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Bio 103, Week 9, Macromolecules and Improbability/Energy

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 progress are we making in terms of understanding life in terms of macromolecules, and how we account for their improbable existence?
Catrina Mueller's picture

During this week's

During this week's discussion, I was reminded of my childhood. The way macromolecules are used in the body paralled very well with the way my sister and I use to play with legos. We would first build the legos according to the directions. After a while, however, we would get bored and deconstruct the parts. We would then construct new creations, often combining the legos from many sets to form one large, complex piece.
Rachel Tashjian's picture

That Crazy Water Wheel.

Okay, here's the crazy water wheel thing as I understood it:

1) It's an improbable assembly because while a wheel is a somewhat predictable shape, a wheel with a bucket attacked to it is not predictable. Throwing those ingredients together would be unlikely to yield the same result.

2) Once the water starts flowing, the wheel is moving downwards, because of gravity/the water pushing it. It's doing something we'd predict it to do, so it's now more probable.

3) BUT! That bucket is still on there. If the bucket is attached to the wheel, it's going to move as the wheel does. And if the bucket is on the bottom of the wheel (which it is), when the water pushes the wheel it makes the bucket move upwards, which is NOT something we would expect to happen. A bucket moving upwards, instead of the predictable and usual direction of downwards, makes it improbable.

Therefore, the wheel is moving down (probable), and the bucket is moving up (improbable), so both an improbable and probable assembly is happening at once.

Please comment if that is incorrect.

Paul Grobstein's picture

water flows up hill

Bingo. Water moving downhill (toward a more probably state) causes other water to move uphill (toward a more improbable state). Issue isn't quite whether we expect it or not (though that's a good touchstone), is the relative probability of starting/ending states. Things go "spontaneously" from more improbable to more probable (second law of thermodynamics). Things going in the other direction can (statistically) do so only when something else changes spontaneously.

Incorrect? Correct? .... Good story?

LaKesha's picture


I really got confused when we began to talk about the water wheel. I'm not sure I quite understood how the water wheel is an example of an improbable assembly if a bucket is attached. What makes the water wheel less improbable when it is stationary than when it is moving? Something else that also surprised me was energy not being created. I could have sworn that I somewhere in my high school years I heard those words. But then I guess is does make sense that it is just a transformation from one state fo energy to another.
Shanika's picture

I was shocked that energy

I was shocked that energy cannot be transferred. How is energy transformed and not transferable? Things that change usually can be transfered, so what make energy different? I guess it kind of makes sense, they do mean two different things. I was relating this notion to my personal experience with gaining energy from another’s action. That is a big difference. If I am playing in a basketball game and I do not have enough energy, my teammates usually say motivational things that affects the way I am feeling. Hold on, so emotions are factors to the way energy is transformed for an individual...Ummmh...i don't know...there have to be some correlation.????

If my energy level is low while playing, it usually becomes high once motivated by my teammates and coaches. I don’t know! I’m trying to play with this notion…BUT????

Since energy transform from another state of energy, how is the energy created before that formed????

Kendra's picture

I knew that energy was

I knew that energy was transformed but not transferred but it was interesting to hear the story that there is no such thinkg as energy independent from matter and that energy is just a way of describing the organization of matter. I found this to be really interesting because I never really realized it before.

I found it cool how we were able to answer the age old question 'if a tree falls and no one is around to hear, does it still make a sound" just by realizing that certain molecules, in this case soundwaves, are not effective unless they interact with other molecules, i.e. the ear. From this I learned that vibrations turns into sound only when it hits the ear, which is an interesting thing to think about.

Samar Aryani's picture

The idea that energy is

The idea that energy is transformed and not transferred was quite surprising to me.  It was interesting how energy is not created, it is just a transformation from one state of energy to another.  In essence, we are transforming energy from an improbable state to a probable state.  It is somewhat of a hard concept to fully grasp because I understand that energy transforms from one state to another but wouldn't you think that after some time when that energy is not being used that it would have to be created again? Maybe I understood the concept wrong but it seems confusing to me. 
andrelle's picture

At first, i was confused

At first, i was confused but now i think that it make sense.  The class seems to be moving back to some of the things that Im familiar to hearing about in high school such as energy being trasnferred and kinetic energy.  It even make sense that we have to eat these macrolecules in order to gain energy.  Everything was making sense until we got to the waterwheel analogy.  I thought that I knew what "propable" and "impropable meant and now I'm starting to think that I never really understod what it meant.

I also think that it's very cool how we learn about macromolecules and their fuctions and use that to help us better understand life and how it works.  Normally, all this tal about periodic tables and molecules would bore me, but now Im starting to appreciate these things and how they work. 

Jen's picture

I'm not sure I quite

I'm not sure I quite understood the water wheel example as being an improbable assembly if a bucket is attached. What makes the waterwheel less improbable when stationary than when moving?
Sharhea's picture

Eating Macromolecules

On Friday, when we initially started talking about us as macromolecules eating macromolecules. It almost sounded like the same reasoning a vegetarian may have for not eating animals and/or animal products. In sense we are eating the same building blocks of life in everything that we eat, whether they are plants or animals. We may break them down into smaller molecules to produce the energy necessary to survive.

Now the waterwheel example, I'm still a little confuse about it. I don't think I understand the connection between the waterwheel and the breakdown diagram of the macromolecules.

LuisanaT's picture

Getting technical

Participants of experiments die for all sorts of reasons, many of which go undetected because the information collected is coming from very one sided lens. The observations are only regarding one overarching aspect of the reaction from the stimulus. But the fact of the matter is that living creatures don’t die from just one cause let alone the same specified cause as everyone else found in a so called “controlled group”, no matter how fixed the environment may seem. The body is tremendously complex and different from one human being to the next, where the simultaneity of interactions and reactions inside and out never ceases to exist. Despite this major technicality when coming to general conclusions that fail to take into consideration every possible interaction that can occur, every single side effect the stimulus might evoke, and these experimentations are necessary evils. The thing is that the risks scientists go through everyday when faithfully declaring to the world the latest breakthrough is the only way for us to really verify the credibility of the set claim. It’s important to put the word out there to see if this story of observation holds true on a worldly level. And that I must say again ties back to the great thing about science; it is constantly open to change and additional information. Science is ever-changing, there are always delayed reactions or results found later effected by the original stimulus. New receptors and detectors being either used or made give rise to an unbounded number of possible secondary responses and therefore unlimited believable stories.

OrganizedKhaos's picture

Meaning and Water Wheels

The discussion about randomness and ordering was very interesting because I like to think about myself as one of those who didn't necessarily believe people had a certain "unpleasantness" in order to be punished and cause suffering but the whole "luck of the draw" concept didn't make too much sense to me so it seemed like a more likely reason whic I chose to accept. But then I began to understand that and i don't feel that knowing about genes gets rid of meaning. The science behind it serves as an explanation but may not be the only reason for that certain "unpleassantness" depending on the background of that person. They should and may still believe that there some bigger meaning to their suffering.

Our discussion progressed making a lot of sense to me but then the water wheel topic came up and the shift and change of water from being probable to becoming more and more improbable as it was going on the water wheel. At first I thought I understood what exactly was being explained but once it was explained over and over i got more confused. Whether water can become more probable or improbable while being in the same state not frozen or anything and only from movement confuses me and I don't see how that can be possibe.

eharnett's picture


I thought that yesterday's discussion in class was interesting; it made me look at energy and matter in a different way.  I always thought that energy was something that was transferred, not transformed...and I never thought of energy and matter as being the same thing and not different entities.  This definitely changes my ways of looking at the laws of thermodynamics, and though it may take me awhile to get use to it, it does make sense to me.

Kee Hyun Kim's picture

since we opened the Pandora’s box of genetic discrimination..

I would like to throw a question out to everybody…


What if we are able to reach a level of science that we can safely identify the different characteristics of the genes and are also able to alter individuals like the movie GATTACA? Where should the line be drawn between science and morality?


I guess the answer is fairly easy when it comes to finding your special person like one of the posters mentioned (although some will disagree) but what if it is directly related to our safety and well being?


What if in the future, ( hypothetically) we are able to identify and even possibly transform genes that causes someone to be violent and susceptible to extremist ideas.


In such a case, should we use science as a tool to identify the ones with such genes?  


Personally I am a bit torn between the two sides. While one side of me says this is infringing upon humanity while the other side of me is saying that by neglecting to do so would be ignoring the rights of other individuals to pursuit his or her happiness. (I guess its similar to the debate of stem cell research)


What do you guys think?

 Oh and today’s conversation about how energy is not a separate entity and therefore cannot be transferred was very interesting… Until know, I thought energy could be transferred like sound wave being transferred through air molecules..  


ekim's picture

on energy and waterwheels.

today's class started out okay, until it got to the waterwheel...i was a bit confused with the idea of the waterwheel's movement causing more probability, while the moving nailed pail caused more improbability. the moving waterwheel and the moving pail are both using kinetic energy, so shouldn't they both be moving toward one or the other (probability or improbability)?

and the 2nd law of thermodynamics said that change occurs from the less probable to the more probable, but also says that entropy increases. correct me if i am mistaken, but isn't increasing entropy increasing disorder-ness, therefore increasing improbability, not increasing probability? so then shouldn't the kinetic energy of the moving waterwheel and pail yield for more improbability?

kgould's picture

I listened to the radio

I listened to the radio discussion about genetic testing. The mentions about genetic discrimination and "biology not being destiny" struck me as interesting concepts.

First off, having watch GATTACA several times in science classes throughout high school, I find the idea of genetic discrimination to be terrifying. It isn't fair to judge someone based on their DNA. No one's perfect. And no one should be. Employers shouldn't gain access to someone's genetic map with the intent of refusing employment if they test positive for certain genes. ...At the same time, employers would want to know if their employees have a high chance of developing some kind of behavioral disorder, right? Especially if it came down to safety? (i.e. someone with access to dangerous substances, like nuclear or biological weapons).  

What about relationships? Certainly, one should be judged based on their actions, not on their DNA are, but if a prospective mate has Huntington's Disease... would one still reproduce with the knowledge that the offspring will encounter the disease later in life?

It's confusing. I know genetic discrimination is wrong, and I don't think I really agree with genetic testing in the first place, but isn't it fair to your spouse if you let them know that your prospective offspring have an 85% chance of developing breast cancer?

No one's perfect, and no one should be perfect. The idea that someday parents might be poking around their child's genome to make them "better" makes me rather ill. Not only does it give some people (those with the means to mess around with genomes) unfair advantage over others, but we're still not entirely certain what genes code for. A lot of genes influence several traits. Going in and changing things simply to make a child "better" is probably not such a good idea.

...but should parents be able to erase genetic disease from their children's genomes? Would they be "better" parents for doing so? Wouldn't it make their children's lives better?...

And "Biology is not destiny." Knowing the randomness of life, there's always a chance, however small, that the genetic disease or disorder isn't going to be expressed. Nothing is set in stone. As I stated earlier, I don't really agree with genetic testing. Is knowing really going to change anything? In some cases, I think knowing makes things worse. Instead of living life normally, one would be anxious and paranoid about each new day. Is that a new bump? Did I have that rash yesterday? Do my hands always shake like that?

Is having a reason for your disease or disorder going to change how you deal with it? Is blaming it on your genes, on your parents, going to make the disease any better?

...I don't think so. Regardless of any reason, isn't it best just to live your life as best you can?

Paul Grobstein's picture

Genes, and "meaning"

Interesting conversation this morning, triggered by Ruth's thought that "randomness ordered by a set of rules ... just seems a little hollow to me". The point, if I understood it correctly, was that if one had a gene with some unpleasant consequence, one would prefer to think there was some reason for that unpleasantness rather than it being simply the "luck of the draw." Interesting counterpoint today during NPR's "Voices in the Family", discussing genetic testing. A caller wanted to know whether genetic testing could help him explain why he'd been suffering, and was pressed by Dan Gottlieb, the moderator, to explain why knowing there was a genetic explanation would make him feel better. Maybe knowing about genes and randomness abolishes "meaning" in some contexts, and creates it in others?