BIOLOGY 103 Fall, 2006

Discussion Notes

• starting places (Paul Grobstein and ...)
• diverse interacting entities exploring new terrain
• with resulting somewhat unpredictable movement beyond current understandings
• to be shared among ourselves and with others

Biology -> Science of life

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

Linear science	Seriously 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

Revisiting Science in Culture: Science as Story Telling and Story Revision Getting It Less Wrong, The Brain's Way: Science, Pragmatism, and Multiplism Thinking About Science: Evolving Stories Science as Story Telling in Action Science as Storytelling or Story Telling? A Conversation About Science Education ... and Science

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"

• Water on Mars? - more
• Life in Mars meteorites?
• Center for Mars Exploration, from NASA Ames
• Deep Sea Life
• Evidence grows for Europa ocean
• Cassini reveals Titan's Xanadu region to be an earth-like land
• Extrasolar Planets
• SETI Institute OnLine

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"

highly improbable assembly bounded energy dependent - "ashes to ashes, dust to dust" semi-homeostatic semi-autonomous reproduces with variation

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

Diversity "neither incidental nor detrimental ... instead essential"

Darwin's Voyage Revisited Why categorize? individually? collectively? Are categories "real", ie reflect things "out there" or simply human constructions? Is there a "right" way to categorize? A more useful way? Making Sense of Diversity: A Conversation at Bryn Mawr College

Interactivity

Change over time

Have to think about not only here/now but also there/then. Life as process: Interdependent diversity, change over time Scales of space/time Levels of organization Interaction Life, like science, is ongoing process of as hypothesis generation and testing? Is it a good scientific story? A useful one?

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

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?)

Internal boundedness vs lack of internal boundedness

Five (or six, or more) Kingdoms:

• Monera (plus) - single cell, prokaryotic, auto or heterotroph
• Protists (plus) - single cell, eukaryotic, auto or heterotroph
• Plants - multicell, eukaryotic, autotrophs
• Fungi - multicell, eukaryotic, heterotrophs, cell wall
• Animals - multicell, eukaryotic, heterotrophs, no cell wall
• ?Viruses?

Discovered some order in diversity: is "clumpy"

• Most things are variants of a small number of things
• Some things that can be imagined (BECAUSE we classified!!!!) don't exist (multicellular autotrophs without a cell wall? multicellular prokaryotes?)

Why "clumpiness"? Things like small number of other things, some kinds of things absent?

Clumpiness in plants

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25 September

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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)

• Diploblasts vs triploblasts - alternate
• Protostomes vs Deuterostomes
• Invertebrates vs Chordates
• Mammals within Chordates
• Humans within Mammals

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?

Classification

• Categories "real", independent of human observers?
• Categories "useful"?
  • Helps to make sense of things, reduce blur
  • Correlations help to predict based on partial information
  • Raises new questions ...
  • Relevance in other cases?

  How make sense of diversity, clumpiness?
  

  • Great chain of being - ordering of organisms along some scale?, no "narrative" character, everything has its place, there is an explanation for everything
  • "clumpy diversity" - any ordering or simply diversity? complexity? some degree of arbitrariness?

  Evolution as way of making sense of diversity? Time as an essential descriptor of life?

  • Makes sense of things being similar to other things, of missing things?, but also raises questions ...,

  • Has life changed over time in appropriate ways?
  • Was there a first organism? a first organism of each kind?
  • Why the PARTICULAR set of organisms we see, and not others?
    
  • Progression? Ranking?
    
  • Time/history as part of explanatory framework? Would it have to come out the same way? Life identical elsewhere? The same here if taped replayed?
  • Similarities between life as process and science as process?

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):

• universe - ~15 billion years
• ,stellar evolution (sun - ~ 5 billion years old, of ~10 billion year life span)
• earth (and life?) - ~5 billion years (150 million human generations)
• humans - ~100,000 years (?) (3,000 human generations)
• recorded human history - ~10,000 years (300 human generations)

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2 October

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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)

• Cyanobacteria
• Impact on earth - alternate

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

• Paleozoic - 540-245 million years ago, Explosion and extinction (Cambrian Explosion and Burgess Shale)
• Mesozoic Era - to 65 million years ago, Extinction (K-T), very probably meteor impact
  • Solar system impact craters
  • Terrestrial impact craters - more
  • Yucatan Peninsula
• Cenozoic - 65 million years ago to present, radiation of mammals (among other things)

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

• Things similar because of common ancestry?
• Non-existing things because didn't/can't work? because not tried?
• Was there a first organism? a first organism of each kind?
• What accounts for appearance of progression? ranking?
• Why does "change" happen? - need both differential survival and randomness to explore.
• Life identical elsewhere?

Evolution includes both slow, continuous change and rapid change

• The latter because exploring some possibilities depends on having explored prior possibilities?
• Would help explain how highly improbable things come into existence.
• Indicates very strong history dependence in accounting for life.

Evolution involves "chance", and hence likely to proceed somewhat differently elsewhere or if repeated

• meteor collisions (and the like)
• dependence on random variation within biological systems

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"?)

• reproduction with variance AND selection
  • Darwin's Finches
  • domestication
  • drug resistance
• Selection forces always changing
• Life itself changes the selection forces
• All existing organisms (including ones that have long evolutionary histories) equally adapted ("successful").
• Genetic randomness ("reproduction with variance") and selection rather than
  • "intelligent design" (see also Intelligent Design and the Story of Evolution: No Need for Drawing Lines in the Sand)
  • transmission of individual experience (Lamarck)
• Relation to cultural evolution, intentionality
  • Brings into existence both?
  • Lateral spread of information more in cultural than in biological evolution?

Images of evolution - "getting it less wrong"?

• Evolution as a progressive tree
• Cladograms
• Darwin?!
• Evolution as increased branching, bush
• Evolution as "non-essentialism"
  • species as diverse groups reproductively isolated from other diverse groups
  • themselves continually undergoing change
• additional changes
  • continous change in branches
  • exchange among branches
  • long time course dynamics

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

• clustered diversity, geographic variation, interdependence
• "adaptiveness" (without normative judgement or hierarchy)
• practical matters, such as plant/animal domestication, the development of antibiotic resistance, human variations having medical and other significances

Evolution (so defined) also raises new questions

• Was there a first organism? How did it/they come into being?
• Can the same mechanisms that account for small scale clustered diversity (micronevolution) also account for larger scale clustered diversity (macroevolution)? For the progressive appearance of more complex organisms?
• How is one to account for large scale patterns of temporal change (eg repeated episodes of diversification and extinction)?
• How much interaction is there between lineage dependent influences on living systems and non-lineage dependent ones (culture and other "horizontal" interactions, information exchanges)?
• What implications does the story of evolution have for the likelihood and character of life elsewhere in the universe? for our own sense of what who we are and where meaning comes from?
• How should new stories and older ones be handled in science classrooms, in education generally?
  
  Question about evolution is not whether it is "true" but whether it offers new and useful ways to make sense of things

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

• Schrodinger
  • Its not movement/change that has to be accounted for, its stasis that requires explanation
• Protein Motion
• Alkanes in Motion
• Time to Think?

Life=Science?

• On-going change, exploration
• No perfection or right answer
• Observation-gathering, hypothesis generation, testing, and repeat

  And ... ?

• Periods of relative stasis interspersed with periods of more rapid change?
• Periods of extensive hypothesis generation with relatively little testing interspersed with periods of extensive testing with relatively little hypothesis generation?
• Periods of data collection interspersed with periods of data compression and loss?
• Getting less wrong - in sense of summarizing more and more observations?
• Strong dependence on history?

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

• Anticipated by Greek atomists (who also inferred life elsewhere in universe)
• Very important advances in 1600's; see Soul Made Flesh by Carl Zimmer, Free Press, 2004

Element	Symbol	Atomic number	Percent in universe	Percent in earth	Percent in human (typical of living organisms)
hydrogen	H	1	91	0.14	9.5
helium	He	2	9	trace	trace
carbon	C	6	0.02	0.03	18.5
nitrogen	N	7	0.04	trace	3.3
oxygen	O	8	0.06	47	65
sodium	Na	11	trace	2.8	0.2
magnesium	Mg	12	trace	2.1	0.1
phophorus	P	15	trace	0.07	1
sulfur	S	16	trace	0.03	0.3
chlorine	Cl	17	trace	0.01	0.2
potassium	K	19	trace	2.6	0.4
calcium	Ca	20	trace	3.6	1.5
iron	Fe	26	trace	5	trace

• no hand atom, foot atom, human or elephant atom, no "live" atom
• nothing BUT atoms?
• therefore ... life is particular (improbable) assemblies of atoms
• of which there are many fewer kinds than there are living organisms
• whence cometh diversity?

• Stereoisomers (enantiomers, optical isomers) - How distinguished by biological systems?

Electron, electron affinities key to many biological processes

• covalent bonds - electron sharing
• ions, ionic bonds
• polar bonds, polar vs. non-polar molecules, (molecules with polar, non-polar regions)

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, http://www.cnn.com/2006/TECH/science/10/11/extinction.mammals.reut/index.html, 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 ... http://news.bbc.co.uk/2/hi/science/nature/6048186.stm?ls ... 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. http://news.yahoo.com/s/nm/20061017/od_nm/britain_stonehenge_dc 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? electron sharing, covalent bonds electronegativity ions, polar bonds how do living systems discriminate between left and right handed molecules?

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

• consequences of polar properties ("hydrogen bonds")
  • water as solvent, reaction facilitator - animation
  • water as contributor to homeostasis - high specific heat
  • cohesive (and adhesive) properties - tall trees, wider striders, capillary action
  • ice floats
• pH, important for higher level assemblies, further flux (the time dimension)
• origins of boundedness in polar, non-polar interactions

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

• diversity
• beginnings of autonomy, homeostasis, boundedness

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

• polor/non-polar
• acidic/basic

"Inorganic" versus "organic" molecules?

• proteins
• nucleic acids
• carbohydates
• lipids
• not mysterious: generally polymers of smaller molecules

• improbable, matter, energy, lots of roles
• more "combinatorial explosion": twenty subunits of quite different characters, so LOTS of variety
• 3-D structure (primary, secondary, tertiary) - alternate
  • importance of primary structure - Sick cell anemia -HBB: The Gene Associated with Sickle Cell Anemia
• enzymes: control mechanisms on flux by facilitating some chemical reactions as opposed to others
  • Specificity - lock and key, 3 D shape important
    • Shape change may be important for breaking down acceleration - alternate
  • both shape and flexibility/shape change important
    • 3 D structure complex in origin, fragile
  • provides understanding of life's ability to discriminate 3-D structures
  • explains temperature, pH sensitivity of living organisms
  • remember hydrogen bonding, ability to change shape, improbability (polymerization by dehydration, energy source)

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

• improbable assemblies of matter, energy content, play variety of roles
• Linear polymers (like proteins, but simpler)
• DNA: information as concept, relation to history dependence of life, human genome project
• "explains" sequence of amino acids in proteins - DNA -> RNA -> protein
  • sickle cell anemia
• double helix: intergenerational transmission of information, "explains" reproduction with variance `
• remember also improbability (polymerization be dehydration, energy source)

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

• energy storage (though less than lipids), structure, recognition(?)
• water soluble (of course)
• multiple structures from simple elements
• cellulose versus starch (structural isomers at next level)
  Why can't eat cellulose?

From hydrocarbons to lipids

• fatty acids to triglycerides
• generally hydrophobic (but also mixed)
• energy rich (improbability plus assembly rules, including oxygen)
• phospholipids central to boundedness of cells
• simple lipids include cholesterol and steroid hormones, important element in sexual identity/behavior
  • Lowering blood cholesterol to prevent heart disease
  • Relationship between blood cholesterol and violent behavior?
  • Cholesterol as a precursor - steroids. possible relation to serotonin Fats/cholesterol in diets - the current story?

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

• Complex web of interdependences - molecules serve multiple roles - transitions and choice points dependent on enzymes
  • complexity - alternate - cell/tissue specificity -
  • pyruvate
  • catabolism - breakdown (decreased improbability
  • Anabolism - assembly (increased improbability)
  • Cyclic breakdown/assembly
• Change one thing ... likely to change other things, somewhat unpredictably
• At deeper level: why do things change (not change) at all?
  • "improbable", "energy-rich", useable as "food"
  • break down "natural", where/how get assembly, the improbable?
    • Remember ATP, NADPH

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)

• Matter: what one can feel/touch, what IS (down to levels of atoms, molecules)
• Energy: everything else (almost), including what accounts for change
  Energy = motion/change (kinetic energy), capacity to cause motion/change (potential energy)

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)

Life as

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

• Why doesn't cellulose/peroxide fall apart?
  • Enzymes and reaction rate
    • Competitive inhibition
    • Non-competitive inhibition
    • Allosteric control
  • Enzymes don't CAUSE chemical reactions, they PERMIT/ACCLERATE/CONTROL them, and are themselves controllable
  • Key is to reduce increased improbabilities needed to get to decreased improbability, 3-D shape important not only for "fit" but also for this, variable shape may be as well
• Sugar won't fall from sky at any appreciable rate without enzymes (BUT, it actually takes more than that, as we'll see)

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

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

• diversity (again) - how account for it? what's its significance?
  • Prokaryotes, eukaryotes ... viruses
  • animals cells vs plant cells
  • common characteristics of cells
    • boundedness
    • ability to transform improbability
    • ability to reproduce (create comparable improbable organization)
    • genetic material
    • semi-autonomy
    • semi-homeostasis (reactivity)
    • eucaryotic cells: internal bounded spaces (compartments)
• scale: microns, tens of microns, a minimum size for life?, why?
  • macromolecule diameter ~ 10^-8 m, so 100 or so across a small cell, need a million macromolecules?
• a maximum size for cells? why? relations to outside world? ... maintenance of internal improbability
• nature of inside world? ... internal coordination
• cell as assemblies of diverse components (and hence themselves can be diverse), creates need for internal (and external) intercommunication/coordination
• the new factors: specialization, interdependence, distributed control

The matter of boundedness

• Displacement, internal movement, shape change
• Cytoskeleton
• Proteins and intracellular movement
• Actin filament assembly/disassembly
• Muscle
• Procaryotes move "autonomously", respond ("adaptively") (alternate)
• Reducing autonomy, responsiveness to molecules (for procaryotes and eucaryotes) (alternate)

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

• Where do proteins come from? - lots of steps from genes
• Turning genes on and off at the transcription level - Alternate
  • Genes CAN be turned on/off - true in multicellular organisms as well - significant in explaining diversity
  • Protein synthesis in some cases "autonomous", can be turned off, become active in response to external change (inhibition removed, rather than "activated") - "adaptive response", "goal directed behavior", homeostatic
  • DNA includes protein coding regions, as well as regulatory regions
• circadian rhythms in cells - "autonomy" based on gene regulation and feedback (more, and more)
• Are lots of other ways to control gene expression - another reason why the relation between genotype and phenotype is not direct

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?

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 is...how 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

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

• An overview - alternate
• Anerobic processes - Glycolysis and fermentation - alternate
• Aerobic processes - The mitochondrion as a specialized compartment with compartments
• The Krebs cycle (complement to dark reactions of photsynthesis)
• And again - electron transport, proton pumping and .... ATP synthase to yield ATP
• ATP as keystone of metabolism

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

• matter, like energy, is not "used", it is transformed, may be recycled
  The fossil fuels
  • there is no free lunch
  • CO₂ and global warming (more)
• 3-D organization of macromolecules critical (not explicit in genetic information), as are molecules other than proteins (ditto)
• are at level of cell already talking about complex interactions among complex, semi-specialized, semi-autonomous parts (the cell as symbiotic system) - cooperation at least as important in biology as competition (Lynn Margulis)

Cellular reproduction - mitosis

• If there's nothing but macromolecules there, why can't scientists make cells? .... when cells can?
  • spatial organization - alternate
  • though see The artificial cell, evolving
• A complex (and beautiful) symphony of interacting cell components, of macromolecular assemblies
• DNA replication .... with protein participation
• interphase/prophase transition - Chromosomes - chromosome condensation, with protein participation
• cell cycle autonomy, regulation - and cancer - alternate
• Independent but coordinated division of semi-autonomous, endosymbiotic(?) organelles
• Reproduction with variance?
  • mutation - but corrected
  • sex without reproduction - antibiotic resistance in bacteria - viruses and flu epidemics - horizontal gene transfer

Lessons from cells about life:

• Life is not any one thing or any one part but rather an ongoing and coordinated dance among lots of different parts
• Three dimensional organization and boundaries are essential to the dance
• Different parts play different roles - are "specialized"
• Signals are constantly moving back and forth among the parts - coordination key
• No simple "cause/effect" relations, elements reciprocally influence one another
• No one is "in charge" - coordination emerges from the semi-autonomous characteristics of the parts and the signals that move among them
• The problem of building a cell, of creating life?, may be at this point more a problem of properly assembling the components than of determining what the components are.
  • Yes, biologists don't know everything; there is still (will always be?) "so much to be learned". Even about the "basics"? Is nature of science?

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

• Cells, rather than macromolecular assemblies as components
• Diversity, need for coordination
• Need to maintain "life" in components

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

Energy-dependence?

• Eating/breathing ... not so much to keep YOU alive as to keep components of you alive
• Cells need ... molecules, oxygen
• Have to consider source ... and distribution (diffusion too slow in large, multicellular organisms)
• Digestive system
  • digestion, diffusion, active transport
  • "essential" things
  • eating regulation
• Respiratory system
  • bulk transport, diffusion
  • who's in control?
• Circulatory system
  • Semi-autonomous but interactive highly improbable assemblies
    • The heart as an example
    • Influenced by other systems, but beats independently
    • Made up of cells each of which can beat independently
    • "life" is in coordination
    • "self" is ... (who controls heartbeat?)
  • As a coordinating system (multiple functions of blood)

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

• The nervous system
  • Complex assembly of cells: neurons
  • Specialized for information transmission, communication
  • Input (sensory) neurons, output (motor) neurons, interneurons
    • Action potentials (ion flow)
    • Chemical intercellular signalling (synaptic transmission)
    • Network specificity, chemical specificity
  • Homeostasis
  • Another example of autonomy
  • Capacity to see, conceive alternatives, create (alternate)
  • Distinction between two parts of nervous system: conscious/unconscious - animate/conscious - where is self?
  • Genes, experiences, and ... personal creation, choice ... "self" is PART of brain, PART of who one is
• The endocrine system
  • Widespread, chemical communication
  • Chemical signals hormones, receptors
    • Steroid hormones
    • Second messangers
  • Interactions - feedback loops
    • Homeostasis
    • Autonomy
• The immune system
  • Self/other distinctions at the cellular level
    • Humoral immunity
    • Cellular immunity
  • At the molecular level - antibodies, membrane associated recognition molecules
  • Source of "appropriate" antibodies?
    • Gene rearrangement (combinatorial explosion)
    • Clonal selection
    • another example of "adaptive" behavior from selection among random variants
    • Interesting issues
      • origin of self/non-self?
      • membrane bound "identification" molecules - uniqueness?
      • early immune system development - autoimmune diseases
      • exchange of genetic information? (alternate)

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 ..."

• Multiple cells from single cell, zygote, fertilized egg
  • Why always back to single cell?
  • Which came first, chicken or egg?
  • Relation to problem of accounting for cell architecture
• Cleavage - multiple cells from mitotic divisions
  • Diversity NOT due to genetic variation
• Gastrulation - formation of basic vertebrate body plan
  • Skewered hot dog, with spaces in wall
  • embryological tissues - ectoderm, mesoderm, endoderm

• Combinatorial explosion again to account for diversity, history dependence
• Gene regulation key to development, dependent on cell movements, cell interactions
  • cell division, differentiation, the stem cell idea
  • makes cloning possible but ...
  • effects of nuclear/cytoplasmic interactions
  • effects of interactions with other cells
  • effects of extracellular, extraorganismal factors
  • stable changes in genetic material

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

• Lymphocytes
• Antibodies and immune specificity
• Antigens, antibodies, cell surface proteins
• Receptor diversity
• Clonal selection

• When facing unknown challenges, try out lots of things, build on what works
  • Contributes to cohensiveness/identity
  • Also threatens it - allergies, autoimmune diseases

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

• Fusion of two genetically different cells, themselves the product of improbable assemblies of specialized cells
  • oocyte from ovary - relevant to evolution: protected cell populations
  • sperm from testis - relevant to evolution: ditto
  • involves special kind of cell division - meiosis - to be returned to
  • had to have chicken before egg?
• Meiosis - an "adaptive" biological diversity generator
  • Haploid, diploid alternation
    • Diploid - pairs of homologous chromosomes
  • Two cell divisions
  • Generation of genetic diversity in Meiosis 1
    • Random assortment/segregation
    • Crossing over
  • Meiosis II equivilent to mitosis
  • Consequence - Mendel's Laws of Inheritance
    • Random segregation
    • Independent assortment
    • Importance, limitations
  • Consequence - "innate" information, individuality, exploration (from interactions of cells is multicellular organism)
  • Sex as play/exploration of novelty, facilitates exploration of gene usefulness in different genetic contexts

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

• Sex chromosomes influence, do not determine
• Hormones (themselves influenced but not determined by genes) influence but do not determine
• Environment/culture (themselves influenced but not determined by genes/hormones) influence but do not determine
• The story teller (itself influenced but not determined by all of the above) influences ...

The "story" from biology (so far)

• All organisms are interactive improbable assemblies, "explorations" of what can be/what works
• Cultures are interactive improbable assemblies that generate new properties
• Individuals are both influenced by and influences on cultures
• Individuals have the capacity to conceive of things as other than they are and to play a causal role in bringing into existence new improbable assemblies

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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