.  They will be tests of your understanding of the principles of biology, not solely tests of your ability to memorize and recall. For test preparation, former tests used for the 2nd half of the semester can be found at Dr. Dini’s website <http://courses.ttu.edu/biol1403-mdini>. Tests may include material covered in previous testing units.  Students are invited to create and submit sample multiple-choice questions for potential inclusion into all tests.  A review session will be held before each unit test, usually on Monday evenings from 5-6.

Tests will be on Tuesday evenings at 6:00 sharp (see schedule for dates) and will last 90 minutes.  You must be prepared to present a photo ID (does not have to be a Tech ID) at all tests; failure to do so can result in the disqualification of your test.  Also, bring two #2 pencils and a pen.  We will provide scantron forms.  Anyone entering the test after someone has completed the test and left the room will not be allowed to take that test.  While tests are scheduled at a frequency of about once a month, the test period on Tuesday afternoons will often be used for optional activities such as discussions of current topics, enhancing study or test-taking skills, administering re-tests, going over old tests, working on sample test questions, etc.  We strongly encourage you to be present for as many of these sessions as you can.  Not all lab instructors are equal.  As a result, it may be necessary to normalize lab scores in certain lab sections at the end of the semester.

5. UNDERSTANDING EVALUATION

Evaluating student performance is a complex and difficult process.  While students cannot be pigeonholed, they can be judged on the basis of their achievements.  Effort is an important component of achievement, but we cannot accurately gauge your effort.  We are limited to measuring achievement by the number of points you earn.  Below are descriptions of typical "A" and "C" students in BIOL 1403/1404 modified from an article in The Teaching Professor, August/September 1993.

The "A" Student -- An Outstanding Student                  The "C" Student -- A Mediocre Student
Attendance: "A" students have virtually perfect               Attendance: "C" students sometimes miss class.  They
  attendance.  Their commitment to the class                    put other priorities ahead of academic work.  In some
  resembles that of the teacher.                                        cases, their health or constant fatigue renders them
Preparation: "A" students are prepared for class.                         physically unable to keep up with the demands of
  They always read the assigned pages.  Their                  high-level performance.
  attention to detail is such that they occasionally                        Preparation: "C" students prepare their assignments
  catch the teacher in a mistake.                                      consistently but in a perfunctory manner.  Their work
Curiosity: "A" students show interest in the class                         may be sloppy or careless.  At times, it is incomplete.
  and in biology.  They look up or dig out what               Curiosity: "C" students' interests are limited to issues
  they don't understand.  They often ask inter-                   like "Do we have to know this for the test?"  They
  esting questions or make thoughtful comments.                        are most interested in coping or getting by.  Their
Retention: "A" students have retentive minds.                   goal is to spend as little time as possible in lab or
  They are able to connect past learning with the                           studying.
  present.  They bring a background with them to            Retention: "C" students only memorized things for
  class and they continually check new information            tests in high school; thus, they bring little background            against what they previously learned.                               to the class.  They will probably take little from it
Attitude: "A" students have a winning attitude.                  because they still use the same poor study habits.
 They have both the determination and the self-              Attitude: "C" students are not visibly committed to the
  discipline necessary for success.  They show                 class.  They participate without enthusiasm.  Their
  initiative.  They do things they have not been                  body language often expresses boredom.
  told to do.                                                                  Talent: "C" students vary enormously in talent.  Some
Talent: "A" students have something special.  It                have exceptional ability, but show undeniable signs
  may be exceptional insight and intelligence.  It                of poor self-discipline or bad attitudes.  Others are
  may be unusual creativity, organizational skills,               diligent, but below-average in academic ability.
  commitment -- or a combination thereof.  These            Results: "C" students obtain mediocre or inconsistent
  gifts are evident to the teacher and usually to                 results on tests.  They have some concept of what is
  other students as well.                                                   going on, but clearly have not mastered the material.
Results: "A" students make high grades on tests --
  usually the highest in the class.  Their lab work is
  a pleasure to read.

                        Grade Distributions for the last two BIOL 1404 Classes
                        spring 2011                               spring 2012
                        A = 11.9%                                 A = 8.1%
                        B = 31.0%                                 B = 32.5%
                        C = 37.2%                                 C = 37.2%
                        D = 15.6%                                D = 15.0%
                        F = 4.1%                                   F = 7.2%
                        W = 6.2%                                  W = 11.2%

NOTE: Letter grade proportions were calculated based on the number of students enrolled on the last day of class, whereas “W” proportions were figured according to students enrolled on the 12th day of class.

6. SUPPLEMENTAL INSTRUCTION

The SOAR Center will sponsor Supplemental Instruction (SI) specifically for BIOL 1404 students.  The student leaders, Jeffrey Chen & Suzanne Alkul, will attend all lectures, and will offer free instructional SI sessions at times and places to be announced.  This is a superb opportunity to get help from a peer who is also an expert.

7. TEST GRIEVANCE PROCEDURES

During the week of Feb. 5-8, fifteen randomly selected lab sections may elect a representative to the Biology Advisory Committee (BAC) following brief presentations by the candidates concerning their qualifications for the position.  This committee of students will meet the Wednesday afternoon following each regular unit test in order to evaluate student comments/criticisms about test items and to forward their recommendations to the course instructors, who will take these recommendations under advisement.  The qualifications to serve on the committee are that the student took BIOL 1403 at Texas Tech and received a "C" or better, and that the student be free Wednesdays from 4-5 p.m.

Suspected errors in the filling in of any part of the scantron form must be brought to the proper instructors' attention within one week of the posting of scores.  Please do not procrastinate; check the posted scores as soon as possible.

8. WITHDRAWAL FROM COURSE

Students who think they should withdraw from the course should be aware that this course is offered only once a year, during the spring semester.  Withdrawal must take place before 5:00 on March 27.  You need not inform the instructor, but it is helpful if you inform your lab instructor and lab partners of your intention to withdraw.  Failure to withdraw properly will result in the grade of “F.”   Students who plan to take this course elsewhere and transfer the credits to Texas Tech must insure that the other institution’s course (a) is designated specifically for majors (not non-majors and not both), (b) has a 3-h laboratory component, and (c) is a course that treats most of the following principles of biology: basic ecology; biodiversity; plant anatomy/physiology, and animal anatomy/physiology.

9. OTHER RELEVANT INFORMATION

Dishonesty on exams, homework, written work or connected with your attendance in lab or lecture will meet with the most serious consequences.  Students are expected to be aware of, and abide by, the University's Honor code.  Plagiarism on written lab reports or essays (copying/paraphrasing from other students or from other sources without giving due credit) will result in the loss of all points for that exercise, at the very least.

Disabling conditions: Any student who, because of a disabling condition (e.g. diabetes, epilepsy, dyslexia) may require special arrangements in order to meet course requirements should contact us as soon as possible so that accommodations can be made.  Students should present appropriate verification from Disabled Student Services, Dean of Students Office.  No requirement exists that accommodations be made prior to completion of this University procedure.  Religious holidays: Any student who will miss tests because of recognized religious holidays should notify us as soon as possible so alternative arrangements can be made.

Can we talk?  We can talk about anything you'd like.  No appointment is necessary to see us during office hours -- just drop in.  If office hours are not convenient, then feel free to make an appointment. You can also e-mail us..  We should tell you that we are not happy to deliver all or part of a lecture to someone who has missed class.

10. SCHEDULING

The final four lectures will be covered as part of the Cumulative Final Exam, which is on Thursday, May 9th, from 10:30 to 1:00 p.m. at locations to be announced in class.










Tentative BIOL 1404 Schedule, 2013
Week    Date     Topic                                                               Text Pages       Notes
1          Jan. 16   Natural Selection                                             476-485 NO 1404 labs this week
1          Jan. 18   Natural Selection/Altruism                                1134-1139        
2          Jan. 21   MARTIN LUTHER KING, JR HOLIDAY                           Labs do meet this week
2          Jan. 23    Altruism/Behavioral Ecology                           1118-1134
2          Jan. 25   Why have sex?                       
3          Jan. 28   Sexual Selection                     
3          Jan. 30   Population Ecology                                         1187-1191
3          Feb. 1     Population Ecology, cont.                                                       Last day to drop w/o penalty
4          Feb. 4     Human Population Growth                               198-200             BAC Elections this week
4          Feb. 6     Community Ecology                                       1194-1215
4          Feb. 8     Indirect Effects
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5          Feb. 11   Ecosystem Ecology                                                                                                   
5          Feb. 12   Test #1 (Intro. through Indirect Effects)
5          Feb. 13   Introduction to Energetics                                142-151
5          Feb. 15   Photosynthesis I                                             184-203
6          Feb. 18   Photosynthesis II
6          Feb. 20   Photosynthesis/Cellular Respiration                  163-181                        
6          Feb. 22   Cellular Respiration II
7          Feb. 25   Angiosperms: Fruits and Seeds                       807-811
7          Feb. 27   Plant Diversity I                                               600-615
7          Mar. 1     Plant Diversity II                                              618-634
8          Mar. 4     Plant Diversity III
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
8          Mar. 5     Test #2 (Energetics through Plant Diversity)              
8          Mar. 6     Viruses                                                           381-394 2nd half of course begins
8          Mar. 8     Prokaryotes I                                                  551-553, 556-565          
9          Mar. 9-17  SPRING BREAK
10         Mar. 18   Prokaryotes II                                                  564-573 NO 1404 labs this week
10         Mar. 20   “Protists”                                                         575-579
10         Mar. 22   Fungi                                                              636-642, 648-652
11         Mar. 25   Invertebrates I                                                 654-673
11         Mar. 27   Invertebrates II                                     674-683 Last day to drop
11         Mar. 29   Invertebrates III                                                683-692
12         Apr. 1   UNIVERSITY HOLIDAY                                                             Labs do meet this week
12         Apr. 3     Invertebrates IV                                               692-695
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
12         Apr. 5     Vertebrates I                                                   697-709
13         Apr. 8     Vertebrates II                                                   709-717
13         Apr. 9     Test #3 (Viruses through Invertebrates)
13         Apr. 10   Vertebrates III                                                  717-724            
13         Apr. 12   Nervous System I                                            1045-1054
14         Apr. 15   Nervous System II                                           1055-1067
14         Apr. 17   Endocrine System I                                         974-982, 984-989
14         Apr. 19   Endocrine System II                                        989-993
15         Apr. 22   Circulatory System I                                        897-904, 913-914
15         Apr. 24   Circulatory System II                                        905-909
15         Apr. 26   Lymphatic/Immune System                              910-911, 929-946
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
16         Apr. 29  Respiratory System I                                       915-922            
16         Apr. 30 Test #4 (Vertebrates through Immune System)
16         May 1   Respiratory System II                                       923-926             Lab practical starts today
16         May 3   Digestive System I                                           880-886
17         May 6   Digestive System II                                          887-895

Wednesday, January 23, 2013

The Evolution of Antibiotic Resistance




I think that the evolution of antibiotic resistance is an interesting and important issue. Below I has listed the expected learning outcomes for this topic in BIOL 1404. Because this topic has widespread medical relevance I have included a lot of additional readings and a powerpoint presentation that I developed for another class last semester. This info is not required, but is only intended to provide more info to interested students.

Expected Learning Outcomes

By the end of the course a fully engaged students should be able to

- discuss the causes of the development of antibiotic resistance

- discuss what we have learned from ecology and evolutionary biology about potentila problems associated with antibiotic use

- discuss what we have learned from evolutionary biology that should help us fight microbial diseases more effectively

Past Exam Questions (answers at the bottom of the post)

In the 1950s, Japanese physicians began to notice that some hospital patients suffering from bacterial dysentery, which produces severe diarrhea, did not respond to antibiotics that had generally been effective in the past.

1. In order for the result described above to have occurred, which of the following must have been true in the population of dysentery-causing bacteria?
(a) there was variation in the susceptibility of the bacteria to antibiotics
(b) antibiotic resistance was heritable
(c) bacteria that were more resistant to antibiotics had higher survival rates than less resistant bacteria
(d) a, b, and c
(e) neither a, b, or c was true


2. What can be done in future to limit the problem of antibiotic resistance in disease-causing microorganisms?
(a) Doctors should only describe antibiotics when appropriate
(b) Doctors should prescribe larger doses of antibiotics
(c) patients should make sure to take all of the pills when antibiotics are prescribed
(d) a and c
(d) a, b, and c

Answers 1. d 2. d

Further Reading

Evolution of Antibiotic Resistance-
http://www.pbs.org/wgbh/evolution/library/10/4/l_104_03.html

Antibiotic resistance: Questions and Answers- CDC
http://www.cdc.gov/getsmart/antibiotic-use/anitbiotic-resistance-faqs.html

Antibiotic resistance- delaying the inevitable (parts 1 and 2) UC Berkeley
http://evolution.berkeley.edu/evosite/relevance/IA1antibiotics2.shtml

HIV the ultimate evolver (parts 1-3) UC Berkeley
http://evolution.berkeley.edu/evosite/relevance/IA2HIV.shtml


When Penicillin Pays: Why China Loves Antibiotics a Little Too Much http://www.time.com/time/world/article/0,8599,2103733,00.html

Here is a link to an article about India I just discovered.
The Super-Resistant Bacteria That Has India 'Hell Scared' http://www.theatlantic.com/international/archive/2012/01/the-super-resistant-bacteria-that-has-india-hell-scared/251731/

Here is an link to an article about what is going on in the US sent to my by a fellow BIOL 1404 students. Thanks!
Antibiotic-Resistant Bacteria Found in 37 U.S. States
http://news.yahoo.com/antibiotic-resistant-bacteria-found-37-u-states-204438989.html

Powerpoint Presentation

Here is a link the the powerpoint presentation I used in another class.

http://www.slideshare.net/secret/rPekyBdLalUvFY

Evolution of Sex







Based on our understanding of natural selection, at first glance sexual reproduction doesn't appear to be advantageous from the female perspective (due to the two-fold cost of sex). However, the fact that sexual reproduction is so common in all groups of organisms suggests that there must be some major benefits of sex that outweight the costs.

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- explain "the two-fold costs of sex"
- discuss possible benefits of sexual reproduction including adaptation to environmental uncertainty and fighting disease
- be able to discuss the problem of the evolution of antiobiotic resistant microbes
- be able to discuss what the medical field may be able to learn from observing how nature fights disease.

Past Exam Question (answer at the bottom of the post)

1. What is the “two fold cost of sex”?
(a) female gametes are twice as expensive to produce as male gametes
(b) the genetic variation produced by sexually reproducing females provides a benefit if there is environmental uncertainty
(c) individuals reproducing asexually pass on twice as many of their genes
(d) a and b
(e) b and c

2. Which of the following hypotheses can explain a benefit of sex?
(a) males pass on more genes in sexual reproduction than in asexual reproduction
(b) the genetic variation produced by sexual reproductions provides a benefit in uncertain environments
(c) females reproducing asexually pass on twice as many of their genes
(d) a and b
(e) b and c


Further Readings

Although I am usually a little skeptical of articles form Wikipedia, this one is pretty good. It goes into more detail than you need to know, but provides some useful information

Evolution of Sexual Reproduction http://en.wikipedia.org/wiki/Evolution_of_sex

Interesting Article by Evolutionary Biologist David Barash

The Good News About Sex http://chronicle.com/blogs/brainstorm/the-good-news-about-sex/43292

Life in Local Playa Lakes

If you would like to learn a little more about local playa lakes-

Playa Lakes http://www.eoearth.org/article/Playa_lake

Drawings of cladocerans similar to those inhabiting playa lakes.










This is what they don't look like.


answer- 1. c 2. b