Remote Ready Biology Learning Activities

Greetings ... Name: Paul Grobstein Date: 2005-08-26 07:31:42 Link to this Comment: 15924

Welcome to the Bio 103 course forum area. This is an interestingly different kind of place for writing, and may take some getting used to, but I hope you'll come to value it as much as students in other courses have.

The first thing to keep in mind is that its not a place for "formal writing" or "finished thoughts". Its a place for thoughts-in-progress, for what you're thinking (whether you know it or not) on your way to what you think next. Maybe simpler, imagine that you're not worrying about "writing" but instead that you're just talking to some people you've met. This is a "conversation" place, a place to find out what you're thinking yourself, and what other people are thinking, so you can help them think and they can help you think. The idea is that your "thoughts in progress" can help others with their thinking, and theirs can help you with yours.

So who are you writing for? For yourself, and for others in our classes primarily. But also for the world. This is a "public" forum, so people anywhere on the web might look in. That's the second thing to keep in mind here. You're writing for yourself, for others in the class, AND for others you might or might not know. So, your thoughts in progress can contribute to the thoughts in progress of LOTS of people. The web is giving increasing reality to the idea that there can actually evolve a world community, and you're part of helping to bring that about.

Glad to have you along, and hope you value/enjoy sharing the activity of trying to make sense of life.

week 1 Name: Paul Grobstein Date: 2005-09-02 16:04:50 Link to this Comment: 15967

Interesting discussion in class today about the "story" of evolution. Thanks, am interested in, among others things, the number of people who wanted a fourth option and why. Looking forward to seeing what you've been thinking this week about science, about evolution, about life (how do we know it when we see it?), any combination of the above, or anything else that you've been thinking about that might help us all get less wrong about life.

What does it mean to be "living"? Name: Lizzy de V Date: 2005-09-02 16:07:01 Link to this Comment: 15968

Today in class, we were asked how we, having landed in the desert, would determine whether or not the things we observed were alive. My immediate response was that it was obvious that the camels we saw were alive, because they were moving. Camels breathe, make noises, eat and drink, and walk. Of course they are living beings. Another student raised her hand and responded that perhaps the camels were not themselves moving, but were in fact being moved by the wind or some other means. While this answer struck me as out of the range of possibility, I realize now that what we are learning in this course is to do just that, to think outside the bubble, to observe and to wonder. What I myself wonder, however, is if through this process we are training ourselves to be skeptics, or to work too hard to see possibilities, rather than accept some of the simpler facts of life. Does it really make sense for me to take the time to wonder "Is it possible that some outside force is actually propelling the inanimate camels across the desert? Might they be robotic creatures or some sort of non-living form?" Is this kind of thought a waste of our time?

Week 1 Name: Iris M Date: 2005-09-03 00:30:27 Link to this Comment: 15969

What is science? We are taught that science is something we do that we can like or dislike and possibly live without. We can actually not enjoy science but we can't escape it. Science seems to be all around us we must only become aware of it. Looking around my room it became apparent to me that most if not all of the items in my surrounding sprung forth from a scientific process. Observations were made by inventors who applied them to create items such as a fan. Science doesn't change but our own thought process and technology change helping us observe better and leading us to be "less wrong." This is important in the question of whether living organisms exist in mars because our list of characteristics for what is considered alive may change over time. Currently we are taught that all organisms fall under living or nonliving and that living organisms have common characteristics, which include: eating, growing and reproducing. However, these are current observations and it may turn out that what we consider non-living may actually be a living thing in mars.

The article about the Langston Ant asks whether the ant has a purpose and it suggests that it doesn’t since it only had a set of directions and that possibly Langston didn’t set out to make the Ant create roads. However, I feel that the purpose of the ant is to follow the directions given to it by it’s creator therefore whether it creates a road or not it has a purpose, which is to follow it's given directions. The jazz improvisation also has a purpose, which is to perform music whether it turns out good or bad.

What is science? what is life? Name: keti Date: 2005-09-04 11:28:28 Link to this Comment: 15975

I found the idea interesting that the web is helping to create a world community, a sort of global network of communication. This implies the existence of a global dialogue in which those with internet access can contribute to, participate in and be educated by the work of others. This seems to relate to the concept of science as a process of “story-telling.” In other words, the discursive element of online information-sharing is much like the conception of Science as a dialogue or discourse. Seen in this light, science is no longer a field comprised of absolutes but is rather a methodology for interpreting and understanding the world. Science is a discursive and perhaps recursive process. Perhaps this explains my abysmal (and short) career as a science student in both middle and high school. One patient science teacher explained to me that science, like religion, requires a “leap of faith”; like the acceptance of God as an absolute force, one must accept the (already-tested and established) facts of science as absolute truths. This “leap of faith” idea unsettled me and I can accept that science is a continually changing and nonlinear process. But at the same time, if it is to be a process of “story-telling” then there does not appear to be any end in sight. Who gets to contribute to this story-telling? Whose words carry the most weight? And while I see the advantages of redefining science as an inclusive rather than exclusive activity, I wonder if this if this inclusiveness is realistic. If there were such a scientific world community would it not (just like the global community of the web) be riddled by misinformation, indecisiveness, even fraud?
To address the question of the nature of life, I would say that life is characterized by its capacity to display emotion. By this I mean that humans identify life as an object (person, plant, animal) to which some sort of emotional capacity can be attributed. While this may not be the most scientific of methods, I think it is the one commonly used by people in their day-to-day lives. How one identifies life affects how they then respond to it. For example, everyone knows that trees and plants are alive. But there are some who feel such a strong sense of attachment to the natural world that to them killing a tree is equivalent to taking a life. While the idea that plants and trees are living things may be universally accepted, the attribution of human emotion/characteristics (which is an individually-generated definition) also carries weight. Consider the expression “life as we know it”: life cannot be defined in absolute terms absent of qualifications as defining life is both a communal and individual process.

Life as we know it. Name: Katie Date: 2005-09-04 14:03:24 Link to this Comment: 15978

After reading Keti’s post, I wanted to respond to two of her points that I think are really interesting. What is life? I think that the statement “life as we know it” serves as a valid answer to this question. Defining life seems to be a reflection of one’s own perspective and perception about what constitutes life. Does it have to move? Does it have to show emotion? Does it have to respond to its environment? There are no Truths in science, so there cannot be specific criterion to differentiate living and nonliving things. I think that the answer lies within the eye of the beholder.

Not only are there differences between living and nonliving things, but there also seem to be different degrees of importance amongst living things. As Keti addresses, in our society a human life is valued more than that of a tree’s. Killing an ant does not carry the same weight as killing a person. Why are some lives more valued than others? Who is to say that my life is more significant than anyone else’s? I think that the answer lies within the eye of the beholder.

Obviously, this is why I chose option four to explain evolution. I have qualms about submitting myself to one conclusion to explain how things came about and how they have evolved. I think that it is really up to the individual to determine, based upon personal observations, morals, values, etc., what they believe to be the “less wrong answer.” Once again, I reiterate that the answer lies within the eye of the beholder.

Name: Nick Date: 2005-09-04 14:36:17 Link to this Comment: 15979

I wanted to respond to Lizzy's post, because I share some of her sentiment about this particular approach to science. I have long believed that science is not much more than a religion, but a religion that required tons of work to get started. It also seems a religion that is continually redefining most of its beliefs, except of course for its focus on rationalism. That being said, I think our relativist approach to science is necessary to keep in mind if science is to be understood fully. There has to be a reason that penicillin doesn't always work, and relativism accounts for it. In this way I think that this approach is important.

I don't think, though, that this approach should be taken so seriously as to lead to the belief that science can't be useful. Science can be, and has been, extraordinarily useful, and there is an undeniably practical element to the Western conception of science which, in my opinion, legitimizes it. The relativist approach to science should not overrule its ultimate usefulness. This is my only hesitation in fully accepting the approach to science we've adopted in the class.

To sum up, then, I agree with Professor Grobstein in that there is no absolute or ultimate truth, but at the same time I don't think this should be taken by anyone to suggest that science can't be beneficial.

stories of life Name: Stephanie Date: 2005-09-04 15:11:27 Link to this Comment: 15981

Two trains of thought on different topics:

It would be very hard to determine whether or not something is living simply by looking at it for a few seconds. In terms of our desert picture, there IS a possibility that the camels are some type of robotic camel and that the grass is fake. However, if you studied these things over a long period of time, you would clearly be able to determine that they were living. They need to eat and drink in order to make energy, which they will then consume. If I remember correctly from high school biology, using energy is one of the properties of every living thing. Another property of life is change, which again, is something that would have to be observed over a period of time. The grass will grow; the camels would grow if they weren’t full grown already and if they were, there would probably be some changes in their physical features over a period of time.

Out of curiosity, I looked up “life” in the dictionary. The property or quality that distinguishes living organisms from dead organisms and inanimate matter, manifested in functions such as metabolism, growth, reproduction, and response to stimuli or adaptation to the environment originating from within the organism. I was wondering if anyone could think of anytime when these things are not all true of a living organism. For example, if a mule is sterile and can’t reproduce, does that mean that it’s not alive?

The other topic that I was thinking about this weekend was the “story of evolution” discussion. I’m confused as to whether a person can believe in a creator and still believe in Story 1: straight evolution. The other question that came to mind was that if there was a creator that wasn’t necessarily initiating “multiple creative events” such as in Story 2, yet was still somehow involved in the process of evolutions, would it be “natural” selection or “divine” selection? And then, what if “natural” and “divine” are actually the same thing?

Name: Sara Date: 2005-09-04 20:46:15 Link to this Comment: 15989

I was thinking about the last part of Stephanie’s comment dealing with the “story of evolution” and like her I was confused and torn about what story to believe. This is the same reason I chose option four in class. The subject of creation has so much gray area that I have trouble believing any one story. I don’t think believing in evolution prevents you in anyway from believing in a creator or the divine. Since there are no “Truths” I think in this case you can create your own truth. On another note the issue of life. How can one begin to define something as vast as life? If a person is in a coma and is on life support is he or she alive? Or are the machines keeping him/her alive actually the living things? How can we decide what is living? If there are once again no “Truths” where do we get our authority?

Name: Date: 2005-09-04 21:24:01 Link to this Comment: 15991

I enjoyed Sara's comments about the definition of life:

"How can one begin to define something as vast as life? If a person is in a coma and is on life support is he or she alive? Or are the machines keeping him/her alive actually the living things? How can we decide what is living? If there are once again no “Truths” where do we get our authority?"

Sara's question about "Truths" was spot on. In order to define something arbitary guidelines are going to be decided on by other human beings, the arbitariness of these guidelines prevents the definition from becoming "Truth." Thus the question becomes an excercise with very little meaning unless a large of powerful group are willing to accept the arbitary definition. This class seems focused on a serious questioning of the established "Truths" of science and by asking the question "What is life?" we are trying to create our own definitive version, isn't this what we are trying to avoid, or is the process of coming to our own definition of life the important part? I apologize for the incoherence of this post, I am not sure it makes any sense.

Brom

Life (and then some). Name: Magda M. Date: 2005-09-04 21:37:41 Link to this Comment: 15992

I find the definition of life that I learned way back in High School bio difficult to get away from; the basic gist of our first semester was that an object was living if it respired. I suppose that's awfully simplistic, but at the same time, "traditional" science has always seemed to me to be about finding ways to state things concretely, to make absolute statements. Being the daughter of two Masters of Agriculture, I'm sure it'll be interesting for me to try to get away from thinking about biology in a linear manner. :)

I suppose that's why I had such a problem saying that the camels were alive just because they moved and because they moved in a complex manner. There are always air drafts, visual interferences, tricks of the light, etc which might get in the way of assessing an object form a distance on a foreign planet and such. Perhaps they were akin to tumbleweeds (which, granted, are organic but dead), instead, or something of that sort created from inorganic matter.

I find "science" a bit more difficult to categorize than life; where do we draw the line between science and simply existing? So much of what we do in our daily lives involves the common things associated with science--learning, exploration of our environment, and experimentation.

Summary of Observations about Science Name: Scott Date: 2005-09-05 05:37:18 Link to this Comment: 15995

Random rambling to begin: I like that people have made a clear distinction between utility and reality. The frameworks through which we see this world have to be seen as relationships with reality rather than records of it. When we split the atom, harness laser power, and use stem cells to learn about genetic codes, we are not describing the real world--we are changing it, shaping it, and making observations about the consistency of the results. Even the light of our eyes, modern Physics tells us, changes what we see in order to permit our seeing it. Let us not forget that our frameworks are as blinding as they are enlightening. Why do you think the Western perspective (framework) is still baffled by acupuncture and those medical monks who can smell a cup of urine and make a very complex, accurate diagnosis of its owner? (has anyone else seen these guys!).

As far as choosing the 'other' category for the story of evolution. Evolution is just a useful framework that helps explain the phenomena of life, but as we have mentioned this past week, it does not tell us secrets of Reality, of Truth. These things don't really exist in my opinion. The subjective and objective distinction is a dichotomy that we imagine, but no person has ever experienced anything objectively because objectivity is a subjective supposition. In life, one does not have to establish beliefs and re-call them as though minds were made to be databases. If science isn't getting us to the sacred realm of Truth, than we can own the truths (the relative kind with a lower case 't') that we arbitrarily decide on a moment to moment basis. By using mystery instead of fighting it, we open up a new realm of experiences, we find frameworks that are useful in providing other kinds of information. Religion is out there for the taking. Truth is a myth, but truths are a choice.

G'Night. Scott.

Name: Matt Lowe Date: 2005-09-05 10:05:06 Link to this Comment: 15997

I have to admit that I have always believed that there is Truth. The idea that the true nature of something is not objectively knowable has caused me tremendous frustration for as long as I can remember. As others have said, the distinction between utility and reality is a valuable one, but for me its best application is a simple reminder that that which is useful is not necessarily reality, or Reality. There must be an equation that accounts for everything. It can be mapped, so how can it not be governed mathematically? Perhaps more accurately, everything is an interplay of discrete movements in space. This movement has to have a mathematical expression, doesn't it? The fact that most likely this will never be discovered only bothers me on a ideological level rather than a practical one. In fact, I feel like my willingness to doubt the accuracy of a story was often inspired by the best stories. Asking myself, "how can that be? how can the way this has been explained actually work?" in response to a wild but usually valid "new summary of observations" has done most of the work of piquing my interest in science, once the seeds were planted.

I do, however, have plenty of experience with people making arrogant conclusions from observation. Having been raised Catholic, I was informed on a regular basis that I was encountering Truth, that the grown-ups around me had figured it out and I needed only to accept their experimental method and I would be tapped in to this knowledge that managed to elude thousands of really, really smart people who work their whole lives to find it. No, thanks, I said from as early as I could articulate it, but maybe it's true that my ancestors found something that is both useful and fits a summary of observations, so to speak. I wonder how it ended up that I was proselytized from the Church to the church of science? Maybe I was so starved for proof that anything based on systematic physical observation was bound to appeal to me. I think it is true, though, that in finding something else that made sense I clung to it with a similar degree of faith as the folks in the pews did.

Evolution Name: Stephanie Date: 2005-09-07 19:46:53 Link to this Comment: 16043

Today in class, we were discussing "how the world might look in a million years" and how humans would probably become extinct someday. This kind of reminded me of planet of the apes.

Well this evening as I was doing some reading for a psych class, I came across a list of a bunch of things that apes can do and be taught. The problem with this is that this has all been done in a "lab" (or zoo) type of setting. Everything such as food and shelter were provided for the apes and they have no reason to "adapt". I was thinking that maybe someone should put apes (or other primates) into a situation where it would be advantageous for them to acquire a new skill and pass the skill on to their offspring. It has been documented that other primates can pass sign language to their offspring, but there is no advantage to having to learn sign language when you are being cared for by humans. It might be somewhat cruel to force animals to adapt like this, but it would make an interesting study.

Thoughts anyone?

week 2 Name: Paul Grobstein Date: 2005-09-09 15:32:48 Link to this Comment: 16071

Let's see. We've talked about what we mean by a "living" organism (and how we might want to broaden that definition to allow for future possibilities), and about not only those characteristics but also interdependent diversity and change over time as things that biologists need somehow to account for. And we've had a look at spatial scales, at size ranges where one does/doesn't see obvious signs of living organisms, life, and improbable assemblies. Any thoughts about any of that? Anything else come to your mind this week that would help us (and others) make sense of life?

the universe Name: katie Date: 2005-09-11 12:06:15 Link to this Comment: 16083

Despite my attempts to free my mind from all school-related matters Friday afternoon, I could not stop thinking about what I had just learned in Biology. After traveling millions of light years away from Earth, we were able to view distant galaxies, stars, and planets. It got me wondering: can we really be it? In the vastness of this universe, can Earth really be the only place that sustains life? Call me an optimist, or a dreamer, (or perhaps on in the same), but I am having great difficulty grappling with the idea that in this truly immense universe, living things only exist on Earth.

Friday’s class also got me thinking about my own significance in terms of the enormity of the universe. If earth is just small part of the Milky Way, what is my significance in the grand scheme of things? If you were to travel far enough away from the Earth, it appears to be just a dot in a lot of black, empty space. So, where am I in this dot, a dot inside of the dot? I know that sounds silly, but I am not sure how to explain all of this to myself and put my life in perspective in comparison to the size of the universe and all that it encompasses.

life elsewhere Name: Nick Date: 2005-09-11 14:57:51 Link to this Comment: 16084

A thought that struck me during class was something I had heard a while back in some science class somewhere, that the conditions on Earth are just right for life (as we know it). Its distance from the sun, the character of the atmosphere, the presence of tons and tons of water - all of this lends itself, at least in the case of Earth, to the creation and sustenance of life. As we moved back from the Earth a bit during class, I had an idea. If Earth is the ideal planet for life in our tiny solar system, maybe our solar system is an ideal system in the galactic sense. If the sustenance of life is primarily based on the Earth's distance from the sun, then maybe the same can be said for our solar system with respect to the center of the galaxy. As far as I know, we know the rough distance from our system to the center of the Milky Way. Maybe, if/when we get out of our solar system in the search for life, a good starting place may be to plot a circle around the galactic center which includes our system, and (if this is at all possible) search in this general area before moving in or out any farther. This is, of course, almost complete speculation on my part, but it struck me as an interesting hypothesis.

Life and the definition thereof Name: Zach Withe Date: 2005-09-11 16:32:08 Link to this Comment: 16085

I keep coming back to the definition of life we've been developing, and I still don't like it. I feel like we're taking too many derivative features of life and imagining them as definitive. Of course, a definition by definition is invented, so technically we could define life as whatever we wanted. Still, I feel that for purposes of understanding the universe, we're best off with a minimalist definition.

I'm trying to look at this one feature at a time. (highly improbable assembly, bounded, energy dependent) seems like the most fundamental set of features to me, although clearly this set includes much that is not life (stars, for example.) Semi-autonomous seems like the next really useful criterion, even though I'm not entirely comfortable with it. Do sea sponges have any semi-autonomous features? And reproduction, while it seems like a no-brainer, has problems we've already discussed. How about mules? And thinking back to the dawn of life, does it seem reasonable that the first billion or so organisms to be formed out of the primordial ooze might have lacked reproductive capabilities, and only later did one form that happened to have that capability? Were those first organisms life? If not, why not?

Where I really become uncomfortable, however, is when we start defining diversity and interdependence into the meaning of "life." These are phenomena of great importance and worthy of study, but I feel that the real question raised is "why does (insert definition of life here) invariably live in diverse interdependent communities". You basically kill the whole subject of study if you just assume that as part of the definition. It's like going back to "why is the world the way it is? Because God said so."

Life Name: Brom Date: 2005-09-11 17:19:57 Link to this Comment: 16088

I really had no idea how big the Universe was until Friday's class. I am still astounded at its size. I think the sheer size of the universe must be pointed to by many who believe in other forms of life, I would think the odds are in favor of there being life elsewhere. Has any mathematician tried to figure out the odds of life elsewhere in the universe?

Another factor leading me to believe that there is probably life somewhere else is based on carbon conversation we had on Friday. The carbon present in our solar system is the product of a supernova. Even if their was only one supernova in the history of the universe there would have to be carbon somewhere else besides here, I imagine the carbon would be thrown out in all directions in the event of the supernova. I think that supernovas are regular occurences so it seems likely to me that somewhere in the universe there is another carbon-based life form wandering around.

Lastly if the life is not carbon-based, what are other possibilities give serious consideration?

Name: keti Date: 2005-09-11 18:18:04 Link to this Comment: 16089

What is life? The American Heritage dictionary defines it as “the quality which distinguishes living organisms from dead organisms” or, alternately, “the interval between birth and death.” My roommate defines it as “everything that’s not rocks.” While the first is an authoritative definition, the second is actually more helpful. It reminds me of a class in which everyone was asked to define modernity. Nobody was able to offer a definitive answer but could only say what modernity was not. In a sense, this mode of classification (defining by opposition) might be more useful in our discussion of the nature of life. Firstly, it seems to go along with the idea of science as a process of getting it less wrong; characterizing life by what it is not as opposed to what it is allows room for error and for new discoveries. It is a way to recognize and classify patterns of life without essentializing the observations made.
I agree with the comments made in the previous forum that the denial of absolute truth does not negate the usefulness of science. That usefulness stems from its ability to tell us something at the most basic level, such as what exactly is that “interval between birth and death”? In our discussion on Friday (or Wednesday?), we talked about the need for scientists to modify their definition of life in relation to new discoveries on Mars. In this context, it would be interesting to consider a classification system which defines by opposition: in other words, life in terms of what it is not as opposed to what it is.

Name: Magda Mich Date: 2005-09-11 19:19:43 Link to this Comment: 16091

I was, like others, amazed at the presentation on the size of the universe. In a way, it was a real eye-opener; we spend so much time focusing on ourselves and on our personal issues that we often forget to take a step back and appreciate that we're part of a much, much larger picture.

I find it almost difficult to believe that the universe is finite; logic tells us it is, but contemplating all of those swirling galaxies really makes it seem like something infinite, something much larger than we're capable of comprehending. That itself got me thinking about how we as humans process things; the human brain, a squishy, grey mixture of cells, is capable of performing all of these intensely complex functions, and it's so tiny in relation to everything else. In that context, it seems highly unlikely that there isn't intelligent life--and how do we quantify "intellect" in that context, anyway?--out there aside from us.

Name: Stephanie Date: 2005-09-11 19:49:57 Link to this Comment: 16092

I have been thinking a lot about the magnitude of the universe. What strikes me is that the probability of us (here on Earth) being the only “life” in the whole universe is so infinitely small. It is highly likely that there are other forms of life out there somewhere. So what does this other life look like? I am curious about how far it has progressed on planets other than our own. If it is relatively new life, there may be only single-celled organisms. Maybe there is a comparable number of species on another planet to our own. Maybe a planet has progress past where Earth is and has more technology and can do things that are way cooler than we can even imagine.

My next question would be this: if there are planets more technologically advanced, which is likely, why have they not made some type of contact with us? Or maybe they have tried and the stories of UFO sightings are not urban legends after all. As a huge fan of the Hitchhiker’s Guide to the Galaxy, this is extremely intriguing to me. I want to travel to other planets and see other forms of life.

As for defining life, one thing we can be sure about is that our criteria for reproduction must be correct. Life anywhere must have a way of making new life, even if it is a way that is unfathomable to us. I would also imagine that life anywhere would need to be an improbably assembly. Perhaps boundedness may not be a property of life on other planets. I could imagine a scenario where there was something quite large and unbounded which ended up being alive. Also, being energy dependent could be different on other planets and we would have to come up with a definition of energy that fits other planets as well as our own. It may be a criteria on Earth for life to be semi-homeostatic and autonomous, but it could differ somewhere else. Of course, I cannot get out of my “earthy” way of thinking and cannot even begin to imagine what type of creatures might exist on another planet.

Then again, maybe Earth is the only place in the whole entire universe that has life. It’s possible, but unlikely.

Life, The Universe, and Everything... Name: Zack Date: 2005-09-11 21:06:42 Link to this Comment: 16093

I've long since abandoned any kind of hope that I'll see proof of extra-terrestial life in my lifetime. It's funny--the more our scientific understanding of the universe increases in detail, the further we seem to be from the kind of space travel necessary to do any kind of universe-exploring. We're left hoping that some superadvanced being will come find us.

Given the enormity of the Universe and the length of time it's been around, I'd say its a safe bet that there is life out there. And, assuming that some of the life has been around longer than us, it's also a safe bet that someone, somewhere, has developed some capacity for long-long-long distance travel. And, were some alien life forms to seek out other forms of life, I would guess that they would look for planetary/solar alignments having conditions for life similar to their own--which would mean that were we to be sought out and visited by an alien form of life, the odds are that they would be similar to us in some way.

I would also imagine that if we (humans) were to develop some way to explore outer space efficiently, which seems highly improbable at the moment, we would go out looking for a planetary system much like our own--because all we know about life involves a very specific situtation.

I'm going through all this guess-work for a reason: while I can be sure that there is other life out in the universe, chances are low that we will ever come into contact with it. And, if we do, chances are that we will not be exposed to some wildly different form of life--instead, the odds are that we'll find life most similar to our own form out of all the many possible configurations in the universe.

The question for me isn't whether or not there is life; instead, I wonder if we will ever be capable of conceiving the true possibilities of life, given the limitations I've written about above.

week2 Name: Iris Date: 2005-09-11 21:35:42 Link to this Comment: 16094

Seeing the universe at different scales surprised me because earth is such a small part of the entire picture. It lead me to question whether there is life some where else, which seems extremely possible since there are so many places that we have not been able to explore. The carbon atoms that became part of the earth came from a super nova, which explodes and sends parts to all directions. There may possibly be a twin earth out there with similar organisms as us or organisms that developed differently than we did, which we may look at and see as not having improbable assembly until focusing on it.
We also discussed interdependent diversity and stated that all organisms are embedded in food life as being a way to recognize life on another planet but this makes the assumption that the organisms of planet X are similar to earth’s living things. Seeing the differences in the planets of our galaxies it seems that organisms in planet X will have differences because organisms adapt to our environments for survival. These differences may have changed them in such a way that they do not need each other to live.
While posting I was also thinking about our periodic table and how we discover new elements. Can there be an element that we haven’t discovered? And if so maybe this element can be sustaining life in another planet. What is the possibility that a supernova spreads this unknown element across galaxies?

Between life and death? Name: Lizzy de V Date: 2005-09-11 22:25:38 Link to this Comment: 16096

In general, I am not one to automatically realize/make connections between science and some of my other interests, specifically art and politics. Sometimes certain statements, however, stand out and help me to realize just how integral science (particularly biology) is in every day life. The definition of alive which Keti provided was one such statement. The politics of Roe vs Wade and other abortion issues have always interested me. While I personally am pro-choice, I thoroughly respect the opinions of others. If we indeed go by the dictionary definition of alive, "between birth and death", then the fetus should not be considered a living being, and the arguments of many of those who are pro-choice are no longer valid. What I find fascinating about this particular concept is that if the dictionary's definition was altered even just slightly, the pro-choice argument could be strengthened far more than it ever has. If an organisms symbiotic relationship with a living being (i.e. a fetus connected to its mother by an umbilical cord) could serve as justification for calling that organism a living being itself, then abortion would be, for a fact, the termination of a life. I realize now that just the basic definiton of the word "life" also defines concepts far beyond the realm of science and biology.

The more things change, the more they stay the sam Name: Matt Date: 2005-09-12 00:30:12 Link to this Comment: 16097

What Lizzie discusses in her comments regarding abortion have been a major sticking point for me for a number of years. It points to a basic difference of definition that I would like to imagine has a reasonably definitive answer. An answer benefitting one side or the other would render the major arguments of the opposition moot, for all intents and purposes. Despite the fact that the argument could be settled with a real definition legitimizing one of the stances, the party lines in real life seem to be guided more by ideology than by an interest in discussing this disconnect and arriving at a rational answer.

To return to the interstellar context, despite the breadth of possibilities our imaginations allow us after seeing the demonstration on friday, a few things (to the best of my knowledge) are pretty universally true. Ill phrase them as questions, because I suspect I'd want to look for confirmation at each step. We know enough to conclude that everything in the universe is matter and energy, correct? That is to say, isn't everything in the universe is made up of protons, neutrons, and electrons, and the energy that makes them interact? Since these subatomic particles are discrete objects, wouldn't everything in the universe be governed by the sort of bean-counting that we perform on earth in our chemistry? The idea is that no matter where you are in the universe, an atom with 82 protons will be an atom of lead. So any complex bit of matter, anything other than a pure element would have to be composed of atoms, arranging themselves the way they arrange themselves on earth, because it seems that atomic forces and charges and interactions would be factual outside of our understanding of them on earth. So if life exists on some other planet, it's going to be composed of atoms and elements the way we are, and moreover, from the same basic collection of atoms and elements (one caveat here is that I can't remember what effect isotopes have on any of this stuff). This, it would seem, cuts down pretty drastically the number of possible forms extraterrestrial life may take. More specifically, it appears to demand that life would take a form Nearer to life on earth rather than Farther. Given this, our ability to distinguish something living from something nonliving would be pretty serviceable in our interstellar travels. Now if we could just get our hands on a ship...

the infinite limitations Name: Scott Shep Date: 2005-09-12 00:38:26 Link to this Comment: 16098

I am still having trouble with the way we are talking about life and life's characteristics. Others have pointed out that the definition can never be set because we have seen so little on our own planet, and I think this point is understated. As far as I can tell, the universe seems to be random, chaotic, irrational, but it also has yielded this thing we are calling life. On an essential level then, life is just a will to power. Some specific molecules happened to connect in ways that made it easier for them to connect again, and as soon as the ability to stay organized came into existence, it stayed in existence. To talk about the more complex problem of order and how it exists with chaos is impossible because our language and our mental frameworks forbid us from understanding paradoxes and supposedly incompatible dualities. What is important is that some organization exists, and at some arbitrary time human beings decided that one type of organization should be privileged over other types because their relationship with the world around them was more homeostatic and it created energy cycles and it was bounded and so on.
What I am arguing is that our particular classification is so evidently random because it is characterizing the results of one “Petri dish” (The Earth) when there are millions of other Petri dishes. Space, time, the limited ways in which human beings perceive the world (I say limited because we could be among millions of aliens all the time, and they could have order on five different sense levels, and they could interact with space and time in completely different ways. We are still stuck in the old mindset where we presuppose that we have an idea of what life is, when we are just drawing random lines in the sand. Maybe rocks are pods that protect aliens who are existing on a different plane of existence before our very eyes, but they experience time a billion faster than we do and they communicate through auratic telepathy. They might not even be able to talk about human beings at all, and look how close we think we are to them. I know this idea sounds crazy, but honestly if we’re talking about the universe and infinite then the craziest possibilities are exactly what we should be talking about. We must humble ourselves and realize that we are so isolated, so ignorant, and the definition of life we create is only useful on a social and political level. As far as truth, we shouldn’t even tempt ourselves with the word definition. Limited inference is more like it.

G’ night
--Scott

Categories Name: Zach Withe Date: 2005-09-16 09:45:08 Link to this Comment: 16173

I'm not satisfied with the treatment that categories of things have gotten so far. I continue to maintain that "categories", as such, are human contrivances. That said, I also agree entirely with the "clumpiness" idea, that there is a pattern to things in nature independent of observation. My thought is only that of the things in nature, which exist in a certain formation for certain reasons, one can detect many different possible patterns, depending on the attributes observed. The patterns are pre-existing, but categorization is not.

week 3 Name: Paul Grobstein Date: 2005-09-18 14:15:01 Link to this Comment: 16185

Reflections on this week? How seriously do we want to take "diversity" as an essential characteristic of life? In the one case we know, here on earth? In general? And how DOES that relate to "classification"/"categorization"? You are, of course, welcome to write about anything else that came to your mind this week. Check out the forum archive index if you want to get back to anything you/others have said.

value-free science Name: keti Date: 2005-09-18 18:47:28 Link to this Comment: 16195

To sum up a few points: evolution helps to account for what we are calling “clumpy diversity”. This means that it is a useful way not only to explain how those clumps came into existence but why there are gaps between them. In other words, the story of evolution is helpful in two ways: 1) in its descriptive capacity and 2) in its capacity to project ideas about possible life forms based on observations of living things (we look at what we know to exist to figure out what might exist). In this sense, the story of evolution is a useful scientific tool for describing patterns of life on earth.
Alternative concepts of evolution (the Great Chain of Being for example) are rejected by scientists on the basis that they are predicated on assumptions. For example, the illustration we looked at in class catergorizes life in hierarchical terms. Placing humans (or God) at the top of the chain suggests that man is the ends of the evolutionary process and attaches a value to science. But the story of evolution, if we are to call it a story, is just as much based on an assumption. This is to say that any story which seeks to explain presupposes that it can explain. The theory of evolution is not so diametrically opposed to alternative stories such as intelligent design. While it may not attach a moral value to science, the story of evolution shows that science is not value-free. In seeking to explain diversity, it assumes that it can explain it.

categories and clumpiness Name: katie Date: 2005-09-18 18:47:51 Link to this Comment: 16196

I agree with Zach that there inherently exists some sort of ‘natural clumpiness.’ I think that because of this natural clumpiness, the human race has imposed categories to serve as tools for organizing these ‘clumps’. These categories can be useful, especially in terms of making it easier for people to look at the world. Without categories, it would be too overwhelming for a human to process everything by itself (whether it be an organism, a concept, or life in general). However, I think that we often get ‘category-happy’ by trying to force things into categories that may not really fit. For example, let’s say there are only 6 categories of plants. If we discover a plant species that does not fit into one of these categories I think that people do not know what to do. Do we create a new category? Do we try to sneak it in to an already existing category? We have become so reliant upon fitting things into categories, that we lose sight of what they are truly useful for. I think that they are helpful in general purposes, but should not be relied upon to explain everything about life. That is simply asking too much.

Name: Nick Date: 2005-09-18 18:54:05 Link to this Comment: 16197

On the subject of diversity... Insofar as science is a utilitarian tool above all, then precise classification schemes are extremely useful for us to understand life for ourselves. Because we are humans, we have a certain way of understanding and naturally categorizing that which surrounds us, and so it is in one sense beside the point to concern ourselves with questions of "natural classification" or "natural diversity" - all that matters is that it makes sense to, and works for, our own needs or desires. In this way, classification is very useful. Blood donors can give to the right people, certain animals can be tested for medicinal purposes before humans, plants can be genetically altered, and so on...Classification is necessary for any of these developments, for good or ill. For whatever reason, the human way of categorizing the world has worked thus far, which would lend evidence to the point that this diversity naturally divides and organizes the world. My point, though, is that the idea of "naturalness", ie what the world would look like to a non-human observer or if no humans were present, is a pretty pointless line of questioning. There is no way to know, and, even if we did know, the world wouldn't look or feel any different to us.

Name: Magda Mich Date: 2005-09-18 20:47:24 Link to this Comment: 16199

I'm still thinking in terms of whether categories we use to organize living things exist or not. I find it very hard to be persuaded that categories exist inherently simply because we have evidence of diversity being "clumpy." I don't think that makes categories inherent; I think it just shows how the human psyche compartmentalizes things to make them easier to handle. I think evolution is the simple reason for clumpy diversity, and I'm content with that; maybe that just makes me stubborn. :)

Name: Brom Date: 2005-09-18 21:12:36 Link to this Comment: 16200

The idea that in no environment in the known world does just one organism exist, rather, that a system of organisms must exist in one environment for any organism to live, intriguiged me. The idea that life is a communal force, that in its very definition it depends on a diversity of organisms created an unexpected feeling of "everything is connected spirituality" within me. I am not really sure what this has to with the rest of the conversation but I found it satisfying and was wondering if others did.

Name: Zack Date: 2005-09-18 22:14:38 Link to this Comment: 16202

Clumpy diversity as a concept isn't unintuitive for me. Professor Grobstein mentioned that most things that have been alive are no longer alive. Clumpiness, it seems to me, could be a result of the difficulty of life--a lot of connecting points between clumps are lost to the past and extinction.

Nick has pointed out that we should not overlook the usefulness of science (in favor its "truthfulness") in our discussion. Categorization then, is a useful tool. Attempts to find similarity between species can lead to discoveries far beyond new arbitrary distinctions. Also, creating categories allows us to get started on our massive project of sorting through this mess of life on the planet. As long as we do not take them for gospel, I think the way we go about it is valid.

order and chaos Name: scott shep Date: 2005-09-18 22:39:30 Link to this Comment: 16204

Although I am reluctant to call anything Truth, I am also willing to admit that the consistent truths of perception (certain laws of physics, biological conceptualization, etc.) have more of an effect on my actual life than theoretical truths of abstract thought. So, looking at diversity and the pursuit of knowledge from a biological point of view, I believe evolution is absolutely the best story we have to describe clumpy diversity. It astounds me how chaos and order are not mutually exclusive, and I think how the two create one another is fundamental to our understanding of the universe. Every time physics makes a break through, it seems that a certain chaos persists inside the order (quantum theory observations). The big question for me is not necessarily creating a detailed account of evolution. It might be a fruitless enterprise to try and explain how the peacock got its patterns or to know precisely the order of evolution from prokaryotes up to humans, because the effects never completely contain the causes within them. Variables will always be overlooked for the simple answer, which is not always the right answer. So to plot the most complex and detailed chronological mapping of human evolution is an invitation for error. Sure, classifying organisms is useful, but only so useful. What is more interesting is this idea that an ordered force appeared despite the disorder and, at least on Earth, proved to find a relationship with the disorder. Things are here because at some point it did them better to be the way they were, and as we see, at times things could evolve because it was better for them to change, or if the changing wasn’t ‘better’ it at least did not bring about their immediate destruction. That is the real craziness—the world makes sense, and it makes non-sense at the same time—not necessarily because we don’t see the whole picture, but because it is fundamentally chaotic and ordered.

G'night
Scott

Week 3 Name: Iris Date: 2005-09-18 22:41:21 Link to this Comment: 16205

I believe diversity exists due to evolution, the constant changing of organisms creating different clumps, and that the empty spaces are simply organisms that never developed or possibly tried to but failed. There doesn’t seem to be anything else that can account for the clumping except the idea that an omnipotent being created it. Without humans, evolution would have still occurred maybe just a bit different but there would still be clumpiness. The categories are there, but we try to go beyond the bigger categories and sometimes this is where we influence the classification method. It becomes tinted by human ideas and beliefs so that each individual may group organisms differently. We may find one small similarity between organisms and group them together even though it may have the same number of similarities with other organisms. What makes one category better than another?? That it causes each clump to be small. So how far do we go in categorizing organisms? Until there’s one left or maybe two?? I was reminded of the movement by the multicultural students at Haverford to have a different box on the application for admission, which took into account that an individual could have more than one race. In their case, human categorization was limiting their choice to only one group and a new category needed to be created.

Name: Norma Date: 2005-09-19 00:46:23 Link to this Comment: 16207

In the past few years, I've come to fear categories, and class this week has made me think again about why. At first blush, categories in many fields of biology seem less dangerous than in other areas I'm used to thinking about. Essentializing members of a racial or religious group has obvious negative implication for how we see perceive particulars and treat individuals. But as the Great Chain of Being that we saw in class shows, it is difficult for the framework we use for categorizing plants and non-human animals to be seperate from our approaches to other sources of information and understanding of the universe.

As the course proceeds, I'll be interested to see how crucial evolution is in diversity. Last week, we seemed to place it at the center of modern biology's categories. Can organisms that evolve from different sources independantly develop significant common characteristics, to the point where they have more in common than species with the same ancestor?

Categorization Name: Stephanie Date: 2005-09-19 12:43:03 Link to this Comment: 16210

I forgot to post before class on Monday, so here it is:

I’ve been thinking about this whole clumpy diversity mess. Everything is viewed by different individuals in a different way. As we have seen from our labs, there are many ways to categorize life that aren’t necessary wrong, but aren’t necessarily fully right either. And for that matter, we may not ever be able to decide who is “less wrong”. As a linguistics/psych major, I have been thinking about how these categories relate to our language and how we always seem to express things in a hierarchy of categories useful to identifying the object. This is also necessarily the way that we categorize life. There are features that are more useful than others in identifying things. But this usefulness is all based on what is useful to humans. Where it might be useful for us to identify that the organism is a bird, then that it is a seagull, then that it is a blackback gull, then that it is an immature female blackback gull, these features might not be useful to a tiger.

Recently, I have been reading about animal communication. Animals too can categorize things, but they categorize them from a different perspective, which is equally as useful to them as well as equally as valid. For example, there is a type of monkey that has a different call for different types of organisms that it may encounter: it has a call for an airborne predator or a ground predator, and it calls louder when the predator is larger. Also, its food call distinguishes whether there is a lot of food or a little food. We can assume from this that other primates can then form categories and lump predators into separate categories for whether they are ground or airborne. We can also assume that animals can categorize things into what can be eaten, what cannot be eaten, what can be reproduced with and what cannot be reproduced with, what is a predator and what is not a predator. Thus, categorization is only as useful as the observer makes it out to be and I think that all categorization is valid and does “exist” in nature, but we cannot say that our way of categorizing things is better than any other.

evolution Name: kate Date: 2005-09-25 21:01:15 Link to this Comment: 16295

After talking in class on Friday about evolution it got me wondering about the process of current human evolution. I wonder if we are slowing or even stopping the process of evolution through our use of modern science and technology to create a race that strives to make people ‘fit in.’ If a child is born with webbed toes, the webbing is usually cut. Why do we do this? What if we were supposed to have this ‘mutation’ as part of the evolutionary process? I’m curious as to who has the authority to say what is a mutation, and what is the norm.

Name: keti Date: 2005-09-25 22:06:50 Link to this Comment: 16297

Our discussion about time scales made me think about the usefulness of science. When we start to consider millions and billions of years, not only does human life seem insignificant but human consciousness seems inadequate. Science is then extremely valuable in that it can describe events that lie outside human comprehension. To say that science is a leap of faith because it explains things outside human scales is a presumptuous statement: it asserts that human life is the eye through which all science and history is seen. But this is not true. Just as it is impossible for us to see tiny objects without a microscope it is also impossible to imagine the world billions of years ago without the aid of science. Science can actually take the place of the human eye and (attempt to) describe places and times outside of human scales.

Name: Norma Date: 2005-09-26 01:38:32 Link to this Comment: 16303

Professor Grobstein asked me to post the following email exchange:


My question: I never quite understood how much the standard current methods of
classifying life depend on evolution. I looked at a biology text book, and
it stressed that evolution was important in classification systems, but I
still don't understand how. When scientists break down life into species,
orders, etc, do they begin with observable differences or their
understanding of evolution? I'm not sure if question makes sense - I know
that diversity of life relates very much to evolution - but it seems to me
that these methods would yield different results. I'm trying to imagine a
classification system based on the final image you showed us in class, and having trouble.

His response:
Classification/systematics existed long before the development of the theory of evolution and
was, as we talked about, a significant part of the development of the
idea of evolution. The breakdown into "species, orders, etc"
actually predated the idea of evolution. What has happened in recent
times is that biologists have been trying to align classification
schemes based on "similarity" (this effort was termed "cladistics")
with classification schemes based on evolutionary descent (ie
biologists are not beginning with one or the other but working on the
problem of how they relate to one another).

For the most part, the alignment is strikingly good but there are and
will continue to be cases where questions arise (remember that, of
course, BOTH "similarity" and "descent" require indirect inferences
from actual observations and judgement calls). Among the issues
that is still in considerable question among biologists is the status
of higher order classification schemes ("macroevolution"). Are these
just larger clumps of smaller clumps of underlying diversity, with
the same processes of reproduction with variance and selection
operating in both cases? or is there something different/additional
going on in macroevolution? Most biologists (myself included) are
inclined to the former notion but there is certainly room for further
exploration on this front.

Yep, the final image I showed in class was intended, in part, to
raise questions (of the sort we discussed earlier) about any effort
to create a definitive classification system. We'll talk more about
this in class. Classification is an interesting, significant, and
quite general problem, not one specific to evolution or biology.
Michel Foucault, in The Order of Things: An Archeology of the
Human Science (1966) suggested that, among others "naturalists,
economists, and grammarians employed the same rules to define the the
objects proper to their own study, to form their concepts, to build
their theories". These rules, Foucalt suggests, have a common
underpinning in "essentialism", a presumption that things are and
have always been actually distinct and that those distinctions
reflect particular distinguishing characteristics (or sets of them)
that also have permanent significance. In these terms, evolution
(and related ways of thinking in other areas) are a major and quite
broad cultural shift in progress, to a way of thinking that
acknowledges much greater continuity among things and, as Foucault
puts it, seeks "the principle of their intelligibility only in their
own development". Things change in time, exist because of pasts, are
connected there, may be more or less similar now than they were then
and will be in the future. And so classification systems are always
and necessarily of use only in the present, and always subject to
change as the things being classified themselves change.

life, the universe and everything Name: Stephanie Date: 2005-09-26 09:50:01 Link to this Comment: 16310

After discussing evolution and the timescale that it occured on, I realize that the realization I made a few weeks ago needed to be drastically changed. When we had talked about how large the universe was, I said to myself "Wow, it is so highly improbably that Earth is the only planet with life on it out there." But now after seeing how long it took even to develop unicellular organisms and then each "cluster" after that, I said to myself, "Wow, it's so hard for life to develop and the conditions have to be just right. It's highly improbable that similar series of changes happened on any other planet except Earth."

So now I am stuck with conflicting feelings about the possibility of life outside of our planet. To one extent, I appreciate the vastness of the universe and realize that we are such a tiny planet, but to another extent, I think that our planet has developed specially: we have living things here.

week 5 Name: Paul Grobstein Date: 2005-10-02 13:24:07 Link to this Comment: 16413

So, we have enough of an overview of life, in space and time, to have a sense of what we need to account for. And, starting with the very small, it looks like we're going to have to try and account for it with .... assemblies of atoms, no more and no less. What do you think? Does the story make sense up to this point? Do you think we can do it? Is it worth trying? Conceptually? Practically?

blah Name: keti Date: 2005-10-02 13:42:08 Link to this Comment: 16414

So, what makes an improbable assembly distinctive from another lies not in which particular atoms constitute it but in the proportions of atoms. This means that possible life forms which might come to exist will be made up by the same atoms from which humans and other animals are constituted. The possible creation or appearance of new organisms lies in the possible assembly of a limited set of atoms. This leads us back to our discussion of clumpy diversity- namely how the gaps between clumps represent either species which once lived but did not survive or organisms which have not yet appeared. Do the rules governing the assembly/proportion of atoms dictate certain possibilities? In other words, is it possible to predict what life forms may come to exist in some distant future?

Name: kate Date: 2005-10-02 21:38:01 Link to this Comment: 16424

I think that Keti addresses an interesting point about predicting what life forms may come to exist in the future, given the possible assembly of only a limited set of atoms. However, given the number of random combinations that could be made from these few atoms, it seems nearly impossible to predict what the future will hold, especially because the environment, which is unpredictable in and of itself, plays such a huge role in the way molecules are formed.

This seems to relate to a chemistry colloquium that I attended last semester in which the professor discussed how changes in the atmosphere have affected the way metals bind in water. He discussed that as one gets deeper and deeper in ocean there is less oxygen, which affects how metals bind and which metals bind. These conditions mimic surface conditions from thousands of years ago when the atmosphere was very different than it is now. Here we see that the atmosphere plays a large role in the way elements are combined. Therefore, in terms of the future, it is difficult to determine what the atmosphere will be like and how it will affect living organisms, especially due to the use of modern technology and its unknown affect on the atmosphere.

I'd like to think I'm different Name: Lizzy Date: 2005-10-02 23:05:55 Link to this Comment: 16425

I want to be willing to accept that everything is made of atoms, just more or less of them. But then I look at the room around me, and think "How can that be possible?" This may seem like a ridiculous thought, but if I'm made up of atoms, and the desk is made up of atoms...why am I living, and its just a desk? I know, I know, improbable assembly. But what if I broke the desk into a million pieces, all of different sizes, some so small they could barely be held. Is that still improbable assembly? Isnt it just dust that looks the same as what would happen if you ground me up? Please tell me that there is more to it than this.

Unity Name: Zach Withe Date: 2005-10-02 23:42:03 Link to this Comment: 16426

So, we're all the same, huh? People and monkeys and ants and plants and rocks and trees and stars? Well, that's hard to get your head around... but it's not a new idea. The first time it occurred to me was some time in middle school, when after having learned the basics of chemistry and physics and evolution, I read in a book that any given water molecule in your body has been around for millions of years, having spent time in rivers, oceans, plants, dinosaurs, clouds, and pretty much everywhere else. It sort of came together for me at that point: So the universe came from the big bang, and the Earth formed out of the universe, and life formed out of the primordial ooze, and we evolved from life... there's no point at which "new stuff" is added. Some parts of the universe happened to end up as rocks, and other parts as humans. The first time I saw this formally presented in an academic setting was in a class on Buddhist Philosophy. The fundamental unity of everything is pretty much the basis of the whole religion. Whoever said that science and religion are opposed clearly hasn't spent too much time around either of them.

week 5 Name: Iris Date: 2005-10-03 00:37:45 Link to this Comment: 16427

One of the questions I had after the Sept 28 class was “where do other religions fit in the discussion of intelligent design vs. evolution? polytheist?” so I was glad when Zach mentioned the Buddhist religion in his comment.
When I first found out we are all composed of atoms, I became ecstatic. It was so long ago that I really don’t remember why. I think given my environment and witnessing people continuously ridiculing each other, being able to say that we are all made up of the same thing was something I clung to. I still find it difficult to look at a table and think about it being made up of atoms because I don’t think in terms of that scale. Yet, if I found out that there is life in another planet I would not be surprised. I would think about them being composed of atoms just like us. I guess it’s harder to think of non-living things being similar to us.

atoms Name: Sara Date: 2005-10-03 09:08:53 Link to this Comment: 16430

This atom thing is pretty intense. I mean the idea that we aren't so special and are made up of the same things as every other thing is a pretty tough concept. And how can something as seemingly simple as arrangement account for such diversity. I feel like I am pretty different from a bacteria but maybe not. Maybe I am so used to the biological heirarchy and thats why it is so hard to understand that we are all the same. With such a limited amount of building blocks could we play with atoms and predict what other living things would look like?

Testable Hypotheses Name: Norma Date: 2005-10-03 09:44:03 Link to this Comment: 16431

As I wrote my lab report, I realized that I had trouble evaluating when a hypothesis is testable. I know that testable hypotheses have to be disprovable, but I’m having trouble figuring out exactly what this means. Professor Grobstein said in lab two weeks ago that the hypothesis “cell size and organism size are linearly correlated” is not testable, I don’t remember why he said it wasn’t, but I think that the problem with this hypothesis is that more data could show a linear correlation. Keti and I hypothesized that larger organisms have larger cells. It seems to me that enough data could prove that cell size is not proportionate to species size – but I’m not sure how this is different
from enough data showing that there’s a linear correlation? How, more generally, should one think about whether a hypothesis is testable?

Name: Paul Grobstein Date: 2005-10-03 10:21:23 Link to this Comment: 16432

I think/hope I'm being misremembered/misquoted. A "testable" hypothesis is one for which there are, in principle, future observations that will DISprove it. What I suggested was NOT a "testable" hypothesis was "there is some relation between cell size and organism size". Since there are an infinite number of conceivable "relations", one could never make a set of observations that would exclude all of them. "Cell size is proportional to organism size" is a more "testable" hypothesis in the sense that there is a well-defined relationship to be evaluated and a give set of observations could in fact show that that relationship does not exist.

Could a more extensive set of observations show subsequently that that relationship does in fact exist? ie that the initial sample was, for example. poorly chosen or too noisy, and that a relationship it doesn't show appears with a larger sample? Yep, I guess that could indeed happen and so one might prematurely reject a "testable" hypothesis. Still, though, it is the ability to make observatiions that falsify the hypothesis rather than to support it that is key to the "testable" idea.

Name: Magda M. Date: 2005-10-06 22:52:29 Link to this Comment: 16489

I'm sure we'll be talking more about this in a later class, but I made the (potentially?) obvious connection between the electric charges of hydrocarbons and their role in the lipid bilayer. This was the first time that the whole point of discussing electric charges in a bio class honestly made sense.

I can't remember if it came up in discussion, but I was just wondering where the charge came from. Are all atoms present in the universe charged either negatively or positively? Are there any neutral atoms? Does it have anything at all to do with the earth's magnetic orientation? Just wondering...

enzymes Name: kate drisc Date: 2005-10-16 19:43:59 Link to this Comment: 16514

Last week we began to touch upon the role of enzymes in biology. I was surfing the web, looking at some of the links on serendip, and saw this cool website (http://bio.winona.edu/berg/ANIMTNS/allostan.gif) that showed how some enzymes need to be activated by something before it is able to perform its function. It got me thinking: How many enzymes in our body are not functioning because they have not been activated? Or, how many enzymes are activated a day?

After looking at the website it also got me thinking about the level of difficulty of finding the component that is the perfect fit to activate an enzyme. On the website it looks like all you need is the special key or the magic password to activate an enzyme, but somehow I fear that it is a bit more complicated.

Water weights Name: Norma Date: 2005-10-16 20:54:08 Link to this Comment: 16515

If water is the same whether in liquid, gas or solid form,why does it change weight? If the same amount of water always contains the same amount of "stuff," shouldn't it weigh the same? Or do the molecules spread out or expand depending on what form the water takes? Can changing the condition of a substance change its weight?

activating enzymes Name: Lizzy Date: 2005-10-16 23:52:18 Link to this Comment: 16517

Kate said in her comment that enzymes need to be activated by something to perform their function (at leat she said something like that). Does this mean that certain nutrients/ ingredients which we ingest activate enzymes, or certain actions. When we exercise, aren't some enzymes activated? Does energy in the body activate enzymes?

Name: Date: 2005-10-17 00:39:56 Link to this Comment: 16518

I was varnishing a kayak this break, and in the haze of the fumes I thought to look at the ingredients, which listed only "aliphatic hydrocarbons". Apparently aliphatic just refers to a molecule where the carbons are strung in a chain - do I remember correctly, that this is basically true of all hydrocarbons? How simple...of course you cover a boat with not just any hard stuff but stuff that is nonporous to water on a molecular level. this revelation partially demystified the applied, product-oriented realm of scientific research: looking for a certain result, work with types of chemicals whose properties are already well-known and combine them till the desired result occurs...

The part about life comes in after the boat gets launched. In the middle of the river, I felt like I had left the living world behind, that I was observing it from a distance. I had long passed the last bug that flew too far from land foundering in the water, and trees and human activity bustled in the distance on the shores. The fact that there was no such separation was proven with just a glance down - the water was packed with white sea nettles (and certainly lots of other stuff). The system is inescapable. The more I think about it, the more plausible seems the claim that the earth itself (or its ecosystem, or its outer layer, or whatever division) is a living thing. Of course, this is problematic in light of the guidelines we have established; for instance, we have never seen the planet reproduce. But, it is definitely an improbable assembly with organized, self-replicating systems that ensure the continuing function of other systems. Even if the "life" of the planet is only metaphorical, it is a useful metaphor, because the planet can be killed. Anyway, maybe the "life" of plants and animals is just another useful metaphor.

The more things change, the more they stay the sam Name: Matt Date: 2005-10-17 00:40:58 Link to this Comment: 16519

sorry, that last one was from me.

week 7 Name: Paul Grobstein Date: 2005-10-23 11:29:04 Link to this Comment: 16586

You're free, as always, to write about whatever you're been thinking about this week. But, if you need something to get you started ... we've spent a fair amount of time at this point looking at macromolecules. What's your feeling about the extent to which macromolecules do/do not help us to understand life? To see how it might in fact be possible to account for the properties of living things that we said had to be accounted for during the first part of the course on the presumption that they are in fact nothing more (and nothing less) than improbable assemblies of atoms?

Name: Norma Date: 2005-10-23 15:15:48 Link to this Comment: 16592

Macromolecules help account for how organism have many of the properties of life that we laid out at the beginning of the course, but how much has what we’ve studied shed light on why organisms have these features? Studying proteins has helped us understand how organisms are semi-homeostatic – enzymes can facilitate self-regulating reactions. We can infer how this ability might be helpful to life, but no clear purpose follows from this property. Macromolecules help explain how organisms are improbably assembled – what components and assembly rules serve as the building blocks for life. The “why” is clearer here, as implied by specific functions, such as the structural stability that proteins provide. Mutations in nucleic acids contribute to variations in reproduction – again, one can speculate about why reproducing with variation might facilitate survival, but examining macromolecules doesn’t provide clues. As far as I can tell, what we’ve studied about macromolecules so far doesn’t shed light on three other properties of life: that organisms are bounded, semi-autonomous and energy dependent.

Protein and Improbability Name: Zach W Date: 2005-10-23 17:25:28 Link to this Comment: 16597

All known life is DNA-and-protein based, correct? That seems even more improbable than the fact that such complicated macromolecules could have come into being by random processes in the first place. It simply seems mind-boggling that only these very specific types of macromolecules are capable of producing the characteristics we attribute to "life". But if that were not the case, why would we not see "life" based on much simpler molecular structures? Even virii are DNA wrapped in a protein sheath. Even the simplest life is constructed on its most basic level of phenomenally complex structures. It just seems odd.

Name: Keti Date: 2005-10-23 20:58:33 Link to this Comment: 16600

I agree to a certain extent that macromolecules help account for the properties of life that we have discussed. My concern is not so much Norma’s question of why organisms have these features; that I can understand. Rather my problem lies with the assertion that the explanation of all life can be reduced to improbable assemblies of atoms. If this is true, how do environmental factors outside the body affect the workings of macromolecules within it? I was thinking of my paper about autoimmmune disorders in which certain genetic regions may contribute to gene susceptibility while unknown environmental factors can “trigger” symptoms as well as affect their post-onset progression. In studies done on identical twins in which one twin is affected by MS, it is can be 50% more likely that the second twin will develop the disease. But this leaves us with another 50% unaccounted for by genetics. So then how are environmental factors outside the body accounted for by improbable assemblies of atoms within it?

Fixing DNA Name: Brom Snyde Date: 2005-10-23 21:48:36 Link to this Comment: 16602

I just finished reading an article in the New York Times about the building of "nanocars" and "nanotrucks" that are capable of carrying molecules to a specific location(the article can be read at http://www.nytimes.com/2005/10/21/technology/21cnd-nano.html). Currently the focus of the research is for the manufacture of computer technology but it got me thinking about its uses in biology particularly to fix DNA. Assuming certain genetic disorders are caused by point mutations, a vehicle that could deliver the correct nucleic acid to the point on the DNA where the mutation has occurred would be invaluable in fixing the problem. Obviously the new nucleic acid has to replace the problematic nucleic acid currently in the DNA, but having a method of delivery at least makes this more feasible. Another idea would be to replace the incorrect nucleic acids on the RNA before it is read by the ribosome and proteins are manufactured. I am not sure if any what I have mentioned is really feasible but the ability to transport individual molecules opens the door for fixing genetic diseases on a moleucular level.

DNA Name: Magda M. Date: 2005-10-23 22:00:48 Link to this Comment: 16603

I still don't quite understand how, during DNA replication, bases are only supposed to connect with certain other bases but then, at times, there's an exception. Why would textbooks and lectures phrase things as if that was always the case, when in reality there is the possibility of one base connecting with another to which it normally doesn't?

Macromolecules Name: Nick Date: 2005-10-24 01:28:53 Link to this Comment: 16606

The more I think about macromolecules, the more astonished I grow. This is especially true with the proteins. Talking in class about the literally endless combinations of amino acids that can be strung together has me amazed that anything can stay alive at all. This is especially true considering the fragility of living systems (ie one misplaced amino acid -> potentially lethal situation). I'm really surprised that more RNA messages aren't messed up somewhere along the line. I guess we have however many years of evolution on our side to make sure that things run pretty well, but it's hard for me to think that more disastrous things don't happen to living systems on a more regular basis, with so many proteins being created at all times. Even if such an occurence were one in a million, this would mean that most living things would fall apart within a fraction of their lifespan.

nano take over Name: Scott Shep Date: 2005-10-24 01:30:55 Link to this Comment: 16607

Responding to Brom’s thoughts about nanotechnology and their potential usefulness for a new way to alter the molecular structure of DNA, I was thinking about the potential danger of nanobots and a new form of evolution. Granted, these Michael Crichton informed worries are not intended to sensationalize the situation, but by creating enormous amounts of infinitesimal bots that can reproduce we are giving them the opportunity to evolve and become dominant, destructive organisms. Regardless of how we program these bots, as soon as they begin replicating themselves they are influenced by the same evolutionary forces as every other self-replicating organism. It takes one mistake in replication, and by mistake I only mean that the nanobot does not accomplish the types of acts that the program designates, and if this mistake makes survival any better for the bots, than these bots will begin to overtake the original bots. I imagine a world where we will be making strains of nanobots to fight defected strains. But the powers of variances and randomness have created something as complex as human beings, and there is no telling the ways which natural variances could make nanobots that could cause irreparable harm to the human race they originally served. DNA seems to work so well not because it is a flawless system, but because replication and translation are happening on such a small scale thousands of times over in different parts of the body that the counterproductive errors will have little success in perpetuating themselves if they are not helping the body that depends on their regeneration. Kind of like a biting the hand that feeds you. What we have to question with nanotechnology is how soon will the “dog” be big enough that he can make the humans his dinner—bypass the hand and go straight for the heart.

Week 7 Name: Iris Date: 2005-10-24 01:59:49 Link to this Comment: 16608

So when an RNA or DNA is coded incorrectly or other mistakes occur how long will it take for corrections to take effect? Will these be passed to future generations(since in class it was stated that our parents' DNA isn't directly affecting us as much as past DNA )? Are these mistakes what causes some cancers? because many doctors state that some cancers are passed down. Can we tell if an error occurred within ourselves or if it came like that?

Name: Lizzy Date: 2005-10-24 09:44:49 Link to this Comment: 16610

Iris' post reminded me of something I have always been concerned about. We have learned it is the DNA of past generations which is passed along, not neccessarily the DNA of our parents. In my family, most of the members of the generations above my parents were killed in the Holocaust at a very young age. Nothing is known about their genetics, about what disorders or ailments they may have had to deal with in their later years. We don't even know much about their health as young people, because of the conditions they were being exposed to during that terrible time period. In such cases, how are we to understand our own genetics without a history to base them on?

Name: Date: 2005-10-24 10:38:54 Link to this Comment: 16612

what i've been trying to figure out is how mutations , which must necessarily occur basically at a very specific, cellular level extend their influence into the other cells of an organ or organism. That is, when mutation occurs, how does the mutation synchronize within the category of cell? is only uncoordinated, destructive mutation able to occur in a living being, with constructive mutation only occuring in the reproductive stage? What is the state of an organ with different, possibly conflicting genes in close proximity? Is there a more central question that I'm missing?

not good Name: Date: 2005-10-30 16:46:47 Link to this Comment: 16699

not good...u didnt help me in my hw...so fu!!!

week 8 Name: Paul Grobstein Date: 2005-10-30 18:47:50 Link to this Comment: 16701

So ... we've finished with macromolecules (for now) and started thinking about "energy" and change. With the starting ideas that living things don't consume energy (or matter), they simply transform it, and that change tends to be from less probable to more probable. What does that (or anything else we talked about last week) make you think/wonder about life, about life as we are trying to understand it in this course?

entropy Name: kate drisc Date: 2005-10-30 19:55:04 Link to this Comment: 16706

At the end of the last class we began to discuss the Second Law of Thermodynamics, which establishes the relationship between entropy levels in isolated systems. I think that it is really interesting that everything is moving towards a more chaotic state. It led to think to about human society as a system. If we did not impose “order”, ie. rules, laws, norms, etc. would our society be moving towards an increased state of chaos? How similar is this “isolated system” referred to in the Second Law of Thermodynamics to human nature and the human system? It is interesting that “order” is not a natural state, and that it is forced on systems to limit the chaos/disorder. It leads to me to question if introducing “order” into systems is really improving it any way, or if we are losing an essential part of that system by inhibiting its natural flow towards chaos.

What matters Name: Iris Date: 2005-10-30 21:30:13 Link to this Comment: 16709

Thinking about isolated systems is a bit confusing because it leads me to question what is an isolated system or how isolated does a system have to be. For example, you stated putting someone in a box with a sandwich would be isolation but is there a natural isolated system (earth, galaxy & universe). This is relevant to the discussion we had earlier in the semester, when looking at larger scales, about the black hole sucking in matter. Doesn't this go against the 1st law of thermodynamics because matter is being consumed? Or is it believed that the black hole has transformed the matter?

The 1st law helps to understand how organisms are connected.

Name: Keti Date: 2005-10-30 22:13:22 Link to this Comment: 16712

The Second Law of Thermodynamics may seem to suggest some interesting ideas about order and chaos, about the nature of society as a chaotic system restricted only by legal structures and institutions. In fact, some political theorists would argue that the world structure is one of anarchy, necessitating governments to combat the anarchic tendencies. While this is all very fascinating, I think it is much more interesting that this movement towards chaos in isolated systems occurs through very ordered processes. Chemical reactions which take place are precise enough that we have equations and formulas to describe them. If change is from less probable assemblies to more probable ones, this change occurs through ordered interactions.

Name: Lizzy Date: 2005-10-30 23:18:00 Link to this Comment: 16713

I agree with Keti that the most interesting part of theories of chaos are how truly organized they ultimately are. Everything happens in patterns, with reasons. Is this actually, perhaps, the main reason we study biology? Without learning the ordered processes which govern our bodies and environments, it really could seem that our lives are a matter of the results of chaos. I'm not sure if most biologists would agree with me, but in my personal opinion, this more philosophical view of life can offer a better understanding to more people than a purely scientific explanation can. Many people are true scientists, but those of us who aren't would like an opportunity to understand why things are the way they are as well.

Name: Magda M. Date: 2005-10-30 23:32:41 Link to this Comment: 16714

I like the idea within the Second Law of Thermodynamics, but I would like to see a few examples of things generally rolling towards a stop. If the natural state of things is inclined towards reaching inertia, why does life continue to function? Why does matter continue to be converted rather than just stopping? The abstract construction of the "law" makes it a bit difficult to see how it applies to biology (whereas it's much easier to see its correlation with physics).

Name: Norma Date: 2005-10-30 23:48:30 Link to this Comment: 16715

In light of Keti's comment that rules so precise that we can describe them by formula govern increasing order: do these rules ever develop? If so, we could view the development of these rules as part of the process of creating order. Keti talked about political systems; humans are part of these systems and are responsible for the imposition of order. Similarly, could rules that increase order develop within an organism, or are they simply derived on pre-existing laws of physics?

On a more basic level, I don't understand why entropy, or disorder, increases when a system moves from a less probable to more probable state. When something becomes more probable it is less chaotic, right? Then how is there more disorder? What would this look like?

Name: Date: 2005-10-31 00:41:37 Link to this Comment: 16716

The fact that life surrounds us seems to disrupt what we know about thermodynamics and entropy. To say that the "base" of everything is chaos and that any kind of organization will only crumble in time is a distressing scientific "truth." However, that kind of reasoning gets us nowhere, even if it is accurate. We must make distinctions between what is unnatural and what is improbable. Life is not an exception to a rule--just an example of a rule that doesn't apply to most situations. And, seeing as how life involves transformations of energy and matter, who is to say that a greater kind of organization will not evolve? Why not think that the more life grows and varies, the more it changes its situation so that the former "improbable assemblies" are now the probable ones?

Name: Zack G. Date: 2005-10-31 00:41:50 Link to this Comment: 16717

The fact that life surrounds us seems to disrupt what we know about thermodynamics and entropy. To say that the "base" of everything is chaos and that any kind of organization will only crumble in time is a distressing scientific "truth." However, that kind of reasoning gets us nowhere, even if it is accurate. We must make distinctions between what is unnatural and what is improbable. Life is not an exception to a rule--just an example of a rule that doesn't apply to most situations. And, seeing as how life involves transformations of energy and matter, who is to say that a greater kind of organization will not evolve? Why not think that the more life grows and varies, the more it changes its situation so that the former "improbable assemblies" are now the probable ones?

Name: Brom Date: 2005-10-31 02:39:38 Link to this Comment: 16718

The argument that "order" is unnatural I think is a flawed one. Order is an improbable element within the closed system that is the universe, but nonetheless order has always been a part of the system. As Keti points the processes that drive the system towards chaos exhibit an order, they dictate that atoms will act a certain way in certain situations. I think it is more useful to think of the processes occuring in the universe within a spectrum of creative or destructive actions. Regardless of where a process falls in this spectrum it is subject to certain theoretical guidelines.

entropy Name: Stephanie Date: 2005-10-31 10:14:11 Link to this Comment: 16721

I've been thinking a lot about entropy (that systems will always move from a more probable state to a less probable state). It seems that this doesn't accound for how things get to the more probable state in the first place. In my csem last semester we talked about this concept in relation to time, but I don't remember what we concluded about it. The example we discussed was this: if you have an egg, it is likely that the egg will break, thus fulfilling the second law of thermodynamics. The egg is in an improbable state, but after it is broken, it is in an probably state. But how did the egg come to be in the improbable state of being an egg? At some point in time, it must have gotten larger and gained matter from its surroundings, becoming more and more improbable of an assembly. How should this be accounted for?

Name: Matt Date: 2005-10-31 10:30:20 Link to this Comment: 16722

Thinking about chaos and order and entropy, I encountered a thought that I couldn't shake. The whole planet full of life, full of improbable assemblies seemed so vast and varied that it occupied the entirety of the planet. All this talk about improbable assemblies made me think about what it would be to be a probable assembly - maybe the crystalline structure of metal ore or packed particles of sedimentary rock. Thinking as big as I could, even to famous natural formations, it seemed that there was nothing that would have been the work of an engineer rather than a sculptor. The enormous gulf between the level of organization in the living versus the nonliving world is overwhelming. Is it just that this latter part lacks certain tools that require enormously detailed and complicated structures to change their own state or ultimately return to a comparatively inert state?

Lucky us.

and on ... Name: Paul Grobstein Date: 2005-11-06 22:26:46 Link to this Comment: 16837

So, we now know something about why sugar doesn't fall from the sky (it does, but so slowly that ...) but not everything (throw some enzymes up there and you still wouldn't get much), so what else is going on with living things? What are these "higher levels of organization we keep mentioning? Is that just a way of saying everything we've learned about atoms and molecules and macromolecules is irrelevant to the real questions or .... ? Your thoughts on that, or anything else that occurred to you last week?

Name: Nick Date: 2005-11-06 22:52:57 Link to this Comment: 16838

This discussion takes us back to our very early discussions of truth and science (ie getting it less wrong, yet using our "knowledge" practically). Macromolecules and "lower" levels of organization are undeniably important to any proper discussion of life, but the discussion of lower levels cannot overshadow the bigger picture, as it were. Macromolecules become useful to living systems only insofar as they function as a part of a larger organization, as in specialized cells. We can't truly understand, for example, a muscle cell without knowing the specific types of macromolecules present, and in the same way, we shouldn't let ourselves get so bogged down in those specific macromolecules as to lose the overall structure and function of muscles. Cells, and organs, and living entities are what give meaning to macromolecules for us, and macromolecules, though important, should only concern us insofar as they help describe cells, organs, and living systems.

its like an oxygen bouncer Name: Scott Date: 2005-11-06 22:56:06 Link to this Comment: 16839

So, if we are going to compare what is going on in autotrophic cells, namely plants, I think a useful metaphor is a dance club where there is an overzealous bouncer. Sugar is created in the sky, but not in high quantities, and even with enzymes it would still not be in high quantities, and this has to do with the structure of the plant cell. We know that photosynthesis moves molecules from a more probable state to a less probable one because hydrogen, which is more likely to stay with its oxygen goes to the glucose molecule. So, I think somehow the structure of the plant cell pulls oxygen away, or kicks it out while light shakes loose the bonds of CO2 and H20. I'm sure this has something to do with chlorophyl, so somehow the properties of oxygen are being used against it so that it gives the hydrogen and carbon a chance to "dance". Either its electronegativity attracts it to a part of the plant that the carbon and hydrogen are less likely to go--a "chill room" of the plant cell where only oxygen can hang out, or some part of the plant structure acts as a bouncer to kick the highly electronegative oxygen molecules out of the vicinity of the glucose. I'm not sure exactly what is going on, but the properties of oxygen are such that the plant structure can use these properties to separate oxygen from its probable molecular configurations, forcing hydrogen and carbon to improbably "hook up", and the result is pretty hot and sweet.

Name: keti Date: 2005-11-06 23:16:44 Link to this Comment: 16840

Let me get this straight...order as we are defining it means the production of disorder. Energy from the sun drives a process through which the less probable becomes more probable. So, the “downhill” movement comes from the fact that things are falling apart and creating more order. If there is always an overall loss of organization, does this means that all processes which sustain life invariably create waste? Furthermore, if one of the links in the chain disappeared or was made to disappear, all life would cease to exist. But if we are saying that it takes spontaneous processes to create improbable assemblies, what’s to prevent one such spontaneous process to occur which does just this- that is, break the chain. I am very troubled by this. Good night.

Probable effects of improbable situations Name: Zach W Date: 2005-11-06 23:41:15 Link to this Comment: 16843

What seems worth remembering to me is that improbable configurations subscribe to the same laws as probable ones. With that in mind, it's easier to see why tremendously improbable systems don't immediately collapse under their own weight. What is improbable is that a living system would spontaneously arise out of unorganized matter. Once organized, it is entirely probable that it will continue to work, just as probably as that the sun will continue to burn or the magma in the Earth will continue to flow. It's just what atoms and molecules in that configuration do.

Name: Lizzy Date: 2005-11-06 23:53:52 Link to this Comment: 16844

To continue with the theme of being puzzled by science...I really am very confused about this whole concept of "improbability". It seems that throughout this entire course, we have been learning to indentify improbabilities in life, in nature, in science. Are we then, in fact, learning that to make any sense of science, we should understand that things do not really make sense? How have we been teaching students facts and equations, if life is really just...random? I realize maybe this sounds like a bunch of mumbo-jumbo, but perhaps it is just more of an improbable assembly of ideas?

probs Name: IM Date: 2005-11-07 03:39:29 Link to this Comment: 16846

I find it amazing that all these improbabilities & probalities together keep us (improbable)going. Since we are improbable, it seems more probable for something to stop working (like the lungs) then us being healthy. We are constantly battling against the probable.

Name: Norma Date: 2005-11-07 03:39:47 Link to this Comment: 16847

I disagree with Nick's argument that we should only pay attention to macromocules insofar as the help us describe cells, organs and living systems. First, I'm not sure if any macromolecule on earth (or in the universe?) could be completely independent from life given how intertwined life is with its environment. Second, even if some macromolecules contribute little or nothing to our understanding of life, they may be interesting in their own right - because of other affects, or for their own sake. While life certainly seems like a more interesting line of inquiry to me, I don't think we should close off others.

order/stability Name: kate Date: 2005-11-07 06:54:48 Link to this Comment: 16848

I have to say that I find it very interesting that “order” depends on the continuing production of disorder. Going back to my example of the humaman system, if we were to apply this concept it would mean that order is being created because of the constant disorder of society. This seems to fit because if the world weren’t disorederly there would be no need for our imposed “order”, ie. rules, laws, etc. I also find it interesting that “stable” order may reflect slower rates of falling apart. This too I think can be applied to the human system, in which a law or certain social construction is created to maintain “order” but upon closer observation the society slowly falling apart, as crime rates increase, laws are no longer followed, etc. and the imposed “order” slowly falls apart. Of course if this were to continue on a grand scale, the world would probably be in a state of anarchy. But, I think that it still think that it is a possible valid relationship between order, stability, randomness and society.

Name: Stephanie Date: 2005-11-07 10:47:43 Link to this Comment: 16851

When you think about falling apart in terms of life and the human body, we are falling apart pretty quickly compared to many substances. Does this mean that every disease we have or injury we incur is causing us to fall apart faster than we would have originally? Could there be a set amount of time that each of us would "fall apart in" if we never had anything wrong with us?

Cells as assembies of macromolecules Name: Paul Grobstein Date: 2005-11-13 18:34:08 Link to this Comment: 16957

So .... cells are assemblies of macromolecules. And that can help us make sense of boundedness and movement/reaction, and semi-autonomy? What do you think of the progress we're making? Of lipids and membranes as slowing down the loss of improbability? Of protein shape change as giving still more important properties of living things, like reactivity and spontaneous activity? Can we quit or is there more to look for?

Name: Keti Date: 2005-11-13 20:06:46 Link to this Comment: 16960

Is the conclusion then, if there ever can be a conclusion in a scientific story without Truth, that life can be reduced to the functioning of macromolecules¡¦? We are saying that macromolecules are important in that they are a part of the bigger picture, that making sense of cells helps make sense of the properties of life (boundedness, semi-autonomy, etc). While I think it is important to look at macromolecules as they fit into larger structures, we then have to look at how organisms themselves fit into larger structures. In other words, this presents us with the question of how humans fit into society. To go back to the diagram linking life and the second law of thermodynamics, at the level of biology, the term ¡°culture¡± is included. How then do the properties we have discussed account for such a thing as culture, given that we have discussed these features in terms of lipids and protein shape. Just as the little yellow box tells us: molecules are important but as they fit into the bigger picture; genes are important as they fit into the bigger picture; humans are important as they fit into the bigger picture. So what is the bigger picture and how does biology account for it?

Name: Norma Date: 2005-11-14 01:40:02 Link to this Comment: 16963

While we've accounting for most of the properties of life, there are all kinds of questions that we must do more to be able to answer. Just thinking about the human digestive system, say: how do we break down food? How does food translate into energy? Why do I need green vegetables? We need to talk more about how cells and organs interact within an organism - and how organism affect their enviroments and each other.

little yellow box Name: kate Date: 2005-11-14 08:28:52 Link to this Comment: 16966

The little yellow box has got me thinking. Molecules, genes, and individuals ¡°are important, they do affect the bigger picture, but they in turn are influenced by and derive significance from the bigger picture that they are part of.¡± However, I think that there is a difference between molecules, genes and humans in terms of ¡°being influenced by and deriving significance from the bigger picture they are part of.¡± I think that molecules and genes seem to be influenced by more mechanical, biology, chemistry and physics while individuals seem to be affected by more intangible concepts like societal norms, values and morals. So, is it easier to identify how molecules and genes are influenced by the bigger picture in comparison to individuals? How do we compare all of these things on the same level?

Explanation from components Name: Zach W Date: 2005-11-14 08:51:46 Link to this Comment: 16967

Life can't be explained simply from the properties of macromolecules any more than a house can be explained from the properties of bricks. Knowing only the properties of brick, you can explain why the house stands up and predict under what circumstances it will continue to stand up and what maintenance it will need. What you can't explain, however, is how the house got there, or why it's organized the way it is. For that, you need either to appeal to higher intelligence - someone built it that way - or a complex chain of historical accident which led to the assembly of a house in this location.

Name: Brom Date: 2005-11-14 10:19:42 Link to this Comment: 16968

As our exploration of life's organization and structure (macromolecules and how they work) continues it seems as if we are moving farther and farther away from determining what life really is, I realize that this is a search for truth and will probably be fruitless but it seems to be a question religion is much more likely to tackle. The study of macromolecules by scientists is interesting for two reasons, first that it does help describe how living things work but secondly it illustrates the methodology that scientists use, the constant reevaluation of current information to develop a new and different understanding of what is going on in the world around them. Science's examination of life and its workings requires a much greater willingness to accept new information and incorporate it your understanding of the world, most religions do not, and this simplicity of most religions( i.e. accept this piecce of information as absolute truth and it will not change in your lifetime) holds attraction for many.

Interesting article Name: Stephanie Date: 2005-11-19 19:26:57 Link to this Comment: 17079

I thought that this article about the Earth was really interesting. Enjoy!

just looking Name: Iris Date: 2005-11-20 20:52:17 Link to this Comment: 17102

Thanks a lot for that link.

Name: Lizzy Date: 2005-11-20 21:41:00 Link to this Comment: 17103

A few classes ago, we were asked whether we would rather learn about how eggplant turns into Norma, or more about the cultural significance of everything we have learned about over the course of the semester. I personally wonder why we can't do both. Sure, I am beginning to understand how eggplant begins the process of turning into Norma...but what does it really mean if the only reason we are interested is that it is kind of funny to wonder "How does eggplant turn into Norma?" Clearly, eggplant does not directly morph into Norma. So, what does this information really mean for us?

culture Name: Iris Date: 2005-11-20 23:10:45 Link to this Comment: 17105

Some people want to learn about how "an eggplant becomes Norma" because it is easier to discuss and come to an agreed upon conclusion than the cultural significance of what we have been learning. It is understandable since the word itself "culture" encompasses many things. I think a little challenge would be fun.

Name: Keti Date: 2005-11-20 23:47:09 Link to this Comment: 17106

I think it is misconception that we can dis-aggregate the question of eggplant becoming Norma from the question of the place of humans within the “bigger picture.” If we return to our earlier discussions of the nature and utility of science, some comments in the forum and in the classroom expressed the idea that the purpose of scientific enquiry lies in its ability to propose new questions and not in its ability to provide definitive answers. What others have chosen to term the “cultural” components (such as the relation of humans to society) are implicit and implicated in the study of biology; that is, studying how eggplant becomes Norma does not preclude a discussion of greater cultural implications. Rather, a discussion of processes at the level of the macromolecule cannot be separated from the processes occurring at the cultural level. The relation between humans and society/culture is an issue implicit in, not exogenous to, the study of biology.

Name: Magda M. Date: 2005-11-21 01:19:41 Link to this Comment: 17108

I agree with Keti; I think biology and sociology are inextricably linked since, as humans, we are biological creatures. There are reasons we interact with other humans in specific ways tied directly to our evolution and place in the food chain. Exploring both the biology and psychology behind that would give us a fuller understanding of people in general.

Name: Nick Date: 2005-11-21 01:53:48 Link to this Comment: 17109

While I do agree with Keti's notion that the "bigger" and "smaller" pictures are inextricably connected, for surely they are, I also think there has to be some point where the discussion will lose whatever ground it has in what we as a society have come to call biology. I don't mean to deter anyone from pursuing those questions they are interested in, but (and correct me if I'm wrong) it seems like these bigger picture questions are more suited to classes in other academic disciplines. For example, I'm not quite sure how essential an understanding of macromolecules is to an understanding of the rise of a society. I think the trajectory of the course at the moment is giving us as a class an interesting biological perspective on the functioning of living systems and their relation to their surroundings, and I'm not sure if broadening our perspective would necessarily make our biological knowledge any more complete.

Name: Brom Date: 2005-11-21 02:26:13 Link to this Comment: 17110

Learning the "eggplant to Norma" material is incredibly useful in understanding not only the natural world, but also the political, social, and economic world. Understanding the rules of biological systems is invaluable in the development of new technologies and products, it also frames political and social debates (stem cell research, differences between the genders). Learning the nuts and bolts of the "eggplant to Norma" problem makes all of us better equipped to engage in the debates surrounding larger social issues.

eggma Name: scott Date: 2005-11-21 03:30:44 Link to this Comment: 17111

I think that the methodology that this class has applied is very useful and should be transplanted into many other discussions concerning society, culture, art, etc. The fact is, the actual knowledge that many of us lack about how biological systems really work on a macromolecular level cannot be discovered despite the quality of our discussions. This class is one place where we actually have the opportunity to ground ourselves in biological information. Biological observations are quite distinct from the observations we can make as active social beings--I can't see photosyntehsis by carefully watching the palm sunday ritual. When this class invites the avalanche of a social context, we will experience more frustration than mind expansion.

bigger picture Name: Kate Date: 2005-11-21 07:55:41 Link to this Comment: 17115

I agree with Keti in that the ties between biology and the larger social and cultural context are inherent and inseparable. We have learned this semester that there are no Truths in science, that science is a process not a thing, and that things are part of science if they are part of the process, not because of any defining characteristic intrinsic to the things themselves and that we must constantly create new stories based upon new observations. In order to create new stories about biology that are “less wrong” we must apply science to society and culture. Furthermore, if there are no Truths in science what is the point of learning all of the science without applying it to the “bigger picture” if we don’t even know what are learning is really fact. The links are too strong to be broken and therefore cannot be ignored. We need to know more about the cultural implications of Norma and why and how eggplant becoming Norma is important in the “bigger picture.” Without the “bigger picture” we only have part of the story.

Name: Norma Date: 2005-11-21 09:49:19 Link to this Comment: 17116

I think I see hints of this sentiment in other comments, but I'm interested in how society shapes the way we understand how I become eggplant - not just the cultural implications of biology - and in examining how useful biological methods are in other disciplines.

Also, I agree with Brom that what we learn in biology can shape debates in other areas. I hope, however, that we maintain the ability to distance ourselves in certain circumstances. For example, in debates about gender differences biological findings about possibilities are important, but we should be wary of what is "natural" and look to what is possible, and to what we want. As humans we have the ability, to a degree, to define society and ourselves - we should look towards what we want to value rather than towards what biology tells us is "natural."

the smaller things Name: kate Date: 2005-11-27 21:24:12 Link to this Comment: 17176

I think that it is really interesting that we characterized life not as one thing or any one part but an “ongoing and coordinated dance” among a lot of different parts and that no on is “in charge.” I can’t help but picture all of my body parts dancing inside of me, performing their specific and specialized functions in order to keep me alive. It is a serious team effort, something that I had not really thought about before. Whenever I think about what keeps me alive, I think about the heart, the brain and the lungs, not ribosomes and mitochondria. However, these components are equally important in sustaining life and therefore should be overlooked. Therefore, I think it is time to give the “smaller things” more attention because I admit to having overlooked their importance in the course of my nineteen years of existence.

Name: nick Date: 2005-11-28 09:59:57 Link to this Comment: 17177

Kate, you bring up a good point. When learning about biology, more specificially anatomy, high schools don't offer information about anything more specific than the cell (at least outside of AP courses) and this course is good for learning about the small things. I would eventually like to know, however, the relation of the small things to organs and the like. I think we're getting a pretty good picture of why cells function as a result of macromolecules, but what is the difference between specialized cells in different organs, in terms of macromolecules. Obviously liver cells aren't the same as muscle cells aren't the same as skin cells etc., and I guess I'm interested in the macromolecular reasons for these differences.

Name: Date: 2005-11-28 10:14:32 Link to this Comment: 17178

THe image that I can't get out of my head is that for every cell in my body is at least one full copy of my entire DNA sequence. That's in the trillions, right? Hearts and brains running every component of me that retains characteristics of larger components. When I shake someone's hand, my hand is surrounding millions of copies of everything you need to end up with the body the hand is attached to. I think I'm in agreement with Nick when I say that what I want to see now is not only the mechanics by which a cell interacts with the cell next to it, but how collective cell action is coordinated and effected.

Name: Matt Date: 2005-11-28 10:15:06 Link to this Comment: 17179

THat was me before.

Name: Stephanie Date: 2005-11-28 10:16:10 Link to this Comment: 17180

I also agree with Kate's point that we haven't paid enough attention to the "smaller things". I remember having to memorize all the different parts of the cell and their functions and we even made an "edible cell" in middle school, but I now have some understanding of these things from a molecular perspective. I have always been a curious person and one of the things that I have been wondering about for probably my whole life is WHY our bodies work-- and not in a philosophical way. Most of us have probably known for a long time that "everything is made up of atoms" but now I can understand the interactions between the atoms that cause our bodies to function in the way that they do.

from cells to multicellular organisms Name: Paul Grobstein Date: 2005-12-04 20:21:15 Link to this Comment: 17293

Whatever you're thinking about is fine, as always, but ... what do you think of the idea that multicellular organisms consist of assemblies .... of living things? and that none of them are "in charge"? that the whole story is "interactions" among a variety of semi-independent parts? Potentially relevant for "bigger" pictures?

I didn't respond to the question but....... Name: keti Date: 2005-12-04 21:45:04 Link to this Comment: 17296

I’m still thinking about cloning. Couldn’t it be, and hasn’t it been, argued that cancer is itself a process of cloning whereby cells continually divide and reproduce themselves? Cancer is an uncontrolled process whereas the cloning of say an animal or human is one under controlled circumstances. Or is it that cloning a human is also “uncontrolled” in that genes influence phenotypic expression but do not determine it since the environment also plays a part.

That said, I don’t like cloning (nor do I like cancer) but to say it is a revolutionary technology is a misnomer; the technology has existed within the human body itself a long time before the thought of cloning a sheep ever entered someone’s mind. Furthermore, I think much of the public fascination with cloning stems from the misconception that it will produce something visually identical (a reaction to the physical as opposed to the biological). But if biologically, carrying a gene does not mean that it will be expressed, isn’t this fascination misplaced?

Teachers anyone? Name: Iris Date: 2005-12-05 02:01:21 Link to this Comment: 17297

When I was in high school, I heard of a study done with identical twins in different environments. Even though they grew up in different places the twins had common interests. In class, someone stated that identical twins are like clones. So if a person is a doctor his clone can possibly be interested in becoming a doctor as well. Not that I would suggest we increase human labor in certain fields but I know NYC needs more teachers.

Basketball and Multicellular Organisms Name: kate Drisc Date: 2005-12-05 08:19:41 Link to this Comment: 17299

This weekend I played in the Seven Sisters Basketball Tournament. While thinking about what to post, I realized the striking similarities between the components of multicellular organisms and a basketball team: they both consist of assemblies of living things, and no one is “in charge” (although there is a captain, she isn’t spewing out commands to her teammates, nor does she play for the entire game, so I think that the parallel still works). Both also require “interactions” among a variety of semi-independent parts, which is relevant to the “bigger” picture. Interactions (ie. communication, passing, setting screens, helping on defense) between teammates are necessary on the floor in order to win, which is the bigger picture. For the basketball team, like multicellular organisms, it is not about an individual who is in charge; it is about each of the individual components working together to serve the larger goal. Without these interactions, the team would surely lose and a multicellular organism would surely not be alive.

terribly basic question, but... Name: Norma Date: 2005-12-05 10:18:20 Link to this Comment: 17302

To what degree is the brain in charge? Doesn't it issue orders?

where we've gotten to ... Name: Paul Grobstein Date: 2005-12-05 11:27:47 Link to this Comment: 17303

No, its not over, of course. You can/should/will go on thinking about biology. And I certainly will, with our semester together an important influence. Thanks all. And so, you last word (for now) ... what has changed (or not changed) this semester in how you think about science and life?

Cooperation - makes it happen - cooperation - work Name: Zach and K Date: 2005-12-05 14:47:09 Link to this Comment: 17306

Cooperation is by far a superior strategy for a group, if everyone buys into it. Cooperative groups grow faster and survive in situations of less resource availability. A member of a cooperative group, while not eating as much as he might want at any given time, is also much less likely to starve. However, in direct competition with a greedy group, a cooperative group will eventually be overwhelmed. Cooperation works as a strategy as long as the cooperative group is able to insulate itself from the greedy group. In the case that the greedy group is capable of expansion, no matter how slow, it will eventually overwhelm the cooperative group by killing off the members at its edges and moving into its territory. However, in cases where the greedy group uses resources faster than the environment can provide them with in the long term, all the cooperative group has to do is keep from dying out completely until the greedy group dies out itself. Left to its own, the cooperative group will then be able to regrow.

From a sociological standpoint, it’s worth noting that the fastest way for a cooperative group to collapse would be for its outer members, in competition with greedy individuals, to become greedy themselves. If the cooperative group cannot “keep its principles”, it surrenders its ability to survive in low-resource circumstances. Thus, even if the cooperative herd is able to stave off an incursion from a greedy group, it will die all the same if it does so by becoming greedy.

Thus, greed sucks hardcore.

The Final Cut Name: Nick Date: 2005-12-06 15:39:21 Link to this Comment: 17323

A few musings. First off, this class showed me that there are those within the science community who accept the fallability of science. It was nice to get a science class from a perspective outside of that which I view as the traditional science perspective. My second change stems from the question of what we've taken to calling "the bigger picture" recently. I've never thought explicitly about the influence of biology on societies, aside from the occasional plague. I've also never seriously thought about society in biological terms (ie a person as a macromolecule or a cell performing a duty to create a larger social organism). I'm still kind of afraid of thinking like this, partly because I value individual human work, and the notion that a human can be scraped away like a skin cell with minimal influence on anything around it makes me extremely uncomfortable.

Name: keti Date: 2005-12-06 21:42:47 Link to this Comment: 17329

I agree with Nick’s comment concerning the fallibility of science. It is comforting to know that scientists themselves see the process of science as one which is ongoing, not static. But this process of scientific discovery/enquiry I think is two-fold. Not only are scientific facts contestable but I think as well the actual scientific process is one which can be rethought. I guess that’s why we talked about the scientific method at the beginning of the semester although I didn’t really see the significance of this discussion at the time. In other words, the course has demonstrated that not only are the “truths” we have come to accept as universal subject to revision but the very way in which science is conducted is also open for revision.

improbability vs. improbability Name: Scott S. Date: 2005-12-07 01:32:46 Link to this Comment: 17331

I think the most important aspect of this class was thinking about all of life in terms of immprobability. These ideas have been floating in my head for a while, vaguely under the headline of evolution, but now the idea of an improbability drive makes so much sense to me. As an improbability drive begins it is interesting how it uses probability as a partner in extending into further complexity. Evolution allows the most probable thing to survive, but in life, that probable survivor develops from an improbable change--language between humans is one of the most improabable things out there, but it came slowly because it is more probable that a species with language would survive against nature and predators. In an infinite universe, everything gets tried out, and in a reproducing system, ie. life, the things that will be tried out are mind-blowing. I definitely have more reason to believe in aliens, things we call ghosts, and all sorts of shit now. I mean, if a species could go virtually unnoticed, wouldn't that be a highly improbable but amazingly helpful life characteristic? Ghosts could be super-evolved life forms and we wouldn't know it for a reason. It really does seem that some parts of the seemingly infinite universe would create the most improbable life-perpetuating forms. Can't get over that.

Name: Brom Date: 2005-12-07 02:49:45 Link to this Comment: 17332

As this class has progressed I have become increasingly amazed that any us are walking around. The shear number of things that need to go right for a human beings, or for that matter, any organism to exist is truly astonishing. On one of its most basic levels all of life is predicated on the movement of an electron, a particle infinitesimelly small, and from the movement of these particles human beings with the ability to express ideas in the abstract emerge, WOW. Before this class I was impressed by the complexity of life but I now have a better understanding of the improbability driving the whole process.

Name: Magda Date: 2005-12-12 23:15:41 Link to this Comment: 17380

Looking back on my comments, I see that as the class progressed I definitely started asking different types of questions. Rather than asking for the meaning of something, I would ask how it showed part of a greater whole that makes up our understanding of biology. I sometimes found the web forum a little daunting, because it seemed less interactive than classroom discussions. Nevertheless, I thought it was very useful in terms of being able to see other people's perspectives on various topics. I found that I learned almost as much from the insights of my classmates as I did from lecture, because while the lecture provided facts and means in which to expand my exploration of biology, the discussions provided me with concrete examples of how my classmates tackled these problems. That was an invaluable resource in finding "jumping-off points" for my own explorations and helped to complicate the questions in a positive way even more.