Fall, 2006

Discussion Notes

4 September

Bio 103 as shared process ... making sense of life

Biology -> Science of life


Raises further interesting/relevant questions ...

Science as process ... of Story Telling and Story Revision

Linear scienceSeriously loopy science
see class thoughts
Science as body of facts established by specialized fact-generating people and process

Science as successive approximations to Truth

Science as authority about "natural world"

Science as process of getting it less wrong, potentially usable by and contributed to by everyone

Science as ongoing story telling and story revision: repeated making of observations, interpreting and summarizing observations, making new observations, making new summaries ... individually and collectively

Science as skepticism, a style of inquiry that can be used for anything, one which everybody is equipped to to/can get better at/be further empowered by, and contribute to - a way of making sense of what is but even more of exploring what might yet be

Science as practical tool, continually being adapted and therefore
  • should be expected to keep evolving rather than to get it "right"
  • is as much about creation as about discovery (multiple possible summaries)
  • the crack is a feature rather than a bug; both "objective" and "subjective play essential roles
  • differences among people are an asset to the process rather than a problem or an indication it isn't working

Distinguishing between forms of story telling: science, authority, belief Which of the following two stories do you prefer?
  1. The earth is flat (Flat Earth Society)
  2. The earth is round
Because of ...
  • personal observations?
  • observations made by others (personally verified or not)?
  • social stories (heard from others)?
  • usefulness?
Relevant observations: Is one or the other story true? Have there been others? Are there others? Will there be?
Which of the following two stories do you prefer?
  1. The sun goes around the earth
  2. The earth goes around the sun
Because of ...
  • personal observations?
  • observations made by others (personally verified or not)?
  • social stories (heard from others)?
  • usefulness?
  • is one or the other story "true"? are there others?
Relevant observations Is one or the other story true? Have their been others? Are there others? Will there be?
Scientific stories are frequently efforts to summarize the widest possible range of observations, always motivate new observations and hence new stories, should never be understood as "authoritative" or "believed in", do not compete with or invalidate other stories. Key issues about scientific stories
  • What observations do they summarize?
  • What new observations do they motivate?
  • Within what contexts are they useful?

11 September

From the forum

To be honest before taking this class not only did I hate science, I also was scared because I thought that this subject was only for geniuses. By taking this class I have not only changed my mind about science I have also learned that all of us can understand it because is part of our daily lives ... Ingrid

I always thought of scientific conclusions as concrete truths, whereas now I know that nothing is ever certain. I tend to take scientific articles too seriously, but now that I know to approach these studies with scepticism, I don't feel as vulnerable ... Sarah M.

I find biology really fascinating in particular because I'm curious about the way the world works (and for that matter, how I work), and biology gives me those answers. Granted, we spent all of last class talking about the fallability of science, but no matter how politically incorrect it is to call something "scientific fact," I'm perfectly comfortable using that term - it doesn't prevent me from realizing that there's always something new to be discovered ... Meagan

One thing that I like about the nature of this biology class is that the so-called truth is in a process of evolution, and finding the truth, in fact, is not as important as the journey or quest itself ... Randomness resonates with me and I was glad to see it plays a part in science, along with getting it wrong ... Sarah G.

Science has always been portrayed as knowing all the answers,and knowing how to apply them to everyday life. To hear that there are a lot of things that science can't explain, and that randomness is relied on after a certain point, is strange. It also brings about the question, if nothing can be proven certain, and if certain things can only be explained, why bother at all? And also, can't randomness be overused to explain things that are possible to find out, but that just haven't been yet? ... cmccnally

The interminable battle between Faith and Science continues ... We spoke in class about the strict, reasonable trial and error process and how it cannot in truth lead scientists to be absolutely sure of anything anywhere in the world. This requires some belief in science then, to TRUST that the sun will rise and set tomorrow and that gravity won't switch off suddenly. And that is where faith quietly comes in ... Carolina (see also Arielle, Annabella and Evolution and Intelligent Design: Perspectives and Resources and The Power of Social Psychological Interventions)

because of recent class discussion involving seriously loopy science and the revelation that white lab coats are not needed to make observations and conduct experiments, I have realized that although I might feel one way about a particular subject, I am going to constantly reevaluate why it is that I feel this way, perhaps make some new observations, and change, or not change, accordingly ... Corey

So with all this talk about the scientific method vs. seriously loopy science, I was a little disappointed to open my brand new $100 (paperback) text book for anthro and find "The Scientific Method Explained" ... "The goal [of science] isn't to establish "truth" in any absolute sense, but rather to generate ever more accurate and consistent explanations of phenomena in our universe." ... Georgia

Harold Osborne, a British aesthetician ... Simone

Genes Called Link Between Life Span and Cancers ... Mia

Which of the following stories do you prefer?

  1. Existing life forms (including humans) are as they are because of a previous and ongoing process of evolution consisting of random change and natural selection (differential reproductive success).
  2. Existing life forms (including humans) are as they are because of repeated creative acts of a supernatural being with a plan and intent?
  3. Existing life forms (including humans) are as they are because of an initial creative act with a supernatural being with a plan and intent?
  4. Other?
Because of ...
  • personal observations?
  • observations made by others (personally verified or not)?
  • social stories (heard from others)?
  • usefulness?
  • is one or another story "true"?
Relevant observations: To be returned to ...
Science as commitment to "summary of observations", "getting it less wrong", continuing meaningful story creation/sharing/revision/evolution

Life as ... process?
(starting where one is, telling a story, getting it less wrong)

Life is ... ?

Practical issue related to really major "getting it less wrong"

Characteristics of a living thing?

What's alive here?Is Langton's ant alive?
from Sahara Meteorite Prospecting from The World of Langton's Ant:
Thinking About "Purpose"
  I believe all things are alive. As another student bravely put forth in class, if it is on the earth, it is living ... it is the notion that the Earth does not fall into the narrow common sense parameters of what is alive (in western thought) that makes it OK to not treat it as if it were alive ... Annabella

if something consciously utilizes nature in order to maintain some sort of active status then it is alive ... Katherine F

inanimate, animate, conscious - useful distinctions?

Defines some of the phenomena that need to be accounted for in course (or, at least, by biologists over time). But is not sharp (mule that can't reproduce?, person in a coma?, Langton's ant?, artificial life?, products of life?, viruses? earth? rocks?) ... maybe life is not something things have (no elan vital) but instead ... ? Maybe there isn't a sharp border between living and non-living things? Like particular stories aren't "scientific" in and of themselves but rather as part of an ongoing process? And the list in any case doesn't include ALL of the things that biologists need to make sense of .... what needed beyond characteristics of a living organism to define "life"?

Additional defining characteristics of life

"neither incidental nor detrimental ... instead essential"
Darwin's Voyage Revisited


Change over time

Have to think about not only here/now but also there/then.
Life as process: Interdependent diversity, change over time

18 September

From the forum

The theme of this week seemed to be the importance of not taking things for granted and not making assumptions: thinking about life, where we came from, and how we continue to exist, things that (ironically) are very easy to ignore ... Hannah

seemingly basic questions have resulted in philosophical and religious arguments and have forced us as students to look beyond what we were forced to memorize in high school biology class. Sadly, my natural response to questions like "what charaterizes life?" is whatever I was force fed in high school. I love the way this class actually forces me to THINK, question, and observe natural phenomena. For example, in retrospect the concept that living things are highly improbable assemblies seems basic, however, it took us an entire class to even come near this conclusion ... Sarah

I think life and death are probably the most important distinguishing categories of all words, but probably the most frightening, since neither can be controlled by humans and both change as time goes on. It's interesting to take what we've learned and break it apart, seeing all the stuff we've just assumed forever, and now actually thinking about it and realizing we may not see it the same way ... Karen

While reading this article, I began to wonder, if people consider the earth to be alive, are the other planets alive as well? What are the reasons or justifications for saying that the earth is alive? Is the earth alive just because there are living things on it or is it something else? If not, could this newly found, puffy planet be alive as well? What about Mars, where water was found recently. If there is life on Mars, is Mars alive too? Just a thought that I hope will spark interesting and informative debate ... One last thing on the same topic of whether or not the earth is alive ... Just because I do not think that the earth is a living thing does not mean, in any way, that I treat it badly ... Corey

Maybe by the end of the semester we'll be able to answer ... questions about whether there is a "right way" to categorize things... Simone

There was one thing I caught it class though that made me think. The possibility of categorizing life into:

  • Inanimate
  • Animate
  • Conscious
I just think this could bring an interesting new way to look at our definitions... Moira

I'm also interested in the idea of a distinction between animate, inanimate, and conscious, and how that applies in medical situations. I had a friend once ... Meagan

Professor Zajonc told us that in the study of science one starts on a large scale and moves to smaller and smaller levels of structure and function. He told us that everything is ordered and makes sense on each level, that it is clear how things function and give rise to the order on the level following them. Eventually though, he said, on the lowest level that science has been able to discover, there is utter chaos. The question here is how does this chaos suddenly jump into order on the next level up? What force creates order out of chaos... Ananda

An Overview: Spatial Scale and Diversity

Spatial scale - at what scales do improbable assemblies exist and how do they relate to one another? alternate

Lessons from working up in scale from human ...

And from working down in scale ...

A Closer Look at Existing Diversity Have sense of spatial scale, existence/potential of life, size (not so good for categorizing), multicell versus single cell (better, why?) Are there other ways of making sense of existing diversity? Is categorization/classification totally arbitrary, simply a "social construction", or does it reflect to some extent characteristics of what is under investigation? are there "natural" categories? and, if so, what does that imply about life?).

Starting with intuitions (as we did with "life", as one always should, in science and elsewhere): what things LOOK like and do
What is similar to what, how similar, how many relevant axes?
Are there "discontinuities" in life's diversity?
Diversity is "clumpy" - the kinds of existing organisms are not randomly distributed among all possible kinds; instead there are lots of variants of a smaller number of more general kinds of organisms

Plants versus animals versus fungi(?)

Autotrophs versus heterotrophs (interdependence)
With cell wall versus no cell wall)
Fungi have cell walls, but different molecular constituents (chitin versus cellulose), are heterotrophs but with external digestion
Can use molecules, like any other feature, to evaluate similarities/differences
Get discontinuities/"clumpiness" (diversity itself an "improbable assembly", not either all possibilities of improbable assemblies nor random assortment of them but lots of variants one some kinds of improbable assemblies, none of others)
(Why no autotrophs without cell walls?)

Taking advantage of technology: Eukaryotes vs Prokaryotes (Monerans: eubacteria and archaea) (Why no multicellular prokaryotes?)

Five (or six, or more) Kingdoms: Discovered some order in diversity: is "clumpy" Why "clumpiness"? Things like small number of other things, some kinds of things absent?

Clumpiness in plants

25 September

From the forum

Another thing that bewildered me during our class discussion on what it is to be 'alive' is that to me being 'alive' always meant to be a THINKING organism capable of COMPREHENDING its purpose in participation of the life cycle. Now, it turns out that my perception of this word is rather egoistic and would be too philosophically coded. My present goal is to diviate from this perception of mine and question how it relates to those, for example, who recycle to keep the Earth ALIVE... Masha

I was raised to always try to see multiple sides to any theory or argument. So I thought this class wasn't going to be as life changing for me as for some of my classmates-which is fine. But then I got to class on Monday and Prof. Grobstein continued the exercise of zooming out on a section of Earth. As our planet contimued to fade into the distance and "nothing", my jaw dropped. I was so suprised by how incredibly, infinitissimily small we really are! Just think about what a big deal our day to day lives are. But really, our entire planet isn't even a speck of dust in the grand scheme of things ... Moira

I think that someone said that atoms and molecules and DNA are not alive. Yet, if those things are not alive, how are we, then, alive? The notion that the composition of non-living things creating living things is paradoxical. Using this notion, it could then be said that the Earth (i.e.- air, dirt, water)is alive. (I think that there is a difference between being alive and living. Living things have a consciousness.)... Kelly

I don't think that it is impossible or completely paradoxical to believe living things are made up from things we consider non-living. We consider a lot of factors when deciding whether or not something is alive, so the collection of non-living material may combine to fit all those criteria, but may not do so independently ... Georgia

We called galaxies and the patterns galaxies make improbable assemblies, but (to my knowledge) the only force present in making those assemblies is gravity. Is gravity really so improbable? Life has many forces working together to assemble its parts (I think), gravity being one but not the only one. And at the atomic level, there are quantum forces, different from gravity, that give atoms their organization. I wonder if these forces are complex enough to be called "improbable" as well? It's interesting that there are forms of organization even at very big and very small levels, but the assembly of life forms seems far more complex that that of galaxies or atoms. There seems to be more going on to keep a person alive than to keep galaxy spinning, which is strange. I guess I'm still not sure what constitutes an improbable assembly ... Hannah

In Wednesday's class, we tried to categorize many different pictures of organisms on earth. There was not one person in the class who agreed with every categorization. Different people have different opinions about different things. Some pictures were more similar to others and then there were a few that looked like they belonged in their own category. I guess what I'm trying to say here is that earth supports a lot of different organisms; there are no two that are exactly alike. Humans are the most obvious example of diversity...ex: even identical twins are not exactly the same. I think it is silly to try to place these organisms into certain categories when we know that they will never truly fit. I think diversity is present on earth for a reason, but I'm not sure what that reason is... Courtney M.

And as we get further and further from thinking we know, the easier it is to live graciously in this world, for how can we look down on anyone as being "ignorant" or "stupid" or any other insult we can think of. And when these ideas do come up into our minds, we may be thoughtful enough to question whether we can know that they are however we are describing them. In other words, we become better able to give everyone more room to be themselves and us ourselves, appreciating one another, our diversity, and our commonalities ... Annabella

why do we feel the urge to categorize everything, even if our categorizations are (more than possibly) wrong? If not knowing/not being sure makes us less vulnerable, why do we even attempt to organize life (be it plant, animal, or human)? ... Cris

Look more carefully at animals (metazoans)

More patterns within patterns (level of internal complexity, embryology)
More clumpiness. and more "arbitrariness"

Why no ventral nervous system with endoskeleton?

Nested Clumpy Diversity

Humans a small part of life, as life (as we know it) a small part of universe (but humans also steadily, perhaps even explosively, experiencing more and more of universe - is that distinctive of humans?


An Overview: Temporal Scale and Evolution

Human natural time scale - seconds to years, perhaps three generations (100 years)

Longer time scales important for biological systems (change where not aware of it):

2 October

From the forum

As we have discussed life in terms of scale, a lot of us have realized that there is a lot more out there that we don't know about than we thought, and it is in our nature to want to know everything, but will that ever be a possibility? ... exploration of the universe brings us back to the question of "why bother" ... Amelia

I found it interesting how prokaryotic cells were the sole form of life for 3.5 billion years, and only in the past 1.5 billion years or so has life really diversified rampantly. Why did this change take so long? ... I guess the answer has something to do with the fact that there was no "need" to become more complicated. As long as a living thing can easily preserve its life, it does not need to make any drastic changes to itself. I think that's a basic tenet of evolutionary theory. Eventually, the ones that worked together became so advanced that the single cells couldn't compete, so eukaryotic organisms came to dominate ... It's also a little unnerving to think that we are only right in the middle of this process of evolution, ... The life forms 1.5 billion years from now could be to us as we are to the prokaryotes of 1.5 billion years ago ... Hannah

"The fairest thing we can experience is the mysterious. It is the fundamental emotion which stands at the cradle of true art and true science. He who know it not and can no longer wonder, no longer feel amazement, is as good as dead, a snuffed-out can." -Albert Einstein

We may not understand the universe, and perhaps questioning it is futile, but we must always hold on to the amazement of everything around us... Hannah (see also Simone B and Applied Neurobiology: Bottom Line, and picture and picture)

the holes in evolutions timeline makes me wonder why we can't fill them in yet. Have we just not found the fossils of those other, arbitrarily connected characteristics of organisms that didn't work so they died off, or are those fossils we seek not even there? Does this give strength to the theory of Intelligent Design? That some powerful, divine (perhaps) figure created us and all that we know with some greater master plan in his/her/its mind? Again, this theory can't be either proven or disproven. So why do we discuss either theory? Why is it that we as humans need to know how we came into being? Or is that exactly what makes us human, our curiosity and thirst for knowledge? ... Corey and Intelligent Design and the Story of Evolution and Perspectives and Resources

it's in these irregularities- these mutations- that new things are created.. but where's the division line between the original, and the new? ... Karen

Humans young, as yet restricted experience, small part of life - BUT also have in us record of much of history of universe
LOTS of time for evolution

Evolution helps to account for diversity/clumpiness, also for ... ordering?

Long, slow, inexorable, inevitable continuous change, progressive improvement? (Evoution as a progressive tree?)

Fossil record - Observations

Earliest life (?) - prokaryotes (> 3 billion years, and getting older)

Plenty of time for subsequent development of improbable assemblies, but ...?
Consistent with progression, but changing what adapted to, and persisting

Next steps? How soon?

Eukaryotes - 1-2 billion years ago (last quarter of life's history to date)
much more improbable than prokaryotes? evolve from prokaryotes? - Endosymbiosis - illustration

Multicellular Organisms - ~600 million years ago (last sixteenth of life's history to date)
VERY improbable?

Stasis and change - THEN slow progressive improvement?

Nope, continued fits and starts

Well then ... humans at least?

Nope - diversification and extinction here too
(see more recent article)
Though there are here, as elsewhere, some reasonably slow, continuous changes
Different time scales reveal different patterns, just as different space scales do
Clumpiness understandable in terms of evolution, but (and) raises new questions
Evolution includes both slow, continuous change and rapid change Evolution involves "chance", and hence likely to proceed somewhat differently elsewhere or if repeated Evolution also helps to account for "adaptiveness" and does include some directionality, but is not toward "perfection" or "better" but rather toward having explored more (increased "complexity"?) Images of evolution - "getting it less wrong"?

Evolution as an "(attempt to) describe places and times outside of human scales"

Random variation (reproduction with variance) and natural selection (differential reproductive success) helps to make sense of Evolution (so defined) also raises new questions

Shorter time scales ALSO important for biological systems - milliseconds, nanoseconds (change where not aware of it)

Why do things change? At small scales, in space and in time, change is fundamental.

Have at small scales, beginnings of an explanation of one fundamental characteristic of life: change, exploration? Have also, at large time scales, some explanation of "adaptiveness", and of "clumpiness"/diversity


Have sense of life as increasing complexity, improbable assemblies of improbable assemblies .... Need to underestand origins of improbable assemblies, of diversity, as well as boundedness, energy dependence, reproduction with variance, homeostasis, autonomy
Will work our way from small scales to large, seeing how much we can account for at each level of organization (improbable assembly)

Remarkable generalization from small scale looking - dissociate ANYTHING, get out elements = atoms

ElementSymbolAtomic numberPercent in universePercent in earthPercent in human
(typical of living organisms)

Living, non-living assemblies not distinguishable by identity of constituents at atomic level
Nor are different kinds of living things
Living assemblies are distinctive in proportions of atomic constituents (improbable assemblies)
Fewer kinds of constituents than of assemblies

What are atoms? How get more from less?

Atoms -themelves combinations of still smaller and fewer constituents Periodic table - another related remarkable generalization

9 October

From the forum
It's funny, because when we talk about evolution and massive changes in class, it seems as if they happen in a matter of years; but, on the contrary, it takes MILLION of years for change to occur ... cmmcnally

I spent years actively protesting our callous and careless treatment of the environment, and spent most of that time very upset and unhappy. But then someone asked me, "Who died and left you to play God?" and those very questions came to me, and it changed a lot. It is another way of asking the same can I know what is good and what is bad? ... Anabella

Humans, however, are not limited to breeding animals, and have explored the possibilities with many plants and other organisms. What does this say about the part we play in our environment, and the future of the species we alter? Is something beneficial to humans always the right thing? Do we always know the consequences of the changes we are making? Those were just some questions that came to mind- not just in thinking about cats- but in our general control over our environment and ecological systems around the world ... Georgia

a developed conscience and ethical morals are part of human evolution, but are they in turn slowing down the process as well? ... M.E.

isn't assuming that we can actually know thatwe aren't the goal of evolution just as human centric? ... Maggie (see also Simone B. and Sarah G

it is up to us to believe what we hear or not and to be bothered about it or not, which is fair. However, is the overridding goal of these discoveries accumulation of knowledge or strive to understand more what is life and where and how else and in what forms it can exist? ... Masha (see also The Nature of Science)

I find the whole concept of chance and connections to be so interesting in Evolution. When you think about it, the two are hardly related except in the area of life ... even water is so complex that it is constantly moving. How much more complex are the eukaryotic cells that we humans are made of and that connect us to something as simple as a blade of grass? ... Kelsey

It is mindboggling to look at one tiny cell under a microscope and imagine that we as humans are merely the same thing, but a community of those cells orgaized and working simultaneously to acheive our state. A single cell seems so simple to us but when combined to create multicellular organism it is amazing to see what complex things can be created ... M.E.

Game of Life

Assembly rules:

Each green location must have either three or four red neighbors and no red location has exactly three green neighbors. Construction rules:
  • Start with any distribution of red and green squares
  • Turn red square green if it has exactly three green neighbors
  • Turn green square red if it has fewer than two or greater than three green neighbors
  • Repeat
"Assembly rules" as a concept

Assembly rules = what is allowed, construction rules = how to make allowable things Assembly rules for atoms into molecules by covalent bonding (electron sharing), see periodic table

Vastly more possible different molecules than numbers of different atoms -
Diversity by combinatorial explosion
Combinatorial rules also create 3-D shapes, central to biological processes

Electron, electron affinities key to many biological processes

23 October

From the forum

You're dating this guy. He's got a nice body and he can read Tolstoy and make witty comments ... What you don't know is that you might be dating him for more than all that. You might be dating him because it's written in your genes ... Meagan H.

The idea that all of us could be carrying around DNA that is not our own blows my mind ... One step further on the path to getting it less wrong: realizing that answers are never absolute ... Moira

Does "electron shell" just help us think about bonding, or is that actutally how an atom looks? ... Hannah M.

So just when we think that we have it all figured out, scientists make new observations, come up with new ideas, and add a new variable which changes everything. According to this article,, the extinctions of rodents and mammal species are greatly influenced by the tilt and orbit of the earth ... Corey

t turns out that the Cambrian Explosion may be less dramatic than it sounds. Scientists may have found a way to explain it as a process rather than a mysterious explosion. In a 653 to 551-year-old limestone deposit in Souther China, the oldest known embryo fossils of primitive sponge-like creatures were found ... ... embryos and embryionic development became more complex as multicellular species became more complex. Even in today's sponges, the embroys are more complex than those of their Cambrian ancestors ... brings to mind the "chicken or egg" question... Simone

I noticed an article online today stating that "they" have noticed that 6 of the 7 wonders of the world no longer exist. Therefore, they are going to come up with a new list. This got me thinking. Somehow, I hadn't considered something such as a "wonder" to be such an arbitrary thing. I thought it had more to do with intrinsic values of the item that it be considered a "wonder"... Annabella

I think that if I had to summarize what I learned so far in this class, I would say that I learned, in the process of analyzing the subject, to ask additional questions that lead me to further understanding ... Masha

Earlier this week, I was eating a chocolate chip granola bar, and noticed how the chips weren't evenly distributed, and the marshmallow pieces were in clumps all over the bar. And then it dawned on me: CLUMPY DIVERSITY... Cayla

I think it's interesting that a lot of the time very different things have similar or the same chemical components and it is up to the architecture to differentiate completely between one thing and the next ... Karen

Where we've been, are going?
Life properties to acccount for
  • improbable assembly
  • bounded
  • energy dependent
  • semi-homeostatic
  • semi-autonomous
  • energy-dependent
  • diversity
  • change over time, evolution
  • can we account for all this using atoms? assemblies of atoms? assemblies of assemblies of atoms? etc? key is architecture, how things put together? inanimate -> animate -> conscious?
  • assembly rules and randomness as generators of diversity? and new properties?
  • how do living systems discriminate between left and right handed molecules?

Water, central to living system as known, example of "emergent properties"

combinations of simple parts (atoms, elements) yield in assemblies (molecules) new properties

keep eyes on electrons, oxygen, charge
on polar vs. non polar
on water
remember three-dimensionality, flux
Overwhelming diversity of molecules (like life)
Any way to make sense of it? Any other useful things to learn at this level?

Functional groups help to make sense of both small and large molecules

"Inorganic" versus "organic" molecules?

Carbon based versus non-carbon based, but inorganic/organic no longer a good distinction for small molecules (large?) Biological molecules distinctive?: macromolecules
Enzymes: Essence of Life?
  • Speed up breakdown, are not themselves broken down
  • U-shaped temperature, pH senstitivies
  • highly specific in what breakdowns they facilitate
  • little men?
  • something in and of itself, not to be explained?
  • specific catalyst that is sensitive to environment?
  • might also account for distinguishing left and right handed molecules?
Proteins, from amino acids via peptide bonds

30 October

From the forum

I spent a lot of time thinking about atoms and their improbable assemblies which do in fact make up everything in the world and beyond. It is fascinating for me to think that we can break down everything in this universe to atoms- not only our bodies but our emotions come from atoms ... I can understand why others, especially in the 18th century, would be disillusioned by the perspective that everything is just atoms, and not something more spiritual or Godly ... I understand the romanticism of believing that there is simply something magic and mysterious about a substance because we have no other explanation for its unique qualities ... Anyway, class has really been pushing me to reflect on ideas that I had never taken much time to consider before, and I am very happy about that. Even our liberal arts education breaks down ultimately to atoms! ... Mia

The most glaring observation that has never been explained by atoms and molecules and assemblies is what makes the assemblies alive? ... Annabella

water is something really different than everything else. It's one thing to hear someone to say this, but seeing the way insects can walk on water, and discussing why ice can float has really helped me understand what I've always been told ... Cayla

water has properties that are not present in any of its constituents alone ... waters properties are a result of its architecture ...How is it that a little collection of hydrogen and oxygen can yeild such astounding results? polar and hydrogen bonds and the idea of electronegativity ... Corey

With all of talk about molecules, it all seemed repetitious and the same old, same old talk about protons, neutrons, etc. But I understood today that an enzyme is something that is extracted, like a 'life force' so to speak of something else and it can be removed! It is strange to think that you can just take something out of a life, especially since before the concept seemed way too Scifi channel to me. What else can you take out of a life? ... Kelsey

I see now the way [enzymes] actually work, literally breaking down the substrate by "forcing" it into a "keyhole." For some reason I had always figured, when I thought about it all, that the way they worked was more complicated than that. Like, maybe they used some kind of potent goo to dissolve the substrate, or something. But it's beautifully simple, really, and I like that. I also better understand the primary-quaternary protein structure, which is another way to make something really complicated out of simple parts, to perform a function none of the parts could complete on their own. The assemblies keep getting more and more improbable! ... Hannah

I wonder if everything actually happens for a reason and we just have to discover the cause to predict the effect, or if we just create this "stories" in the attempt to link cause and effect but have got it all terribly wrong. Disturbing thought ... Priscila

Where we've been, are going?

Diversity/new properties from atoms/assembly rules
Polar (water)/non-polar distinction begins to account for boundedness
Macromolecules from assemblies of molecules
Proteins as linear sequences of amino acids complexly twisted/folded in 3D space

  • Single amino acid change can make a big difference
  • Shapes quasi-stable, can vary
Enzymes as proteins, fit/induced fit helps to account for
  • temperature sensitivity of living organisms
  • pH sensitivity of living organisms
  • discrimination of right handed/left handed molecules
Proteins also relevant for other things (including boundedness regulation, energy)
How account for improbable assembly of amino acids?

Nucleic acids , from nucleotides

Water solubility and energy yield (given availability of O2) is (relatively) easy to predict from a characterization of the improbable assembly of atoms in sugars. Sweetness is not. Why? (relevance to the tree falling in the forest problem?)

Changes in proteins likely to affect not just one thing but lots of things (hence we don't evolve cellulose digesting enzymes? ... see The gastrointestinal system: an introduction and Animal nutrition and digestion for more on ruminants

Carbohydrates, sugars (monosaccharides to polysaccharides) - alternate

From hydrocarbons to lipids

Living systems are molecules, macromolecules constantly in flux ...

6 November

From the Forum

The map we saw today of reactions that are constantly happening in the human body was amazing. Thinking about the complexity and dynamic nature of all those reactions, I am astounded that we can ever really feel like we are at rest. Which reminded me of our earlier conversation about our place in the universe. Just like there are improbable assemblies on very small scales and very large scales, there are also constant motions and reactions occuring on small and large scales which we seem unable to directly perceive ... Hannah

The heart is very utilitarian: It takes care of itself and it takes care of the other organs in the body. However, the heart must respond to the amount of oxygen available (as taken in through the lungs and as perceived by the brain) and perform accordingly ... Arielle

If you can change how you think when you are having a panic attack to calm yourself down and regulate your breathing again, is your heart really taking care of itself? ... Georgia

After our lab on heart rates, I wondered about what else can affect the proper and delicate inner workings of our heart. One of the most common acts that incites high heart rates (among other things) is smoking ... Cris D

As we were trying to determine what accounted for different heart rates, we couln't really find a pattern. I guess what we learned is that there is no direct or definite correlation with the causes of heart rate ... Angie

this blood thinner/rat poison story was a perfect example of the multiple funcitons of chemicals and how the quantity of a certain chemical has everything to do with the difference between life and death. My Grandmother NEEDS the blood thinner for her heart fibrilations, while the rat poison nearly KILLED my adorable dog ... Simone B

Although class this past week was interesting, I did find it a bit hard to follow. I spent some time this weekend reading about fat and cholesterol levels and how they effect our bodies ... Mariellyssa

It is really amazing that the slightest changes in the assembly of atoms or in a molecule can lead to things as different as a human and a rock ... Kelly/a>

Accounting for change ... and stability
(and their relation to order, chaos, etc)

Some other versions of thermodynamics:
  • You can't win
  • You can't break even
  • You can't get out of the game

For Newton's Laws of Motion

For Thermodynamics:
First Law of Thermodynamics - in any isolated sytem (the universe) the total energy/matter remains constant Second Law of Thermodynamics - in any isolated system (the universe) change is always from less probable to more probable states (entropy increases)

Diffusion as the archetype of life - improbability and flux (increasing disorder) driving increasing improbability (increasing order)

  • Random change underlies all biological organization, with "order" resulting from it
  • "Only in the co-operation of an enormously large number of atoms do statistical laws begin to operate ... All the physical and chemical laws that are known to play an important part in the life of organisms are of this statistical kind". "Order" (improbable assemblies) are forms of stability within flux
  • Things "spontaneously" fall apart, at different rates (probability increases)
  • One set of things falling apart can cause other sets of things to get together (probability decreases)
  • "Order" depends on continuing production of disorder (with more falling apart than getting together)
  • "Stable" order may reflect
    • dynamic equilibria (purely statistical)
    • slower rates of falling apart

Adding the time/change dimension to life (at the molecular level)

Sun (plus? alternate) as source of driving improbability
Need to capture, use improbablity to make improbability
Take advantage of "quasi-stable" improbability, "energy" in chemical bonds

Can "trap" improbability in chemical bonds ("potential energy")
Carbohydrates (all macromolecules) high order/improbability/"free energy" -

How do enzymes fit into this picture? Enyzmes as regulatable regulators of falling apartness, adjusting the size of the hole Enzymes as couplers of catabolic and anabolic processes, of falling apart and building - transforming improbability from one state to another

Life as

is not entirely fantasy.

13 November

From the Forum

A lot of times it seems like anything that's "natural" is called good and anything "man-made" is called bad, but now I realize that "good" and "bad" are meaningless labels for chemicals. How can a chemical not be 'natural'? Because it was made in a lab? That's silly. People are nature too! :-) ... Meagan

The notion that our waste cannot actually be destroyed or really ever disposed of is a worrying idea. While there are certain things that can be recycled, other things are not. This got me thinking about the processes that different elements undergo to become harmful waste. Presumably, if we are able to create waste we should be able to retrace the steps and return it to its previous state. I am sure, this is not that simple (or it would have already been done), but this idea of re-arranging environmentally damaging waste into, harmless waste is an interesting one ... Priscilla (see also Sarah G)

If the nature of the World is to move from a less probable assembly (order) to a more probable (chaos)than the human life is unnatural in our universe. We are an unnatural assembly because we are against what is really supposed to happen ... Kelsie

It is counterintuitive to be told that the most probable state for life is disordered, but it does make sense. We are taught to try to organize ourselves, our lives, our rooms, etc. When really they are MEANT to be disorganized. That small things such as us growing older, or leaves falling off of trees are all extensions of the Big Bang is something that forces me to take a much larger outlook on life. I neve thought of myself as something that was in a constant state of flux, not actually solid, or something that is in an inevitable state of falling into disorder. This world, which appears so full of improbable assemblies, is actually more disorderly than orderly, and that's the way it should be. The next time I clean my room, instead of lamenting my inability to keep it together when I notice piles accumulating on the floor, I will embrace this as part of life's water wheel... Moira

Moira's comment about disorder while cleaning your room really got me thinking. I wasn't able to visualize the disorder/order concept before. But now I see our rooms and itÕs like Š bam Š disorder. And disorder is the easiest way to leave things. Making a mess is supposed to be what happens. So when little kids leave food/toys everywhere, they're just doing what's more natural in the world, creating disorder. Maybe we need to follow the kids' example and make a mess. ... Maggie

I liked Moira's comment about things being naturally disordered, and how it is a human inclination to put everything in order. This relates to our discussions of classifications, and how it is so difficult to find the right categories in which to place different species of plants and animals. Just as it is diffcult to keep something in its place- when its natural tendency is to spread out and disperse energy, according to the second law of thermodynamics. While it isn't directly related, I found it interesting that a process that occurs on a smaller, molecular level, reflects larger activity among species. Perhaps plants and animals evolving into new species, interbreeding, and the mutations of different genes are a way of disorganizing the existing "order" in the world. Things are progressing into a natural state of variation and as they remain in flux and change they are diffusing characteristics into as many new life forms as possible... Georgia

I think it's important to remember that all science-knowledge acquisition involves a leap of faith because so many of these stories are based on past observations and none have the benefit of prophetic future observations to confirm themselves ... I loved that our second lab on "Oneself as a Biological Entity" coincided with this week's lectures on thermodynamics. Anytime we are reminded that we ourselves are part of this uncertain yet trustworthy system of science is an important process ... I also wanted to discuss the idea of probable/improbable assemblies in the context of reproduction. My mom said she never believed in G-d until she had children ... Human beings are improbable assemblies, much like the camel from the photograph, and not even speaking of Darwin's theory of evolution, but our own evolution from sperm-and-egg to living, breathing person is at odds with the idea that everything tends towards disorder ... Arielle scientists discovered that sea urchins actualy possess many genes previously thought unique to vertebrates, along with an immune system of unprecedented complexity ... Simone B

The urchin "shares more than 7,000 genes with humans". How can an organism that has so many similarities with the human, look so different and have completely different fucitons. Again, it all goes back to if two things have certain constituents in common but constructed differently, they become very different organisms ... Corey

Maybe it never ends... maybe the flux does last forever, as there was nothing before the big bang, and that could just have as well been defined as an ending instead of a beginning (even though all new beginnings come from endings..) ... Karen

As the water being poured into the wheel becomes more probable and the water in the cup becomes more improbable, our current stories are the cup of water, becoming more improbable, while our new stories are the water being poured into the water wheel, becoming more probable ... Kelly S.

The waterwheel system of energy exchange is amazing. It's interesting how life could not exist without ATP, but we can't call ATP the key to life because life could not exist without enzymes or other proteins (ie DNA, RNA) either, or without carbohydrates. There is no one molecule responsible for life, at least not for life on Earth... Hannah

Enyzmes as regulators of falling apartness, adjusting the size of the hole, and couplers of falling apartness to putting togetherness - Themselves regulatable

Moving On: Cells as Organized Spatial Arrays of Macromolecules
How DOES Sugar Get Made Anyhow? (among other issues)

6 CO2 + 6 H2O --*/*--> C6H12O6 + 6 O2

*/*: in the presence of light, enzymes, and organized spatial arrays of molecules

C6H12O6 + 6 O2 --*/*--> 6 CO2 + 6 H2O

*/* in the presence of organized spatial arrays of molecules, including enzymes AND simultaneously ADP -> ATP

  • As with energy, living systems do not consume matter, they transform it
  • Transformations are cyclical and involve linked transformations
  • Non-spontaneous transformations are driven by spontaneous ones
  • Enzymes and their shape changes are critical
    • for facilitating spontaneous reactions
    • for linking spontaneous and non-spontaneous reactions
  • Organized spatial arrays of molecules are essential
The "cell theory" - All living organisms are either cells or assemblies of cells

What are cells? Why a needed level of organization for life?
Why must there be a "cell" to have life? How can cells be both "distinct entities and building blocks"?

Cells as energy-dependent, semi-autonomous, semi-homeostatic, reproducing, bounded improbable assemblies of molecules/macromolecules

The matter of boundedness

Life requires not only ways to speed up spontaneously occuring breakdown (enzymes) but also ways to slow it down

Membranes the key to boundedness, both of cell and within cell (are also important framework elements, organizing other macromolecules)

Movement, and autonomy ... understandable in terms of proteins
"the discussion of lower levels cannot overshadow the bigger picture"

Molecules ARE important, DO affect the bigger picture, but they in turn are influenced by and derive significance from the bigger picture they are a part of

Genes ARE important, DO affect the bigger picture, but they in turn ...

Individuals ARE important, DO affect the bigger picture, but they in turn ...

Stories ARE important, DO affect the bigger picture, but they in turn ...

Gene regulation - More on responsiveness/autonomy at the single cell level

20 November

From the Forum

The last part of the article contradicted one of the points of class this week and last: that life uses the entropy of the universe instead of fighting against it. One of the scientists, George Whitesides, said, "The way of the universe is to go from order to chaos... but on the occasion when life was created, that was reversed and the universe went from chaos to order. Finding the answer will take input from a wide variety of fields." But we think the answer is that life uses the waterwheels moving from improbable to probable to create energy. Life on other planets would almost certainly have to do the same thing... Hannah (see also Amelia)

So volcanic activity, or at least the stirrings of, still characterizes the moon. As I discussed earlier, the earth is a lively source of volcanic activity and other sub-crust motion. Is the moon alive? Is our planet alive? Are there degrees of being alive? Scientists had written off the moon as "deader than a door nail," an idiom referring to an object that I can claim with great confidence is devoid of life. But with this new evidence of subterranean motion, the moon appears to be less dormant than we thought and thus more lively/alive. I like to think about celestial bodies as living - all it takes is creative verb changes to ascribe life-traits to seemingly non-alive entities ... Arielle

But I do think that it is a really interesting idea that was brought up that if the earth is alive, then it is humans that are the ultimate parasite/earths agent. I have never thought of it like that and it is a new perspective on how people interact with their environment. However, this whole idea goes off the assumption that the eath is a living entity unto itself...which it is not. Now that it is later in the semester and we, as a class, better understand certain traits that characterize things to be alive, I think that my point is more clear. Can the earth reproduce with varients? Is it energy dependant? It is semi-homeostatic or semi-autonomous? No. Although the earth SEEMS to be alive and moving and interacting, that does not mean that it is. It SEEMS that I am standing still, when in fact all of the atoms and cells in me are actually moving ... Corey

To quote the phraseology of The Lion King (Disney), we are all connected in some way, shape or form. Be it the 'circle of life' or otherwise ... Kelsey (see also)

I know that in the past without intention I tended to distinguish the mind and the brain as two separate entities- the brain being the organ that is the key to our existence and keeps us alive, while the mind is more ethereal and abstract; it is the mind that thinks. However, we all think so differently, as the results of the lab clearly demonstrated, so what does that mean to say about the differences in our brains and what confluence of elements determine how our minds think? The science and biology of thinking is ridiculously intriguing, especially when we can bring it back to the atoms ... Mia

Responsiveness/autonomy depend on energy (transformation of improbability) - Where/how does that get in game?

27 November

From the Forum

In response to the idea that the earth is not alive, I must object. I do not agree in the slightest that our class has honed in on the fact that the earth is not alive. After all, we never came up with a set of parameters that we agreed on that defined what it meant to be alive. Paul put forward some ideas and we agreed to hold the class under those presumptions for the sake of discussion ... Annabella

I agree with Cory. I don't think that the earth is alive ... So there aren't any absolutes. But that also means that the earth isn't absolutely alive, either ... Maggie

I agree with Maggie about absolutes and is the earth absolutely alive or not? ... Annabella

How can we be sure what alive is exactly then? This class has directed me to question what we have always known because it has been what is taught. There also seems to be a distinction between the conscious and inanimate. How do we know what really goes on in the 'minds' of trees if they even have minds? ... Kelly S.

I dream every day and I remember my dreams since I was five years old..what is that beat that creates them? (and I am not talking Freud at all now since in this case the 'scientific'answer would interest me a lot more)What is that muscle that constantly works in my brain creating images, playing with pictures I see around me (referring, for example, to the pictures we looked at today), living basically its own life? Maybe everything I see is not actually the way it really can I know? Maybe it is just the work of my brain and, paraphrasing a famous monologue from 'Macbeth', maybe I am just a poor player who creeps on the stage created by my mysterious brain ... Masha

From A Midsummer Night's Dream

That you have but slumber'd here
While these visions did appear.
And this weak and idle theme,
No more yielding but a dream,

From The Tempest

We are such stuff
As dreams are made on, and our little life
Is rounded with a sleep.

I find that interesting, that what I have been looking at for years is really just a backwards image of what is there or more importantly, what my brain has taught me to see. It is very very extreme for me to think that sometimes what I see, isn't really there. I guess it gives you a concept of perception; what I see isn't what my fellow human sees and vice versa ... Kelsey (see also Kelly S)

it's interesting to think that we may be who we are because of thoughts stored in our subconscious, making us react and think the way we do, and these atoms that make up the parts that make up these thoughts..that these thoughts, in essence, are some translateable form of molecules or atoms ... Karen (see also Reflections)

IÕve begun to wonder if all of the new trends in genetic engineering really improve the quality of life. By altering the gene sequence in wheat we may be producing more wheat at a quicker rate and be able to feed more people, but is the quality of life really improved? Sure I spend less on produce at the grocery store, but are these fruits, vegetables, and grains just filling our stomachs and not nourishing the rest of out bodies? Americans seem to have quickly accepted genetically engineered food and few have questioned it. The benefits of genetic engineering adjust themselves well to the principles of capitalism, but in Europe bans on genetically engineered food have been instituted ... Simone

Looking back and forward - link(s) between life and the second law

Or ... on "what's another reason why sugar doesn't fall from the sky?"
Photosynthesis the starting point ....... 6 CO2 + 6 H2O + light -> C6H12O6 + 6 O2

Cellular respiration the link to metabolism and the return part of life cycle ......C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O + 32-34 ATP

Given spatial arrays of macromolecules that can do the link:

Improbability drives the creation of

  • molecules
  • macromolecules
  • spatial arrays of macromolecules
  • cells, organs (including brains), people, culture, ecosystems, biospheres?

Problem of creating a living cell is problem of assembling intricate architecture of large numbers of molecules, macromolecules?

General principles from the discussion of energy at the cellular level, beyond energy per se

Cellular reproduction - mitosis

Lessons from cells about life:

4 December

From the Forum

I think that it is very dissapointing how little we know. You always hear about how far science and medicine have come. And how, with all we know now, we are so much more capable to heal and explore. But as we talk more and more in class, I find that there are so many things that are still complete mysteries ... How can our modern medicine/scientific communities tout knowledge when there is still so much to be learned? ... Moira

I enjoyed reading Cris' comment about the Golden Ratio ("pleasing to the eye and, almost mystically, is naturally occuring") ... Basically, I've come to find that concepts like improbable sequences make more sense and seem more valid with mathematical ideas to support them. I find it amazing that nature is not random, life is not random. It fits ... Sarah G

The lab this week really got me thinking about how while many mixes of traits follows a set ratio (3:1 or 9:3:3:1),there are always exceptions to the rule. The traits that my partner and I looked at had a ratio of 2:1:1, which was unlike most of the other groups. The possiblilites were seemingly endless, and that was just for fruitflies, which appear to be a lot less complex than mammals. It is mind boggling to think of all the genes in something so small as a fruit fly, but it is even more astounding to think about genes and their effects on humans ... ... Cayla

I found this article very interesting because it focused on the fact that such drastic, and life altering (no pun intended) events have taken place Corey

When I am in the space of feeling that everything I believe is borne in my imagination, all of a sudden I am much more understanding and compassionate than when I think there is a reality out there, and I know something about it ... Annabella

I feel that there is so much more in this universe than what is known, clearly ... Mia

there is movement on very small scales (cells) and very large (expansion of the universe). Not only are we in constant motion, but we're moving really fast! And still...we can't sense it ... Hannan (see also Kelly and Mia on cell animation

Yesterday in class we discussed the difficulty of spatially arranging organelles in relation to each other to create a cell and how it is impossible for humans to synthesize a cell. But aren't we able to male cells? If not, what is cloning? I know it has to do with replication, but isn't it essentially the formation of a new cell? ... Amelia

Multicellular organisms as improbable assemblies of cells having three-dimensional structure, boundaries, internal boundaries/spaces, energy dependence, autonomous/homostatic properties, reproduction with variance

Key points:
  • Lots of different sets of organized cells, lots of different cells
  • Sets and cells all themselves alive, as well as being parts of living thing
  • Need "differentiation" (specialization), organization (coordination)
  • Where get lots of different cells? in organized form?

Making sense of diversity - morphological tissues as intermediate level of organization between cells and organs/organ systems

Boundaries and spaces from epithelia - regulate movement of materials


11 December

From the Forum

today's lab brought to mind the age old debate of whether or not an organism is the way it is because of its environment or its heredity. Sadly the lab didn't further any evidence for either concept because we only proved that both things can effect the organism. Which is a good enough answer for most, but not for those who want to know that answer to the debate. But personally, it reminded me of how much goes into life. We are made of complex devices (atoms, molecules, cells, systems,etc.) and on top of that, we are made part because of the environment that we live in. For example, I grow better when I eat in my environment that has food for me; what would I do for substance if I lived in an area without my usual sustenance? I would have to adapt or die, and this would change myself and my offspring...etc. I guess it just goes to prove that there is always a 'what if' to every aspect of our lives... Kelsey

I don't think he could actually knock himself out by holding his breath...because if he could, as soon as he blacked out his body would take a breath and then he would become conscious again ... Hannah

this would make SAD a disturbance in the circadian rhythm, the 24-hour pattern that normally aligns the sleep-wake cycle with all the other bodily rhythms ... Corey

nature can still penetrate the artificial shelters we have created for ourselves (buildings, heating devices) to assert human dominance over nature ... Arielle

I learned a lot about the capacity of my brain and mind, and how totally out of control one can be with regards to his or her behavior ... Mia

What good are our gifts of reason and free will if we don't use them? ... Sarah G.

trees, plants, etc. are "alive" but they do not possess the ability to reason or think. However, if we were alive without our conscious, would we really be human anymore? Does our conscious make us human is what I guess I'm really asking ... Amelia

Semi-autonomy, homeostasis, adaptiveness and ... the self? Coordinating systems

How make complexity - development of multicellular organisms

How get elaborate, three-dimensional assemblies of diverse elements? Development (alternate) as guide, further insight into diversity, background for "cloning" issues ... see also Cloning: Past, Present, and ..."

Organized diversity despite (because of?) genetic homogeneity
Differentiation and morphogenesis dependent on gene regulation ...
  • Nuclear/cytoplasmic interactions
  • Cell/cell interactions
  • Cell/environment interactions
  • Genes influence everything, do not determine anything

A noteworth exception, the immune system ... making productive use of randomness (continued)

Where does zygote come from? (more on making productive use of randomness)

Development of the individual (and of culture): sex/gender

The "story" from biology (so far)

Thanks all for participation in this process this semester. Keep learning, thinking, acting, imagining, "getting it less wrong". Keep in touch.

To be continued

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