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Bio 103, Week 7, Working Up From Atoms ...

Paul Grobstein's picture

Glad you're here, to share explorations of life. If you're registered in Biology 103, remember to log in before posting here. Others are welcome to contribute without logging in. Such comments though will be checked to avoid spam postings and so be delayed in appearing.

In any case, remember that this isn't a place for polished writing or final words. Its a place for thoughts in progress: questions, ideas you had in class (or afterwords), things you've heard or read or seen that you think others might find interesting. Think of it as a public conversation, a place to put things from your own mind that others might find useful and to find things from others (in our class and elsewhere) that you might find useful. And a place we can always go back to to see what we were thinking before and how our conversations have affected that. Looking forward to seeing where we go, and hoping you are too.

You're free to write about anything that came into your mind this week. But if you need something to get you started, what do you think of the idea that the diversity of organisms and living phenomena can be made sense of in terms of asemblies of a small number of simpler things, ie atoms and molecules?  Is it, will it become, a good story?
LaKesha's picture

How Different are WE?

Now I ever thought I would hear atoms and molecules again because I planned to never take a chemistry class again but I feel like I learnefd something new. Or I should say I actually thought about it more in depth this time. We are ALL made up of atoms. I think that is sooo cool because we are all made up of the same thing but are ALL different because of the different formations of the atoms and molecules. I guess if I would have gave chemistry a chance I might have liked it...nevermind I take that back.
kgould's picture


Trying to learn biochemistry has always been difficult for me. I just can't seem to wrap my mind around it. Or, at least, I couldn't. It seems much more approachable now.

I can appreciate the idea that different assemblies of atoms make for different properties. And I am interested in the idea that there is no one atom that makes "life."

It does make me wonder, however, why humans have always sought for that one ingredient that makes something alive. Why couldn't they accept life as an assembly of different units and properties?

Mary Roach's book, Stiff, discussed Duncan MacDougall and his efforts to find the weight of a human soul. He weighed six terminally ill patients as they died in an attempt to see if they did indeed weigh less, suggesting that their soul had left their lifeless bodies.

His experiment was a little iffy; MacDougall used a very small sample size and had trouble determining the exact time of death (without disturbing the scale), which was imperative to the experiment. Thus the test ended with no satisfactory conclusion (although MacDougall reported that a human soul weighed 21 grams).

It's an interesting experiment, none-the-less.

PS2007's picture

I didn't realize we would be

I didn't realize we would be talking about chemistry in this class, but I guess to fully understand biology (or any other science) you need a basic understanding of chemistry. Even though it was unexpected, I really enjoyed learning about chemistry from a more theoretical perspective. When I was in high school we mostly just memorized formulas and solved problems, and I didn't realize what chemistry actually had to do with the big picture. Our class discussions helped me realize how chemistry and biology work together to create life.
Kee Hyun Kim's picture

Finally some certainty

The fact that all living - non living organisms are created of same atoms and cannot be distinguished provided some comfort to my confused state of mind. Now that we know that living and nonliving things are composed of the same atoms, I would like to find out more about the difference of composition between living and non living things.


What intrigued more, however, is how all these different atoms are connected to each other. How they find their counterpart (similar to us finding that special person) that will successfully compliment whatever charge they may have (negative or positive). Also, the difference a single atom or a single connection can make was very interesting (the example of alcohol we talked about in class)




Catrina Mueller's picture

Not having a "human" atom

Not having a "human" atom or an "alive" one really struck me. Before, I had thought carbon as being the "alive" atom. Carbon, however, does not make the compound "alive". It just happens to be the things that are/were alive, but it is in other stuff also. Before, I would have said that carbon was the key to "life", but now that I think about it, there cannot be any specific "life atom".

Jen's picture

I enjoyed the lab very much

I enjoyed the lab very much this week; a lot of the time, we couldn't get correct readings, especially for myself; I was flat-lining a lot of the time. But I especially enjoyed the freedom of being able to create our own trials to determine the underlying process that controls heart rate.

As to class, I find it interesting that one proton can make one atom completely different from one another, can produce something with totally different properties and behavior. I mean, if we created a building out of bricks but we put the bricks in different patterns, it would still be a brick building; but if you put different numbers of protons together in atom, you either get a gas or an alkaline metal or any number of different building blocks. How does that work out, exactly? Why does that happen?
Shanika's picture


Diversity seems to be a strong factor in many of our class discussions. The idea to actually relate the word diversity with structures of molecules explaines that the word diversity can be used in many ways, contexts...etc.

The lab on thursday was a great. My partners and I found that when performing exercises our heart rates increased. As stated in our lab forum, one of the reasoning for this reult can be that when our heart beats were at rest our blood was flowing at a steady pace, when we did the exercises our heart pumped faster causing the blood to go through our body faster. We found that there is a correlation between one's heart a rate and the flow of one's blood. What we could not understand was why was our blood pressures lower after performing an excerise, rather higher????

Overall I enjoyed myself!!!!! YAY!!

MarieSager's picture

I was really interested by

I was really interested by the statement that elephants and humans consist of the same atoms. I had never thought of it like that, and it brings up the question of how we are different? In class, everywhere really, the answer to that question (of why humans and animals are different) has always been hard to answer. But, according to class this week, the difference lies in assemblies of atoms. And even the differences between a person's hands... it all comes down to differences in composition. And then to think that composition, which implies some kind of order can and does originate out of randomness... and at such a small scale... its all mind boggling.

cmcgowan's picture

Class this week was

Class this week was interesting because it made me think of molecules and atoms in relation to my life. The one thing that I found especially interesting was the when we discussed the 3-D shapes of atoms in relation to diversity. I had never really realized that two things could be made out of the same atoms, yet end up being completely different depending on the order of their assembly. It is intruiging to think that thephysical differences of two things are possibly the result of just one small difference in their biological assembly. This makes me wonder how much variation can their can actually be between different forms of life. 

I feel like I have been getting a lot out of the lab portion of this class. Lab can sometimes be very frustrating because we are left on our own to come up with procedures and explanations but this is great because we aren't told to look up the answers in a text book. I like that we have to try and create our own stories, and I like that we often come up with a variety of ideas that conflict and we often leave lab feeling a little bit stumped. Its nice to know that we worked towards finding some sort of answer by creating our own story rather than just mindlessly repeating what we have read or been told by others.  
OrganizedKhaos's picture

Molecular Diversity

This weeks dicussion in class led to a lot of questions about the small things when compared to the bigger picture, life. The idea that we are all made of three simple atoms sort of takes away our specialness but also the random combinations which makes us differen adds to the specialness that we all possess. It reminds me about the ethanol and ethane discussion how the placement of one atom can either kill or someone or get you drunk.

I feel comfortable with the story that we are all made from basic atoms and have our own uniqueness and specialties due to random combinations.

ekoike's picture

Diversity... as a result of formations of atoms

This week's discussion really fueled interesting conversation in the class that made me fully realize the importance of "improbable assemblies" (on a molecular and minute level) that make up various organisms.

What really struck me this week as very significant was the realization of how even one atom or molecule less in an "assembly" can produce very very different things. One main example of this was in the example that was brough up in class about Carbon Monoxide versus Carbon Dioxide. One causes deadly harm to humans if inhaled and the other is what is produced when we exhale.... the fact that even the most smallest changes in atomic structure can cause such a drastic change is rather alarming.

In my head, for some reason, I often associated these two as completely different, but in fact when you simply look at the structures of the two bonds, I noticed how little difference they have...

This made me think further on the whole biodiversity/"Are humans special?" discussion that we were having last week. If in fact some organisms have similar genetic makeup (with very minute differences in smaller molecular structures) to each other (such as gorillas, chimps and orangutans vs. humans) and such close common ancestors, does this mean that we can discount them as not as "special" as humans?

Samar Aryani's picture

My comments on class is

My comments on class is pretty much the same as the ones written above.  The conversation on Wednesday were particulary interesting especially when discussing the diversity that exists within structures of molecules that have the same components can and are different in the overall outcome.  This was fascinating because it shows that diversity still exists at this small of a level. 

Also, our discussion on how such things as water, salt, and hydro-cloric acid are built.  It was said that the electrons join together with other electrons in order to reach their desired number.  From this process, we get water, salt, and so on.  This was fascinating because I never thought about it with that way. 


Rachel Tashjian's picture

Up and Atom.

I really enjoyed this week's discussion and lab. I guess I have a few questions/thoughts. On Monday, we said that living and nonliving assemblies are not distinguishable by "the identity of their atomic constituents" (in other words, everything is made up of the same things). I know that there's a difference in the number of types of elements that make up an organism (and in the design/"pattern," as we saw on Friday). But if it's all made of the same thing, doesn't that mean that at the most basic level, the "clumps" we see in, say, species, is not present at the most fundamental level?

Second, I really liked that on Friday, we talked about things using more scientific terms than we normally do. I would not have expected to enjoy that, but I think I liked it because when we used those terms, we then asked what the practical implications were. I think that's the main reason I was able to follow everything we were talking about.

Third, lab was kind of a lesson in experimental methods for me. First, we were convinced for a bit that I was a zombie (or, more realistically, had really low blood pressure) because I wasn't getting a read on the thumb pressure reader thing. We figured out after about 20 minutes that the problem was actually with the reader (it had been working on and off). As a result, we didn't get to do as many trials as we wanted to, and didn't get to try as many variables, either. We were really nervous putting our post together, because it seemed like we didn't have as much data (and thus, we assumed, not as much to say) as other groups. I didn't think, however, that the data we got with the faulty reader should have been thrown out, and my partners and I were able to get some interesting information from it (and a bigger lesson about experiments in general). We also were concerned that since my BPM didn't change while listening to rock music or watching a funny video (we hypothesized my BPM would go up), this data was no good, since it proved nothing. But for me (and, I think, my partners), it proved that it's difficult to get a really accurate result on this kind of experiment because of the pretense of an experimental setting. If I had been hanging out with my friends listening to music, the result probably would have been much different.

Kendra's picture

When we began to

When we began to incorporate the periodic table and talk of the different molecular bonds in class discussions, I panicked. This was because I decided to take a biology course in order to avoid any chemistry, which was my worst nightmare last year. But now I realize that the two are, of course, interconnected and that studying the periodic table helps us to better understand the molecular diversity of living organisms. I, too, think it is a good story that everything is made out of the same constituents but in different arrangements.

I thought the point that 'there is no atom that makes us alive, rather a group of atoms' is a good one to recognize. One example about molecular diversity that really stuck out to me was the difference between ethane and ethanol,how one can kill you if ingested while the other just makes you drunk. Theyare both made of the same constituents, but that one oxygen atom makes all the difference.

Also, I found myself questioning what makes a molecule left handed or right handed? It just seemed like an interesting way to differentiate certain molecules.

eharnett's picture

It is a good story

I believe that the idea of atoms making us a diverse is a good story.  The fact that we are all made up of the same components but in different ways makes sense.  Also, the way that the same molecule can have so many different structures and therefore make life so much more diverse is fascinating.  Just thinking about the different arrangements, combinations etc. is mind boggling.  We've only talked about hydro carbons so far-so it’s interesting to think about all of the other different types of molecules and their varieties of structures.  I do believe that diversity stemming from the simpler components to structures is a good story.

kcough's picture

I'm really enjoying this

I'm really enjoying this discussion about atoms-it's fascinating, since they are what makes all of us up. I'm a little confused about the left and right-handed molecules, however. First of all, why are they called that? What is it that makes them left or right handed? And how/why do living organisms discriminate between them if they only differ in their shape? Why is shape so instrumental in showing the differences between organisms? And does this only happen with hydro-carbons? Why only hydro-carbons?

That's lots of questions and not so many answers, I know.

I thought that polar molecules were fascinating as well-so that's why humans are what, 70% water is it? Makes a bit more sense now.


ekim's picture

on molecular diversity.

all living things are made up of the same constituents (atoms). this makes sense to me. all living things are made up of the same constituents, but are different because of the arrangement thereof. this makes even more sense to me.

this story simply harks back to our discussion of clustered diversity, no? no matter what scale we look at things (from the universe to atoms), there is diversity in clumps, arrangements, boundedness, etc.

and those clumps, arrangements, boundedness in turn account for diversity.

it just keeps going in circles.

so if it keeps going in circles, is there ever a limit to molecular diversity? to atomic arrangements?

LuisanaT's picture

One final note on humans being special

The only way I can fairly consider humans as “special” is on an evolutionary scale. We have significantly expanded the range in the variety of combinations as a result of our own specializations. Human beings have introduced for the first time, from my knowledge, concepts like religion, currency, opposable thumbs, etc, adding to the grid from the diagram “themselves undergoing continuous change” (/biology/b103/f05/evolclassif.jpg) we observed in a previous lecture.