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 Simone B and Applied Neurobiology: Bottom Line, and )

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)

To be continued [an error occurred while processing this directive]