Why do we yawn?

New research into the biological basis of yawning will be published soon in the journal Animal Behaviour (news summary can be found here). Researchers at Binghamton University used a species of parakeet as a model organism, since they have relatively large brains, and do not exhibit contagious yawning, as has been seen in humans and other animals.

In their study, they subjected the birds to three different temperature conditions: Warm, normal (control) and slowly increasing. They found that only the third condition had a significant effect on yawning frequency. Their conclusion is that yawning functions as a brain-cooling mechanism, much like a cooling fan on a laptop. When the environment is cooler than the body/brain temperature, taking air in quickly will function to cool the facial blood, which in turn will cool the brain. This leads to an increase in arousal, so those early morning yawns may function similar to a cup of coffee in providing a jolt of energy.

This explains the most common occurrences of yawning. Exhaustion and sleep-deprivation have been shown to increase brain temperature, so yawning in these states would make sense. In addition, yawning may be able to be used as signs of brain cooling problems, which occur in diseases such as multiple sclerosis.

The authors also point out that yawning should no longer be viewed as a sign of boredom, but as an indication of attentiveness. I will try to remember that during my next PowerPoint lecture.

Chapter 19 PowerPoint

As usual, I will be online moderating comments til 10.00 or so tonight.

Chapter 16 review packet answers

Here are the answers to the answers to chapter 16 review packet. If you need more explanation for any of the answers, leave a comment and I will respond.

Interactive question 16.5
a. helicase.....................................................h. DNA polymerase
b. Single-strand binding potein.................i. RNA primer
c. DNA polymerase.....................................j. primase
d. leading strand.........................................k. replication fork
e. lagging strand......................................l. 3' end of parental strand
f. ligase..............................................m. 5' end of parental strand
g. Okazaki fragments

Multiple choice
1. c....................................12. d
2. a...................................13. e
3. b.................................. 14. a
4. a...................................15. d
5. b...................................16. e
6. a...................................17. c
7. b...................................18. d
8. e...................................19. e
9. e...................................20. c
10. a.................................21. a
11. e

Animations

Here are the links for the DNA replication and the transcription/translation animations. I had some problems getting the Flash movies to load using Firefox, but found that IE worked fine.

As a quick aside, please be careful when you use internet resources to study. Be sure that the information you are getting is from a reputable source. A student in block 1 today had some questions about the "5-inch cap" on mRNA, and what it meant that rRNA "forms a gibbet." The student stated that the information came from a website. Upon Googling, I found the site, and the entry on RNA types. I scanned a few of the other posts, and found that grammer is a bigger issue than getting facts wrong. However, the info about RNA is pretty bad.

There is a 5' (five prime) cap added to mRNA molecules. The problem may have come from misreading the prime symbol (') as the symbol for inches, as in I am 5'10" tall. However, the symbol for inch is ", not '. And if the cap were 5 inches long, assuming that each nucleotide is 3.4 Angstroms apart, there would be approximately 370,000,000 nucleotides in the cap. Seems a little much, cosidering the whole human genome is only 3,000,000,000 base pairs.

As far as the gibbet....I have no idea where that came from.

So please be midful of this when searching for help online.

Thanksgiving naps - is it the tryptophan?

We most likely all know someone who, after a large Thanksgiving meal, will move to the couch and take a nap, possibly blaming the high level of tryptophan in turkey for making them so tired. So what is tryptophan, is there a high amount in turkey, and does it really make us sleepy?


Tryptophan (see figure at left) is one of the 20 naturally occurring amino acids that make up the proteins in our body. Since humans are unable to synthesize tryptophan from basic building blocks, we must consume it in our diet. There are ten essential amino acids that we must consume in adequate amounts: Arginine (only for young), histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

So where does the link between tryptophan and sleep come from? Tryptophan is a precursor in the synthesis of two important signaling molecules, serotonin and melatonin (see pathway at right). Serotonin is a neurotransmitter that has multiple effects in both the central and peripheral nervous system. In the CNS, it has been shown to regulate sleep and mood. The effects of the hormone melatonin are opposite those of serotonin: What one inhibits, the other will activate.

So is there enough tryptophan in turkey to account for the sleepiness we feel after Thanksgiving dinner? According to this chart, turkey falls somewhere in the middle range as far as grams of tryptophan per 100 grams of food, with 0.24 g tryptophan per 100 grams of turkey. Compare this with egg whites, which have 1.00 g tryptophan per 100 g (dry), or Parmesan cheese, which has 0.56 g tryptophan per 100 g. Additionally, tryptophan is converted to melatonin in the intestine, where it functions to regulate digestion (peristalsis). Very little of this intestinal melatonin will enter the blood stream to get to the brain and make us feel sleepy, although there is evidence that if there is an excess in the intestine, some melatonin will leak into the blood stream. There is also a link between extra tryptophan in the diet and melatonin in the bloodstream. This increase in melatonin level has been shown to cause a phase shift the body's circadian rhythm, the normal cycle of resfulness and alertness that is common in all living things. This phase shift may make our bodies think it is later than it actually is, which contributes to a feeling of sleepieness. Interestingly, this phase shift may also contribute to feelings of wakefulness later in the night.

However, these studies were done in rats and chickens with pure tryptophan introduced directly to the stomach. The problem with this is that you do not eat a big plate full of tryptophan on Thanksgiving, or even a big plate of only turkey. You eat a big plate of turkey, stuffing, mashed potatoes, gravy, dinner rolls, pumpkin pie, etc. Adding all these extra nutrients will affect the absorption of melatonin into the bloodstream. Another problem is that tryptophan works best to stimulate sleep on empty stomach - something that is very rare after Thanksgiving dinner.

So what causes the sleepies? There are a few other suspects associated with Thanksgiving dinner. Carbohydrates, such as the starch found in potatoes, stuffing and bread may indirectly lead to an increase in tryptophan in the blood. Fats tend to slow down digestion of all parts of the meal, which makes digestion take longer and lead to longer periods of fullness. If there is alcohol served at dinner, it will function as a general depressant of the central nervous system.

In my opinion, the most likely culprit is simply the size of the meal. The typical Thanksgiving dinner contains more than 4000 calories. The USDA recommends about 2500 calories per day, so some people are basically eating two days worth of food in one sitting. When you are digesting, the body diverts blood flow away from the extremities and brain to the digestive system. This is why it often feels colder outside after eating - less blood in the extremities to keep them warm. Less blood to the brain means less oxygen, which may make you feel tired. There are a few calorie calculators out there for you to try to regulate your food intake. They are not perfect, but they will give you a rough idea of how much you are eating.

So what should you do? I am going to eat a small breakfast, probably not much lunch and try to go light on the appetizers. Then I can eat as much at dinner as I want to, and not worry about it. Thanksgiving is only once a year, might as well celebrate. Its not like the football games are going to be any good.

Genetics problems review answers/explanation

Here are the answers and explanations for the genetics review problems from class today. There will be a few problems on the test. I will be online till around 10.45 or so tonight if you have any questions.

1. Colorblindness is a sex-linked, recessive trait. Remember that sex-linked traits are on the X chromosome, which means that men only have one copy of the gene. In this example, we are told that the man has colored vision, so his genotype must be X^CY. The woman also has colored vision, so she could be X^CX^C or X^CX^c. Since one of her sons is colorblind, she must be X^CX^c, since sons inherit their X chromosome from their mothers.

2. This is a relatively simple dihybrid cross. If we use B for brown eyes and b for blue eyes; and H for brown hair and h for blonde hair, the genotype of the man is BbHH, and the woman is bbhh. Doing the cross, their children have a 50% chance of being BbHh and a 50% chance of being bbHh. Answering the question posed on the sheet, there is 0 chance their children will have blue eyes and blonde hair.

3. This is an example of a dihybrid cross where one of the genes displays incomplete dominance - red and white flowers give pink. We are crossing two F₁ plants, so the phenotype of both parents is TtRr. For this type of dihybrid cross with complete dominance, we would normally expect the 9:3:3:1 ratio. However, with incomplete dominance there is a new phenotypic class, since the heterozygous individuals are distinct from the homozygous dominant individuals. The expected phenotypic ratios are then 3 tall, red-flowered; 6 tall, pink-flowered; 3 tall, white-flowered; 1 dwarf, red-flowered; 2 dwarf, pink-flowered; and 1 dwarf, white-flowered.

4. A dihybrid cross with a lethal allele. If an individual is homozygous recessive for the l allele, they will not survive, and are not counted in the phenotypic ratios for the answer. The parental genotypes are LlBb and Llbb. After throwing out the individuals with the lethal gene combination, the phenotypic ratio in the offspring is 1 normal-legged, brown; 1 normal-legged,white; 2 deformed-legged, brown; and 2 deformed-legged, white.

5. Gene linkage. You absolutely must know how to analyze these types of data, and tell the difference between parental and recombinant phenotypes. The data that are presented are from a testcross on the F₁ generation. The genotypes for this cross are CcShsh crossed with ccshsh (remember, a test cross is always performed with a homozygous recessive individual). The phenotypes of the parents are colored, full seeds and colorless, shrunken seeds.

If we assume that these genes are going to follow the Mendelian laws of inheritance, we predict that the offspring would have equal numbers of the four possible phenotypic classes: colored, full; colored, shrunken; colorless, full; and colorless, shrunken. HOWEVER, that is NOT what the data show. Two of the phenotypic classes, colored, full seeds and colorless, shrunken seeds are MUCH more common than the other two. These two common phenotypes are called the PARENTAL phenotypes, since they resemble the parents of the cross. The other two phenotypes, which are much less common, are called RECOMBINANT phenotypes, since these gene combinations do not exist in the parental generation.

To calculate the map distance, we need to calculate the recombination frequency, which is simply the percentage of offspring that show recombinant phenotypes. For this problem, the answer is (515 + 489) / 8368 = 12%. This means that the genes are 12 map units apart.

6. This is an example of epistasis - one gene is influencing the expression of a second gene at a second location. In this case, dogs that are homozygous recessive for the e gene will be yellow, regardless of what alleles are at the location that determines pigment color (B for black and b for chocolate). The phenotypes of the parents are BbEe. Doing the cross results in a 9 black to 3 chocolate to 4 yellow labs.

7.

...........7..........3...................15..................5..........
-----/-----------/----------/---------------------------/-------------/---
.....b..........d...........a...........................c.............e

8. This is a simple incomplete dominance cross. The heterozygous individuals have green flowers. A cross of two green flowers gives results of 1 blue, 2 green and 1 yellow.

9. The genotype of the woman must be ii, since that is the only possibility for type O blood. Her baby, with type A blood, must have at least one i allele from the mother. Therefore, the babies genotype must be I^Ai. The I^A allele must come from the father. The only man with an I^A allele to contribute is man #2.

10. Pedigree A is an autosomal recessive trait. Pedigree B is a sex-linked trait because many more males exhibit the trait than females (7 vs 2). Pedigree C is a dominant autosomal trait. To differentiate recessive and dominant traits, there are a few things to look for. First is that recessive traits tend to skip generations. Look at generations I and III in pedigree A. For a dominant trait, at least one parent must exhibit the trait in order for it to be passed on to the offspring.

11. I treated this example like a regular dihybrid cross, but in this case the dominant allele will change based on the sex of the individual. The two parental genotypes are BbXX and BbXY. For female offspring, there will be 3 with hair for every 1 bald; and for males there will be 1 with hair for every 3 bald.

Genetics test

The test on genetics will be on Thursday, Nov 20. It will cover chapters 14 and 15. I have included two large PowerPoint presentations below. Both cover much more than we went over in class, and probably more than will be on the test.





And please remember to bring a #2 pencil for the test.

History in (and of) Photos

As we enter into our discussion of DNA, I would like to take the time to point out the interesting story behind one of the more well-known photographs in science.



The photo shows up everywhere, it is used as the frontspiece to the chapter in our textbook, and is probably found in every biology textbook published since 1970 or so. As a biologist, I think it ranks with this picture in historical importance; maybe not in total brain power, but at least in terms of the public consciousness. More people have seen the picture of Watson and Crick than of the 1927 physics meeting.

So what is the history of this picture; why, how, and when did it become so famous and widely used?

The picture was taken by Anthony Barrington Brown on May 21, 1953, about a month after publication of Watson and Crick's results on April 25. There were a total of eight photographs taken that day, of which three are commonly reproduced: the famous one above, the slightly less staged version shown below, and one more of Watson and Crick drinking tea (or coffee) in their office. The other prints are not widely reproduced, and a Google Image search failed to uncover them.



Barrington Brown's own account of the day the photographs were taken is interesting. A friend of Barrington Brown's contacted him and asked him to take some pictures for a story that would be sent in to Time magazine. Barrington Brown describes his first meeting with Watson and Crick, and the circumstances behind the posed pictures:

I was affably greeted by a couple of chaps lounging at a desk by the window, drinking coffee. "What's all this about?" I asked. With an airy wave of the hand one of them, Crick I think, said "we've got this model"
[...]
Anyway, I had only come to get a picture so I set up my lights and camera and said "you'd better stand by it and look portentous" which they lamentably failed to do, treating my efforts as a bit of a joke. I took four frames of them with the model and then three or four back with their coffee.

The picture was not used by Time, nor did it appear in a story in the campus newspaper Variety. Barrington Brown was paid 52 pence for the photos, and they were forgotten by all, including the photographer. Up to the awarding of the Nobel Prize in 1962, there appears to be no record of the photos being widely published or distributed.

In 1968, James Watson's autobiographical tale of the discovery of the DNA sttructure, The Double Helix was published. The popularity of the book greatly increased demand for pictures of the pair, and the Barrington Brown photo, which appears in the book, best seemed to capture the personalities of the researchers. Barrington Brown has never received royalty payments for the use of his photos, though he is actively pursuing them now.

In the past 40 years, the photographs have achieved near iconic status, not just of Watson and Crick's discovery, but of scientific research in general. A testament to the iconic stature of the photograph is the fact that Watson and Crick got together nearly 40 years later in an updated version of the photograph.

Cell Division Test

If you can figure out why Dr. H had his son pose for this picture, you will receive 5 bonus points on the test Wednesday.


Post your answer as a comment. Be sure I know who you are from your user name.

Basis for gender identity

Regarding our discussions in class the last few days, I have done some research into gender identity and gender roles. I found a few good articles, including this one by Ghosh and Walker, which is geared toward the medical/scientific community, this one by Brown, which is more for the public, and I found the short story I had mentioned, X: A Fabulous Child's Story, which I highly recommend reading.

First, some definitions (from the first article by Ghosh and Walker), first of gender identity and gender role:

Gender identity is defined as a personal conception of oneself as male or female (or rarely, both or neither). It is intimately related to the idea of gender role, which is defined as the outward manifestations of personality that reflect the gender identity. Simply put, gender identity is a self-label; gender role is a label given by society because of behavior and appearance. For example, if a person thinks of himself as a male and identifies himself as such, then his gender identity is male. However, his gender role is male only if he demonstrates typically male characteristics in behavior, dress, and/or mannerisms.

So gender is more of a social/psychological construct than an absolute biological outcome. Biology does determine the sex of an individual, which is often confused with the term gender:

The 2 terms sex and gender are often used interchangeably in the vernacular. However, [...] these words are not synonymous. [...] Sex, from the Latin word sexus, is defined by the gonads, or potential gonads, either phenotypically or genotypically. It is generally assigned at birth by external genital appearance.

If an intersex condition is present, one sex is often chosen with the intention of making social interactions and rearing simpler. Gender comes from the Latin word genus, meaning kind or race. It is defined by one's own identification as male, female, or intersex; gender may also be based on legal status, social interactions, public persona, personal experiences, and psychologic setting. Stating that sex is biologically determined, whereas gender is culturally determined, is fair.

So obviously, sex is determined by basic biology - XX for females, XY for males. The Y chromosome is the key; it encodes a gene named SRY, or testes determining factor (TDF). During the first 8 weeks of gestation, all fetuses are female. Around the eighth week, TDF is expressed, which leads to the development of testes. The testes begin producing testosterone, which is then converted to dihydotestosterone, the key hormone in virilization (making the fetus male). In the absence of the Y chromosome,the fetus will continue along the female developmental pathway. So that explains sex, what about gender identity?

Unfortunately, much of our understanding of gender identity stems from studying gender identity disorder patients, in which the process of gender identity development is believed to have misfired. This may be a useful strategy, but it is also like trying to figure out how a car runs by visiting a junkyard.

It is thought that the intrauterine hormone exposure sets a gender bias early in fetal development, which explains why female sex most often aligns with female gender identity, and male sex with male gender identity. There are other prenatal factors:

The environment in which a baby is reared with respect to gender begins to take shape prior to birth. Prenatal ultrasonography now allows the sex of a fetus to be determined quite accurately. In families who receive this knowledge of the child's biological sex, parental planning and reactions are often tailored by it. Names, items of clothing and toys, even specific thoughts about the baby, may be different depending on the anticipated sex. Thus, a preformed idea of the child's preferences is in place even before the child is delivered.

So a mother thinking about her child as a "boy" or "girl" and buying blue or pink drapes for the nursery has an effect? Personally, I am not sure about that, it seems like a stretch.

After birth, the parents are instrumental in reinforcing gender roles: little girls are hugged and cuddled with more, little boys wrestle and play with trucks. (According to Ghosh and Walker, this is more evident with fathers than mothers.) Gender identity may come from and be reinforced by these parentally-installed gender roles, and by 3-4 years old identity may be firmly set. Interestingly, gender-variant behavior seems to be better tolerated in females ("tomboys") than in males ("sissy-boys"), at least in Western society.

Looking at some biological bases of gender identity, there are a few chromosomal abnormalities and other mutations that can lead to sex or gender issues. In Turner's syndrome, the individual has only one X chromosome (XO genotype). These individuals are anatomically female, but are often infertile. Although the gender identity is usually reported as female, the infertility may lead to questions about gender role. Klinefelter's syndrome results from an extra X chromosome (XXY). Because of the presence of the Y chromosome, the fetus will generally develop as male. However, during puberty blood testosterone levels are lower than normal (XY) males, which leads to appearance of secondary female sexual characteristics, such as gynecomastia. These can lead to psychological problems and questions about gender identity.

Non-chromosomal causes include congenital adrenal hyperplasia (CAH) and androgen insensitivity syndrome. In CAH, a genetically female (XX) fetus is exposed to high levels of the hormome cortisol while in the uterus. This leads to enlarged external female genitalia, which sometimes are mistaken for male genitalia at birth. If the diagnosis is not made until puberty, as was often the case, these children were often raised as males, which can lead to gender identity problems when the female sex is revealed.

So is there a biological basis for gender? Since gender is a social (for gender roles) or psychological (for gender identity) construct, biology cannot be the only determinant. However, as outlined above for the disorders, there may be biological factors that influence gender. It seems to me that how a child is raised, the parental influence on gender roles, is the most important factor.

Mitosis lab website

Follow this link for the online mitosis lab.

Follow the link on the site in the upper left corner for Onion Root Tips.

Ms. Drust AP Biology Class

I am pushing back the cellular respiration test until Friday. I realized that some of the questions deal directly with the lab and I want to be sure that you guys have all the data for the lab and test. Please make sure to pass it on.

Nobel and IgNobel

In case you missed it, the 2008 Nobel Prizes were awarded last week. The prize for physiology and medicine was split between three researchers, one who discovered human papilloma virus (HPV) and its link to cancer. The other two researchers were among the fist to discover human immunodeficiency virus (HIV) and its link to AIDS. There is a fair bit of controversy over who should get credit for the discovery of HIV. The Nobel committee decided to reward the French group, while ignoring the American contribution. Of course, I may be a little biased, since Robert Gallo is at the University of Maryland.

The prize for chemistry went to three researchers involved in isolating, cloning and basic research on green fluorescent protein (GFP). GFP was first isolated in jellyfish, and has lead to a revolution in molecular biology. Most likely, there are few molecular research laboratories that do not use some form of GFP in research right now. And you can make cool stuff like this. Or this. Or... yeah you get the idea.

As important as the Nobel Prizes are, there is an interesting take on them here. Very interesting read; if you have time and are contemplating a career in the sciences I highly recommend reading it.

Almost as prestigious as the Nobel Prizes are the IgNobel Prizes, which

honor achievements that first make people laugh, and then make them think. The prizes are intended to celebrate the unusual, honor the imaginative -- and spur people's interest in science, medicine, and technology.

The list of 2008 (and past years) winners can be found here. Which award would you rather receive?

Chapter 9 review packet answers

To help you study for the respiration test on Thursday, here are the answers to the chapter 9 review packet handed out in class on Tuesday.

Interactive questions

9.1 C₆H₁₂O₆, 6 CO₂, energy (ATP + heat)
9.2 a. oxidized b. oxidizing agent c. reduced
9.3 a. oxygen b. glucose c. Some is stored as ATP and some is released as heat
9.4 a. electron acceptor or oxidizing agent b. NADH
9.5 a. glycolysis: glucose --> pyruvate b. Krebs cycle c. ETC and oxidative phosphorylation d. substate-level phosphorylation e. substrate-level phosphorylation f. oxidative phosphorylation The top two arrows show electrons carried by NADH to the ETC
9.6 a. 2 ATP b. 2 glyceraldehyde phosphate (not important for this class) c. 2 NAD+ d. 2 NADH e. 4 ATP f. 2 pyruvte
9.7 a. pyruvate (from glycolysis) b. CO₂ c. NADH d. CoA e. acetyl CoA f. oxaloacetate g. citrate h. CO₂ i. NADH j. CO₂ k. NADH l. ATP m. FADH₂ n. NADH
9.8 a. intermembrane space b. inner mitochondrial membrane c. mitochondrial matrix d. ETC e. NADH + NAD+ f. NAD+ g. H+ h. 2 H+ + 1/2 O₂ i. H₂O j. ATP synthase k. ADP + P_i l. ATP
9.9 a. -2 b. 4 c. Krebs cycle d. 32 or 34 e. 38 f. 2 g. 6 h. 2 i. 2 j. 2
9.10 Respiration yields up to 19 times more ATP than does fermentation. By oxidizing pyruvate to CO₂ and passing electrons from NADH through the ETC, respiration can produce a maximum of 38 ATP compared to the 2 net ATP that are produced by fermentation.

Test Your Knowledge
1. a 15. c
2. a 16. c
3. c 17. b
4. d 18. d
5. e 19. c
6. d 20. e
7. c 21. c
8. e 22. b
9. b 23. d
10. b 24. e
11. a 25. a
12. e 26. e
13. c 27. c
14. e 28. d

I am not overly concerned with the Structure your Knowledge questions. You have a cellular respiration overview chart that we filled out the first day of respiration that has all the important information on it.

Respiration PowerPoint

This is a powerpoint that covers all of chapter 9, cellular respiration.



Not all of this information was presented in class.

Additional Lab Review

Hey guys,

I just wanted to remind you that the lab bench website is a great resource. I might look it over for the test if I was an AP Biology student.

Osmosis Review PowerPoint

Make sure you know the definition of isotonic, hypotonic and hypertonic, and what happens to a plant or animal cell when placed in each type of solution. If you have questions, I will be try to be online Sunday night, though I have been having problems with my internet connection at home.

Good luck on the SATs.

Weekend events - not science related

If you are looking for something fun to do this weekend (and maybe earn a few brownie points from Dr. H) the 31st annual John Ragone road races will be held this Sunday in East Brunswick.

I am entered in the 5K race, which starts at 1 pm. If you come out early, you can cheer on my son in the kid's Pumpkin Dash at noon.

The course map can be found here.

Hope to see you there.

Don't believe the hype

It's amazing what that one extra grape chromosome can do for you.

clipped from Feel Younger Live Longer Only 1 grape in the world has the extra chromosome to do this and we've purchased most of the world's supply. Enter password BE86817. | Cool Home Stuff Find interesting DIY projects, new home improvement products and fun household gadgets! |

A Positive Definition for Prokaryotes

This article highlights some of the current thought behind the need for a positive definition of "prokaryote." The current definition is negative: Cells that don't have a nucleus (nuclear membrane) are not eukaryotes, so they are prokaryotes. Negative definitions are not scientifically useful, since they only allow members to be excluded from the group, not included in another group. You have a nucleus, you don't belong in this group.

This new positive definition is based on molecular data rather than morphological observations. The old format has two major groups, the prokaryotes and the eukaryotes.

The current textbook paradigm for biological diversity and evolution is based on what I will call the prokaryote/eukaryote model. This posits that there are two kinds of cells: prokaryotic, those without nuclei (specifically, without nuclear membranes) and eukaryotic, those with a classical membrane-bounded nucleus. The model further posits that the former gave rise to the latter.

This "textbook" definition states that prokaryotes appeared first, and slowly evolved into eukaryotes. However, modern molecular analysis does not support this.

Molecular-sequence comparisons, first of ribosomal RNA genes in the late 1970s and of many other genes since, replaced analyses based on morphological subjectivities (such as the presence or absence of a nuclear membrane) with credible maps of evolutionary relationships between genes. These sequence comparisons have rendered the prokaryote/eukaryote model obsolete.

Analysis of the rRNA sequences results in the following evolutionary tree:



This illustrates that eukaryotes and archaea are more closely related than archaea and (eu)bacteria. So putting archaea and bacteria together in a group does not make evolutionary sense when the molecular biology is taken into account.

The article concludes with a call to remove the term "prokaryote" from the textbooks.

I believe it is critical to shake loose from the prokaryote/eukaryote concept. It is outdated, a guesswork solution to an articulation of biological diversity and an incorrect model for the course of evolution. Because it has long been used by all texts of biology, it is hard to stop using the word, prokaryote. But the next time you are inclined to do so, think what you teach your students: a wrong idea.

Our textbook has chapters on prokaryotes. I will do my best to refer to them as arcaea and bacteria.

Macromolecule powerpoint

If you have any questions/concerns about the test material, I will be online until 10.30 tonight. Post your questions as a comment and I will respond as quickly as possible.

Water PowerPoint

Found it.

Enzyme PowerPoint

PowerPoint for sections 8.4 and 8.5.



I will post the water review PowerPoint as soon as I find the CD where I have it saved. Hopefully it is in my computer at home.

Change in test material

The material to be covered on the test on Thursday has been adjusted. The test will only cover chapters 1 -4 and sections 8.4 and 8.5. Chapter 5 (Structure and Function of Macromolecules) will NOT be on the test Thursday. Chapter 5 will be presented in class on Wednesday, and we will finish chapter 5 after the test. There will be a test on chapter 5 sometime next week, most likely Tuesday or Wednesday.

McCain and science

As promised, here are John McCain's answers to the 14 top science questions facing the next President of the United States. For a side-by-side comparison of the two candidates, click here.

Jury duty and schedule changes

So I was able to get off with only one day of jury duty (Friday), since the court of New Jersey allows teachers to claim a "hardship" and be excused from three weeks of service. The case actually sounded sort of interesting (man murders girlfriend, claims self-defense. Not sure how the dismemberment part fits as self-defense...) but missing three weeks of school would have been a little much.

In order to get back on track, we are going to have to make a few adjustments to the schedule for this week. The new schedule will be as follows:

Monday - Enzymes and energy
Tuesday - Enzyme activity lab
Wednesday - Macromolecules review
Thursday - Test on Unit 1 (Chapters 1 - 5)
Friday - Microscope review

The review day scheduled for Tuesday was cut out, so that we will only be one day behind the original schedule. If you want extra review before the test, I will be in room 216 after school on Tuesday.

New Poll

New poll on the left. Be sure to vote and make your voice heard.

Obama and Science

Barack Obama responds to questions on US science policy. John McCain has said he will also provide answers to these questions. When McCain's responses are posted, they will be linked.

Summer ecology review PowerPoint

Here is the PowerPoint to review the summer ecology packet. Test is on Thursday.

More Handouts

More first-day-of-class handouts. The syllabus for September and blog contract.

Chapter 1 powerpoint

Here is a Power Point presentation for Chapter 1 of the textbook. Quiz on this material is on September 8 (Monday).

Class procedures handout

Here is a copy of the classroom procedures handout that was distributed on the first day of class. Be sure to review them and share them with your parent/guardian. The signature sheet should also be signed and returned before the end of the first week of school (9/5/08)

Welcome

Welcome to AP Biology at Monroe Township High School. This site will be used throughout the year to supplement and expand on the material covered in class. Be sure to check periodically throughout the semester for important information, and feel free to leave a comment.