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Lou FCD



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Joined: Jan. 2006

(Permalink) Posted: Aug. 20 2008,20:11   

Steve suggested over on the BW that I open a thread to blog about the Biology course I'm taking in my first semester in college.  Here it is.

A little about the course:

It's Bio 111, with a lab, and it's the first course along my way to a Biology Education degree.  

The instructor, who I'll just name "Doc" for now, earned his bachelor's at Ohio State, his master's at University of North Carolina Wilmington, and his PhD at North Carolina State.  Along the way, he taught various places, including at Coastal.  He's been teaching there for (if I recall correctly) 22 years or so.

The text we're using is Biology, Eighth Edition, by Campbell & Reese et al, and the lab manual is Biology, Ninth Edition, by Sylvia S. Mader.

I have the lecture at 8:00 AM on MWF, and the lab is Mondays from 11:00 to 2:00.

Monday's lecture was mostly course introduction, reviewing the syllabus, that sort of thing.  With a bit of time left in the class period, Doc opened the floor to questions.  I asked him about his background, and hence the biographical content above.

Monday's lab consisted of some discussion of the Scientific Method, evidence, and making observations, creating hypotheses, predictions, and testing, and making conclusions.  There was more than a little stress placed on the idea that in Science, we don't prove things, we disprove them or we say that evidence supports our conclusions.  A lot of that discussion can be found in various forms all over this board, or at your friendly neighborhood Science blog or ScienceBlog.

We then played some cards.  Specifically, we did a class demonstration of a game called Eleusis.

The idea of the game is to demonstrate the Scientific Method in a way that students can relate to it.

One person is designated "Nature".  Nature draws a small envelope from a larger one, and inside the smaller envelope there is a rule for a sequence of cards.  The rule might be "Black Red Black Red" or "2,4,6,8" or something having to do with the four suits of cards.  Each of the smaller envelopes contains a different rule, and each is numbered (ie. Rule #6)

Nature picks two cards out of the deck and lays them on the desk to begin the sequence.

The other members of the group then make their initial observation of the first two cards and form a joint hypothesis about the rule (writing it down of course).  They then find a card in the deck to test their hypothesis, and hand the card to Nature, who places is either next in the sequence if it fits the rule, or perpendicular to the last card that fit the sequence if it does not.  The group then observes the "test result" and progresses from there until they are confident they have figured out the rule.

One thing Doc really stressed was that Nature was to remain absolutely silent, never ever giving the rule.  Not during the process, not when the group is sure they have it, not during the comparisons later, not ever.  The idea being of course, that Nature really doesn't ever tell us if we're right.  There is no right.  There is only supported or not supported by the evidence.

After the class demonstration, the class broke into three or four smaller groups and each group played this game for some time.

Afterwards, each group sent a representative up to the board to write down their theories about the rules.  It sort of mimicked a portion of the post-peer review experiment replication process, in that each group was repeating the exact same experiments and then comparing results.

None of the groups finished all ten rules.  There was overlap on many of the rules that were completed, and in some, all the groups got the same answer.  In others, there were two or three groups that had different answers for the same rule.

We then discussed what happens in Science when one group of scientists does an experiment, but other scientists get differing results from the same experiment.  It seemed to be very instructive to the class.  They got it.

Moving on, cross posting from the BW, here are my notes and thoughts from this morning's lecture:

Quote (Lou FCD @ Aug. 20 2008,11:24)
Great introductory bio lecture this morning.  Living vs. nonliving stuff, hierarchies, stressing on evidence, that sort of thing.

One thing Doc really spent some time on was the difficulty in defining life, and how any definition of life has to encompass so much.

Some notes:

Over the thin skin of the earth, the only place we know for sure that life exists, we've documented and catalogued:

over 350,000 species of plants, over a million species of animals (BEETLES!!!), and thousands upon thousands of fungi, protists, bacteria.  Given that we have documented about 1.8 million species of life, here's some context:

That's life on earth now.
Water covers 70+% of the surface area and 99% of the volume of the known biosphere.  We've explored perhaps 5% of that.
Over 95%, and perhaps as much as 99% of all species ever are now extinct.
Earth is a dust mote in the context of the cosmos

Any definition of life would have to cover the species we know, the species that are extinct, the species that live in the vast majority of the Earth we haven't even been to, and then still cover any life we might find elsewhere.

Holy crap, that really is overwhelming in that context.

He also mentioned Justice Potter Stewart's famous quote about pornography from the 1964 Jacobellis v. Ohio case, "I know it when I see it".  It was an interesting aside.

Another interesting note from today's lecture:

Discussing the definition of Science, our working definition is 'an evidence-based way of learning about the natural world'.

and allow me this little quote on the subject of evidence, from my prof:

"...not just because it's written in a book somewhere."

Dogs and cats came up in the context of heredity, and I imagine that it wasn't accidental.  Sort of the wind up for the pitch to follow later, I think.

I'm loving my Biology class, in case anyone couldn't tell.


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afarensis



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(Permalink) Posted: Aug. 20 2008,22:03   

Brilliant! I'm going to have to see if I can find that game.

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Lou FCD



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(Permalink) Posted: Aug. 21 2008,05:07   

Quote (afarensis @ Aug. 20 2008,23:03)
Brilliant! I'm going to have to see if I can find that game.

The only thing you really need are several decks of regular playing cards, a large manila envelope, several small manila envelopes, and little strips of paper for the rules. Just print them out and cut them up.

Doc had a really big set of cards for the class demonstration to make it easy for everyone to see.  They were probably about 12" X 18" or something.  Instead of placing them on the desk, he used magnets to put them up on the white board.

Also, it works best if there is a minimum group size of four.  Then each person takes a turn at being Nature.

I have to wonder if there might even be an electronic version.

Hey, there's a Wikipedia entry, even.

ETA:More info about the game, and a page with the rules

ETAA: Also, when writing the rules remember to keep it simple.  Each rule should only play on one variable, and the variables were restricted to suit, value, and color.  So


Quote
Hearts, Spades, Diamonds, Clubs, Clubs, Diamonds, Spades, Hearts


or

Quote
Each card increases by two: 2, 4, 6, 8, 10, Q, A, 3, 5, 7,...


or

Quote
Red, Red, Black, Black, Red, Red, Black, Black


would be good rules for the demonstration.

ETAAA: We just let the group pick the card out from the deck and hand it to Nature, who did the placing of the card, rather than the way the rules on that page state.

Also there was no hint from Nature.  Nature was not to speak at all (mimicking real Nature, who NEVER gives hints), not even saying "correct" or "incorrect".  Even after the lab was over, we didn't know which rules the different groups got right or wrong.

Edited by Lou FCD on Aug. 21 2008,06:23

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Reciprocating Bill



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(Permalink) Posted: Aug. 21 2008,07:45   

Quote (Lou FCD @ Aug. 21 2008,06:07)
   
Quote (afarensis @ Aug. 20 2008,23:03)
Brilliant! I'm going to have to see if I can find that game.

The only thing you really need are several decks of regular playing cards, a large manila envelope, several small manila envelopes, and little strips of paper for the rules. Just print them out and cut them up...

Reminiscent of the Wisconsin card sort, used in neuropsychological testing. A task very sensitive to particular forms of brain damage, esp. to the frontal lobes, which mediate executive functioning.

The subject is presented cards (created for the purpose) and required to deduce a rule governing their classification, which is indicated by which of two piles each card is placed in. The rule is generally quite simple.

Once the subject is consistently employing the rule to predict where each card will be placed, the rule changes. Suddenly, some of their answers are wrong.  

The measure is how long the subject persists in applying the old rule, which no longer works, before deducing the new one. Persons with frontal brain damage often deduce the original rule quickly, but persist in applying it long after it has ceased to be appropriate.

(WAD? Behe? Meyers? Step over here...)

ETA: You go, Lou.

--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

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J-Dog



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(Permalink) Posted: Aug. 21 2008,08:07   

Quote (Reciprocating Bill @ Aug. 21 2008,07:45)
The measure is how long the subject persists in applying the old rule, which no longer works, before deducing the new one. Persons with frontal brain damage often deduce the original rule quickly, but persist in applying it long after it has ceased to be appropriate.

(WAD? Behe? Meyers? Step over here...)

ETA: You go, Lou.

How embarrassing for them - and perceptive of you to notice this!

The entire ID charade, and their entire careers and lives summed up as a footnote about an error in thinking.

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Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10

Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08

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Lou FCD



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(Permalink) Posted: Aug. 21 2008,11:18   

Oh, I almost forgot.  During the first lecture, I totally stole a line from David Heddle.  It was perfect, and classic.

Doc asked, "Anybody know what the difference is between this class, Bio 111, and the other Biology class, Bio 110?"

To which I shamelessly replied, "That other class is 'Biology for Poets'."*

Big laughs from the class, and a valiant effort at repressing a smirk from Doc.  He nearly succeeded.

*A similar line about Physics classes appears in Heddle's novel, Here, Eyeball This!, which I am currently reading in my "spare" time.  Here's a hat tip, Heddle!

Edited by Lou FCD on Aug. 21 2008,12:19

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JonF



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(Permalink) Posted: Aug. 21 2008,11:35   

Quote (afarensis @ Aug. 20 2008,23:03)
Brilliant! I'm going to have to see if I can find that game.

Invented by Robert Abbott in 1956. Martin Gardner wrote about it in Scientific American in 1959. Abbott updated it in the 70's.

Eleusis and Eleusis Express

  
Lou FCD



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(Permalink) Posted: Aug. 21 2008,11:54   

Quote (JonF @ Aug. 21 2008,12:35)
 
Quote (afarensis @ Aug. 20 2008,23:03)
Brilliant! I'm going to have to see if I can find that game.

Invented by Robert Abbott in 1956. Martin Gardner wrote about it in Scientific American in 1959. Abbott updated it in the 70's.

Eleusis and Eleusis Express

hmph.  Not paying attention in class, Jon?

*ahem*

 
Quote (Lou FCD @ Aug. 21 2008,06:07)
Hey, there's a Wikipedia entry, even.

ETA:More info about the game, and a page with the rules


Edited by Lou FCD on Aug. 21 2008,12:54

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Albatrossity2



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(Permalink) Posted: Aug. 21 2008,12:05   

Lou

Thanks for starting this thread. Our classes start on Monday, and I am up to my eyeballs in things that I need to do before then, but I will follow with interest your exploits at Coastal Carolina. Our class here is not a traditional lecture/lab course like yours; it is in the studio format and thus is sorta experimental. But lots of things that are done in the traditional formats are still adaptable for us, so keep posting!

--------------
Flesh of the sky, child of the sky, the mind
Has been obligated from the beginning
To create an ordered universe
As the only possible proof of its own inheritance.
                        - Pattiann Rogers

   
Venus Mousetrap



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(Permalink) Posted: Aug. 21 2008,12:13   

I play a card game called Mao, which sounds like this only less useful. One of the rules is that you can't be told the rules, and that you have to deduce them as people play. The core rules are simple (lay cards of like suit, or like value, some cards have special effects like the 8 reversing direction of play, etc.) but the reward for winning (by losing all your cards) is that you get to add a new rule of your own invention, which must then be deduced by the other players.

This eventually results in lots of rules acting at once, which is why the game has an explicit Point of Order which can be called if two players need to decide if their rules are clashing and which takes priority, etc.) It's neat. Unless, in my case, you utterly wreck the game by suddenly doubling the number of suits to 8 and making it near impossible to win, and they wouldn't let me cancel my rule *grumble grumble*

  
Lou FCD



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(Permalink) Posted: Aug. 21 2008,12:35   

Venus,

Yeah, I think I read something about the similarity to Mao on the Wiki page or something, though I've never played Mao.

Bill and Alby,

Thanks, I hope you guys enjoy reading about the class, and maybe find something useful.  I'm certainly enjoying the class thus far, both the lecture and the lab.*

*disclaimer:  I was just thinking about sending Doc an email with a link to this thread, and my opinion of the class as stated in this thread is in no way affected by my desire to suck up for an A.  :)

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Wesley R. Elsberry



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(Permalink) Posted: Aug. 21 2008,12:56   

Quote

The measure is how long the subject persists in applying the old rule, which no longer works, before deducing the new one. Persons with frontal brain damage often deduce the original rule quickly, but persist in applying it long after it has ceased to be appropriate.


People with perseverative frontal lobe damage never switch rules in the Wisconsin card sort. This is despite the fact that such patients may be able to describe the WCS procedure, plan a strategy for changing rules, and express an expectation that they will, this next time, manage to switch rules.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
Assassinator



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(Permalink) Posted: Aug. 21 2008,13:03   

Nice thread Lou, the course sounds really good. As you might now I spent 1 year doing a Bio-Informatics Bachelor, ofcourse with a biology class. But what shocked me is that we spend almost no time on the scientific method, how science works etc. How can you ever properly work with science if you don't know the basics?
Anyway, I'de love to do a similair biology course some day, but I don't think I can do that here in the Netherlands. I wonder how that works at your place Lou, how can someone at your age and no proper biology history (wich would be the case with me) end up in a university biology class. What kind of biology course is it anyway? Can you get a Master with it, or is it just for 1 year?
I bet it works very different over there in the US.

  
Lou FCD



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(Permalink) Posted: Aug. 21 2008,13:12   

Quote (Assassinator @ Aug. 21 2008,14:03)
Nice thread Lou, the course sounds really good. As you might now I spent 1 year doing a Bio-Informatics Bachelor, ofcourse with a biology class. But what shocked me is that we spend almost no time on the scientific method, how science works etc. How can you ever properly work with science if you don't know the basics?
Anyway, I'de love to do a similair biology course some day, but I don't think I can do that here in the Netherlands. I wonder how that works at your place Lou, how can someone at your age and no proper biology history (wich would be the case with me) end up in a university biology class. What kind of biology course is it anyway? Can you get a Master with it, or is it just for 1 year?
I bet it works very different over there in the US.

Assassinator,

This is just the first semester of my very first year.  I'm just like a kid who just graduated secondary school.  In fact, most of the students (though not all) in all of my classes are exactly that.  I'm "The Old Man" in a classroom mostly full of kids.  (In fact, I've been given that exact nickname in my English class...)

It's a lot of fun, but it'll be two years at Coastal for me to get an Associate's degree in Biology Ed., then I'll have to transfer to the University of North Carolina - Wilmington to finish my Bachelor's degree (another two years, if all goes well).  Then I can get certified to teach in a secondary school.

Until then, I'm just another poor Uni student making his way, just older and with a messed up neck and back.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Assassinator



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(Permalink) Posted: Aug. 21 2008,13:51   

Aaa, I thought you were just doing a loose biology course for 'shits & giggles'. But you're actually wanting to become a biology teacher, I wish you good luck with that ;) My mom (snicker) did something similair, but she got a much lower degree for a primaire school teacher assistant. I'm still very proud of her, that she managed to do that while also having to run a family.

I don't think I'll ever do something similair, but I still would like to experience biology in a true educational setting. I hope that's possible, first I'll have to focus myself on my Journalism Bachelor. There are still some scientific opportunities with that, I can alwayse dive into science journalism. In the meantime I'll just follow this thread about your educational adventures.

  
Lou FCD



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(Permalink) Posted: Aug. 22 2008,10:53   

This morning's lecture was teh awesome.

Doc started with some announcements, a reminder to get a composition book and a folder for lab, and a reminder about the Science Club.  There is a 2hr canoe paddle on the New River and a shore clean up thing on September the 6th.  After my English class I stopped by the Doc's office and gave him the $2 for membership, though obviously I can't do the canoe thing, for physical reasons.  If I'm free that day, I may see if I can just meet the club at the clean-up site.

Does membership in the Science Club make me an official Science Geek now?  I mean, I've even paid the dues and all! I'd like to be part of the Official Science Geek Club.  I mean, that's part of the benefits package, right?  Plus, Science Geeks have the hottest chic ... uh... I mean that means nothing to me because I'm married.

Ok, on to the lecture, y'all quit distracting me with the pleasures and temptations of the flesh:

Doc started out by going over the levels of biological organization that we ended with on Wednesday, and laid out that we'd be covering the bottom levels mostly in Bio 111, and why.  Seeing as how you have to understand the basics of the building blocks before you can really start to understand the higher levels, it makes sense that we're going to be spending our time at the levels of cells and their constituent parts (molecules, atoms, subatomic particles).  We'll be skipping up to the Population level in the last unit of the course.

Bio 112 will focus on the upper levels.

For anyone not familiar who might be reading this, here's what we're talking about, from the top level down.  Each level consists of members of the next lower level.  It's pretty straightforward.

 
Quote
Biosphere
  Ecosystems
     Communities
        Populations
           Organisms
              Organ Systems
                 Organs
                    Tissues
                       Cells
----------------------------------------------
                          Molecules
                             Atoms
                                Subatomic Particles


So doc drew a analogy between Bio 111 and the foundation of a house.  It takes months to put in the foundation, and it's critical to get it right, because the rest of the house, while quick and easy to put up in comparison, requires a good foundation.

So, why are we dealing with cells?  Cells are the basic structural and functional units of life.

Structural ----> All living things are made up of cells
Functional ---> All the Unity of Life functions occur at the cellular level

So then he posed the question of why are cells alive and why are their constituent parts (molecules) not alive?  (Hence the line in the organization level diagram above.)

Emergent Properties

The properties of a level of biological organization not present in lower levels, resulting from the interactions of their constituent parts.  Emergent Properties are in most cases unexpected, and not predicted from knowledge of the properties of the lower level parts.

EX 1: Water
Water is made up of hydrogen and oxygen, two flammable gases
But water, as a result of the interaction of hydrogen and oxygen is a non-flammable liquid (at room temperatures)

EX 2: Sodium Chloride
Sodium is a highly reactive explosive silvery metal
Chlorine is a toxic gas
Table salt is vitally necessary for life

EX 3: Tree
Carbon Dioxide gas and liquid water interact to form a 500 kilo tree.

(Note: The question was posed by Doc: "Where does a seed get all the stuff to make a tree?"  I was surprised that I'd never really thought about where the wood comes from.  Obviously not the soil, as Doc pointed out, or the tree would be in the middle of a big hole.  Where does all that stuff come from?  CO2 and water.)

So then we came back to The Diversity and Unity of Life

1859 (I wanted to yell out the significance of this date when he wrote it on the board and left it hanging there all alone.)

"On the Origin of Species" by Charles Darwin

Doc talked about Darwin's voyage on the Beagle briefly, then dove in head first.  (As an aside, I kept an ear out for groans or clucking tongues, but didn't notice anything untoward.)

Descent with Modification

--All organisms are related by descent from a common ancestor ---> explains the unity of life.

--Populations change over time as they adapt to new or changing environments through the process of Natural Selection ---> explains the diversity of life.

 
Quote
"Descent with Modification is the only idea that explains both of these characteristics of life."


Doc then put up a table regarding generations of our ancestries:

 
Quote
Generation - Ancestors
1                  2  <----- 6,000,000,000 people on earth now
2                  4
3                  8
4                16
5                 32
6                 64
7                128
8                256
9                512
10             1024


So the question was, "why were there fewer people on earth two hundred years ago (about generation 10) than there are now? Why weren't there 1024 * 6B?"

The answer of course is that we share ancestors.  There were some ooos and aaaas at the impact of the numbers when it dawned on people that 1024 people were in their family tree in one generation just 200 years ago.  I'm the family armchair genealogist, so I had that moment years ago, but I remember it well.

To illustrate Descent with Modification, Doc drew a graph similar to the following:



and explained that each red dot was a species.

Then he filled in the ancestry tree thus:



Then he boxed in all the extant species, and explained that the reason that all life have cells and DNA and metabolism is because of heredity from the common ancestor.



And then explained that DNA replication is not perfect, and that errors occur and adaptation to the environment takes advantage of that to produce speciation:



So if a line of heredity develops trait X, its descendants will have trait X, and if another line develops trait Q, its descendants will have trait Q.

The lecture was straightforward and easy to follow, I imagine even for someone who doesn't hang around a bunch of Science Geeks.  Good day, for sure.

Quote
All images are clickable for larger versions at my Flickr page.  Created by me, and licensed for use as you see fit.


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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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dogdidit



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(Permalink) Posted: Aug. 22 2008,11:43   

Years ago (more years ago than I care to calculate just now) I took a college class in (classical) quantum mechanics. The professor didn't assign a text, but instead explained that all the material for the class would be presented on the blackboard during his lectures. Therefore (1) it was important to attend every lecture, or at least get notes from a buddy, and (2) it was important to take comprehensive notes! But the professor made it abundantly clear that good note-taking alone was insufficient; he strongly recommended that we re-copy our notes after class. His theory was that when we re-copied the notes, the study material would have to pass from our eyes to our hands, and would therefore have a good chance of encountering our brains along the way, where some of it might stick.

I took his advice. It was very effective.

Dude, keep up this blog and you are going to be a serious biology-knowing science geek fer sure.

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"Humans carry plants and animals all over the globe, thus introducing them to places they could never have reached on their own. That certainly increases biodiversity." - D'OL

  
Lou FCD



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(Permalink) Posted: Aug. 22 2008,11:59   

Quote (dogdidit @ Aug. 22 2008,12:43)
Years ago (more years ago than I care to calculate just now) I took a college class in (classical) quantum mechanics. The professor didn't assign a text, but instead explained that all the material for the class would be presented on the blackboard during his lectures. Therefore (1) it was important to attend every lecture, or at least get notes from a buddy, and (2) it was important to take comprehensive notes! But the professor made it abundantly clear that good note-taking alone was insufficient; he strongly recommended that we re-copy our notes after class. His theory was that when we re-copied the notes, the study material would have to pass from our eyes to our hands, and would therefore have a good chance of encountering our brains along the way, where some of it might stick.

I took his advice. It was very effective.

Dude, keep up this blog and you are going to be a serious biology-knowing science geek fer sure.

Love the thought.  If it works as well as it should, I'll have to keep that in mind for when I start teaching.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Henry J



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(Permalink) Posted: Aug. 22 2008,12:08   

Quote
(Note: The question was posed by Doc: "Where does a seed get all the stuff to make a tree?"  I was surprised that I'd never really thought about where the wood comes from.  Obviously not the soil, as Doc pointed out, or the tree would be in the middle of a big hole.  Where does all that stuff come from?  CO2 and water.)


That's sort of like when somebody puts a clipping from a flower in a pot with only water in it, and it somehow grows - without even any access to any dirt. :p

  
cogzoid



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(Permalink) Posted: Aug. 22 2008,12:10   

I wish I did the same thing.  A physics prof I had in college described his method when he was a student.  He would recopy the entire lecture in pen in a new notebook every night, correcting mistakes and carefully redrawing diagrams, etc.  He still has those notebooks and uses them to construct his own lectures.  Most undergrad physics hasn't budged in a hundred years, so they work just fine.  Of course, I didn't hear the story until I was done with classes in grad school.  By then it was too late!

  
Spottedwind



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(Permalink) Posted: Aug. 22 2008,15:51   

I wanted to quickly throw out a word of thanks and support for this thread.  Not only is it great that you are going back to college, but I love hearing about it.

I received my BS in Wildlife Biology 7 years ago but am not yet in my field; heck, I'm not even in biology right now.  I've got a simple state job that pays the bills, but it leaves me missing science to no end.  For the past few months, I've been lurking here, PT, and many other places (when our internet filters let them through) to try to get a fix when I can.  I'm still applying for jobs, volunteering at a zoo, and trying to remember that I'm still young and that there is no maximum age to begin an entry level position.  Still, I get discouraged sometimes and it seems like a cubicle farm is all I'll ever see.

You posting about the classes kind of helps me to re-energize.  Coming here in general does that, but to see your excitement about learning is kind of contagious.  I feel like I haven't used much of my knowledge in the past few years and reading over this thread is a great mental exercise.  How much do I remember?  Did I ever learn that?  It helps me to gain a bit more confidence to get up, dust off, and keep trying.

But I digress.  I wish you the best of luck on the entire endeavor and thanks again for posting about it!

(This post ended up longer than planned...I've been meaning to de-lurk for sometime...guess I waited too long  :D )

  
Lou FCD



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(Permalink) Posted: Aug. 22 2008,16:28   

Quote (Henry J @ Aug. 22 2008,13:08)
That's sort of like when somebody puts a clipping from a flower in a pot with only water in it, and it somehow grows - without even any access to any dirt. :p

Yeah, exactly!  I just never really thought about it.  It's magic!!!!  :)  (No son, it's science.)

 
Quote (cogzoid @ Aug. 22 2008,13:10)
I wish I did the same thing.  A physics prof I had in college described his method when he was a student.  He would recopy the entire lecture in pen in a new notebook every night, correcting mistakes and carefully redrawing diagrams, etc.  He still has those notebooks and uses them to construct his own lectures.  Most undergrad physics hasn't budged in a hundred years, so they work just fine.  Of course, I didn't hear the story until I was done with classes in grad school.  By then it was too late!


I think I might apply the same technique to my precalc class, especially since between the notes and the homework, I'm about halfway through my notebook already anyway!

 
Quote (Spottedwind @ Aug. 22 2008,16:51)
I wanted to quickly throw out a word of thanks and support for this thread.  Not only is it great that you are going back to college, but I love hearing about it.

I received my BS in Wildlife Biology 7 years ago but am not yet in my field; heck, I'm not even in biology right now.  I've got a simple state job that pays the bills, but it leaves me missing science to no end.  For the past few months, I've been lurking here, PT, and many other places (when our internet filters let them through) to try to get a fix when I can.  I'm still applying for jobs, volunteering at a zoo, and trying to remember that I'm still young and that there is no maximum age to begin an entry level position.  Still, I get discouraged sometimes and it seems like a cubicle farm is all I'll ever see.

You posting about the classes kind of helps me to re-energize.  Coming here in general does that, but to see your excitement about learning is kind of contagious.  I feel like I haven't used much of my knowledge in the past few years and reading over this thread is a great mental exercise.  How much do I remember?  Did I ever learn that?  It helps me to gain a bit more confidence to get up, dust off, and keep trying.

But I digress.  I wish you the best of luck on the entire endeavor and thanks again for posting about it!

(This post ended up longer than planned...I've been meaning to de-lurk for sometime...guess I waited too long  :D )


Thanks for joining the conversation, Spottedwind.  I'm glad this thread helps you to pick yourself up, and also that it moved you to delurk.  

Besides being the one productive job that I might be able to do with my screwed up spine, part of the impetus for me doing this is the desperate need for teachers in our area.  Here in Onslow County, NC, we're expecting an influx of about 11,000 Marines (or maybe more) in the next few years, plus their families, plus civilian support staff, plus their families.  All totaled, we're expecting 40k to 200k people (depends on exactly what the Corps does, and whose figures you're looking at).  That means there are going to be a boatload of kids needing teachers in the not too distant future.  And some of those teachers will need to be Science teachers.

It's not a bad place to live if you can deal with the ultra-right-wing nationalism that runs a little rampant in a military town.  Just something for you to consider.

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deadman_932



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(Permalink) Posted: Aug. 22 2008,17:01   

Dear Mrs. Lou,

       I'm sorry to be the bearer of bad tidings -- but this drawing by one of Lou's classmates has come to my attention:


       Your friend, deadman_932

P.S. Notice how your husband is altering his appearance to seem younger and Spicoli-like in class. Possibly just for his nefarious purposes.



Edited by Lou FCD on Aug. 22 2008,19:10

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Lou FCD



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(Permalink) Posted: Aug. 22 2008,17:47   

LOL

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Assassinator



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(Permalink) Posted: Aug. 22 2008,17:56   

I actually had something like that back in my early high-school years. The only difference was that the uber cute/hot biology teacher was really short, and I already was friggin huge. That switch of positions also gives an...interesting perspective, from my point of view ;)

  
Arden Chatfield



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(Permalink) Posted: Aug. 22 2008,17:59   

Quote (deadman_932 @ Aug. 22 2008,15:01)
Dear Mrs. Lou,

       I'm sorry to be the bearer of bad tidings -- but this drawing by one of Lou's classmates has come to my attention:


       Your friend, deadman_932

P.S. Notice how your husband is altering his appearance to seem younger and Spicoli-like in class. Possibly just for his nefarious purposes.

If Lou doesn't give you Post of the Month for that, he needs to be fired.

PS: The scare quotes around 'Doc'? The perfect touch!

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Lou FCD



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(Permalink) Posted: Aug. 22 2008,18:11   

Quote (Arden Chatfield @ Aug. 22 2008,18:59)
If Lou doesn't give you Post of the Month for that, he needs to be fired.

PS: The scare quotes around 'Doc'? The perfect touch!

I haven't made a POTM graphic.  Will that hold you over?

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Arden Chatfield



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(Permalink) Posted: Aug. 22 2008,18:13   

Quote (Lou FCD @ Aug. 22 2008,16:11)
Quote (Arden Chatfield @ Aug. 22 2008,18:59)
If Lou doesn't give you Post of the Month for that, he needs to be fired.

PS: The scare quotes around 'Doc'? The perfect touch!

I haven't made a POTM graphic.  Will that hold you over?

I guess it will have to do.  :angry:

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Arden Chatfield



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(Permalink) Posted: Aug. 22 2008,18:17   

Quote (Lou FCD @ Aug. 22 2008,14:28)
Besides being the one productive job that I might be able to do with my screwed up spine, part of the impetus for me doing this is the desperate need for teachers in our area.  Here in Onslow County, NC, we're expecting an influx of about 11,000 Marines (or maybe more) in the next few years, plus their families, plus civilian support staff, plus their families.  All totaled, we're expecting 40k to 200k people (depends on exactly what the Corps does, and whose figures you're looking at).

Perhaps I'm being a bit obtuse, but what's this about? I mean, I assume this is all a result of our killing uppity Muslims for their oil defending democracy in the Middle East, but why all those people in the next few years? Is that Marines returning, or some new massive buildup for an invasion of Iran that no one's told me about?

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Lou FCD



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(Permalink) Posted: Aug. 22 2008,18:44   

Quote (Arden Chatfield @ Aug. 22 2008,19:17)
Perhaps I'm being a bit obtuse, but what's this about? I mean, I assume this is all a result of our killing uppity Muslims for their oil defending democracy in the Middle East, but why all those people in the next few years? Is that Marines returning, or some new massive buildup for an invasion of Iran that no one's told me about?

No, that's a base-reorganization thing (read: base closures), where the Marines displaced from other locations will be transferred to Camp Lejeune.

Those figures don't include Marines that would return from abroad should the next PotUS pull our collective asses out of the fire.  So add lots of baby making to that, for several years down the road.

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deadman_932



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(Permalink) Posted: Aug. 22 2008,23:16   

Quote (Arden Chatfield @ Aug. 22 2008,18:13)
 
Quote (Lou FCD @ Aug. 22 2008,16:11)
 
Quote (Arden Chatfield @ Aug. 22 2008,18:59)
If Lou doesn't give you Post of the Month for that, he needs to be fired.

PS: The scare quotes around 'Doc'? The perfect touch!

I haven't made a POTM graphic.  Will that hold you over?

I guess it will have to do.  :angry:

Id like to thank all the little people that made this possible. Finally my jelousy-ridden peers have aknolejed  aknowliged  seen my geniuseness and awarded me that which has alluded such lunimaries as John A. Davidson,  Larry Farfleman, Louis and even that so-called Newton of Informations, William Dembski.

I stand before you even grander than before and a giant among pigmies. You may bask in my radiunce. But this thread is not about me, it is about Lou. (HAHAHA! I WIN!!!1!1)

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Arden Chatfield



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(Permalink) Posted: Aug. 23 2008,19:00   

HAR HAR THIS IS LOU

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EyeNoU



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(Permalink) Posted: Aug. 24 2008,06:51   

Been doing any "experiments" while at college, Lou?



  
rhmc



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(Permalink) Posted: Aug. 24 2008,07:35   

Quote (dogdidit @ Aug. 22 2008,12:43)
he strongly recommended that we re-copy our notes after class.

i will vouch for that method of learning.

  
Lou FCD



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(Permalink) Posted: Aug. 24 2008,09:09   

Quote (EyeNoU @ Aug. 24 2008,07:51)
Been doing any "experiments" while at college, Lou?

Geez, I wish.

By the time Friday rolled around, I was in pretty bad shape.  It's taken all weekend for the pain to start easing up enough to concentrate well.

Speaking of which, I have a precalc quiz tomorrow and a bunch of homework due Wednesday, so I'd better get to it.

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Lou FCD



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(Permalink) Posted: Aug. 24 2008,13:11   

I've reformatted the posts for proper blogging and posted them at Crowded Head.

It occurred to me that it might be good fodder for the Tangled Bank, so I've submitted the most recent one to Dr. PZ.

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Lou FCD



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(Permalink) Posted: Aug. 26 2008,16:44   



My notes and thoughts from Biology 111, for Monday, August 25, 2008. The entire series can be found here in blog post form. To go to this post directly, click here.

We began Monday's lecture where we left off on Friday (which is always a good place to start). Doc put the tree of life back up on the white board, and we did a quick review of what we went over on Friday regarding inheritance and emergence.

We then began to work a bit on Natural Selection, using Salmon as an example.

Natural Selection
Variation within a Population + Heredity + Differential Reproductive Success* = Natural Selection


Doc stressed that Natural Selection works at the Population level, and not at the individual level.  It's important to stress this, as it's the beginning of the explanation of why dogs don't give birth to cats, that tired old moronic Creationist standby.

Salmon

We talked about the life cycle of the salmon. Salmon breed and spawn up river, in fresh-water lakes. The young remain in the lake until they are ready, then swim downstream to the ocean. Once out on the ocean, they mature. When they are ready to breed, they return up the same river in which they were born, spawning in the same waters as their parents did.


There is a natural variation in the body size of adult salmon. Remember We're talking about adult salmon size, not babies. That becomes important in a moment.



This is a gill net. It is the tool used by commercial fishermen to catch salmon. Of course, the fishermen want to catch the largest fish, to maximize the price they get per fish. To accomplish this, the net is sized with large holes between the strands, so that smaller fish get through.



The way a gill net works is that as the fish swim through, the large ones get partially through, then can go no further. In an attempt to escape, the salmon back up. At that point, their gills get caught in the net.

So what happens is that in a river fished with commercial gill nets, the smaller fish have a selective advantage, and live to breed another season. This imparts a genetic tendency toward smaller size salmon, as smaller salmon tend to have smaller offspring.

In a river not fished with commercial gill nets, the larger fish have a selective advantage, as they outsize a certain proportion of their natural predators.  The predators pick off the smaller fish, and that population of salmon will tend to have larger offspring. The larger fish have a smaller pool of predators large enough to eat them, so the larger salmon have an advantage here, and tend to live longer - long enough to breed. It's good to be bigger than the guy who wants to eat you.



Looking back at the tree of life chart, one population can be said to acquire trait Q, a smaller size, and the other population trait X, a larger size. As other changes take place due to other selective pressures that differ in the two populations of salmon, there may come a speciation event.

Again, speciation does not occur at the individual organism level, but at the population level. Descent with Modification is an emergent property at the population level.

Chapter Two - The Chemical Context of Life

This was pretty basic chemistry stuff.

There are 92 naturally occurring elements ---&gt; about a dozen are important to biology

Molecular Formulas

Water: H2O

Salt: NaCl

An atom is the smallest unit of an element.

Atoms are composed of subatomic particles

Symbol  Particle  Charge  Mass

p+        Proton      +    1 Dalton**
n          Neutron     0    1 Dalton
e-         Electron     -     ? 1/1800 Dalton


The number of p+ in a molecule an atom = the atomic number: each element has a unique atomic number.


Naturally Occurring Elements in the Human Body
(From the chart on page 32 of the textbook)


Symbol   Element   Atomic Number   Percentage of Human Body Weight

Elements making up about 96% of human body weight

O           Oxygen              8                        65.0
C           Carbon               6                        18.5
H           Hydrogen            1                         9.5
N           Nitrogen             7                         3.3

Elements making up about 4% of human body weight

Ca          Calcium             20                       1.5
P            Phosphorus        15                       1.0
K            Potassium         19                        0.4
S            Sulfur                16                       0.3
Na          Sodium              11                       0.2
Cl           Chlorine             17                       0.2
Mg          Magnesium        12                       0.1

Atoms normally are electrically neutral.

Number of p+= number of e-



Electrical attraction stablizes orbits, as the protons and electrons attract one another due to opposite electrical charges, but protons will repel each other and electrons will repel each other due to same electrical charges. Bear in mind that sketch is not to scale.

Note the protons and neutrons clustered in the nucleus, which gives the nucleus a positive charge.

Lab notes will have to wait, as I have Spanish and Precalc homework that needs attention. (Preview hint: we got to play with live termites!)


*Individuals with certain traits produce more offspring than those with other traits.

** The unit of mass for subatomic particles is the Dalton (also sometimes known as the Atomic Mass Unit or AMU), named for John Dalton, the modern developer of Atomic Theory.

     
Quote
From whence came the art:

The first image is of our textbook, Biology, Eighth Edition, by Campbell & Reese.

Other images created by me, using the salmon from wikipedia commons, and are free to do with as you see fit.


Edited to correct a transcription error, courtesy of Henry, below.

Edited by Lou FCD on Aug. 26 2008,22:55

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Richardthughes



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(Permalink) Posted: Aug. 26 2008,16:55   

PotW!

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Wesley R. Elsberry



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(Permalink) Posted: Aug. 26 2008,18:37   

Lou FCD:

 
Quote

So what happens is that in a river fished with commercial gill nets, the smaller fish have a selective advantage, and live to breed another season. This imparts a genetic tendency toward smaller size salmon, as smaller salmon tend to have smaller offspring.


Iteroparous species breed multiple times over a lifetime. Semelparous species breed once in a lifetime.

The negative selective effect described for gill nets will be stronger for semelparous rather than iteroparous species. IIRC, the explanation hinges on the age-specific distribution of V_x, "reproductive value". Depending on that distribution and the specifics of the heritability of size at a given age, it could actually be the case that positive selection for the trait would be favored in an iteroparous population despite universal exposure to gill-nets. Essentially, if the selective disadvantage in loss of V_x at the oldest age classes is more than balanced by increased V_x in the younger age classes, positive selection for the trait will continue.

Consequence: the example is undercut by describing its application to iteroparous species. The example should, for pedagogical purposes, refer only to the case for semelparous species.

A similar argument as what I outlined above underlies Medawar's hypothesis of senescence.

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Wesley R. Elsberry



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(Permalink) Posted: Aug. 26 2008,18:41   

“Evolution Makes a Mockery of Fishing Policy”

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Lou FCD



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(Permalink) Posted: Aug. 26 2008,21:08   

Thank you, Rich, but the Doc really should get the credit.  I just took notes.  :)

Wesley, I appreciate the explanation and the link to your post.

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Henry J



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(Permalink) Posted: Aug. 26 2008,21:28   

Quote
The number of p+ in a molecule = the atomic number: each element has a unique atomic number.


I think that should read p+ in an atom, rather than in a molecule.

Quote
(Preview hint: we got to play with live termites!;)


Hopefully not in a wooden building! ;)

Henry

  
Lou FCD



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(Permalink) Posted: Aug. 26 2008,21:52   

Quote (Henry J @ Aug. 26 2008,22:28)
Quote
The number of p+ in a molecule = the atomic number: each element has a unique atomic number.


I think that should read p+ in an atom, rather than in a molecule.

 
Quote
(Preview hint: we got to play with live termites!)


Hopefully not in a wooden building! ;)

Henry

Quite right, Henry.  Sorry.

I'll fix it when I can.

ETA: fixed.

Edited by Lou FCD on Aug. 26 2008,22:55

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Lou FCD



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(Permalink) Posted: Aug. 28 2008,16:03   



My notes and thoughts from Biology 111, for Monday, August 25, 2008. The entire series can be found here.

Lab on Monday was another really fascinating demonstration of the Scientific Method. We even got to play with real live bugs - termites, to be specific. The college keeps a colony of them, which is just cool in and of itself.

So the lab opened with Doc having us split into groups of three and four again, and then handed out a blank sheet of white paper to each group, along with a red ball-point pen and a small paint brush. Each group was instructed to make a circle on the paper using the red pen.

Then the fun part started.

Doc walked around to each group with a little tupperware container, beginning with our group. When she saw what he had in the tupperware, my female lab parter immediately got a little squicked out. Termites!

Just seeing her squirm was worth the price of admission, but by the end of the lab she was fine, as long as she didn't have to touch them with her hand. Fortunately for her, that's what the paintbrush was for. Once the termite was on the paper, the paintbrush was for wrangling the termite without squishing him. All we had to do was make sure he didn't wander off the paper.

So I had the paintbrush, because Squicky Britches was still icking out, and all of a sudden, something totally unexpected happened.

Our little termite had begun to follow the red line in a circle! He was like a little NASCAR driver, in a continuous left turn.

We started hollering at the other groups, telling them all about how brilliant our little termite (who I'd named Fred) was. About that time, other groups were still receiving their termites, and everyone was standing or craning to check out our little prodigy.

Then one at a time, other termites began to find the red circles, and sure enough, they started racing around their own little tracks.

Doc let us just be fascinated for a while, which was way cool of him. I don't think anyone in the room was anything short of amazed at this behavior. Eventually though, it was time to get to work. What was causing this behavior in the termites? Our mission, whether we chose to accept it or not, was to figure it out.

Observation:

Given a white sheet of paper with a red circle in ball-point ink and a live termite, the termite tends to follow the red line. A second termite (who we named Ginger, though my lab partners are much too young to understand the significance) exhibits the same behavior.

Question:

What causes the termites to tend to follow the red line?

Hypotheses:

We formed four hypotheses in the beginning, the testing of which is the focus of this lab.
  • Hypothesis #1) The termite prefers to travel in a circle.

  • Hypothesis #2) The termite is attracted to the color red.

  • Hypothesis #3) The termite is attracted to a chemical in the ink.

  • Hypothesis #4) The termite is following the indentation in the paper made by the pressure of the pen.


Testing Hypothesis #1


  • Prediction: Using the original red ink pen, a square is drawn, and if the termite simply prefers to travel in circles, then it will not follow the square.

  • Observation: The termite follows the square, though it has a little trouble with the corners at first.

  • Conclusion: The termite does not simply prefer to travel in a circle, and the hypothesis is falsified.


Testing Hypothesis #2

  • Prediction: Using a black ball-point pen, a circle is drawn and if the termite is attracted to the color red, then it will not follow the black circle.

  • Observation: The termite follows the black circle even better than it follows the red circle.

  • Conclusion: The termite is not simply attracted to the color red, and the hypothesis is falsified.


Testing Hypothesis #3
  • Prediction: Using a colored pencil, a circle is drawn and if the termite is attracted to a chemical in the ball-point ink, then it will not follow the circle.

  • Observation: The termite does not follow the circle at all, and basically ignores the circle completely, crossing its path many times.

  • Conclusion: The termite might be attracted to a chemical in the ball-point ink that is not present in a colored pencil, and the hypothesis is supported by the evidence.


Testing Hypothesis #4
  • Prediction: Using the tip of a pen cap, a circle is drawn without making a visible mark, and if the termite does not follow the circle, then it is not simply following the indentation in the paper made by the pressure of the pen.

  • Observation: The termite does not follow the circle at all, and basically ignores the circle completely, crossing its path many times.

  • Conclusion: The termite is not simply following the indentation in the paper made by the pressure of the pen, and the hypothesis is falsified.



At this point, we were fairly confident that we were on the right track. It was time for our break, so Doc passed out little covered petri dishes to each group with pieces of wet paper towels in them. We put Fred and Ginger into our dish, and went for our break. Fred was not looking very good at this point, and seemed to need a rest from all that racing around he'd been doing, so the timing worked out pretty well.

While on break, it occurred to us that we might want to find out exactly what it was in the ink that termites found attractive, but one of the rules to the lab was that we could use anything in the room to test our hypotheses, but nothing else.

Upon returning from break, we asked Doc if we might have another termite, as Fred was looking rather peaked. He happily obliged us, and we tested various other writing implements to observe the behavior of our new termite. Our new termite really zipped around the circle made by Squicky Britches' black bic pen, so we named him Speedy.

It then occurred to us to check another black ball-point, to see if there might be some inks the termites preferred over others. Sure enough, Speedy showed a definite preference for Squicky Britches' bic over my zebra.

Thinking about the ink and the petri dishes, we wondered if the attractive chemical might be just moisture, plain old H2O in the ink.

  • Hypothesis #5) The termite is attracted to the moisture content of the ball-point ink.


Testing Hypothesis #5
  • Prediction: Using the tip of a mechanical pencil dipped in bottled water, a circle is drawn, and if the termite does not follow the circle, it is not simply attracted to the moisture content of the ball-point ink.

  • Observation: The termite does not follow the circle at all, and actually seems to avoid the dampness left on the paper.

  • Conclusion: The termite is not simply attracted to the moisture content of the ball-point ink, and the hypothesis is falsified.



We talked a bit with Doc about our experiment to this point, and he reminded us that we were allowed to use anything in the lab to test our hypothesis further. Looking around, Squicky Britches (who was so wrapped up in termite wrangling at this point that she wasn't squicky at all) noticed the transparency papers that Doc had lying on the other end of the lab table. As a control measure, we drew a fresh circle on fresh paper with Squicky Britches' bic, and retested Speedy on that circle. As expected, he followed the circle without a problem.


Further testing of Hypothesis #3

  • Prediction: When a circle is drawn and the termite is separated from the paper by a transparency film, if the termite follows the circle, then it is not simply attracted to a chemical in the ball-point ink.

  • Observation: After anthor control in which the termite followed a fresh circle directly on a fresh paper, the termite did not follow the same circle when separated from the paper by a sheet of transparency film.

  • Conclusion: The termite might be attracted to a chemical in the ball-point ink, and the hypothesis is still supported by the evidence.


So this was another really fun lab for us to practice our Scientific Method skills. Sadly, I don't think Fred survived it.
     
Quote
From whence came the art:

The first image is of our textbook, Biology, Eighth Edition, by Campbell &amp; Reese et al.


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Henry J



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(Permalink) Posted: Aug. 28 2008,18:01   

http://www.tolweb.org/Isoptera

Cute little guys, huh?

  
carlsonjok



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(Permalink) Posted: Aug. 28 2008,18:21   

Quote (Lou FCD @ Aug. 28 2008,16:03)
So this was another really fun lab for us to practice our Scientific Method skills. Sadly, I don't think Fred survived it.

Crap. I just wrote a $300 check for my annual termite contract and all I needed to do was draw a ballpoint pen line from my house down to the road.    :angry:

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It's natural to be curious about our world, but the scientific method is just one theory about how to best understand it.  We live in a democracy, which means we should treat every theory equally. - Steven Colbert, I Am America (and So Can You!)

  
Lou FCD



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(Permalink) Posted: Aug. 28 2008,18:49   

Our guys kinda looked like this:



Carlson, yeah, who knew?

It's BigExterma, screwin' us over, keepin' the TRUTH from the PUBLIC!!!11!!!1!!ONE!!!

Editated to complete my scrambled thought.

Edited by Lou FCD on Aug. 28 2008,19:52

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utidjian



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(Permalink) Posted: Aug. 28 2008,20:30   

Lou,

Outstanding series of posts. I haven't taken any regular biology classes since HS (physics major.)

One other test I thought of for your termites might have been:

Hypothesis: Is it the ink alone or an interaction with the ink and the paper.

Prediction: It is the ink alone. Mark out a new circle with the best ink (Squitchy Britches black pen) on the transparency film or on a clean sheet of frosted glass (so the ink will actually adhere.) See if the termite follows the ink.


Thanks again for a great series of posts. I will be watching this thread regularly.

-DU-

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bystander



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(Permalink) Posted: Aug. 28 2008,20:46   

Leave us hanging!! I wants to know the answer  :angry:

You left out disembodied telic entity pushing the termites around using wormholes in the space time continum.

Which is the correct answer no matter what your mere evidence shows. Teach the controversy !1!!one!!

  
Lou FCD



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(Permalink) Posted: Aug. 28 2008,21:32   

Quote (utidjian @ Aug. 28 2008,21:30)
Lou,

Outstanding series of posts. I haven't taken any regular biology classes since HS (physics major.)

One other test I thought of for your termites might have been:

Hypothesis: Is it the ink alone or an interaction with the ink and the paper.

Prediction: It is the ink alone. Mark out a new circle with the best ink (Squitchy Britches black pen) on the transparency film or on a clean sheet of frosted glass (so the ink will actually adhere.) See if the termite follows the ink.


Thanks again for a great series of posts. I will be watching this thread regularly.

-DU-

Thanks DU. I'm still working on yesterday's lecture notes, and of course I have the lecture again tomorrow morning...

Hopefully, I'll get caught up by Saturday sometime.

Squicky Britches actually did try writing on the transparency, just as we were supposed to return Fred, Ginger, and Speedy to Doc. (Somehow, there must be a Snow White joke in there somewhere...) She couldn't get the ink to stick though, so we let it go.

Glad you're reading.

 
Quote (bystander @ Aug. 28 2008,21:46)
Leave us hanging!! I wants to know the answer  :angry:

You left out disembodied telic entity pushing the termites around using wormholes in the space time continum.

Which is the correct answer no matter what your mere evidence shows. Teach the controversy !1!!one!!

Yeah, so do we. Nature never told us the answer, and neither did Doc. We're pretty confident in our hypothesis, given the evidence we have in hand.

Of course, a week from Monday, new evidence may come in and refute our hypothesis, in which case we'll look at whether we have to make some adjustments or if we have to scrap it altogether and start down another path.

As my Pop always says, "Some days'll be like that."

For the moment though, we have no evidence of disembodied telic entities, ghosts, or leprechauns pushing the termites around. We're sticking with the substance in the ink hypothesis for the moment.

:)

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Zarquon



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(Permalink) Posted: Aug. 28 2008,22:20   

termites and ink

  
qetzal



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(Permalink) Posted: Aug. 28 2008,22:24   

Quote (Lou FCD @ Aug. 28 2008,21:32)
For the moment though, we have no evidence of disembodied telic entities, ghosts, or leprechauns pushing the termites around. We're sticking with the substance in the ink hypothesis for the moment.

:)

Maybe you should check for quantum coherence in their microtubules. I'm sure TP can help you with experimental design.  :D

  
Lou FCD



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(Permalink) Posted: Aug. 28 2008,23:15   

Quote (Zarquon @ Aug. 28 2008,23:20)
termites and ink

HA! iz gud siensy guy!

Can I have my PhD now, or do I have to wait until the end of the semester?

 
Quote (qetzal @ Aug. 28 2008,23:24)
 
Quote (Lou FCD @ Aug. 28 2008,21:32)
For the moment though, we have no evidence of disembodied telic entities, ghosts, or leprechauns pushing the termites around. We're sticking with the substance in the ink hypothesis for the moment.

:)

Maybe you should check for quantum coherence in their microtubules. I'm sure TP can help you with experimental design.  :D

I just don't even want to go there.

:)

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Louis



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(Permalink) Posted: Aug. 29 2008,04:56   

Quote (Lou FCD @ Aug. 29 2008,05:15)
[SNIP]

Can I have my PhD now, or do I have to wait until the end of the semester?

[SNIP]

YOU can have a PhD right now! Be just like Kent Hovind and other famous creationists!

Just mail your cheque for $2000 to my home address, make payable to me, and I will send you a genuine, authenticated PhD certificate from GB* University.

Louis

*Stands for "Gullible Bastard".

--------------
Bye.

  
Albatrossity2



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(Permalink) Posted: Aug. 29 2008,11:00   

Quote (qetzal @ Aug. 28 2008,22:24)
Quote (Lou FCD @ Aug. 28 2008,21:32)
For the moment though, we have no evidence of disembodied telic entities, ghosts, or leprechauns pushing the termites around. We're sticking with the substance in the ink hypothesis for the moment.

:)

Maybe you should check for quantum coherence in their microtubules. I'm sure TP can help you with experimental design.  :D

Dang it, I was going to suggest the same thing. You gotta be quick here!

Interestingly, the bacterial symbionts in termite guts were the first case where tubulin (and microtubules) were found in prokaryotes. Here's an old  reference from Science. This is one of the bits of evidence for Margulis's endosymbiont hypothesis; cilia and flagella might have arisen from prokaryotic endosymbionts that were like modern spirochetes.

Perhaps TP can tell us if the prokaryotic microtubules and the termite microtubules exhibit quantum properties...

--------------
Flesh of the sky, child of the sky, the mind
Has been obligated from the beginning
To create an ordered universe
As the only possible proof of its own inheritance.
                        - Pattiann Rogers

   
dvunkannon



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(Permalink) Posted: Aug. 29 2008,11:57   

Quote (Albatrossity2 @ Aug. 29 2008,12:00)
Quote (qetzal @ Aug. 28 2008,22:24)
 
Quote (Lou FCD @ Aug. 28 2008,21:32)
For the moment though, we have no evidence of disembodied telic entities, ghosts, or leprechauns pushing the termites around. We're sticking with the substance in the ink hypothesis for the moment.

:)

Maybe you should check for quantum coherence in their microtubules. I'm sure TP can help you with experimental design.  :D

Dang it, I was going to suggest the same thing. You gotta be quick here!

Interestingly, the bacterial symbionts in termite guts were the first case where tubulin (and microtubules) were found in prokaryotes. Here's an old  reference from Science. This is one of the bits of evidence for Margulis's endosymbiont hypothesis; cilia and flagella might have arisen from prokaryotic endosymbionts that were like modern spirochetes.

Perhaps TP can tell us if the prokaryotic microtubules and the termite microtubules exhibit quantum properties...

Yeah, I learned way too much about termite guts reading Margulis' Symbiosis in Cell Evolution but the tubulin hypothesis never caught on the way mitochodria and chloroplasts did. Now if flagella had their own DNA...

--------------
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Stephen Elliott



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(Permalink) Posted: Aug. 30 2008,13:00   

Quote (Lou FCD @ Aug. 28 2008,18:49)
Our guys kinda looked like this:



Carlson, yeah, who knew?

It's BigExterma, screwin' us over, keepin' the TRUTH from the PUBLIC!!!11!!!1!!ONE!!!

Editated to complete my scrambled thought.

I like this thread for many reasons.

1) Your enthusiasm is evident.
2) You have got me reading my Campbell Reece BIOLOGY Sixth Edition again.
3) Doing a writeup here will help you (and possibly me) in understanding the book.

As to learning tips. I have not heard he writeup one before but it sounds damned good. Here is one I came to late in life: Pre-read lessons, highlight what you do not understand. If you still do not understand when it is covered in class, ask questions until you do.

For me: I find it hard just to remember facts (but I am sure the re-writing would help), if I understand the process I tend to remember better.

  
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: Aug. 30 2008,19:15   



My notes and thoughts from Biology 111, for Wednesday, August 27, 2008. The entire series can be found here.

Wednesday's lecture began with a review of atomic structure, including a reminder that our e- * diagrams are 2D representations of 3D space.

Then we moved on to some more basic chemistry.

We focused mostly on electrons, and will continue to, as electrons are what determines reactivity of an atom, and reactivity is what's really vital to biology.

e- orbits are called e- shells or energy levels. Each e- orbital can hold up to 2 e-.

The first energy level has one orbital, because it's so small, and electrons, having all the same negative electrical charge, repel each other.

The second and third energy levels each contain 4 orbitals, each energy level then is capable of holding 8 e- (2 e- in each orbital).

Then doc talked about how electrons fill from the innermost energy level, out.

e- contain Potential Energy due to location or structure.

Potential Energy is energy stored up that can be used to do work. For instance, because our lecture room is on the second floor, I have more potential energy than the student just below me on the first floor. Should a hole open up under my seat, I would fall down, releasing that potential energy as kinetic energy. That energy would be doing work, like breaking the table below me, breaking my bones, or with a water wheel type contraption the energy released by my falling could be used to produce electricity.

Now, in order to get that potential energy, I had to walk up the steps, doing work, trading kinetic energy for potential energy. So to get energy out, I first had to put energy in.

Remembering that the potential energy in my body on the second floor is caused by my distance from the center of gravity of the planet, likewise the potential energy of an electron is caused by its distance from the nucleus of an atom (though the force involved here would be electromagnetism rather than gravity). The further from the nucleus an e- is, the more potential energy it has.

e- must be in an orbital. They don't free range within the atom, and they tend towards the lowest energy level in which they can squeeze. Changing orbitals requires a change in energy. Energy into an electron causes the electron to move into higher energy levels, and energy released from an electron causes the electron to move to lower energy levels. This is often denoted by ?E, pronounced "delta E".

Doc used the example of sugar. Where does the energy we get from sugar come from? Ultimately, the sun imparts the energy to the plant via the leaves. Sunlight strikes the leaves of the sugarcane plant causing an excitement of electrons, and the plant stores that energy as potential energy. When we eat the sugar, our bodies change that back into kinetic energy, giving us a sugar rush. Thus in the end, we are eating sunlight.

So before we go any further with the notes, let's take a look at the elements we're discussing. In biology, most of the elements we're going discuss are going to be found within the first 18 elements on the periodic table. Let's have the standard periodic table, with those elements highlighted. (The original table here is from the National Institute of Standards and Technology, NIST. The electron distribution table is from a scan of page 36 in our textbook. I have put the two images together to help visualize the sections of the periodic table that we'll be discussing.)



Next up, we talked about orbitals, arrangement of electrons in those orbitals at different energy levels, and the notation we use to describe all that. The remainder of this discussion will reference this electron distribution diagram, found on page 36 of our textbook (at my blog, you can click for a larger version, hosted at my Flickr account):



Let's look now at a few elements on this chart. The obvious place to start is at the beginning, so we'll start with Hydrogen.



In this image, I've highlighted Hydrogen (H). A hydrogen atom consists of one e- and one p+. There are no neutrons in the nucleus of a stable hydrogen atom. The single electron travels in the orbit described. For our purposes, we're going to ignore the nucleus for the time being. In this notation, we're mostly concerned with electrons and their orbits.



Comparing that to Helium (He), we see that in this notation, we're not going to separate the electrons on opposite sides of the atom as they physically would tend to be, we're just noting that there are two e- in this orbit. Atoms in the same row on the periodic table have the same number of shells, and in the first electron shell, there is one orbit. Each orbit will hold up to two e-. It's easy to think of this first shell as being so small that the charge of the e- (which repel each other) are just so close that they won't allow any more electrons in the vicinity.

Further out, in larger shells, each shell will consist of four orbits, but again, each orbit can only hold 2 e-. The outer e- shell of a given atom is referred to as the valence shell. The number of e- in the valence shell is of utmost importance to chemical reactions, and thus to biology.



In the second row then, we would expect to find two e- shells, and indeed, here is Lithium (Li). Notice that Li has the inner shell full (2 e-) and then begins to work on the next shell, with its third e-. Electrons always fill out the shells from the inside out, from closest to the nucleus, to furthest from the nucleus.



Remember that except for the innermost one, e- shells each contain four e- orbits, and each orbit holds two e-. Now, each of those orbits in a shell will take on e- before any of them will take a second e-. Thus the notation for Beryllium shows a second electron in the valence shell, but in a separate orbit from the first e-.



Boron (B) takes a third e-, in a third orbit of the second shell, and then we come to Carbon ( C ). Carbon has four valence e-, one in each orbit of the valence shell. Each of the four e- orbits of the valence shell now has a single electron.



The next element, Nitrogen (N), has five valence e-, and the fifth one can now go in the first orbit of the valence shell, since each orbit in the shell now has one electron.



Predictably, Oxygen then takes a sixth e- in the valence shell (for a total of 8 e-) and it goes in the second orbit.



At this point a patterns should be emerging. Notice that in the first column, all the elements have one valence e-, in the second they all have two, etc.



In the eighth column, all the elements have 8 valence e- (except He), meaning that their valence shells are full. The elements in this column are referred to as the Noble Gases, or the Inert Gases. Elements with full valence shells are non-reactive. They are happy with the number of e- they have, and tend not to interact with other elements.

Atoms are most stable when they have NO unpaired electrons. Natural things tend toward their most stable state. A stack of bricks is less stable than those same bricks all flat on the ground. Likewise, elements tend towards having full valence shells.

We can say then that the reactivity of an atom depends on the number of unpaired valence e-. This becomes very important for biological chemistry.

Now that we had a good idea about valence e-, we could take that information and apply it.

Chemical Bonds

We began our discussion of chemical bonds with the first type, which is called Covalent Bonding.

There are a couple ways for atoms to find e- to fill up their valence shells. They can steal one from another atom (called ionic bonding, discussed in the next lecture). But like in life, bigger atoms are better at this than small atoms. To quote Doc directly,

   
Quote
"If you want to be successful at taking something from someone else, you had better be bigger than them, or they will whoop your ass and take it back. Hydrogen is the smallest atom, so it will always be the whoopee, not the whooper."


So hydrogen goes a different route. It shares electrons. This is called a covalent bond.



In this fashion, two hydrogen atoms can each fill their valence shell (they each now have two e- in the valence shell). They are sharing a single pair of electrons, so this is a single bond.

We can write this in a number of ways.

There is the molecular formula

H2

The structural formula

H-H

and the Lewis Dot diagram

H:H



Oxygen, having two spots to fill in its valence shell, will share two pairs of electrons, and Nitrogen, 3. In the quick sketch I did above (forgive the lack of neatness there...), the molecular notation, the structural notation, and the Lewis Dot Diagram are given for Oxygen and Nitrogen, the two most abundant elements in the air we breathe.

The lecture ended there. On Friday, we discussed electronegativity. I'll get those notes up (hopefully) by tomorrow.

* remembering our shorthand, e- means electron, p+ is for proton, and n is for neutron.
   
Quote
From whence came the art:

The first image is of our textbook, Biology, Eighth Edition, by Campbell &amp; Reese et al. The electron distribution table is from page 36 of that textbook, and I have highlighted portions of it in the various images above to assist in visualization.

The Periodic Table of the Elements is from the National Institute of Standards and Technology, NIST.


Edited to clean up a butchered sentence.

Edited by Lou FCD on Aug. 30 2008,21:53

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Lou FCD



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(Permalink) Posted: Aug. 30 2008,19:16   

Quote (Stephen Elliott @ Aug. 30 2008,14:00)
I like this thread for many reasons.

1) Your enthusiasm is evident.
2) You have got me reading my Campbell Reece BIOLOGY Sixth Edition again.
3) Doing a writeup here will help you (and possibly me) in understanding the book.

As to learning tips. I have not heard he writeup one before but it sounds damned good. Here is one I came to late in life: Pre-read lessons, highlight what you do not understand. If you still do not understand when it is covered in class, ask questions until you do.

For me: I find it hard just to remember facts (but I am sure the re-writing would help), if I understand the process I tend to remember better.

Thanks Stephen.

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Albatrossity2



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(Permalink) Posted: Aug. 30 2008,20:09   

Lou

I think that your understanding of the basic material may be better than some of my students.  Here is an email, rec'd tonight, from a student in my intro bio class. The name is withheld to protect the innocent...
 
Quote
I was reading the textbook and I am now confused.

On page 4, it defines Atoms as "...the fundamental building blocks of all substances, living and non-living."
Then on page 22, it goes on to say that ... "Atoms differ in the number of subatomic particles, but all have a nucleus..."
--- Back on page 8, it told me that bacteria & archaea are single-celled organisms, but that they are prokaryotic, meaning that they have no nucleus..
..Farther back still, on page four, it says in short : atoms join together to make molecules, and molecules (become organized into?) make cells...

So as I said I am confused.  Is the textbook saying that some molecules are formed without atoms?  If so, what are they made of?

..Or is page 22 incorrect about all atoms having nuclei or is there something else ?

Thanks for clearing this up


--------------
Flesh of the sky, child of the sky, the mind
Has been obligated from the beginning
To create an ordered universe
As the only possible proof of its own inheritance.
                        - Pattiann Rogers

   
Lou FCD



Posts: 5377
Joined: Jan. 2006

(Permalink) Posted: Aug. 30 2008,20:41   

Quote (Albatrossity2 @ Aug. 30 2008,21:09)
Lou

I think that your understanding of the basic material may be better than some of my students.  Here is an email, rec'd tonight, from a student in my intro bio class. The name is withheld to protect the innocent...
 
Quote
I was reading the textbook and I am now confused.

On page 4, it defines Atoms as "...the fundamental building blocks of all substances, living and non-living."
Then on page 22, it goes on to say that ... "Atoms differ in the number of subatomic particles, but all have a nucleus..."
--- Back on page 8, it told me that bacteria & archaea are single-celled organisms, but that they are prokaryotic, meaning that they have no nucleus..
..Farther back still, on page four, it says in short : atoms join together to make molecules, and molecules (become organized into?) make cells...

So as I said I am confused.  Is the textbook saying that some molecules are formed without atoms?  If so, what are they made of?

..Or is page 22 incorrect about all atoms having nuclei or is there something else ?

Thanks for clearing this up

*headdesk*

LoL, thanks for the chuckle.

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Henry J



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(Permalink) Posted: Aug. 30 2008,21:35   

Chemistry atomic nucleus != Biological cell nucleus !!

:p

I suppose though that somebody first learning two different fields at once could get confused when those two fields use one of the same words but for different things.

Henry

  
Louis



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(Permalink) Posted: Aug. 31 2008,04:23   

Quote (Albatrossity2 @ Aug. 31 2008,02:09)
Lou

I think that your understanding of the basic material may be better than some of my students.  Here is an email, rec'd tonight, from a student in my intro bio class. The name is withheld to protect the innocent...
 
Quote
I was reading the textbook and I am now confused.

On page 4, it defines Atoms as "...the fundamental building blocks of all substances, living and non-living."
Then on page 22, it goes on to say that ... "Atoms differ in the number of subatomic particles, but all have a nucleus..."
--- Back on page 8, it told me that bacteria & archaea are single-celled organisms, but that they are prokaryotic, meaning that they have no nucleus..
..Farther back still, on page four, it says in short : atoms join together to make molecules, and molecules (become organized into?) make cells...

So as I said I am confused.  Is the textbook saying that some molecules are formed without atoms?  If so, what are they made of?

..Or is page 22 incorrect about all atoms having nuclei or is there something else ?

Thanks for clearing this up

{Blinks}

{Cries}

{Sound of Louis' heart breaking}

Wow...just wow.

Look, I don't want to come over all elitist or anything but the concept of an atomic nucleus and the concept of a biological nucleus were things I understood before I went through puberty. This might explain a few things dammit! On the other hand it might not! ;-)

It's really hard to think back to a time where the concept of an atom (for example) was not something I understood to some useful degree. So whilst I might come across as unsympathetic to this student (and others), believe me I'm not, I just NOW have a hard time intuitively, initially, grasping the "before atom" thinking, my failing, not the student's. I think it's a little terrifying that a college freshman doesn't have that understanding tucked away, but that aside, whoa!

Lou, you seem to be going through the "Bohr atom"/basic idea of orbitals and bonding stuff atm. Have they mentioned s orbitals/p orbitals etc yet? Pauli exclusion principle etc? If not, I hope you get to learn about it because it will make better sense of some of the questions I'll bet you have about atoms/molecules when presented with the "Bohr atom" version. Any chem help or conversation you desire, I'm happy to help with.

Louis

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Reciprocating Bill



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(Permalink) Posted: Aug. 31 2008,06:13   

This raises the distinct possibility that George W. believes that Nuke-U-Lar weapons of which he has control are packed with eukaryotes.

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Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

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Albatrossity2



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(Permalink) Posted: Aug. 31 2008,06:52   

Quote (Henry J @ Aug. 30 2008,21:35)
Chemistry atomic nucleus != Biological cell nucleus !!

:p

I suppose though that somebody first learning two different fields at once could get confused when those two fields use one of the same words but for different things.

Henry

Yeah, I am used to these cases where a word, as used in biology, needs to be distinguished from the usage of the same word in everyday parlance (e.g. fitness). This is the first time that I have had a student get confused about a word which you really only encounter in science!

The sad part is that college prep tracks in KS high schools have a year of chemistry and a year of biology. Either this student did not graduate from a KS high school, or some school someplace is doing a truly wretched job of evaluating the learning of their students. Or both...

Anyhoo, I did have to wait a bit before replying, just to staunch the bleeding from the site where my head hit the desk a few times. Here's what I wrote back  
Quote
It seems that your confusion comes about because the word "nucleus" is used for two different things, in two different fields (biology & chemistry).

The word "nucleus" comes from a Latin root meaning core, center, or kernel, The word "nut" comes from the same root.
In chemistry the nucleus of an atom is the core, consisting of protons and neutrons, around which the electrons orbit.

In biology the nucleus of a cell is the highly organized DNA-containing center of a eukaryotic cell, which is visible in a light microscope. Prokaryotes also have DNA, but it is not as organized, and is not visible in a light microscope.

So the word means a different thing in these two different contexts. I'm sorry that is the case, but sometimes biologists and chemists can use the same word to mean different things. In fact, even in astronomy the word means something else. The "nucleus" of a comet is the central core of that structure as well.

hope this helps

See, I'm not a mean atheistic professor all the time  :)

--------------
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Stephen Elliott



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(Permalink) Posted: Aug. 31 2008,07:18   

Quote (Albatrossity2 @ Aug. 30 2008,20:09)
Lou

I think that your understanding of the basic material may be better than some of my students.  Here is an email, rec'd tonight, from a student in my intro bio class. The name is withheld to protect the innocent...
 
Quote
I was reading the textbook and I am now confused.

On page 4, it defines Atoms as "...the fundamental building blocks of all substances, living and non-living."
Then on page 22, it goes on to say that ... "Atoms differ in the number of subatomic particles, but all have a nucleus..."
--- Back on page 8, it told me that bacteria & archaea are single-celled organisms, but that they are prokaryotic, meaning that they have no nucleus..
..Farther back still, on page four, it says in short : atoms join together to make molecules, and molecules (become organized into?) make cells...

So as I said I am confused.  Is the textbook saying that some molecules are formed without atoms?  If so, what are they made of?

..Or is page 22 incorrect about all atoms having nuclei or is there something else ?

Thanks for clearing this up

I know that I shouldn't, but I do laugh. Although it is sad, it is also kinda funny that we are becoming more stupid.

Actually it isn't. It is damned wrong that pupils are getting less educated at the same time that the sum of human knowledge is increasing.

  
Reciprocating Bill



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(Permalink) Posted: Aug. 31 2008,07:54   

No way I wasn't aware of this distinction by some time in elementary school.

Your student's question reflects an astonishing and dismaying level of ignorance. Period.

If this is at all typical we are in real trouble.

--------------
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- David Foster Wallace

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Albatrossity2



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(Permalink) Posted: Aug. 31 2008,09:26   

Quote (Reciprocating Bill @ Aug. 31 2008,07:54)
No way I wasn't aware of this distinction by some time in elementary school.

Your student's question reflects an astonishing and dismaying level of ignorance. Period.

If this is at all typical we are in real trouble.

Thankfully it is not typical; I ported it over here because it was, in my 10+ years coordinating our intro course, unique.

Frankly I wondered for a bit if the student was just kidding me. But I figured I had to answer it just in case it was a serious question. I think it was...

Is there a corollary to Poe's Law for college students?

--------------
Flesh of the sky, child of the sky, the mind
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csadams



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(Permalink) Posted: Aug. 31 2008,09:43   

Quote (Albatrossity2 @ Aug. 31 2008,06:52)
The sad part is that college prep tracks in KS high schools have a year of chemistry and a year of biology. Either this student did not graduate from a KS high school, or some school someplace is doing a truly wretched job of evaluating the learning of their students. Or both...

. . . or some KS schools have mis-labeled courses as "chemistry" or "physics" for purposes of Qualified Admission, when in fact they're general physical science courses geared toward prepping students for the KS state assessments.

If a KS high school graduate hasn't completed the Regents college prep track, the student can still enter a state university with an ACT composite >= 21.  Or the student can graduate in the top one-third of their high school class and be admitted to a state university.

Alb, I'm not sure how the QA requirements have helped get more students ready for college, with the requirements being so low.  But if(when?) your science-impaired students hail from out my way, let me know and I'll get right on it . . .

*********************
Lou - wow!  What an experience you're getting!  You might think about checking out some summer workshops out your way.  GLOBE has a lot going on in Hampton, VA; essentially, you get paid to learn.  How sweet is that??

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Lou FCD



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(Permalink) Posted: Aug. 31 2008,09:47   

Quote (Louis @ Aug. 31 2008,05:23)
Lou, you seem to be going through the "Bohr atom"/basic idea of orbitals and bonding stuff atm. Have they mentioned s orbitals/p orbitals etc yet? Pauli exclusion principle etc? If not, I hope you get to learn about it because it will make better sense of some of the questions I'll bet you have about atoms/molecules when presented with the "Bohr atom" version. Any chem help or conversation you desire, I'm happy to help with.

Louis

Thanks Louis. If I have any questions, it's good to know I have back-up I can call on. I really appreciate having all you guys standing by.

The p shells and s shells are on deck, in the next section of this chapter of our book.  I imagine we'll get to them on Wednesday (Monday is a holiday here).

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Lou FCD



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(Permalink) Posted: Aug. 31 2008,09:49   

Quote (csadams @ Aug. 31 2008,10:43)
Lou - wow!  What an experience you're getting!  You might think about checking out some summer workshops out your way.  GLOBE has a lot going on in Hampton, VA; essentially, you get paid to learn.  How sweet is that??

Hey awesome! Getting paid to learn can't be anything but good.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Henry J



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(Permalink) Posted: Aug. 31 2008,19:09   

Quote
Have they mentioned s orbitals/p orbitals etc yet?


Didn't sound like it. I thought about mentioning that in the transition metals the electrons are added in the next to highest shell instead of the highest, but decided to wait to see if that was the next chapter. (Also in the "rare earths" the new electrons are added to the second shell from the top.) It's because those orbital have the next higher energy level, and additions are made to the lowest still empty energy level, even when that's not the top shell. It's also why the transition metals aren't overly different from each other chemically - their outer shells are all 1 or 2 electrons (with 1 (or is it 2?) exceptions where the "outermost" shell is actually empty).

Henry

  
Henry J



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(Permalink) Posted: Sep. 01 2008,19:21   

Addendum to my previous post: it's Palladium, symbol Pd, atomic number 46, that has no electrons in its "outermost" (5th) shell.

Henry

  
Lou FCD



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(Permalink) Posted: Sep. 01 2008,20:58   

Quote (Henry J @ Sep. 01 2008,20:21)
Addendum to my previous post: it's Palladium, symbol Pd, atomic number 46, that has no electrons in its "outermost" (5th) shell.

Henry

Now you're just trying to confuse me, Henry.

Besides, I don't care 'bout no damned Palawhocaresium because it's not in the first 18 elements and is currently irrelevant to the material.

Now stop trying to screw up my head with your materialist trans-Argon nonsense!

:)

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Henry J



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(Permalink) Posted: Sep. 01 2008,21:07   

I just thought of something else. Some biological species have lost traits considered normal for members of the containing clade. So palladium is sort of analogous: it's to the periodic table what those species are to their clades.

Henry

  
Henry J



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(Permalink) Posted: Sep. 01 2008,21:08   

Quote
Now stop trying to screw up my head with your materialist trans-Argon nonsense!


Name a non-materialistic element! :p

Henry

  
Louis



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(Permalink) Posted: Sep. 02 2008,06:21   

Quote (Henry J @ Sep. 02 2008,03:08)
Quote
Now stop trying to screw up my head with your materialist trans-Argon nonsense!


Name a non-materialistic element! :p

Henry

Narativium? Terry Pratchett's element of fiction.

Randomium? An element very useful for "explaining" why some reaction has or hasn't worked.

Crossfingersandhopelikehellium? An element in the same group as Randomium. Principle component of dusty crap that desperate students leave/place in flasks of reactions that repeatedly fail in the vain hope that some hitherto unheard of catalytic effect occurs. Not to be confused with molecular sieves or solid state catalysis.

Technecium? Well, it was made (up).

Louis

--------------
Bye.

  
dogdidit



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(Permalink) Posted: Sep. 02 2008,07:42   

Unobtainium has many popular uses in engineering.

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dogdidit



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(Permalink) Posted: Sep. 02 2008,07:50   

Quote (Henry J @ Aug. 31 2008,19:09)
 
Quote
Have they mentioned s orbitals/p orbitals etc yet?


Didn't sound like it. I thought about mentioning that in the transition metals the electrons are added in the next to highest shell instead of the highest, but decided to wait to see if that was the next chapter. (Also in the "rare earths" the new electrons are added to the second shell from the top.) It's because those orbital have the next higher energy level, and additions are made to the lowest still empty energy level, even when that's not the top shell. It's also why the transition metals aren't overly different from each other chemically - their outer shells are all 1 or 2 electrons (with 1 (or is it 2?) exceptions where the "outermost" shell is actually empty).

Henry

SPDF!! I thought I had succeeded in forgetting all that. Thanks for nothing.

I'd imagine Reese and Campbell would cover just enough QM to understanding the how's and why's of chemical bonding, but never haven studied biology I am ignorant of just how much QM and chemistry foundation would be needed. Certainly an understanding of bonding energy would be important.

I've been eyeing up Lou's textbook; would all agree it's a pretty good choice for an autodidact self-learner?

--------------
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Albatrossity2



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(Permalink) Posted: Sep. 02 2008,08:11   

Quote (dogdidit @ Sep. 02 2008,07:50)
I've been eyeing up Lou's textbook; would all agree it's a pretty good choice for an autodidact self-learner?

Campbell et al. is a good textbook; there are a number of good textbooks in introductory biology.

I have been reviewing intro bio textbooks for a number of years. IMHO the best one (and it may be out of print) is Burt Guttman's Biology (McGraw Hill). It is a comprehensive tome, written in an engaging style, and very suitable for auto-didactery. Burt taught for many years at Evergreen College in Olympia WA, and is by all accounts an excellent teacher. He is also a good birder, so he has many useful talents :-)

--------------
Flesh of the sky, child of the sky, the mind
Has been obligated from the beginning
To create an ordered universe
As the only possible proof of its own inheritance.
                        - Pattiann Rogers

   
Henry J



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(Permalink) Posted: Sep. 02 2008,14:18   

Quote (Louis @ Sep. 02 2008,05:21)
Randomium? An element very useful for "explaining" why some reaction has or hasn't worked.

Is that related to randomonium?

  
Louis



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(Permalink) Posted: Sep. 02 2008,14:45   

Quote (Henry J @ Sep. 02 2008,20:18)
Quote (Louis @ Sep. 02 2008,05:21)
Randomium? An element very useful for "explaining" why some reaction has or hasn't worked.

Is that related to randomonium?

One period above, two above pandemonium.

Louis

--------------
Bye.

  
deadman_932



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(Permalink) Posted: Sep. 02 2008,15:33   

Quote (Louis @ Sep. 02 2008,14:45)
Quote (Henry J @ Sep. 02 2008,20:18)
 
Quote (Louis @ Sep. 02 2008,05:21)
Randomium? An element very useful for "explaining" why some reaction has or hasn't worked.

Is that related to randomonium?

One period above, two above pandemonium.

Louis

Pfft. More like "Bolognium." Wretched Brits.

BTW: MY GENES R NUKULAR!!

--------------
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Lou FCD



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(Permalink) Posted: Sep. 02 2008,19:31   



My notes and thoughts from Biology 111, for Friday, August 29, 2008. The entire series can be found here.

Forgive the delay, but I've had a ton of stuff to work on.

On Friday, we started out with a review of covalent bonding. Doc re-stressed that in covalent bonding, atoms are sharing one or more pairs of electrons.

Let's take another look at our covalent bonding notation:



Now note that the two Oxygens share two pairs of e- and the two Nitrogens share three pairs of e-, as noted by the lines and by the dots between them. Also note that in the Lewis Dot diagram, all valence e- are depicted, regardless of whether they are involved in the bonding.

Let's throw some more elements together with covalent bonds:



And to really point out the sharing, I've circled and colored to highlight which e- belong to which element:


In this diagram, we can now really see that each element now has a full valence shell, by sharing e- part time with its neighbor.

Electronegativity

Electronegativity can be defined as the ability of an atom to attract e- to itself when in a compound.

Ignoring the Noble Gases (because they have full valence shells and don't tend to interact with other elements), we can roughly divide our Electron Distribution diagram into three parts. To the left side of the diagram we have elements that are very electropositive. It's much easier for them to lose a few e- to wind up with a full valence shell than to grab six or seven e- from somewhere else.  In the center, elements are electroneutral, where they can sort of go either way. To the right of the diagram, are the electronegative elements, which only need an e- or two to fill their valence shell, and thus are more likely to take than to give.

This becomes important especially when we start discussing ionic bonds.

So if atoms are fairly close in terms of elelectronegativity, they will tend to share e- equally, and there is an even distribution of charge around the molecule. We call that a nonpolar colvalent bond.

If the atoms are further apart in terms of electronegativity, the more electronegative atom will tend to pull the shared e- more towards itself, and the distribution of charge around the molecule will have a very slight uneveness to it. We call that a polar covalent bond.



Water is a good example of a polar covalent bond. Because the Oxygen atom is highly electronegative and the Hydrogen atoms are very electropositive, the shared e- spend more time around the oxygen atom than the hydrogen atoms. Although the molecule maintains a net charge of zero (10 p+ and 10 e- in total), it does have a very slight negative charge on the Oxygen end and a very slight positive charge on the Hydrogen ends. That charge is denoted with the lower case Greek letter delta (?). Note that the atoms of a water molecule do not line up in a straight line like the atoms of a Carbon Dioxide molecule.

Ionic Bonds

Attraction between a cation and an anion.

Ionic bonds form when the difference in electronegativity between two atoms is great.



Sodium, for instance, is very electropositive, being way over on the left side of the diagram and having only one e- in its valence shell.



Chlorine is very electronegative, being way over on the right side of the diagram and having seven e- in its valence shell.



Sodium and Chlorine, side by side for a good look.



When they get together, Chlorine doesn't share an e- with Sodium, it steals one completely. This of course upsets the normal balance of an atom, where it usually has the same number of p+ and e-. When this happens, the atom becomes an ion. Because the Sodium ion has one fewer e- (10) than it has p+(11), it now has a net charge of +1, and it's called a cation. The Chlorine ion has one more e- (18) than it has p+(17) , so it has a net charge of -1 and is called an anion.

Remember that opposite charges attract each other. The Chlorine anion will now attract the Sodium cation, and they will form an ionic bond. This is not actually a molecule, but rather an ionic compound. Bonds only form molecules through covalent bonds.

Chapter 3

Water and the Fitness of the Environment

Water has several emergent properties that make it essential for life on Earth.

Hydrogen Bonds



Water is a polar molecule, and can form Hydrogen Bonds. That very slight polarity we mentioned earlier now becomes very important, as we begin discussing how water molecules attract each other, with what's known as Hydrogen Bonding.

This is where the lecture left off, to be continued on Wednesday, 3 September.
 
Quote
From whence came the art:

The first image is of our textbook, Biology, Eighth Edition, by Campbell & Reese et al. The electron distribution table is from page 36 of that textbook, and I have highlighted portions of it in the various images above to assist in visualization.

The Periodic Table of the Elements is from the National Institute of Standards and Technology, NIST.

Other images by me and are licensed under the Creative Commons Attribution- NonCommercial- Share Alike 3.0 License.


Edited by Lou FCD on Sep. 02 2008,22:10

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Henry J



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(Permalink) Posted: Sep. 02 2008,22:37   

Quote
When they get together, Chlorine doesn't share an e- with Sodium, it steals one completely.


THIEF! Somebody call the copper! Otherwise those ions might a salt somebody.

Henry

  
Richardthughes



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(Permalink) Posted: Sep. 02 2008,22:41   

Chemistry puns. You're like a high-brow version of my Dad!

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"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
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Henry J



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(Permalink) Posted: Sep. 02 2008,23:40   

I wonder if that's good or bad?

Henry

  
Richardthughes



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(Permalink) Posted: Sep. 02 2008,23:45   

Quote (Henry J @ Sep. 02 2008,23:40)
I wonder if that's good or bad?

Henry

It would make you a genetic precursor to me.

I can think of no worse insult!

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
Assassinator



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(Permalink) Posted: Sep. 03 2008,06:13   

Quote (dogdidit @ Sep. 02 2008,07:50)
I've been eyeing up Lou's textbook; would all agree it's a pretty good choice for an autodidact self-learner?

I won't say per definition. I've been discussing with someone over ID and evolution for about a year now. The guy also has read Biology from Campbell and calls himself an auto-didact, but if you see him talk about evolution and all the subjects around it... Imo, you should always keep some experts on the field around to clearify things. Especially with things like biology and evolution, which include so many other subjects (nuclear physics for example) and the sometimes necessary backgrounds, it's incredibly difficult to teach yourself. But still, I can recommend Campbell. It helped me understand a lot of stuff about various subjects.

PS: I'de like to thank Lou for this 'blog'. Because of this, I can make better notes during class and see the value of typing them over. It will really help me getting my Bachelor ;)

  
dogdidit



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(Permalink) Posted: Sep. 03 2008,07:41   

Quote (Assassinator @ Sep. 03 2008,06:13)
     
Quote (dogdidit @ Sep. 02 2008,07:50)
I've been eyeing up Lou's textbook; would all agree it's a pretty good choice for an autodidact self-learner?

I won't say per definition. I've been discussing with someone over ID and evolution for about a year now. The guy also has read Biology from Campbell and calls himself an auto-didact, but if you see him talk about evolution and all the subjects around it... Imo, you should always keep some experts on the field around to clearify things. Especially with things like biology and evolution, which include so many other subjects (nuclear physics for example) and the sometimes necessary backgrounds, it's incredibly difficult to teach yourself.

A valid point. Truth to tell, unless I intend to work in the field (and I don't) there is really not much chance of me reaching the level of understanding of even a bachelor's degree candidate. Books are fine but the social transactions of mentoring relationships (starting with professor-student and going on from there...and lasting a lifetime) are absolutely essential. That is partly why I struck out "autodidact"; this is not at all the same as picking up a manual on LISP or perl and banging out some code, and even in engineering there is essential knowledge that can only be gained with the help and guidance of mentors. Not everything is written down in books. And the relative importance of all that is written is not always evident.

What I am looking for is a deeper undertanding that what can be gained from reading books written for the lay public. I can withstand a higher level of technical detail. Engineering is not much help but I do have a Physics bachelors that I dust off from time to time. The fundamentals never change; that's why they are called...well, you get the idea.

 
Quote
But still, I can recommend Campbell. It helped me understand a lot of stuff about various subjects.
Dank u wel, Assassinator!

ETA: Thank you Albie as well for your recommendations.

--------------
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dogdidit



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(Permalink) Posted: Sep. 03 2008,07:48   

BTW Lou, if you want to master the elements of the periodic table, I highly recommend a mnemonic.

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"Humans carry plants and animals all over the globe, thus introducing them to places they could never have reached on their own. That certainly increases biodiversity." - D'OL

  
Paul Flocken



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(Permalink) Posted: Sep. 03 2008,08:57   

Quote (bystander @ Aug. 28 2008,21:46)
Leave us hanging!! I wants to know the answer  :angry:

You left out disembodied telic entity pushing the termites around using wormholes in the space time continum.

Which is the correct answer no matter what your mere evidence shows. Teach the controversy !1!!one!!

I think the zero energy photons have more to do with it than the wormholes.  :p

--------------
"The great enemy of the truth is very often not the lie--deliberate, contrived, and dishonest, but the myth, persistent, persuasive, and unrealistic.  Belief in myths allows the comfort of opinion without the discomfort of thought."-John F. Kennedy

  
Paul Flocken



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(Permalink) Posted: Sep. 03 2008,09:11   

Quote (Louis @ Sep. 02 2008,07:21)
Quote (Henry J @ Sep. 02 2008,03:08)
Quote
Now stop trying to screw up my head with your materialist trans-Argon nonsense!


Name a non-materialistic element! :p

Henry

Narativium? Terry Pratchett's element of fiction.

Randomium? An element very useful for "explaining" why some reaction has or hasn't worked.

Crossfingersandhopelikehellium? An element in the same group as Randomium. Principle component of dusty crap that desperate students leave/place in flasks of reactions that repeatedly fail in the vain hope that some hitherto unheard of catalytic effect occurs. Not to be confused with molecular sieves or solid state catalysis.

Technecium? Well, it was made (up).

Louis

Tardium-The most essential element for the synthesis of tard in creationist brains.  The most common source of tardium is family bibles.

--------------
"The great enemy of the truth is very often not the lie--deliberate, contrived, and dishonest, but the myth, persistent, persuasive, and unrealistic.  Belief in myths allows the comfort of opinion without the discomfort of thought."-John F. Kennedy

  
Lou FCD



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(Permalink) Posted: Sep. 03 2008,09:32   

i can haz kwiz 2day.

I think I got them all, but I have a question about it regarding the Lewis Dot Diagram of a double covalent bond between N and H on the end of a molecule.

Wouldn't that put four e- in the H's valence shell? (There was a similar situation where an H was single bonded between two C atoms.)

I'll diagram it if that's not clear.



Edited to add image. We were given a molecule something like the first structural diagram, and required to draw the Lewis Dot Diagram.

Wouldn't this suggest too many e- in the valence shell of the circled Hydrogen?  (4)

Edited again to fix an unrelated issue with the diagram.

Edited by Lou FCD on Sep. 03 2008,11:03

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Louis



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(Permalink) Posted: Sep. 03 2008,10:03   

Quote (Lou FCD @ Sep. 03 2008,15:32)
i can haz kwiz 2day.

I think I got them all, but I have a question about it regarding the Lewis Dot Diagram of a double covalent bond between N and H on the end of a molecule.

Wouldn't that put four e- in the H's valence shell? (There was a similar situation where an H was single bonded between two C atoms.)

I'll diagram it if that's not clear.



Edited to add image. We were given a molecule something like the first structural diagram, and required to draw the Lewis Dot Diagram.

Wouldn't this suggest too many e- in the valence shell of the circled Hydrogen?  (4)

Something is very askew with that diagram.

If you consider that diagram to be an H bond between two molecules, it seems to be an interaction between a carbene derived from ethane and formaldehyde under basic conditions. My guess is something else is going on!

You've mentioned a nitrogen in the molecule, redraw that interaction, 'cos there ain't no N in there!

My guess is you have the diagram wrong.

The C-H single bond is sufficiently polar (you've mentioned electronegativity already) to be coordinated by a metal, iron complexes with pentane spring to mind, but my guess is that at the level of chem you are doing this is way off topic.  I'm guessing they haven't introduced you to carbenes and deprotonated formaldehyde yet! (And they don't interact like then when they do!)

So your instinct is right, 4 electrons around an H atom indicates a big no no. (Standard caveats about obscure excited states apply, none of which are relevant to basic theories of bonding).

The 4 valent hydrogen means check your diagrams, 'cos they ain't the accurate banana.

Louis

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Lou FCD



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(Permalink) Posted: Sep. 03 2008,10:10   

ah give me a few. I forgot they were straight out of the book. I have them in front of me and I'll give you the exact problem.

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Lou FCD



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(Permalink) Posted: Sep. 03 2008,10:26   

Ok, here's the actual question and what I did with it, which doesn't seem right, but given that the bonds are supposed to represent pairs of e-, I don't what what else I could have done with it.



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Albatrossity2



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(Permalink) Posted: Sep. 03 2008,10:40   

Quote (Lou FCD @ Sep. 03 2008,10:26)
Ok, here's the actual question and what I did with it, which doesn't seem right, but given that the bonds are supposed to represent pairs of e-, I don't what what else I could have done with it.


Well, I'm no chemist (nor do I play one on TV), but any diagram that has a hydrogen making two bonds with two different carbons is not depicting a real molecule...

--------------
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As the only possible proof of its own inheritance.
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Lou FCD



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(Permalink) Posted: Sep. 03 2008,10:40   

Quote (Lou FCD @ Sep. 03 2008,11:26)
Ok, here's the actual question and what I did with it, which doesn't seem right, but given that the bonds are supposed to represent pairs of e-, I don't what what else I could have done with it.


Nevermind. I read the instructions on the quiz paper but not the ones in the book, which gave the option of saying it was nonsensical.

Damnit.

Same goes for the N question.

RTFB!

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Richardthughes



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(Permalink) Posted: Sep. 03 2008,11:08   

I are lernin!

keep the posts coming.

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"You magnificent bastard! " : Louis
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Lou FCD



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(Permalink) Posted: Sep. 03 2008,11:27   

Quote (Richardthughes @ Sep. 03 2008,12:08)
I are lernin!

keep the posts coming.

If I don't learn to read the instructions, Rich, you might want to carefully reconsider that request.

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Louis



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(Permalink) Posted: Sep. 03 2008,11:29   

Quote (Lou FCD @ Sep. 03 2008,16:40)
Quote (Lou FCD @ Sep. 03 2008,11:26)
Ok, here's the actual question and what I did with it, which doesn't seem right, but given that the bonds are supposed to represent pairs of e-, I don't what what else I could have done with it.


Nevermind. I read the instructions on the quiz paper but not the ones in the book, which gave the option of saying it was nonsensical.

Damnit.

Same goes for the N question.

RTFB!

Look up the term "agostic". It's a word used in organometallic chem (mostly).

The chances of an agostic hydrogen bridging two uncomplexed, uncharged carbon based molecules........unlikely. Comes back to electronegativity again. The polarity of those bonds isn't sufficient to make the formal bond being shown there. If you're talking about hydrogen bonds the sure, they can and do happen, but representing them as "formal" covalent 2 electron bonds is not representing them as they really are. Even a dative bond is more "formal" than a hydrogen bond (H-bonds are really through space interactions of dipoles).

That diagram is not precisely nonsensical, but it IS nonsensical given the information you have been given. Like I said, unless you are dealing with (obscure) high energy states and weird gas state bonding modes, you're not dealing with something "real".

For given values of the word "real"! :-)

Yeah that was helpful Louis!

Louis

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(Permalink) Posted: Sep. 03 2008,11:34   



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Louis



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(Permalink) Posted: Sep. 03 2008,11:34   

I will translate that last post into sensiblese when I am a) not off work for the day, b) not drunk, c) not 2 hours away from my friend's wedding rehearsal, d) not drunk, e) not waiting for a cab, and f) not drunk.

There may be a recurring theme.

Well there is when I can spell "theme" the first time.

Louis

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Richardthughes



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(Permalink) Posted: Sep. 03 2008,11:37   

Quote (Lou FCD @ Sep. 03 2008,11:27)
Quote (Richardthughes @ Sep. 03 2008,12:08)
I are lernin!

keep the posts coming.

If I don't learn to read the instructions, Rich, you might want to carefully reconsider that request.

Reading the instructions, like asking for directions, is the domain of the female. Those that say you can't put a square peg through a round hole have not witnessed the brute force and ignorance school of inquiry.

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"You magnificent bastard! " : Louis
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Henry J



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(Permalink) Posted: Sep. 03 2008,22:48   

Quote
Nevermind. I read the instructions on the quiz paper but not the ones in the book, which gave the option of saying it was nonsensical.


Well the nerve of the professor, requiring the student to know how to recognize nonsense when he sees it. How can people from here know how to recognize nonsense when they spend all their time arguing with, uh... Oh. Never mind.

Henry

  
Lou FCD



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(Permalink) Posted: Sep. 05 2008,09:27   

I just wanted to take a minute to say that my prof rocketh.

Apparently I wasn't the only one who didn't RTFB, and he "was in a good mood" (direct quote), so he didn't crucify us for not labeling the screwy molecules, if we drew them out reasonably correctly according to the given structural diagram.

I wound up with 11 out of the 12 possible points.

Given that, and that my Spanish instructor also didn't crucify us on spelling on our first quiz (and I got the extra credit problem which made up for all my mistakes, giving me a 100), it's not been so bad an ending to the week.

I got my precalc quiz and my labs back Wednesday night, and maxed them all out at 100s too.

I'm ready for the weekend.

:)

--- over which I have an English essay to write for Monday and my first exam (Spanish) to study for on Tuesday.

:(

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Albatrossity2



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(Permalink) Posted: Sep. 05 2008,09:34   

Quote (Lou FCD @ Sep. 05 2008,09:27)
I'm ready for the weekend.

:)

--- over which I have an English essay to write for Monday and my first exam (Spanish) to study for on Tuesday.

:(

We give our first exam in intro Biology on Monday night.

There are 792 students in 10 sections currently enrolled. It's a logistical nightmare.

Frankly, I'm convinced it is easier to study and take a test than it is to write it, proof-read it, make two versions to discourage cheating, distribute it to 7 exam rooms, and get it graded. The students have no clues about this, of course; they are focused on one exam (theirs). And they are all convinced that we are trying to flunk them. Little do they know that I am as anxious (maybe more anxious) to see those grades as they are. I want them to do well, and I'm bummed when they don't.

Good luck on your exam, Lou. And thanks for keeping us posted on your progress there!

--------------
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As the only possible proof of its own inheritance.
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Lou FCD



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(Permalink) Posted: Sep. 06 2008,17:15   

Quote (Albatrossity2 @ Sep. 05 2008,10:34)
Good luck on your exam, Lou. And thanks for keeping us posted on your progress there!

Thanks Alby, and you're welcome.

My blog is getting kinda like the fridge was for my kids when they were in grade school (as is this thread), an observation which I find endlessly amusing.

:)

I realize I'm a little behind on posting the notes and hope to catch up soon, but as I said, I have a paper to finish and some studying to do.

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jeffox



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(Permalink) Posted: Sep. 07 2008,21:14   

Hiya Lou!

I just got done with my first week back at school.  As a geology major, my main course is Minerology/Petrology; but I'm also taking Pre-Calc and an intro to Archeology class.

You wrote above:

Quote
I got my precalc quiz and my labs back Wednesday night, and maxed them all out at 100s too.


I took my first quiz on Thurs. and think that I did well - but I haven't seen the result yet.  We're currently on line equations and quadratic formula derivation.  Neh. . . :)

My Archeology instructor is very animated, likes to quote James Brown, and is a joke-a-minute kind of guy.  I don't anticipate any problems there.

Min-Pet is going to be a lot of work, but should be rewarding as a major "core" course for me.  Plus we have all kinds of field trips (two weekenders, one going as far as the Black Hills in SD) and I get a really cool hammer!!

I had Chem last semester, and (maybe) in the above, the bond is actually a C-C bond, with the H bonding to one or the other?  Anyway, I got a B+ in that course, but did a lot of work and kinda forgot a lot already.  :P

Best of luck to all of the school returnees!  Have fun and learn lots.

  
Henry J



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(Permalink) Posted: Sep. 08 2008,11:26   

Quote
My Archeology instructor


But does he carry a whip, wear a hat, and look like Harrison Ford? ;)

  
Lou FCD



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(Permalink) Posted: Sep. 08 2008,14:27   

Quote (jeffox @ Sep. 07 2008,22:14)
Hiya Lou!

I just got done with my first week back at school.  As a geology major, my main course is Minerology/Petrology; but I'm also taking Pre-Calc and an intro to Archeology class.

You wrote above:

Quote
I got my precalc quiz and my labs back Wednesday night, and maxed them all out at 100s too.


I took my first quiz on Thurs. and think that I did well - but I haven't seen the result yet.  We're currently on line equations and quadratic formula derivation.  Neh. . . :)

My Archeology instructor is very animated, likes to quote James Brown, and is a joke-a-minute kind of guy.  I don't anticipate any problems there.

Min-Pet is going to be a lot of work, but should be rewarding as a major "core" course for me.  Plus we have all kinds of field trips (two weekenders, one going as far as the Black Hills in SD) and I get a really cool hammer!!

I had Chem last semester, and (maybe) in the above, the bond is actually a C-C bond, with the H bonding to one or the other?  Anyway, I got a B+ in that course, but did a lot of work and kinda forgot a lot already.  :P

Best of luck to all of the school returnees!  Have fun and learn lots.

Here's to us, Jeff!

May we learn lots, and share the wealth.

(and now I'm three lectures and a lab behind in posting my notes.... I really need to get caught up on that!)

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(Permalink) Posted: Sep. 08 2008,15:04   

Oh, almost forgot.

We turned in our lab reports for the termite lab today, in the first part of lab.... to each other.

Each person in each group turned over their lab report to someone from a different group. We're peer reviewing before final drafting.

So next Monday, each group gets their copies of the lab report back from the various reviewers, and then we take the critiques and redraft our papers for final turn-in the following week.

That's pretty cool.

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jeffox



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(Permalink) Posted: Sep. 08 2008,23:19   

Henry J wrote above:

Quote
But does he carry a whip, wear a hat, and look like Harrison Ford?  


No, not really.  He does talk a lot about drinking "40's" out of brown paper bags.  :)  Really, he's quite the cat, and a real quick wit, too boot.  

One student made a kinda goofy comment about how cattle, on average, orient themselves with their heads to the north.  The instructor's immediate reply was that that was because they're fed cow magnets.  Being that I've spent a lot of my life in and around farming communities, I actually knew what a cow magnet was.  I almost hit the floor laughing.  Sharp, that one.  :)

Note to city-folks:  A cow magnet is a small, rounded-edged cylinder of steel that is magnetized and fed to cattle to make all the iron-based garbage they eat collect in their stomachs and not go into their intestines where that shit can really cause problems.  They're about 2 inches long and about 1/4 inch in diameter.  The metals that cows eat include parts of old barbed-wire fences, nails, old building materials, etc.  A lot of farmers in the olden days just threw garbage out into their fields to get rid of it.  More than anybody really wanted to know, but there it is.   Moo, y'all.  :)   :)   :p

  
JohnW



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(Permalink) Posted: Sep. 09 2008,11:22   

Quote (Lou FCD @ Sep. 08 2008,13:04)
Oh, almost forgot.

We turned in our lab reports for the termite lab today, in the first part of lab.... to each other.

Each person in each group turned over their lab report to someone from a different group. We're peer reviewing before final drafting.

So next Monday, each group gets their copies of the lab report back from the various reviewers, and then we take the critiques and redraft our papers for final turn-in the following week.

That's pretty cool.

Anonymous peer review (drawing reports randomly) would have been more realistic, and much more entertaining.  You're much more likely to hand out an authentic merciless kicking if you're safe from reprisals.

To make it a truly accurate simulation, you should drop enough little hints for your victim to be all but certain who did the dirty deed - but unable to prove a thing.

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OWKtree



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(Permalink) Posted: Sep. 09 2008,14:02   

Quote (Richardthughes @ Sep. 03 2008,11:37)

Reading the instructions, like asking for directions, is the domain of the female. Those that say you can't put a square peg through a round hole have not witnessed the brute force and ignorance school of inquiry.


The "elegant" male solution for getting a square peg into a round hole requires the use of a lathe.

- Kurt

  
Spottedwind



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(Permalink) Posted: Sep. 09 2008,14:09   

Quote (Albatrossity2 @ Aug. 30 2008,21:09)
Lou

I think that your understanding of the basic material may be better than some of my students.  Here is an email, rec'd tonight, from a student in my intro bio class. The name is withheld to protect the innocent...
     
Quote
I was reading the textbook and I am now confused.

On page 4, it defines Atoms as "...the fundamental building blocks of all substances, living and non-living."
Then on page 22, it goes on to say that ... "Atoms differ in the number of subatomic particles, but all have a nucleus..."
--- Back on page 8, it told me that bacteria & archaea are single-celled organisms, but that they are prokaryotic, meaning that they have no nucleus..
..Farther back still, on page four, it says in short : atoms join together to make molecules, and molecules (become organized into?) make cells...

So as I said I am confused.  Is the textbook saying that some molecules are formed without atoms?  If so, what are they made of?

..Or is page 22 incorrect about all atoms having nuclei or is there something else ?

Thanks for clearing this up

You know, it's funny, I never really thought of the ambiguity about 'nucleus'.  They were just two different concepts with two different words, in my mind at least.

I mean, I know that it's the same word, but...I don't know, it was just different.  Probably partially due to the fact that I am inclined to biology more than chemistry, so cells come to mind more often than atoms, but still.

On one hand, at least the student paid enough attention when reading to even notice that it was the same word used.  That's at least somewhat observant.

On the other hand...that should never have left middle school, let alone high school.  Maybe even elementary school.

Scary, funny, and strange all at once.

  
Spottedwind



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(Permalink) Posted: Sep. 09 2008,14:24   

Quote (Lou FCD @ Sep. 08 2008,16:04)
Oh, almost forgot.

We turned in our lab reports for the termite lab today, in the first part of lab.... to each other.

Each person in each group turned over their lab report to someone from a different group. We're peer reviewing before final drafting.

So next Monday, each group gets their copies of the lab report back from the various reviewers, and then we take the critiques and redraft our papers for final turn-in the following week.

That's pretty cool.

Forgot to add, I really enjoyed reading about the termites.  Something I didn't know and another fascinating about nature.  Cool!

How sad of a nerd am I that the development of a hypothesis was nearly as much fun as the termites themselves?  I know it's very School House Rock!, but learning is awesome!

  
JohnW



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(Permalink) Posted: Sep. 09 2008,14:58   

Quote (OWKtree @ Sep. 09 2008,12:02)
Quote (Richardthughes @ Sep. 03 2008,11:37)

Reading the instructions, like asking for directions, is the domain of the female. Those that say you can't put a square peg through a round hole have not witnessed the brute force and ignorance school of inquiry.


The "elegant" male solution for getting a square peg into a round hole requires the use of a lathe.

- Kurt

Too girly.  If it doesn't fit, get a bigger hammer.

--------------
Math is just a language of reality. Its a waste of time to know it.
- Robert Byers

  
BWE



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(Permalink) Posted: Sep. 10 2008,03:54   

Quote (Lou FCD @ Sep. 05 2008,09:27)
I just wanted to take a minute to say that my prof rocketh.

Apparently I wasn't the only one who didn't RTFB, and he "was in a good mood" (direct quote), so he didn't crucify us for not labeling the screwy molecules, if we drew them out reasonably correctly according to the given structural diagram.

I wound up with 11 out of the 12 possible points.

Given that, and that my Spanish instructor also didn't crucify us on spelling on our first quiz (and I got the extra credit problem which made up for all my mistakes, giving me a 100), it's not been so bad an ending to the week.

I got my precalc quiz and my labs back Wednesday night, and maxed them all out at 100s too.

I'm ready for the weekend.

:)

--- over which I have an English essay to write for Monday and my first exam (Spanish) to study for on Tuesday.

:(

The one class I remember my grade in was pre-calc. I got an A on the first 4 out of 5 equally weighted tests and a B- in the class.

That worried me IIRC because I had calc the next quarter after summer break and it was required for science majors.

But that had to do more with distractions and so forth... I'm sure you'll sail through.

Why are you taking Spanish?

--------------
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When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

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Reciprocating Bill



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(Permalink) Posted: Sep. 10 2008,06:30   

Quote (jeffox @ Sep. 09 2008,00:19)
Note to city-folks:  A cow magnet is a small, rounded-edged cylinder of steel that is magnetized and fed to cattle to make all the iron-based garbage they eat collect in their stomachs and not go into their intestines where that shit can really cause problems.  They're about 2 inches long and about 1/4 inch in diameter.  The metals that cows eat include parts of old barbed-wire fences, nails, old building materials, etc.  A lot of farmers in the olden days just threw garbage out into their fields to get rid of it.  More than anybody really wanted to know, but there it is.   Moo, y'all.  :)   :)   :p

(slaps forehead)

So these refrigerator magnets are supposed to go IN the refrigerator.

DUH!

--------------
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BWE



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(Permalink) Posted: Sep. 10 2008,06:59   

Quote (Reciprocating Bill @ Sep. 10 2008,06:30)
Quote (jeffox @ Sep. 09 2008,00:19)
Note to city-folks:  A cow magnet is a small, rounded-edged cylinder of steel that is magnetized and fed to cattle to make all the iron-based garbage they eat collect in their stomachs and not go into their intestines where that shit can really cause problems.  They're about 2 inches long and about 1/4 inch in diameter.  The metals that cows eat include parts of old barbed-wire fences, nails, old building materials, etc.  A lot of farmers in the olden days just threw garbage out into their fields to get rid of it.  More than anybody really wanted to know, but there it is.   Moo, y'all.  :)   :)   :p

(slaps forehead)

So these refrigerator magnets are supposed to go IN the refrigerator.

DUH!

I worked as a butcher for around 10 years. (I grew up in the country)

Cow magnets pick up a lot of things you wouldn't think of a cow eating but one thing I never figured out was the iron filings, little tiny metal needle shaped bits of metal stuck on them. Some cows are plumb full of magnets and those I figured were covered with bits rubbed off the other magnets but even if they only had a few the same stuff covered them. I imagined they were sucking the iron out of their spinach.

--------------
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

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Lou FCD



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(Permalink) Posted: Sep. 10 2008,19:47   

Quote (BWE @ Sep. 10 2008,04:54)
The one class I remember my grade in was pre-calc. I got an A on the first 4 out of 5 equally weighted tests and a B- in the class.

That worried me IIRC because I had calc the next quarter after summer break and it was required for science majors.

But that had to do more with distractions and so forth... I'm sure you'll sail through.

Why are you taking Spanish?

A foreign language is required both for my associate's at Coastal and for my bachelor's in the UNC system (to which I'll transfer), and I took both French and German in high school.  I thought this time around I'd take something actually useful.  :)

Besides which, it should really be an easy A, and it would be handy for realsies here.

Speaking of precalc distractions, just as class started this evening we got word of a possible tornado headed our direction (by way of my neighborhood), and the building's classes all emptied into the first floor hallway.

We hung out for about 15 or 20 minutes before we got the all clear, and could go back to class. No sightings on the ground that I'm yet aware of, but frankly I'm exhausted and in a great deal of pain tonight, so further investigation will wait until tomorrow.

Right now, I just want to put the precalc quiz behind me (I think I did pretty well) and go to bed.

The days are starting to run together, now.

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jeffox



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(Permalink) Posted: Sep. 10 2008,22:40   

A furly odd occurance today.  I went to my new job (making sandwiches at the campus cafeteria) a few hours earlier today to take in my first Geology Club meeting and do some power schmoozing.  :)  After the Club's meeting, there was about an hour before I had to go to work.  So, there I was, hanging out on the commons when I noticed a fairly large group of students clustered around someone speaking.  Sort of.  I got closer and ended up actually participating.  :)

It was this cat.

Straw men, evidentiary double standards, misidentification, historical revisionism, you name it, he spewed it.  If a question was too difficult, he danced around it.  Thin-skinned and nervous as he spoke, he denounced everything he felt wasn't up to his biblical standard(s).  

I lit into him on a number of issues, and I wasn't alone.  He had little support, mostly people asking him to clarify his point(s).

He's a poor dancer, and came off as a total tard.  He even said that Dawkins made himself look bad in Expelled.  I about died with laughter at that one.

I will say that I developed a great deal of respect for the students at UWEC.  They treated him with respect, for the most part, and yet engaged him on his inconsistencies and political obtuseness.  

I guess school isn't just about book-learning.  It was an interesting day today.

Otherwise, like you wrote, Lou; my days are beginning to blend together also.  Second quiz tomorrow in Precalc.

I hope that all the other current students are having a good time and learning a lot, too!

  
Louis



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(Permalink) Posted: Sep. 11 2008,04:14   

Quote (Lou FCD @ Sep. 11 2008,01:47)
[SNIP]

...and I took both French and German in high school.  I thought this time around I'd take something actually useful.  :)

[SNIP]

Don't knock it, UK foreign policy and "special relationship" with the USA is based on the fact that we mostly cannot be arsed to learn French.* ;-)

Louis

*Needless to say, as a Francophile, this is a policy I profoundly disagree with.

--------------
Bye.

  
dvunkannon



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(Permalink) Posted: Sep. 11 2008,09:48   

Quote (Louis @ Sep. 11 2008,05:14)
Quote (Lou FCD @ Sep. 11 2008,01:47)
[SNIP]

...and I took both French and German in high school.  I thought this time around I'd take something actually useful.  :)

[SNIP]

Don't knock it, UK foreign policy and "special relationship" with the USA is based on the fact that we mostly cannot be arsed to learn French.* ;-)

Louis

*Needless to say, as a Francophile, this is a policy I profoundly disagree with.

I thought half the language was French already. (Obviously not necessary for previous sentence.)

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huwp



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(Permalink) Posted: Sep. 11 2008,10:48   

Hey, if you've studied French AND Spanish then you'll know Portuguese - ask AFDave.

  
Louis



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(Permalink) Posted: Sep. 11 2008,11:46   

Quote (dvunkannon @ Sep. 11 2008,15:48)
Quote (Louis @ Sep. 11 2008,05:14)
Quote (Lou FCD @ Sep. 11 2008,01:47)
[SNIP]

...and I took both French and German in high school.  I thought this time around I'd take something actually useful.  :)

[SNIP]

Don't knock it, UK foreign policy and "special relationship" with the USA is based on the fact that we mostly cannot be arsed to learn French.* ;-)

Louis

*Needless to say, as a Francophile, this is a policy I profoundly disagree with.

I thought half the language was French already. (Obviously not necessary for previous sentence.)

Of course it is, we just don't admit it.

Louis

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Lou FCD



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(Permalink) Posted: Sep. 11 2008,11:51   



My notes and thoughts from Biology 111, for Wednesday, September 3, 2008. The entire series can be found here.

We left off before the Labor Day break with polarity and the ability to form hydrogen bonds.

The polarity of the water molecule, having an oxygen to one side and the two hydrogen atoms to the other, gives the molecules a slight attraction to charged molecules, since the oxygen end is going to have a slight negative charge and the hydrogen end is going to have a slight positive charge. This is caused by the unequal sharing of valence e- between the oxygen and the two hydrogens. Because the oxygen pulls harder on the shared e-, they are going to spend more time toward the oxygen, increasing its negative charge a little, and away from the hydrogens, increasing their positive charge a little (actually decreasing their negative charge a little, to be accurate).

That little bit of polarity will cause the oxygen end of one water molecule to be attracted to the hydrogen end of another water molecule (or any other positively charged molecule), and though the effect is small in one pair of molecules, it adds up with millions of molecules.

This is what causes the meniscus in a test tube or a glass of water. The water toward the edge, closest to the glass, is attracted to the glass, pulling itself up a little to stick to the sides. It's also the cause for the ability to fill a glass slightly over the edge.

Emergent Properties of Water

1. Cohesion and Adhesion

Cohesion is the ability of water (in this case) molecules to stick to each other by hydrogen bonding

Adhesion is the ability of water (in this case) to stick to other polar molecules.

In our previous example of the test tube or glass, cohesion would be responsible for the water overfilling the glass without spillage, and adhesion would be responsible for the meniscus.

They'll also cause the water level inside a glass straw to be higher than the water level of a beaker in which the straw is placed. The thinner the straw, the greater the disparity between the water levels, as there are fewer water molecules in the center, far away from the glass. In the center, gravity will tend to overcome the hydrogen bonding, but at the sides, where the water is close to the glass, the hydrogen bond is strong enough to overcome the gravitational pull.

In another example, it's the cause of a little bit of water acting like glue between two glass plates. The sum of all those hydrogen bonds makes it very difficult to separate two wet panes of glass.

In biology, this is how a plant gets water from the ground to the leaves. Little teeny veins in the tree attract the water molecules, which adhere their way up against gravity to the leaves, where it evaporates.

This lecture was rather short, due to the pop quiz Doc gave that day, and here is where it ended.

Quote
From whence came the art:

That image is of our textbook, Biology, Eighth Edition, by Campbell &amp; Reese et al.


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(Permalink) Posted: Sep. 11 2008,11:57   

Quote (jeffox @ Sep. 10 2008,23:40)
Otherwise, like you wrote, Lou; my days are beginning to blend together also.  Second quiz tomorrow in Precalc.

Yeah, took my second last night, think I did pretty well. We'll be having them every Wednesday night from here out.

Got my Spanish exam from Tuesday back this morning:

100

(two small misspellings and one use of the wrong verb - I used soy instead of estoy - but I nailed the extra credit)

I seem to be keeping mi cabeza above la agua.

Quote (jeffox @ Sep. 10 2008,23:40)
I hope that all the other current students are having a good time and learning a lot, too!


I'll second that emotion.

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Ra-Úl



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(Permalink) Posted: Sep. 11 2008,12:16   

Quote (Lou FCD @ Sep. 11 2008,11:57)
Quote (jeffox @ Sep. 10 2008,23:40)
Otherwise, like you wrote, Lou; my days are beginning to blend together also.  Second quiz tomorrow in Precalc.

Yeah, took my second last night, think I did pretty well. We'll be having them every Wednesday night from here out.

Got my Spanish exam from Tuesday back this morning:

100

(two small misspellings and one use of the wrong verb - I used soy instead of estoy - but I nailed the extra credit)

I seem to be keeping mi cabeza above la agua.

Quote (jeffox @ Sep. 10 2008,23:40)
I hope that all the other current students are having a good time and learning a lot, too!


I'll second that emotion.

Uhmmm . . . "el agua." Feminine nouns beginning with a stressed 'a' (or 'ha') take the "el" article in singular form, and the "las" def. article in plural: "las aguas." Why? Revenge for English spelling. Really.

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Lou FCD



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(Permalink) Posted: Sep. 11 2008,15:52   

Quote (Ra-Úl @ Sep. 11 2008,13:16)
Uhmmm . . . "el agua." Feminine nouns beginning with a stressed 'a' (or 'ha') take the "el" article in singular form, and the "las" def. article in plural: "las aguas." Why? Revenge for English spelling. Really.

heh, thanks. We hadn't gotten to that yet, but I remember agua from Sesame Street.

:)

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BWE



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(Permalink) Posted: Sep. 11 2008,18:20   

I read in one of the recent science mags (science news maybe?) that the quantum effect of the water molecule have a lot to do with the emergent chemical properties and that water made with deuterium is fundementally different in that the bond is much tighter or something like that.

[/blithering]

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Louis



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(Permalink) Posted: Sep. 11 2008,18:32   

Quote (BWE @ Sep. 12 2008,00:20)
I read in one of the recent science mags (science news maybe?) that the quantum effect of the water molecule have a lot to do with the emergent chemical properties and that water made with deuterium is fundementally different in that the bond is much tighter or something like that.

[/blithering]

Not entirely blithertastic my friend.

Ask yourself why (for example) hydrogen sulfide or hydrogen selenide don't behave the same way as water (in their liquid states). Elements from the first period tend to be unusual for their group by virtue of their comparatively small atomic radius and high electronegativity (simple explanation. More complex stuff involves maths, quantum mechanics, and depending on how far one wants to go, molecular orbital theory).

Isotope effects (H to D for example) can alter the strength of the bond sufficiently to noticeably affect the dissociation constants or the pka for example.

Oops, I appear to have got all excited and mildly chemical again. Apologies.

Louis

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dogdidit



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(Permalink) Posted: Sep. 11 2008,22:26   

Quote (Louis @ Sep. 11 2008,18:32)
   
Quote (BWE @ Sep. 12 2008,00:20)
I read in one of the recent science mags (science news maybe?) that the quantum effect of the water molecule have a lot to do with the emergent chemical properties and that water made with deuterium is fundementally different in that the bond is much tighter or something like that.

[/blithering]

Not entirely blithertastic my friend.

Ask yourself why (for example) hydrogen sulfide or hydrogen selenide don't behave the same way as water (in their liquid states). Elements from the first period tend to be unusual for their group by virtue of their comparatively small atomic radius and high electronegativity (simple explanation. More complex stuff involves maths, quantum mechanics, and depending on how far one wants to go, molecular orbital theory).

Isotope effects (H to D for example) can alter the strength of the bond sufficiently to noticeably affect the dissociation constants or the pka for example.

Oops, I appear to have got all excited and mildly chemical again. Apologies.

Louis

You mean second period, correct? That is, home of oxygen, nitrogen, and flourine, the chief electronegative culprits in hydrogen bonding? I'm not nitpicking, I just want to make sure I understand. My college physics never got this far. Excuse me for being a noisy kibbitzer.

It seems to me that "hydrogen bonding" is a bit mislabelled; it's more to do with the electronegative elements than hydrogen. I read somewhere that even carbon can participate in "hydrogen bonding".

ANYHOO- Lou, hydrogen bonding is pretty critical in biochemistry. The two complementary strands on DNA are held together with hydrogen bonds. And I believe hydrogen bonding also plays a role in protein folding. So you're going to spend some time studying it, I imagine.

As for deuterium chemistry, I am slack-jawed. The extra neutron is electrically neutral, and can interact with the electron cloud only weakly (literally), I thought, so WTF? Guess I needed to stay in school a little longer.

Louis, if I had a cap, I'd doff it. *cap-doffing motion*

BWE, let me borrow this:
</blithering>

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BWE



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(Permalink) Posted: Sep. 11 2008,23:02   

dogdidit, after I read the article I called a friend of mine who works at Hanford as a researcher and asked him if they were letting heavy water into the columbia since I'm downstream and all. He said, "I don't know".

WHat!?

You should know dammit.

But I didn't say that. I only thought it.

The thing that made it noteworthy for me was that the QM of the atom affected the chemistry in such a major way.

Here is the online article! I googled 'science news heavy water.'

http://www.sciencenews.org/view....fferent


The interbitlitweb is neet.link

ETA: here is a bit of it:
Quote
The length of bonds connecting water molecules could demonstrate quantum effects and help explain some of water’s weirdness.
access
HEAVY CONNECTIONSThe distance between oxygen and the heavier deuterium in a D2O molecule in liquid heavy water is three percent shorter than the distance between oxygen and hydrogen in an H2O molecule; and the hydrogen bond (dotted) is four percent longer in heavy water than in light. Click image twice for a larger view.J. Korenblat/Science News

Heavy water is not just heavier. Swapping each H in H2O with a D — hydrogen’s isotope deuterium — changes many of water’s properties. Heavy water is poisonous, and its freezing point is 4° Celsius, instead of 0°. Those differences may reveal that quantum effects rule in ordinary water, researchers have now found.

The results, reported in an upcoming Physical Review Letters, could shed light on quantum theory’s relevance for ordinary water, which is the medium for most of the action inside living cells. The work could also help explain some controversial findings on how biological molecules behave in water.


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Henry J



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(Permalink) Posted: Sep. 11 2008,23:12   

Quote
The extra neutron is electrically neutral, and can interact with the electron cloud only weakly (literally),


Is it that it interacts weakly with the electrons, or simply that it doubles the inertia of the atom it's in, making it more resistant to getting shoved around by outside forces? (Also heavier gravitationally, of course.)

Henry

  
jeffox



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(Permalink) Posted: Sep. 11 2008,23:36   

Oh, ya ya, da fish get bigger in heavy water, butcha can't eat 'em.

:)   :)   :p

  
Louis



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(Permalink) Posted: Sep. 12 2008,03:07   

Quote (dogdidit @ Sep. 12 2008,04:26)
Quote (Louis @ Sep. 11 2008,18:32)
     
Quote (BWE @ Sep. 12 2008,00:20)
I read in one of the recent science mags (science news maybe?) that the quantum effect of the water molecule have a lot to do with the emergent chemical properties and that water made with deuterium is fundementally different in that the bond is much tighter or something like that.

[/blithering]

Not entirely blithertastic my friend.

Ask yourself why (for example) hydrogen sulfide or hydrogen selenide don't behave the same way as water (in their liquid states). Elements from the first period tend to be unusual for their group by virtue of their comparatively small atomic radius and high electronegativity (simple explanation. More complex stuff involves maths, quantum mechanics, and depending on how far one wants to go, molecular orbital theory).

Isotope effects (H to D for example) can alter the strength of the bond sufficiently to noticeably affect the dissociation constants or the pka for example.

Oops, I appear to have got all excited and mildly chemical again. Apologies.

Louis

You mean second period, correct? That is, home of oxygen, nitrogen, and flourine, the chief electronegative culprits in hydrogen bonding? I'm not nitpicking, I just want to make sure I understand. My college physics never got this far. Excuse me for being a noisy kibbitzer.

It seems to me that "hydrogen bonding" is a bit mislabelled; it's more to do with the electronegative elements than hydrogen. I read somewhere that even carbon can participate in "hydrogen bonding".

ANYHOO- Lou, hydrogen bonding is pretty critical in biochemistry. The two complementary strands on DNA are held together with hydrogen bonds. And I believe hydrogen bonding also plays a role in protein folding. So you're going to spend some time studying it, I imagine.

As for deuterium chemistry, I am slack-jawed. The extra neutron is electrically neutral, and can interact with the electron cloud only weakly (literally), I thought, so WTF? Guess I needed to stay in school a little longer.

Louis, if I had a cap, I'd doff it. *cap-doffing motion*

BWE, let me borrow this:
</blithering>

LOL Yeah I meant first period....excluding that OTHER first period containing H and He above it. ;-)

Sorry for being confusing.

As for isotope effects, the mass of the atom in a bond has an effect. And wouldn't you know it Wikipedia has something on it. See here. It's all to do with charge/mass and the way a bond vibrates (in classical terms. The QM version is more complicated). I loves me some physical organic chem.

This is very important in biology BTW. Getting a large amount of deuterium in you can seriously affect certain rate critical enzyme catalysed reactions. This is what is technically known as a "bad thing" in clinical terms!

Louis

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Louis



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(Permalink) Posted: Sep. 12 2008,03:10   

Quote (Henry J @ Sep. 12 2008,05:12)
Quote
The extra neutron is electrically neutral, and can interact with the electron cloud only weakly (literally),


Is it that it interacts weakly with the electrons, or simply that it doubles the inertia of the atom it's in, making it more resistant to getting shoved around by outside forces? (Also heavier gravitationally, of course.)

Henry

The second one.

Louis

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BWE



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(Permalink) Posted: Sep. 12 2008,03:20   

Also, if this turns out to be repeatable:
Quote
Rübhausen says the difference in bond lengths could help explain some surprising results he and his collaborators reported last year. His team was comparing RNA made with ordinary organic molecules to RNA made of those molecules’ mirror images. Their goal was to shed light on why life always uses one type of molecule rather than the other.

Chemically, the molecules and their mirror images should be identical. But the researchers found small differences in the energy it takes to excite electrons in the two types of RNA — but only when the RNA molecules were suspended in ordinary water. When the researchers repeated the experiment in heavy water, the differences disappeared.


It will quite possibly be very important.

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Louis



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(Permalink) Posted: Sep. 12 2008,04:40   

Quote (BWE @ Sep. 12 2008,09:20)
Also, if this turns out to be repeatable:
Quote
Rübhausen says the difference in bond lengths could help explain some surprising results he and his collaborators reported last year. His team was comparing RNA made with ordinary organic molecules to RNA made of those molecules’ mirror images. Their goal was to shed light on why life always uses one type of molecule rather than the other.

Chemically, the molecules and their mirror images should be identical. But the researchers found small differences in the energy it takes to excite electrons in the two types of RNA — but only when the RNA molecules were suspended in ordinary water. When the researchers repeated the experiment in heavy water, the differences disappeared.


It will quite possibly be very important.

I'd be careful with this. RNA is big, I'd have to check the original data out to be comfortable with what is being claimed. Is that from the above linked stuff, or do you have a reference for it? I'm dead interested so lemme have a look!

When you have large molecules with large numbers of asymmetric centres (and planes and axes and tertiary structure etc) it is very, very, VERY hard to confirm that you have each asymmetric element perfectly opposed in your enantiomeric partner molecules. Sure, optical rotation, circular dichroism and complex NMR experiments etc can give you a huge amount of information about molecular symmetry. It's even possible they've synthesised short RNA pieces (or even large ones) from different chiral pools of molecules and made sure that no other stereoisomers crept in (practically impossible to do 100%, but not too bad at 99.9%!) and got X-ray structures. Even then remember that they are dealing with billions of billions of molecules in each sample, racemisation of asymmetric centres is a spontaneous process.

It could be some solvation effect with heavy water, it could even be due to exchange processes at labile hydrogens.

ARGH! I'm going to have to go and look this up now aren't I? Thanks BWE, like I need MORE excuses to hunt through the lit for entertaining science. ;-)

Louis

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BWE



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(Permalink) Posted: Sep. 12 2008,04:53   

It's from the link above. I wanted to see if anyone follows my links. :)

And yeah... I can't imagine the lab procedure.

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BWE



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(Permalink) Posted: Sep. 12 2008,04:57   

http://rnajournal.cshlp.org/cgi/reprint/13/11/1877.pdf

Here ya go.

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Lou FCD



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(Permalink) Posted: Sep. 12 2008,05:38   

Quick note before school this morning:

Yep, Doc is spending a lot of time really emphasizing the importance of Hydrogen bonding in biology.

I skimmed the heavy water discussion, but I'll try to squeeze in some time this afternoon to check it out. Thanks for that, fellas.

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BWE



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(Permalink) Posted: Sep. 12 2008,05:45   

Sorry to hijack your thread but it's important you get the facts before you go off to face a professor who will likely tell you that God doesn't wear panties.

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dogdidit



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(Permalink) Posted: Sep. 12 2008,06:54   

Quote (Louis @ Sep. 12 2008,03:10)
 
Quote (Henry J @ Sep. 12 2008,05:12)
   
Quote
The extra neutron is electrically neutral, and can interact with the electron cloud only weakly (literally),


Is it that it interacts weakly with the electrons, or simply that it doubles the inertia of the atom it's in, making it more resistant to getting shoved around by outside forces? (Also heavier gravitationally, of course.)

Henry

The second one.

Louis

Ah, hadn't considered momentum. I heard hoofbeats and thought of zebras. Great discussion, Louis and BWE! Though it's more science than I can handle right now (7:30 am and in a seriously un-caffeinated state). I'll flatter myself by pretending I'll read up and understand it later.

BTW Henry J is right, we shouldn't be ignoring gravity; why, it's the strongest force in the universe doncha know!  :p

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Albatrossity2



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(Permalink) Posted: Sep. 12 2008,07:13   

Besides the discrete effects on individual reactions, deuterium (in water) has interesting effects on whole organisms. One of the more well-studied effects is the ability of heavy water to slow down circadian rhythms, which are fairly resistant to manipulation by lots of other chemical and physical agents. Here's a classic paper in that area.

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BWE



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(Permalink) Posted: Sep. 12 2008,07:18   

I'm going to start a new thread for this. Can a moderator move the other posts in heavy water? I feel like it's stealing some of Lou's spotlight.  ???

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Lou FCD



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(Permalink) Posted: Sep. 12 2008,11:48   

Quote (BWE @ Sep. 12 2008,08:18)
I'm going to start a new thread for this. Can a moderator move the other posts in heavy water? I feel like it's stealing some of Lou's spotlight.  ???

It's fine, BWE. Besides, I only have a one way button for the Wall, so it's something Wesley might have to do if it's important to be over there. Otherwise, you could just post a link back to here for the beginning of the discussion.

*****

I got my first English essay back today.

See it here, at Crowded Head: My Country Bleeds for Thee

I dun got a A.

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(Permalink) Posted: Sep. 12 2008,12:12   

Quote (dogdidit @ Sep. 12 2008,05:54)
BTW Henry J is right, we shouldn't be ignoring gravity; why, it's the strongest force in the universe doncha know!  :p

Yeah, ignoring gravity can sometimes have sidewalk effects.

  
Tracy P. Hamilton



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(Permalink) Posted: Sep. 12 2008,12:45   

Quote (BWE @ Sep. 12 2008,03:20)
Also, if this turns out to be repeatable:
Quote
Rübhausen says the difference in bond lengths could help explain some surprising results he and his collaborators reported last year. His team was comparing RNA made with ordinary organic molecules to RNA made of those molecules’ mirror images. Their goal was to shed light on why life always uses one type of molecule rather than the other.

Chemically, the molecules and their mirror images should be identical. But the researchers found small differences in the energy it takes to excite electrons in the two types of RNA — but only when the RNA molecules were suspended in ordinary water. When the researchers repeated the experiment in heavy water, the differences disappeared.


It will quite possibly be very important.

Betcha it won't be replicated.  Pun intended.

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Tracy P. Hamilton



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(Permalink) Posted: Sep. 12 2008,13:02   

Quote (dogdidit @ Sep. 12 2008,06:54)
Quote (Louis @ Sep. 12 2008,03:10)
   
Quote (Henry J @ Sep. 12 2008,05:12)
   
Quote
The extra neutron is electrically neutral, and can interact with the electron cloud only weakly (literally),


Is it that it interacts weakly with the electrons, or simply that it doubles the inertia of the atom it's in, making it more resistant to getting shoved around by outside forces? (Also heavier gravitationally, of course.)

Henry

The second one.

Louis

Ah, hadn't considered momentum. I heard hoofbeats and thought of zebras. Great discussion, Louis and BWE! Though it's more science than I can handle right now (7:30 am and in a seriously un-caffeinated state). I'll flatter myself by pretending I'll read up and understand it later.

BTW Henry J is right, we shouldn't be ignoring gravity; why, it's the strongest force in the universe doncha know!  :p

The following may take a bit of work, but it will be worth it for those who really want to understand the PRIMARY kinetic isotope effect.  Here is a wikipedia article with a picture that may illustrate why H and D have different bond properties.  http://en.wikipedia.org/wiki/Morse_potential

See those green horizontal lines?  They denote harmonic vibration energy of (v+0.5) times Planck's constant times frequency.  
Frequency is sqrt(k/mass), where k is the curvature of the parabola.  
E=1/2 k (r-re)^2, the second derivative of E with respect to r is k.  
Force is -dE/dr, or -k (r-re).  
F = -k (r-re) is Hooke's Law.

H is lighter than D, so the frequency is higher for H than D, and the green lines are higher for H than for D.  This analysis carries over to the blue curve, and blue horizontal lines, just more complicated.  However, you can't get out of the green well, which is infinite (i.e. harmonic oscillator breaks down), so in real life you have the blue curve.

The lowest energy any molecule can have is with v=0.  The v=0 level is lower for D, so the D0 is larger for D.  D0 is the bond energy.  So R-D bonds are stronger than R-H bonds.

What about bond distance?  The bond vibrates back and forth, but one can see from the blue curve that for a particular energy, the amount of stretch exceeds the amount of compression, so that the average distance is greater than re.  Since the energy level for D is lower than H, the stretching and compression are both smaller, but the stretch more so, so that re is shorter for R-D.  

R is boring organic stuff of interest only to Louis.

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BWE



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(Permalink) Posted: Sep. 12 2008,13:35   

Tracy,
I wrote down the equations from the Wiki page and tried to figure it out but I'm sadly lacking.

I'm reading "A Stubbornly Persistent Illusion: The Essential Scientific Works of Albert Einstein" right now because I told myself I'm going to understand relativity thoroughly before I die. Halfway through the general theory I figured out the equation in the special theory that explains why mass has a discrete energy value.

In QM I've figured out some of it, like I can calculate the Hamiltonian sometimes, given enough info (I understand that doesn't make sense too :) ). And I can follow the examples for Schrodinger's equations. But the second I put away my notes and books, I can't do shit with it.

And now, even though there's a new LGH powered up, and we can build computers and nanomaterials and cosmology and all that, I have a sneaky suspicion that no one really gets relativity. Or at least not most people who ought to. Is there any justification to my suspicion?

--------------
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When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

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Louis



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(Permalink) Posted: Sep. 12 2008,14:12   

Quote (Tracy P. Hamilton @ Sep. 12 2008,19:02)
[SNIP]

R is boring organic stuff of interest only to Louis.

LOL This is undoubtedly true.

That reminds me of the comedy banter I've had with those of an inorganic/physical bent.

Louis

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Tracy P. Hamilton



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(Permalink) Posted: Sep. 12 2008,15:08   

Quote (BWE @ Sep. 12 2008,13:35)
Tracy,
I wrote down the equations from the Wiki page and tried to figure it out but I'm sadly lacking.

I'm reading "A Stubbornly Persistent Illusion: The Essential Scientific Works of Albert Einstein" right now because I told myself I'm going to understand relativity thoroughly before I die. Halfway through the general theory I figured out the equation in the special theory that explains why mass has a discrete energy value.

In QM I've figured out some of it, like I can calculate the Hamiltonian sometimes, given enough info (I understand that doesn't make sense too :) ). And I can follow the examples for Schrodinger's equations. But the second I put away my notes and books, I can't do shit with it.

And now, even though there's a new LGH powered up, and we can build computers and nanomaterials and cosmology and all that, I have a sneaky suspicion that no one really gets relativity. Or at least not most people who ought to. Is there any justification to my suspicion?

Just use my equations, and the picture from wiki.  It will be much easier.

--------------
"Following what I just wrote about fitness, you’re taking refuge in what we see in the world."  PaV

"The simple equation F = MA leads to the concept of four-dimensional space." GilDodgen

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BWE



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(Permalink) Posted: Sep. 12 2008,15:18   

Have you seen my avatar? I think they might be testing the wrong thing..

Thanks. Now I'm reading the paper I linked earlier.

--------------
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

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Lou FCD



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(Permalink) Posted: Sep. 12 2008,15:33   



My notes and thoughts from Biology 111, for Friday, September 5, 2008. The entire series can be found here.

On this day, Tropical Storm Hannah was expected to hit, so the college closed at 1 PM. Although that was well after the end of our scheduled lecture, Doc (if I recall correctly) cut the class a bit short to give folks headed home a little extra time.

So in the previous lecture, we had left off discussing Cohesion and Adhesion, the first of the emergent properties of water on the table for discussion. With this lecture, we picked up with the next emergent property on the list.

2. Moderation of Temperature

Water has a relatively high specific heat, which means that water can absorb and release large amounts of heat with little change in temperature.

To discuss this topic, it helps to first have an understanding of the difference between heat and temperature.

Heat is the total amount of kinetic energy in a body.

Temperature is the average kinetic energy of the particles in a body.

To illustrate this, we discussed the comparison of a hot cup of coffee to the Arctic Ocean.

While the temperature of the cup of coffee is higher, there are many fewer molecules in that cup than there are in the Arctic Ocean. The Arctic Ocean's greater number of molecules each have lower amounts of kinetic energy (hence the lower temperature) but the sum, the aggregate, the total amount of heat is higher, simply because a lot of little bits of heat add up.



It takes much change in energy to change the temperature of water due to Hydrogen bonding and the crystalline structure of water (even as a liquid, as hydrogen bonds are formed and broken, water has a basically crystalline structure).

The Hydrogen bonds are strong enough that each of them takes a certain amount of energy to break, so much of the heat coming onto the surface of the ocean from the sun is used in breaking those bonds, leaving less energy to impart to the water molecules directly. This energy absorption helps to keep the sun from baking the planet.

Reformation of the hydrogen bonds in the cold winter releases that heat back into the atmosphere, keeping the planet from freezing over.

This ties into the next part of temperature moderation.

Water has a relatively high heat of vaporization

Heat of vaporization is the amount of energy needed to go from a liquid to a gas. This is also due to Hydrogen bonding.

Water's State of Matter


Solid ---------> Liquid ---------> Gas
0°      HEAT                HEAT      100°


Evaporation lowers the average temperature of the water left behind.

Evaporative cooling ---> We use this technique as sweating. Plants use this in the leaves, which then draws water up through the plant from the ground (remember the Hydrogen bonding thing from the last lecture?).

Rain forests are so rainy because of the vast amount of evaporative cooling, which saturates the local atmosphere. All that water vapor then cools, condenses, and falls as rain because it's now heavier than the surrounding air.

The ocean temperature close to our shore varies between the low single digits in the winter to the upper twenties in the summer, so that's a thirty degree temperature difference over the course of the year.

In the desert, the temperature ranges from around zero at night to 50° or more during the day.

Water is a great temperature regulator.

We closed out the lecture with a short discussion of the gulf stream, and how that moderates the climate of the British Islands despite their high latitude. We compared Ireland specifically to the city of Moscow, Russia, which is at about the same latitude.

The one is nicknamed the Emerald Isle because it's lush and green. The other, not so much.

   
Quote
From whence came the art:

The first image is of our textbook, Biology, Eighth Edition, by Campbell &amp; Reese et al.

Other images by me and are licensed under the Creative Commons Attribution- NonCommercial- Share Alike 3.0 License.


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stevestory



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(Permalink) Posted: Sep. 12 2008,17:50   

I think this might be the most useful thread ever created at AtBC.

   
simmi



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(Permalink) Posted: Sep. 12 2008,18:51   

Quote (stevestory @ Sep. 12 2008,18:50)
I think this might be the most useful thread ever created at AtBC.

I agree wholeheartedly.  And to be honest, Lou, I totally didn't know that you didn't do any college biology.  Your posts fisking teh tard were so good I assumed you had advanced training in bio.  Please keep the updates coming! (without sacrificing your work, of course)

This thread also inspired me to join in with my own stories of new beginnings (I'm just starting my PhD), but then I remembered I have my own blog which I've been neglecting.  Off to write some posts...

  
Lou FCD



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(Permalink) Posted: Sep. 12 2008,19:22   

Quote (stevestory @ Sep. 12 2008,18:50)
I think this might be the most useful thread ever created at AtBC.

Thank you Steve. That's some pretty high praise.

 
Quote (simmi @ Sep. 12 2008,19:51)
 
Quote (stevestory @ Sep. 12 2008,18:50)
I think this might be the most useful thread ever created at AtBC.

I agree wholeheartedly.  And to be honest, Lou, I totally didn't know that you didn't do any college biology.  Your posts fisking teh tard were so good I assumed you had advanced training in bio.  Please keep the updates coming! (without sacrificing your work, of course)


:)

Actually, my last biology class was a 9th or 10th grade Microbiology class that bored me to tears. The teacher was dry as a bone as I recall, and I think I squeaked by with a C. That would have been 1983ish?

Whipping up on TARD sometimes takes little more than clear thinking. It doesn't take a biologist to know that "Evilution sucks, therefore the Bible is true" isn't the greatest of arguments. Most of the time, in fact, one need only observe the TARDic tendency towards self-inflicted gunshot wounds to the feet to get a good laugh.

 
Quote (simmi @ Sep. 12 2008,19:51)
This thread also inspired me to join in with my own stories of new beginnings (I'm just starting my PhD), but then I remembered I have my own blog which I've been neglecting.  Off to write some posts...


Some linkage, please? I mean, if my little thread here is going to be someone's inspiration, I should at least get to see the fruits of my labor.

:)

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stevestory



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(Permalink) Posted: Sep. 12 2008,19:32   

Quote (Lou FCD @ Sep. 12 2008,20:22)
Quote (stevestory @ Sep. 12 2008,18:50)
I think this might be the most useful thread ever created at AtBC.

Thank you Steve. That's some pretty high praise.

All the praise belongs to you. While lots of us have scientific knowledge, you're the only one bringing it here on a regular basis so that others might learn.

   
Henry J



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(Permalink) Posted: Sep. 12 2008,21:02   

Quote
It doesn't take a biologist to know that "Evilution sucks, therefore the Bible is true" isn't the greatest of arguments.


Yeah, if the argument consists of some equivalent to "biologists have as a group continuously overlooked such and such basic thing that would totally change their minds if they'd only pay attention to their critics", well, that hardly takes expertise to recognize the illogic.

Henry

  
Lou FCD



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(Permalink) Posted: Sep. 17 2008,09:30   

First Biology exam was this morning at 8. I think I did pretty well, and none of the questions seemed very difficult, frankly.

So, either I know the material very well and I did well, or I'm talking out my ass and I blew out badly.

Tomorrow I should be able to get back to posting up notes, and hopefully I can get close to caught up on them by the weekend.

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Henry J



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(Permalink) Posted: Sep. 17 2008,13:47   

Quote (Lou FCD @ Sep. 17 2008,08:30)
or I'm talking out my ass and I blew out badly.

That could depend on what you had for lunch... :p

  
Stephen Elliott



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(Permalink) Posted: Sep. 17 2008,14:49   

Quote (Lou FCD @ Sep. 17 2008,09:30)
First Biology exam was this morning at 8. I think I did pretty well, and none of the questions seemed very difficult, frankly.

So, either I know the material very well and I did well, or I'm talking out my ass and I blew out badly.

Tomorrow I should be able to get back to posting up notes, and hopefully I can get close to caught up on them by the weekend.

Why don't you use this site to help on all your courses? Rather than rewrite your notes to paper do it to here.

You will still get the initial benefit of rewriting and also the secondary benefit of people here who are experts on the subject correcting you sometimes.

It is not asking people to do your work for you if you respond with your own thinking. It would just be even more interesting discussions. Provided that is that you made a new thread for each subject.

It would be like having many instructors/profs and make interesting reading. IMO. Pretty sure I would also learn a few things. Just a thought.

  
Henry J



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(Permalink) Posted: Sep. 17 2008,22:32   

Is the course still on chemistry, or is it getting into actual biology?

Henry

  
Lou FCD



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(Permalink) Posted: Sep. 18 2008,05:50   

Quote (Stephen Elliott @ Sep. 17 2008,15:49)
Why don't you use this site to help on all your courses? Rather than rewrite your notes to paper do it to here.

You will still get the initial benefit of rewriting and also the secondary benefit of people here who are experts on the subject correcting you sometimes.

It is not asking people to do your work for you if you respond with your own thinking. It would just be even more interesting discussions. Provided that is that you made a new thread for each subject.

It would be like having many instructors/profs and make interesting reading. IMO. Pretty sure I would also learn a few things. Just a thought.

Stephen, while in principle that is a great thought, I'm finding I barely have time to copy my Biology notes. As it stands, I'm somewhere around four lectures and a pair of labs behind now. (Though the labs will require only a little time to write up.)

Yesterday I had the exam, then a second essay to turn in for English, and a ton of precalc homework and labs to finish up, and a quiz in precalc last night.

The issue really with Biology is that for the notes to make sense (at least to me), I need to draw pictures, and that takes a little time.

For Spanish, there's the special characters, though I've switched to the international keyboard and that would speed things up.

With precalc, there's fractions and radicals and graphs, etc., that just don't translate well to the web without a lot of time consumption.

The English stuff would be easy though, as I'm writing on the computer anyway and the lectures are pretty much note free. The instructor usually takes a point about the upcoming essay and meanders through analogy after analogy. I posted my first essay on my blog after I got it back, and will probably continue to do that as they are returned to me.

 
Quote (Henry J @ Sep. 17 2008,23:32)
Is the course still on chemistry, or is it getting into actual biology?

Henry


Henry, we're currently hitting the chemical structures of functional groups, so we're sort of making the transition now.

Monday's lecture for instance, was on amino acids, peptide bonds, polypeptides, proteins, and we closed out with a first look at nucleic acids.

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(Permalink) Posted: Sep. 19 2008,17:30   



My notes and thoughts from Biology 111, for Monday, September 8, 2008. The entire series can be found here.

We left off on Friday discussing the second important emergent property of water, the property of temperature moderation.

On Friday, we began with the third emergent property of water that is critical to biology.

3. Solid form of water is less dense than the liquid form

In other words, ice floats. First we took a quick look at what generally defines each state of matter at room temperatures (we didn't delve into plasmas etc)
States of Matter
Solid
Constant Shape, Constant Volume
Liquid
Constant Volume, Changing Shape
Gas
Changing Volume, Changing Shape

So we can say that generally speaking, the state of matter is dependent on its density and the fixity of its bonding. Ordinarily, the solid state of matter is more dense than the liquid state, and this unusual property of water has a very important consequence for life.



Water is its most dense at 4°.

Because ice floats, the top of a body of water will freeze first in the winter. Because of the moderation of temperature, water (in this case, ice) is a good insulator from heat. What this means is that the floating ice on a body of water hinders the escape of heat from below the ice, and the ice then acts as a thermal blanket, preventing the underlying water from freezing solid. This gives life below the ice a place to continue living, even in the coldest of arctic winters.

4. Solvent Ability

Before we can discuss water's ability to act as a solvent, we need to define some terms.

Solution - A homogeneous mixture of 2 or more different substances

Solvent---> The dissolving agent.

Solute---> The substance that dissolves

So when you salt a pot of water on the stove, the water is the solvent, the salt the solute, and the mixture is a solution.

Water has the ability  to dissolve more different substances and in greater quantity than any other solvent. (It's not universal however, or it would dissolve the container that holds it, etc.)

Salinity

Solution    Seawater         Blood
H2O         96.5%        99.1%
Salt          3.5%         0.9%

The difference in salinity between the body and the seawater is why salt water tastes so salty to us, despite the fact that the salt concentration is only 3.5%.



Salt is an ionic compound, and water dissolves it because of the charges of each of the ions involved. Water's polarity is attracted by its slightly charged poles to the charges of the ions. Because the Sodium is positively charged (a cation), the slight negativity at the Oxygen end of a water molecule is attracted to the Sodium. Conversely, the Chlorine ion is negatively charged (an anion), so the slightly positively charged hydrogen end of the water molecule is attracted to the Chlorine. The water sort of forces the salt ions apart through hydrogen bonding, and so the Sodium is separated from the Chlorine.

The solubility of sugars (for instance) works a little differently, and we cover that a bit later on.

Polarity and electrical charge are the keys to water solubility, and water's polarity and hydrogen bonding are what make it such and excellent solvent.


Oils on the other hand, are non polar molecules. That's why oil will separate from water.

Oil doesn't repel water so much as it just doesn't dissolve in water.

We say that Oils are hydrophobic.

Hydrophilic --->Attractive to water (NOT interchangeable with water soluble, though! ---> Cotton is hydrophilic but not water soluble. Cotton and starch are entirely made of cellulose (a sugar). It's components are water soluble. So we can say that being non-water-soluble is an emergent property of cellulose.

Hydrophobic ---> Not attractive to water.

At this point we moved on to pH.



pH ---> A measure of the concentration of Hydrogen ions in a solution.

H+ is a Hydrogen atom that has lost an e-, and what remains is just a p+

We denote H+ concentration thus: [H+] (where the brackets mean "concentration of" whatever is between them, in this case Hydrogen ions).

Some notes about the scale:

The pH scale is a negative logarithmic scale, meaning that each increase of 1 unit on the scale is a decrease of H+ concentration by a factor of 10. So a solution with a pH of 8 has ten times less [H+] relative to [OH-] than distilled water. A solution with a pH of 9 has ten times less [H+] relative to [OH-] than the previous solution, and 100 times less than distilled water.

A small change in the pH number can mean a big change in the balance of [H+] to [OH-]. At 7, [H+] = [OH-], and the solution is said to be neutral. I find it helpful to think of the pH scale as a balance type of scale. When a solution is neutral, it balances evenly between the [H+] and the [OH-].

Thinking about it, this makes sense, as ideally all the H+ and OH- in water should be joined together as H2O.

Also note that the body needs to be regulated relatively closely. Normally, the pH of human blood is between 7.35 and 7.45. A few tenths of a unit of pH one way or the other is fatal. Too many H+ or OH- floating around would make for a very bad day.

One last note: [H+] in distilled water is 10 to the -7 mols/L. This is where the 7 comes from in the pH of water, and the scale is based on that.

1 mole = 6.02 x 10 to the 23. This number is known as Avogadro's number, and is a handy little number to keep in your back pocket.

The lecture ended there, and we picked it up on Wednesday.
     
Quote

From whence came the art:

The first image is of our textbook, Biology, Eighth Edition, by Campbell & Reese et al.

Other images by me and are licensed under the Creative Commons Attribution- NonCommercial- Share Alike 3.0 License.


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Lou FCD



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(Permalink) Posted: Sep. 19 2008,19:52   

Got the exam results back today, and was a bit disappointed. Made some dumb mistakes and wound up with an 88. The highest score in all the sections was a 91, so I know I shouldn't feel too damned bad, but damn it.

Most of the 8 that I missed, I looked at the answer I gave and thought, "What the hell was I thinking????"

One of them was "Which of these is the molecular formula for Maltose?" I forgot to drop the two Hydrogens and the Oxygen from the dehydration synthesis, and answered C12H24O12.

What's worse, the very next question was something like "How does Maltose form from Glucose?", and I answered the question correctly.

Damnit. Some days I want to beat my head on a wall and hope some sense gets osmosified in there.

I did help out in the Science Garden later this morning, though. That was some pleasant down time.

Edited by Lou FCD on Sep. 19 2008,20:53

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(Permalink) Posted: Sep. 19 2008,20:25   



My notes and thoughts from Biology 111 Lab, for Monday, September 8, 2008. The entire series can be found here.

In this lab we mostly talked about metric system measurements, then went about taking measurements of various things. Honestly, it was pretty mundane stuff for the most part, and I didn't enjoy this lab nearly as much as the first two, though I understand the necessity of it.

We used rulers, calipers, and a scale to take measurements of wooden blocks, dowels, and plastic balls, then calculated their volume and surface area.

We measured the room temperature and the temperature of cold tap water and ice water, and water on a boiling plate, as well as skin temperature.

Then, in the most interesting part of the lab, we measured each other's tibias, and then each other's heights (as well as a real dead guy's tibia). We recorded the tibia length and height of everyone in the lab, and for homework we created scatter plots and trend lines with those numbers.

It was pretty straightforward stuff, really, and well... kinda boring except for the dead guy's bone that Squicky Britches refused to touch. That was a source of mild humor.
Quote
From whence came the art:

The first image is of our textbook, Biology, Eighth Edition, by Campbell &amp; Reese et al.

Other images by me and are licensed under the Creative Commons Attribution- NonCommercial- Share Alike 3.0 License.


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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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(Permalink) Posted: Sep. 19 2008,21:16   

And here I thought a mole was a small burrowing mammal... :)

Henry

  
Texas Teach



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(Permalink) Posted: Sep. 19 2008,21:35   

Quote (Henry J @ Sep. 19 2008,21:16)
And here I thought a mole was a small burrowing mammal... :)

Henry

I had a professor for freshmen chem that had actually gotten someone to make him a pair of plush moles to use in class.  They had Velcro in the middle that held the front and back ends together.  After using them for quite some while to make points about moles and half moles, he dropped the back ends of both into a beaker and asked the class what he was holding.

The answer:  500 mL of mole-asses.

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"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

  
Lou FCD



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(Permalink) Posted: Sep. 19 2008,22:01   

Quote (Doc @ today in class)
Hydrogen ion runs into the police station. "Help, help!"

Policeman: "What's wrong?"

Hydrogen ion: "Someone stole my electron!"

Policeman: "Are you sure?"

Hydrogen ion: "Yeah, I'm positive."


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(Permalink) Posted: Sep. 19 2008,22:06   

man, that's one of my 3 horrible physics jokes. The only good one is

Cop: "You know how fast you were going?"
Driver: "Not a clue! But I know exactly where I am!"

   
Lou FCD



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(Permalink) Posted: Sep. 20 2008,13:18   



My notes and thoughts from Biology 111, for Wednesday, September 10, 2008. The entire series can be found here.

In the last lecture, we had left off with a discussion of pH and [H+]. We started this lecture by finishing up with pH.

Remember that pH is a negative log scale, so as [H+] goes up, pH goes down.

We came to definitions right off the bat.

Acid --> Any substance that increases [H+] of a solution. This is accomplished by donation of H+ ions (p+, since a Hydrogen without an e- is just a p+)

HCl ---> H+ + Cl-

Hydrochloric acid will break down in solution into its constituent parts, thus directly increasing the [H+] and lowering the pH of the solution.

Base --> Any substance that decreases [H+] of a solution. This can be accomplished in one of two ways:

Donation of OH- to combine with H+ already in the solution

NaOH ---> Na+ + OH- ---> OH- + H+ ---> H2O

Oven or drain cleaner, Sodium Hydroxide, will break down in solution into its constituent parts, one of which is a hydroxide ion. The hydroxide ion combines with H+ in the solution to make water, thus lowering [H+] and raising the pH of the solution.

Sucking up of H+

NH3 + H+ ---> NH4+

Ammonia, NH3, will pick up an H+ and become NH4+, thus directly decreasing [H+], and raising the pH of the solution.

Then we moved on to Chapter 4: Carbon and the Molecular Diversity of Life



Organic Compounds ---> Carbon based compounds

Hydrocarbons ---> Hydrogen and Carbon, joined together in non polar covalent bonds. There is a lot of potential energy in these bonds due to the maximum distance from the nucleus of the shared valence e- pairs. These bonds also make for hydrophobic molecules, due to the non-polarity.



Hydrocarbons are built on a skeleton of these Hydrogen and Carbon bonds, with other stuff added on. Remember that Carbon has four unpaired valence electrons, so it can form four covalent bonds. Hydrogen has one unpaired valence electron, so it can form one covalent bond.

This makes for a very nice set-up between Carbon and Hydrogen, where the carbon atom can form bonds with four Hydrogens, or three Hydrogens and another carbon, or two Hydrogens and two other Carbon atoms. Using this technique, nature can and does form chains of Carbon atoms surrounded by Hydrogens. These are called hydrocarbons, and form a skeleton upon which nature can build almost infinitely complex molecules. We can even think of the surrounding Hydrogens as plug covers for interchangeable parts.



Hydrocarbons form non-polar covalent bonds, and since the shared e- are equally far from each of the nuclei of the two atoms, that gives the bond its high potential energy. That's why Hydrocarbons are so attractive as fuels. There's lots of bang for the buck.

Of course, the big problem is that it takes about 300,000,000 years to make Hydrocarbons, due to the fact that they're made from decayed organic material (i.e. dead plants and animals). As a species, we're using the planet's available Hydrocarbons much faster than they are being made. It doesn't take a genius to work out the math here.

There are four main classes of organic compounds in living things that Bio 111 is going to cover.

Carbohydrates ---> C, H, O
Lipids ---> C, H, O (sometimes N & P)

Proteins ---> C, H, O, N, S

Nucleic Acids ---> C, H, O, N, P

Functional Groups

1. Hydroxyl Group

A Hydroxyl Group, is just an OH- that replaces a Hydrogen atom as in this Hydrocarbon.



Ethane is a Hydrocarbon molecule, and by exchanging one Hydrogen for an OH-, we change it to ethanol. Ethanol is better known as "grain alcohol" or "ethyl alcohol". Note that the ending "ol" always denotes an alchol. Note too that we keep the Hydrogen in the OH- portion of the molecule separate from the other Hydrogens in the molecular formula, to point out that it's not just another Hydrogen hanging off the main skeleton, but is associated with the Oxygen.

2. Carboxyl Group



A Carboxyl Group is made up of a Carbon, two Oxygens, and a Hydrogen, in the form COOH.

When latching onto a Hydrocarbon skeleton, it will ditch the H+, leaving it with a Carbon single bonded to a negatively charged Oxygen, and double bonded to another Oxygen. Because it donates that H+, it is an acid (lowers pH of a solution), and the negative charge makes it very attractive to water (hydrophilic).

3. Amino Group



An amino group is NH2, a Nitrogen and two Hydrogens. It will pick up an H+ from a solution, making it a base, and also hydrophilic.

4. Phospate Group



A Phosphate Group is a Phosphorus bonded with two negatively charged Oxygen atoms, one regular Oxygen atom, and double bonded with one Oxygen atom. It's molecular formula is PO42- or sometimes OPO32-, to separate the double bonded Oxygen.

Here is where the lecture ended. Although I asked in a later lecture about the odd bondings here that seem to break the rules that we earlier set forth, Doc basically said, "It's complicated, and you don't need to know that for this class, though you'll learn about it in a Chemistry class if you take one." Ok, fair enough.

Quote
From whence came the art:

The first image is of our textbook, Biology, Eighth Edition, by Campbell &amp; Reese et al.

Other images by me and are licensed under the Creative Commons Attribution- NonCommercial- Share Alike 3.0 License.


Edited by Lou FCD on Sep. 21 2008,17:58

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Texas Teach



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(Permalink) Posted: Sep. 20 2008,14:08   

Quote (Lou FCD @ Sep. 20 2008,13:18)
Here is where the lecture ended. Although I asked in a later lecture about the odd bondings here that seem to break the rules that we earlier set forth, Doc basically said, "It's complicated, and you don't need to know that for this class, though you'll learn about it in a Chemistry class if you take one." Ok, fair enough.

This is close to what I tell the introductory students in my physical science class.  For the more clever ones, I also point out that Lewis' dot diagrams are a lovely model, especially for electron bookkeeping, but the real world doesn't care whether our little models work out neatly.  (The patch on his model is to have the one extra bond spread around each of the positions, which lowers the energy.)

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(Permalink) Posted: Sep. 20 2008,18:10   

Quote (Texas Teach @ Sep. 20 2008,15:08)
Quote (Lou FCD @ Sep. 20 2008,13:18)
Here is where the lecture ended. Although I asked in a later lecture about the odd bondings here that seem to break the rules that we earlier set forth, Doc basically said, "It's complicated, and you don't need to know that for this class, though you'll learn about it in a Chemistry class if you take one." Ok, fair enough.

This is close to what I tell the introductory students in my physical science class.  For the more clever ones, I also point out that Lewis' dot diagrams are a lovely model, especially for electron bookkeeping, but the real world doesn't care whether our little models work out neatly.  (The patch on his model is to have the one extra bond spread around each of the positions, which lowers the energy.)

The Intelligent Designer is Microsoft?

Geez, that explains a lot!

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(Permalink) Posted: Sep. 21 2008,00:21   



My notes and thoughts from Biology 111, for Monday, September 8, 2008. The entire series can be found here.


There are four main classes of organic compounds in living things that Bio 111 is going to cover.

Carbohydrates* —> C, H, O
Lipids —> C, H, O (sometimes N & P)
Proteins* —> C, H, O, N, S
Nucleic Acids* —> C, H, O, N, P


* Carbohydrates, Proteins, and Nucleic Acids are Macromolecules, meaning "really honkin' big".

1. Carbohydrates - Sugars - all "ose" endings mean "sugar".

"Carbon Water"

They have a C:H:O ratio of 1:2:1, so the basic carbohydrate formula would be CH2O

a) monosaccharides --> "one sugar" - these are the simple sugars, and contain between 3 - 7 C atoms in them.

A Few Simple Sugars

C Atoms     Molecular Formula     Group Name
3               C3H6O3                       triose
5               C5H10O5                     pentose
6               C6H12O6                     hexose



We're going to stick with the hexose group for a bit, because it's pretty common, and useful to illustrate several things in biology.



Because of the interchangeability of parts, a compound with the formula C6H12O6 (for instance) can actually wind up being arranged in more than one way. When compounds are arranged differently but share a molecular formula, they are called isomers ("same part"). Glucose, Fructose, and Galactose are three simple sugars, all hexose sugars, but have their atoms arranged differently. They are isomers that organisms use for energy.

Each of these hexose isomers have 7 C-H bonds (they are hydrocarbons, and remember that C-H bonds are nonpolar covalent bonds, having a great deal of potential energy)

Monosaccharides often rearrange themselves a little bit from the structural diagrams to the right, and fold in on themselves to make a hexagonal shape. There are illustrations of the process in the textbook.

b) Disaccharides --> "two sugars" - these are simply two sugars linked by a covalent bond.

Since all the bonding places are taken up by atoms in the monosaccarides, a place needs to be make for the link between the two simple sugars. This is accomplished by a dehydration synthesis, also known as a condensation reaction.

The OH- at a place on one sugar will be attracted to the H+ on another sugar. They will each leave their parent sugar molecule and combine to form a water molecule, leaving an unpaired electron in the valence shell of one Carbon in each of the sugar molecules.



This is where the hook-up occurs.

When a galactose and a glucose combine, the resulting disaccharide is called lactose and is found in milk.

When two glucose molecules combine, the resulting disaccharide is called maltose, and is used in brewing.

We can't use disaccharides for energy, so our bodies add water back into the disaccharide, in a reverse process known as hydrolysis. This breaks the disaccharide back into two monosaccharides, something our body can use for energy.

c) Polysaccharides --> "many sugars" - many monosaccharides linked by covalent bonds. These are macromolecules, and can be hundreds to thousands of monosaccharides linked together.

Polymer --> "many parts" --> large molecule made of many small and similar molecules.

Monomer --> "one part" --> one of the small molecules.

Some polymers of glucose are used by organisms to store energy, some to do other things, like build structure.

Plants use starch for energy storage.

Animals use glycogen for energy storage.

Plants use cellulose for structure.

An emergent property of these polymers is that they are not water soluble. This is the means by which they store the energy inside cells (otherwise they would just dissolve inside the cell which is mostly water).

They are stuck inside the cell until needed, much like a school bus brought in pieces into a classroom and then assembled. In order for the organism to use the energy stored therein, the polymer must first be broken down by hydrolysis.

In order to digest cellulose, water and cellulase are needed. Animals don't make cellulase in their bodies, and so can't digest cellulose. Hearkening back to the termite lab, remember that termites subsist on a diet of wood. Wood is made of cellulose. How do they do that? They depend on little microorganisms to digest the cellulose for them.

Breakdown of any -ose (sugar) is facilitated by a corresponding -ase. Breakdown of lactose needs lactase, etc.

2. Lipids --> Of our four classes with which we began this lecture, lipids are the only ones that are not macromolecules.

It's a diverse class that includes fats and oils, steroids, and phospholipids. Fats and oils are long chains, while steroids are ring structured.

This class is made of mostly C and H, with just a little O. Fats and oils are nonpolar molecules, and so are not water soluble.

Fats and oils = triglyceride --> 1 glycol + 3 fatty acids. The difference between fats and oils is density, and I'll have lovely little drawings of them for you in the next lecture.

Edited to correct the ate/ase mistake pointed out by keiths
           
Quote

From whence came the art:

The first image is of our textbook, Biology, Eighth Edition, by Campbell & Reese et al.

Other images by me and are licensed under the Creative Commons Attribution- NonCommercial- Share Alike 3.0 License.


Edited by Lou FCD on Sep. 21 2008,17:48

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(Permalink) Posted: Sep. 21 2008,01:45   

Quote (Lou FCD @ Sep. 20 2008,22:21)
In order to digest cellulose, water and cellulate are needed. Animals don't make cellulate in their bodies, and so can't digest cellulose.

Lou, I think you mean "cellulase" rather than "cellulate".
Quote
Breakdown of any -ose (sugar) is facilitated by a corresponding -ate. Breakdown of lactose needs lactate, etc.

Ditto here.  You really want to say
Quote
Breakdown of any -ose (sugar) is facilitated by a corresponding -ase. Breakdown of lactose needs lactase, etc.

The distinction is important.  A lactate is completely different from a lactase, for example.

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keiths



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(Permalink) Posted: Sep. 21 2008,01:49   

Quote (Lou FCD @ Sep. 20 2008,22:21)

This is where the hook-up occurs.


Dig the dehydration sex.  But why does she get to have an orgasm while he doesn't?

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(Permalink) Posted: Sep. 21 2008,06:12   

Quote (keiths @ Sep. 21 2008,02:45)
Quote (Lou FCD @ Sep. 20 2008,22:21)
In order to digest cellulose, water and cellulate are needed. Animals don't make cellulate in their bodies, and so can't digest cellulose.

Lou, I think you mean "cellulase" rather than "cellulate".
 
Quote
Breakdown of any -ose (sugar) is facilitated by a corresponding -ate. Breakdown of lactose needs lactate, etc.

Ditto here.  You really want to say
 
Quote
Breakdown of any -ose (sugar) is facilitated by a corresponding -ase. Breakdown of lactose needs lactase, etc.

The distinction is important.  A lactate is completely different from a lactase, for example.

You're right. It was late.

Thanks for the correction.

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(Permalink) Posted: Sep. 21 2008,06:23   

Quote (keiths @ Sep. 21 2008,02:49)
Dig the dehydration sex.  But why does she get to have an orgasm while he doesn't?

Because I ran out of gas and the artistic editing ended prematurely.

XVIVO better look out. There's a new animator in town.

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(Permalink) Posted: Sep. 21 2008,08:09   

Quote (Lou FCD @ Sep. 21 2008,06:23)
XVIVO better look out. There's a new animator in town.

Better tell ERV to keep an eye on it for you, or it might appear in one of the Dr Dr's talks.  Something about how materialist biochemistry leads to corruption of our youth.

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Lou FCD



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(Permalink) Posted: Sep. 21 2008,11:39   

Quote (Texas Teach @ Sep. 21 2008,09:09)
Quote (Lou FCD @ Sep. 21 2008,06:23)
XVIVO better look out. There's a new animator in town.

Better tell ERV to keep an eye on it for you, or it might appear in one of the Dr Dr's talks.  Something about how materialist biochemistry leads to corruption of our youth.

Well, it is licensed under the CC, so as long as they abode by the terms of that...

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(Permalink) Posted: Sep. 22 2008,08:05   

I'm so glad you are continuing these...except that this is the area of biology that I was always weakest. :)  So it's probably actually a good thing to go over these basics again.

I admit, I'm an organism (and above) level person.  I just understand that more and it fascinates me more.  Not that the chemical, cellular, etc level isn't amazing...I just don't follow it as well.

Also, to all those adding in the discussion...thanks to you too.  The extra info and clarification is great.

  
Lou FCD



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(Permalink) Posted: Sep. 23 2008,06:36   

I'm trying to get them caught up, Spottedwind.

I noticed that on my exam, there was a significant cluster to the questions I missed, and that cluster was in the area of notes I hadn't put online yet.

Copying the notes really does seem to help.

I was disappointed: I got an 88. The highest score in all three sections was a 91, and the median score was in the 60s. One of the questions I missed was the molecular formula of maltose. What did I do wrong? I forgot to take out the water molecule from the dehydration synthesis.

Hence the graphic above that will ensure that I never ever repeat that mistake. The sugar porn has a purpose, and was not at all gratuitous.

At the moment, we're actually doing the tour of the cell, and as I sat through the lecture taking notes, I couldn't help but be reminded of The Inner Life of the Cell, and as Doc explained the different functions of different parts, I could visualize parts of the animation. I kept thinking, "Oh! so THAT'S what that thingy was that did thus and so".

The images were especially strong in my mind when we started talking about the Endoplasmic Reticulum, the Transport Vesicles, and the Golgi Apparatus. In a way, it was kind of odd to have a picture in my mind of what was going on before I could name the parts, rather than the usual way of naming things and then seeing pictures of them.

I <3 XVIVO.

Lab yesterday was kind of cool, in that it was the first time we got to use microscopes. (We have monocular compound light microscopes, fyi.) It was sort of a let-down when I was looking at my cheek cells, though. I guess I was expecting to see all the cool stuff we had been discussing in lecture yesterday morning. I saw a circle with a blob in it.

:(

WE NEED MORE POWER SCOTTY! REVERSE THE DAMNED POLARITY OR SOMETHIN', WILL YA'?

Edit to add: On the upside, I also got my second English essay back yesterday - I got an A+

Edited by Lou FCD on Sep. 23 2008,07:38

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(Permalink) Posted: Sep. 23 2008,20:16   



My notes and thoughts from Biology 111, for Monday, September 15, 2008. The entire series can be found here.

The class started with a reminder that the next class period (Wednesday the 17<sup>th</sup>) would be our first exam.

Then there was a short review of Hydrocarbons generally, and carbohydrates specifically, just to get us back to the place where we had left off.

We picked up this lecture with our discussion of Lipids.

2. Lipids

Triglycerides ---> Fats &amp; Oils



Glycerol + 3 Fatty Acids

When a glycerol molecule, C<sub>3</sub>H<sub>5</sub>(OH)<sub>3</sub> (the vertical part on the left of the image), picks up three fatty acids (the long strings of C and H on the right), they combine to form a triglyceride.

Triglycerides are fats and oils. If the long fatty acid chains all remain straight, each carbon bonding with two Hydrogen atoms and its two neighbor Carbon atoms, the triglyceride can pack densely, and thus becomes a solid at room temperature. This is a saturated fat.



If one or more of the long fatty acids develops a "kink", ie two Carbons double bond and dump a Hydrogen, the stack can not pack as densely, and thus becomes a liquid at room temperature. This is an unsaturated oil. If there is one kink, it's a monounsaturated oil, and if more than one, it's a polyunsaturated oil.

Ta-da. It was kind of cool to suddenly understand the difference between them after having heard the terms for so long in reference to food labels.

We can measure energy in units called calories.

Because of fat's high percentage of hydrocarbons (all along those fatty acid chains), it has a high caloric content. For comparison, a gram of fat contains 9 calories, while a gram of carbohydrates contains 4 calories. Remember that those Hydrogen - Carbon bonds are high energy content because of the non-polar covalent bond.

Some properties of solid fats:

They are good insulators. (whales, walrus, Rush Limbaugh, etc. are good examples.)

They also make good shock absorbers. Vital organs are wrapped in fat, especially where not protected by bone.

3. Proteins

Life on earth is protein based.



Proteins are macromolecules. They are polymers of amino acids.

On the left of this structural diagram of an amino acid is the amino functional group, and on the right, the carboxyl functional group. Note the Oxygen and the Hydroxide dangling off the end there. Those two really make an amino acid hydrophillic.

Note the big R in a circle. Checking the Periodic Table, you'll note that R is not an element. R is used as a place holder for whatever plug and play molecule might go there in any given amino acid. There are hundreds of different amino acids, depending on what gets plugged in there. Living things use twenty different amino acids to make proteins.

The R is what makes each of them different.

Amino Acids

There are three groups of amino acids.

Nine of them are nonpolar ---> They are made almost entirely of C and H

Six of them are polar.

Five of them are electrically charged  ---> two are negatively charged, and three positively charged.

There's a nice amino acid chart on page 79 of our text book that shows these amino acids in their groups, and it will be important all semester. I won't bother to reproduce it here, though.



When two amino acids hook up, it's by a dehydration synthesis, similar to what we saw before in sugars. In this case though, we call it a peptide bond.

When two amino acids form a peptide bond, it's called a dipeptide. three is a tripeptide, and more than three is a polypeptide.

Long chains of amino acids, about when they reach 100 or so in a chain (not a hard and fast number), are called proteins. The average length of a protein in the human body is about 400 amino acids long.

There are three levels of protein structure that we looked at:

A) Primary Structure ---> proteins are a sequence of amino acids. A dipeptide can have 400 different possible primary structures (20 possible amino acids in the first position, 20 in the second = 20 X 20 = 400). A tripeptide can have 8,000 (20 X 20 X 20), a polypeptide of four amino acids 160,000 (20 X 20 X 20 X 20), etc. Remember, with proteins we're talking about at least about 100 amino acids long. The sequence of amino acids is critical at each and every location.

B) Secondary Structure ---> Hydrogen Bonding causes kinking, curling, twisting, etc, causing a protein to look like a twisted or knotted slinky.

C) Tertiary Structure ---> Complex 3D shape caused by the R groups interacting with each other and with the water solution in which they reside. The long molecules are electrically charged in places, polar in places and nonpolar in other places. The nonpolar parts are hydrophobic, the polar parts hydrophilic. So the nonpolar parts tend to wind up in the middle, while the polar parts and the fully charged parts tend to wind up around the outside, close to the water.

The end shape of a protein is determined by its primary structure and the Hydrogen Bonds, and the shape determines its function, much like the shape of a key determines which lock it will open.

Denaturation, the unwinding of the protein, is a result of broken Hydrogen bonds. Extreme heat or pH will denature a protein, and since shape determines function, a denatured protein will cease to function properly (or at all). High fever for instance (body temp of 42 or 43°) will denature the body's proteins and cause death. Death is bad.

Functions of Proteins

Body structure ---> Much of the body's structure is formed by proteins.

Contraction ---> Contraction of muscles (how you move) is a function of proteins

Enzymes ---> are proteins

Transport of molecules through the body

Hormones ---> insulin, growth hormone

Receptors ---> I apparently forgot to write down what Doc said about this.

These are just a few of the many functions of proteins.

4. Nucleic Acids

Macromolecules ---> Biggest of organic molecules

Polymers of nucleotides

pentose, phosphate group, nitrogenous base

Two types of Nucleic Acids ----> Ribonucleic Acid (RNA) and Deoxyribonucleic Acid (DNA)

We'll discuss these more later on, but here's where the lecture ended.

The following class period was our first exam, so there were no lecture notes for Wednesday, September 17<sup>th</sup>. We picked it up on Friday, September 19<sup>th</sup>.

Quote
From whence came the art:

The first image is of our textbook, Biology, Eighth Edition, by Campbell &amp; Reese et al.

Other images by me and are licensed under the Creative Commons Attribution- NonCommercial- Share Alike 3.0 License.


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Henry J



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(Permalink) Posted: Sep. 23 2008,23:25   

Quote
Some properties of solid fats:

They are good insulators. (whales, walrus, Rush Limbaugh, etc. are good examples.)


You came close to owing me a new keyboard with that one. :p

Quote
A dipeptide can have 400 different possible primary structures (20 possible amino acids in the first position, 20 in the second = 20 X 20 = 400). A tripeptide can have 8,000 (20 X 20 X 20), a polypeptide of four amino acids 160,000 (20 X 20 X 20 X 20), etc.


What if one protein is identical to another one flipped around? Seems like that formula would double count the ones that aren't their own inverse. (e.g., ABCAB and BACBA, where the letters are arbitrary amino acid units, are really the same polypeptide.)

Henry

  
Lou FCD



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(Permalink) Posted: Sep. 24 2008,05:36   

Quote (Henry J @ Sep. 24 2008,00:25)
Quote
Some properties of solid fats:

They are good insulators. (whales, walrus, Rush Limbaugh, etc. are good examples.)


You came close to owing me a new keyboard with that one. :p

Quote
A dipeptide can have 400 different possible primary structures (20 possible amino acids in the first position, 20 in the second = 20 X 20 = 400). A tripeptide can have 8,000 (20 X 20 X 20), a polypeptide of four amino acids 160,000 (20 X 20 X 20 X 20), etc.


What if one protein is identical to another one flipped around? Seems like that formula would double count the ones that aren't their own inverse. (e.g., ABCAB and BACBA, where the letters are arbitrary amino acid units, are really the same polypeptide.)

Henry

I had the same thought, Henry. I don't think the point was a specific number, but rather a simplified illustration of just how important and varied the sequence is when dealing with proteins. We certainly weren't tested on the exact number of possible sequences of amino acids in a dipeptide.

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(Permalink) Posted: Sep. 24 2008,07:13   

Quote (Henry J @ Sep. 24 2008,00:25)
{snip}


What if one protein is identical to another one flipped around? Seems like that formula would double count the ones that aren't their own inverse. (e.g., ABCAB and BACBA, where the letters are arbitrary amino acid units, are really the same polypeptide.)

Henry

Close, but not quite.

If a polypeptide is a real palindrome - abcdeedcba, for example - then, yeah, you just have the same compound.  Your example, however, is of two entirely different compounds, because you must read from only one direction.

I like to use the example of the elephant parade in Disney's "Dumbo."  Amino acids have a trunk, the -COOH end, and a tail, the HHN- end.  A peptide bond is solely a trunk-to-tail arrangement, and you must read the parade starting with the first elephant - the one whose trunk is not connected to another elephant's tail.  (It's perfectly OK to call the amino end the trunk and the acid end the tail, I'm just giving an illustration.)

"Nutrasweet" brand artificial sweetener is a dipeptide called aspartame, see http://www.chm.bris.ac.uk/motm/aspartame/aspartameh.html . If you reverse the order of the amino acids, then you have an entirely different compound which does not have the same chemical properties.

Just like at the end of "Dumbo," when the original boss-lady elephant is at the rear end of the parade and Dumbo's Mom is now the leader.

Same elephants, but a different parade.

ETA:  hunh, I can't get a "subscript" tag to work.  Oh well.

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Wesley R. Elsberry



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(Permalink) Posted: Sep. 24 2008,07:19   

Why not?

Use square instead of angle brackets...

Wh<sub>y</sub> no<sup>t</sup>?

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(Permalink) Posted: Sep. 24 2008,09:09   

Quote (fusilier @ Sep. 24 2008,08:13)
I like to use the example of the elephant parade in Disney's "Dumbo."  Amino acids have a trunk, the -COOH end, and a tail, the HHN- end.  A peptide bond is solely a trunk-to-tail arrangement, and you must read the parade starting with the first elephant - the one whose trunk is not connected to another elephant's tail.  (It's perfectly OK to call the amino end the trunk and the acid end the tail, I'm just giving an illustration.)

Oh, right, because



would not be the same as



because the R1 in the first image would be close to the acid end, while in the second it would be close to the amino end of the dipeptide, giving the two completely different shapes, and thus functions.

Edited by Lou FCD on Sep. 24 2008,10:09

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(Permalink) Posted: Sep. 24 2008,09:10   

Quote (Wesley R. Elsberry @ Sep. 24 2008,08:19)
Wh<sub>y</sub> no<sup>t</sup>?

Use square instead of angle brackets...

Wh<sub>y</sub> no<sup>t</sup>?

When you hit the preview button, the bbcode has been changed to html code, Wesley. Same when you hit submit, then try to go back and edit.

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(Permalink) Posted: Sep. 24 2008,10:08   

Quote (Lou FCD @ Sep. 23 2008,20:16)


If one or more of the long fatty acids develops a "kink", ie two Carbons double bond and dump a Hydrogen, the stack can not pack as densely, and thus becomes a liquid at room temperature. This is an unsaturated oil. If there is one kink, it's a monounsaturated oil, and if more than one, it's a polyunsaturated oil.



Trans fats are like the unsaturated one you mention, except that the double bond does not introduce a kink, so trans fat does not lower lipid density like the good unsaturated oils.  The health risk of trans fat is actually higher than saturated fat.

Quote



Denaturation, the unwinding of the protein, is a result of broken Hydrogen bonds. Extreme heat or pH will denature a protein, and since shape determines function, a denatured protein will cease to function properly (or at all). High fever for instance (body temp of 42 or 43°) will denature the body's proteins and cause death. Death is bad.



I find denaturing of protein at 42 hard to believe! It is possible I suppose.

 
Quote


Functions of Proteins

Receptors ---> I apparently forgot to write down what Doc said about this.



Receptors are proteins that "receive" ligand molecules and in turn produce a change in the receptor that produces a signal of some sort.  Regulation is done via the production of these molecules.  

An example is G-protein coupled receptors.

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