BIOLOGY 103
Fall, 2001

Notes

5, 7, 9 September:
NICE discussion of science on Wednesday. Thanks
What is science? Why can't it "get it right"?

Science = life?

Science as "summary of observations", "getting it less wrong"

Life is ... ?

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

10, 12, 14 September:

I was wondering the same sort of thing during Friday's class, trying to imagine how the concept of "summaries of observations" could be presented in an elementary classroom. I think I've decided that "traditional science" is actually just easier for the teacher, which is probably why it is taught that way. I think we may underestimate children if we think they couldn't grasp the concept of expanding knowledge through experimentation (as opposed to finding it). After all, as previously discussed, in that way science is exactly like life, so it is something children are already involved in. However, wouldn't presenting truth as nonexistent (rather than as something unattianable through human thought) be a very dangerous thing in a classroom?
... Christy Cox

... scientists aren't in search of truth at all, because in science there has to be some sort of evidence--people have to be able to see, hear, taste, touch, smell, or somehow physically register the observations that are made.
... Tua

I think that science, along with all other disciplines, are merely ways of interpreting the world and improving the lives of people according to the philosophies of the times. For example, the scientific discovery of DNA, and Darwin's theory of evolution would not have been as widely accepted, nor perhaps even pursued were it not for the more materialistic atmosphere that resulted from the Protestant Reformation, the Industrial Revolution, and the spread of Socialism. These economic, religious, and scientific breakthroughs were all attempts to better describe the world we live in, and by using these better descriptions, we would be able to improve the state of the world.
... Margaret Pendzich

i find it helplessly depressing to think of life as a series of mistakes one after another. at the same time, that seems to be the class consensus, and perhaps it's my consensus, too.
... Kat Fallon

Yet when science tries to involve it self in Biology, the science “of life” how does it avoid it’s own cultural framework? As a class we had a hard time talking about life on Europa because all of our descriptions of what life might be like were initially human centered…It took us a while to figure out that something didn’t have to “move” in order to be alive. Can we see and understand life without being self-referential?
... Heather Shelton

What seems more likely would be that "life" (I guess we still haven't defined that word) on another planet would have evolved in a completely different direction and would therefore have different characteristics. Just because we can't imagine it, doesn't mean it couldn't exist.
... A.B.

I felt like it was an interesting way to see how science and life are intertwined. We may find that our definition of life evolves as we explore through observation on other planets because just like anything else in science, we have defined life through a series of observations.
... Leah Rayner

While the description of life if I were landing on Europa would have to be based around physical aspects, I think that what life actually is, is far more than what we made it in class. Life can be that short period of time between when something is born and when it dies, or it can be every single moment within that time. Sure, life can be motion, reproduction, growth, and interactions with the environment, but why can't it be memories, sights and emotions? ... We ARE astonished by the obvious perhaps. After all, that's what life is all about.
... Sarah Sterling

I was looking through the book, and I saw how varied "life" was -- for example, they showed pictures of the molecules that make up chlorophyll, then they showed a chloroplast, then a single plant cell, then the tissue, then a single leaf, then a tree, then a forest, where all kinds of organisms interact. All of this, from the tiny cell to the huge forest, is life. In the same way, science encompasses a huge area. Science tries to make sense of the cosmos, of outer space, of the oceans, and also studies the tiniest molecules, splits atoms, tries to map genes. The small and the big all come together. Kinda cool, huh?
... Rachel Moloshok

A living organism ... ?

Defines some of the phenomena that need to be accounted for in course (or, at least, by biologists over time). But not ALL of them .... what needed beyond characteristics of a living organism to define "life"?

Interdependent diversity, change over time




Similarities between science and life?

How "make sense" of diversity?

Arrange in order of size

Human perspective relevant: Technology dependence of observations
Limited range of observations? of sizes of organisms?

17 September:

Yet when science tries to involve it self in Biology, the science “of life” how does it avoid it’s own cultural framework? As a class we had a hard time talking about life on Europa because all of our descriptions of what life might be like were initially human centered…It took us a while to figure out that something didn’t have to “move” in order to be alive. Can we see and understand life without being self-referential?
... Heather Shelton

Contemporary taxonomy, according to our textbook, is primarily focused on establishing how closely various species are related -- how much of their genetic inheritance they share with one another. Why, I wonder, is that so important to us? Why do we seem driven to classify things according to how like or unlike us they are? ... Do we reduce our chances of evolutionary "success" by restricting what it means to be human and then assuming that humanity is the desired state?
... Claudia Ginanni

The previous posting asks why humans are driven to classify things according to how they relate to themselves. I ask: "How can we avoid this tendency?" ... We acknowledge our differences by comparing oursleves to each other as humans and recognizing the idiosyncrasies of our species in comparison to other living beings.
... Joelle Web

the social characteristic of banding together in stress is not a human one. this kind of response is mirrored in other species. it is intersting to note that an injured water buffalo, hunted by a pride of lions, recieves protection from fellow buffalos that encircle him and display they're horns.
... Viv

People get caught up studying theories and models or they get caught up in their own work and chores, and they forget about the life aspect. Life may go on after tragedies, but the value of that specific life (its stories and information) are gone. Science, and biology especially, aren't just about classifying things, but connecting and interacting with other living organisms.
... Emi

I think part of our definion of life may need to include the fact that it is irreplacable. ... And, to relate this to the recent tradgedy, no matter what actions this country takes against anyone now, the lives lost can't be replaced. Killing people can't be taken back, because life is that aspect of an organism which can't be regenerated or replaced.
... Sasha

In our class, we have learned that in order for our lives to go on, we need diversity throughout our biosphere. Yet, here we are trying to destroy something different from us, just because we don't know all the facts. If only we, as a country, could realize just how precious diversity is to us.
... Rebekah Rosas

Too often, we seem to consider ourselves the final, perfect product of evolution. This thought led to another, more pessimistic thought (I'm sorry; I don't usually think this way). In the wake of all this tragedy it occured to me that perhaps humans are WORSE off than other species. After all, what other species kills its own kind out of something other than need; what other species has created things like discrimination and racial hatred; what other species has invented "tools" that serve no purpose other than to hurt others? It makes me wonder how and why we became this way?
... A.B.

I feel insensitively intellectual in trying to understand Tuesday's tragedy as part of the human evolutionary process. If evolution implies advancement, then it would seem that any and everything that occurs in our world somehow betters it. ... How has Tuesday's tradgedy advanced us? What role will it play in our evolution?
... Charlotte Ford

see also 11 September 2001

it seems we can very easily recognize an "improbable assembly," what would we recognize as a probable assembly? I think this can be answered by making some sort of observations reguarding chaos versus order, however the very idea can also be argued against using the parts-of-me-in-a-bag illustration. If I put all of my parts in a bag and spill them out, odds are not good that I will get me on the floor. But if I spill them out once (in what might seem a chaotic and probable assembly), aren't the odds equally slim that I will ever get that "probable" assembly again?
... Christy Cox

Size scales - at what levels do improbable assemblies exist and how do they relate to one another?

1. Larger things are improbable assemblies of smaller things
2. Improbable assemblies exist at a most scales (though see Alvarez)
3. Different features apparent at different scales; at larger scales, smaller wholes become invisible parts
4. Both very small and very large scales are important for understanding life.
5. There exist lower and upper(?) bounds for living organisms ... as we currently know them
6. Existing observations are greater than in past, but clearly incomplete
7. Can distinguish smaller, single-celled from larger, multicellular organisms
(Why no big unicellular organisms? - need for communication/integration?)

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 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
Are there "discontinuities" (is there "clumpiness"?) in life's diversity?

Plants versus animals versus fungi(?)

Autotrophs versus heterotrophs (interdependence)
With correlates (e.g. 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 (Protists) vs Prokaryotes (Monerans: eubacteria and archaea) (Why no multicellular prokaryotes?)

Five (or six, or more) Kingdoms:

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

Look more carefully at animals (metazoans)

More patterns within patterns (level of internal complexity, embryology)
More clumpiness

Why no ventral nervous system with endoskeleton?
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?

How make sense of diversity, clumpiness?
Great chain of being - ordering of organisms along some scale?
Evolution ... ? Go on to time, and its scales.

21, 24 September:

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

It's frightening to me to think that a species that has so much power while, at the same time, being so ignorant of the larger scheme in life and the consequences that the actions taken now will affect the future. ... Julie Wise

.many Americans were able to unite...to cope with the tragedy..yet..as quick as I was able to group plants today in categories ..people were quick enough to place me under the category of being a threat to the US...since all they can see is my brown skin... Monica Bhanote

As there are more and more discoveries scientific categories evolve. As different races of people in the United States learn more about those with skin color that differs from their own their definitions of race evolve. I wonder how much scientific observation it will take until our society realizes that skin color is not an adequate way to classify ... Leah Rayner

In our own species we seem to either hate variety and supess it, or to ignore it so we can all be the same. I think we should be impressed with similarities and differences all the time. ... Sasha

Sasha commented how we either suppress or ignore our variety. I agree that we don't appreciate the small differences that we do have. Biologically, we aren't all that diverse because we haven't given evolution a chance to experiment. For the most part, we find others similar to oursleves and huddle together in small groups. On Friday, we began to think about what effect time might have on this whole process. Just as with diversity, many people ignore and suppress change. I wonder, as a species which doesn't like change or diversity, what, in evolutionary terms, are our chances of survival over time? ... Tua

One thing we must endevor not to forget is that we are still in the process of evolving. ... I think it extremely important for us to recognize what we may become, and how the consequences of our actions may have an effect on that. ... Rianna

I am proud to be a thinking and feeling being that grows within this world and shares this world with so many different people ... Celina

In case anyone's forgotten, let me remind you of the huge world that we share with the all the animals and plants and trees and bugs and oceans and deserts. And of how old the earth is, and how much things change. ... Rachel Moloshok

every day scientists, with the aid of technological advancements, are unearthing new species. will these 'missing links' help to smooth out some of nature's "clumpiness"? ... Viv

Our textbook paraphrases Darwin's second inference: "Survival in the struggle for existence is not random, but depends in part on the hereditary constitution of the surviving individuals. Those individuals whose inherited characteristics best fit them to their environment are likely to leave more offspring than less-fit individuals." (p 420) How does this apply to the human species? Does it apply to individuals, or cultures, or only to the human race in its entirety? It isn't logical to call a mother of 10 better adapted than an infertile woman, is it? ... Charlotte Ford

the overwhelming role evolution plays in explaining non-human animal behavior coupled with the number of examples of human behavior that are consistent with evolutionary theory make evolution a viable tool in explaining the diversity of life ... Rebecca Roth

When looking at the big picture, we tend to look at life as insignificant - we are so small compared to the cosmos and our lives are so short compared to eternity. We do live and die, and yet we don't. Maybe we won't be remembered within a few centuries, but isn't it amazing to think that the people we see now are show some of the history of the human race through their physiology and that we may perhaps someday have offspring who will in turn give some part of us to future generations? ... Emi Arima

when I look at our species in the context of geological time, I wonder if we should consider the technologies we've developed as part of the evolutionary process. Or perhaps they will ultimately have the effect of retarding the evolutionary process, since one of the things we try to do with them is to alter our environment to suit us. ... Claudia Ginanni

Scale and Evolution: Time Scales

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):

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?

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?

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
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 does include some directionality, but is not toward "perfection" or "better" but rather toward having explored more (increased "complexity"?)

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 also 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)

1 October

The concept of time is generally associated with scales and improvement, or change continuing in a certain direction. For once, we must disassociate evolution with time ... Life does not evolve on the straight path of time. It is difficult for me to understand time without the notion of a pattern. Where is life going? Is it going forward, backward or staying in the same place? ... Ilana Moyer

During a recent C-Sem class discussion my professor mentioned how old the text we were reading was. While Herodotus’ Histories are extremely old compared to what we can conceive, I couldn’t help but think of the age of “life as we know it”. Considering the age of life the text is quite new. My problem with this idea is that I can’t even begin to imagine anything before human life. This incomprehensible quality of science has always bothered me. How do I get beyond having little faith in science because there are so many questions and very few answers? We can continue to come up with hypotheses for what the earth was like before our time but we will never really know ... Millicent Bond

Our history of life is often a story of ever-increasing complexity. This increase in complexity begins with life's prehistory: hydrogen atoms are compressed into more-complex helium atoms as suns form, helium molecules become more-complex atoms of heavier elements including carbon when suns die; carbon atoms become parts of huge, complex organic molecules. Then we go from prokaryotic life to eukaryotic life to multicellular organisms and so on, building organizations of organizations, with complexity always increasing. And the possibilities of diversity increase with complexity. Of course, the reverse process is going on all the time -- things are constantly decomposing and breaking down into less complex components -- but that narrative doesn't seem so compelling. Perhaps that's because it seems so much more probable.

But the process of thought sometimes seems to be more nearly analogous to the deomposition process. We feel that we have understood something only when we have taken it apart into its constituent parts -- the simpler (and thus less diverse) the basic components, the better our analysis has been. Then we feel that we have achieved order ... Claudia Ginanni

its hard to think of oneself as an evolving species. as humans, we detatch ourselves from the process or believe we have mastered it through technological advancement. it is only when we realize that this ongoing process of exploration will continue as long as life does that we see the lack of control we have over it. it is strange to think that like whales that "are believed to be descended from terrestrial, 4 legged animals," we too exhibit signs of an evolving species. Our pinky toes are slowly shrinking, and more and more people have wisdom teeth that never grow out of the gums; it makes you wonder what kinds of adaptations we as a species will exhibit in the future. ... Viv

The last few classes have raised a rather interesting paradox for me. As we talked about time and how OUR history (the history of humans or even the history of multicellular organisms) occupies such a very small percentage of time as a whole, it made me feel rather insignificant. On the other hand, the more we study how "improbable" our assemblies are, the more I'm struck by how amazing it is that we're here thinking, feeling, and acting. It's strange to feel so trivial on one hand, and yet so unique on the other hand ... A.B.

Need to account for patterns in space and time at multiple scales
Improbable assemblies, adaptiveness, diversity, change
Can get that from improbable assemblies of physical elements (atoms)?

Remarkable generalization - dissociate ANYTHING, get out elements = atoms

ElementSymbolAtomic numberPercent in universePercent in earthPercent in human
hydrogenH1910.149.5
heliumHe29tracetrace
carbonC60.020.0318.5
nitrogenN70.04trace3.3
oxygenO80.064765
sodiumNa11trace2.80.2
magnesiumMg12trace2.10.1
phophorusP15trace0.071
sulfurS16trace0.030.3
chlorineCl17trace0.010.2
potassiumK19trace2.60.4
calciumCa20trace3.61.5
ironFe26trace5trace

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

"Assembly rules" as a concept

Assemble rules for atoms into molecules by covalent bonding (electron sharing)

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

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

8 October:

Overwhelming diversity of molecules (like life)
Any way to make sense of it? Any other useful things to learn at this level?

"Inorganic" versus "organic" molecules?

Carbon based versus non-carbon based, but no longer a good distinction for small molecules (large?)

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

Classes of biological(?) macromolecules (and related constituents): lipids, carbohydrates, nucleic acids, proteins ... polymerization, dehydration reactions

Proteins, from amino acids

Nucleic acids , from nucleotides

Carbohydrates, sugars (monosaccharides to polysaccharides)

From hydrocarbons to lipids

27 October:

Have diversity, improbable assemblies of parts, macromolecules. Assembly rules define possible things that can be, not what IS, nor what leads to change from one thing to another ... For that, need to take about energy, energy dependence

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)

First Law of Thermodynamics - in any isolated sytem (the universe) energy remains constant

Second Law of Thermodynamics - in any isolated system (the universe) change is always from less probable to more probable states Diffusion as the archetype of life - improbability and flux (increasing disorder) driving increasing improbability (increasing order) Sun (plus?) 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" - why doesn't cellulose fall apart without enzymes?

Anabolic and catabolic processes coupled, break things down to build things up, always create "waste"

Can do same thing in the absence of light (Alexis Hilts), which also raises an interesting issue with regard to circadian rhythms (Susanna Jones).

29 October - 2 November

I was fascinated by the link in our lecture notes to low cholesterol levels' correlation with violent behavior, and by a classmate's suggestion that this could help explain violent behavior in "developing" nations. It's never as simple as nature or nurture; they both inform each other--but how much control do we have over our actions/reactions? To what extent do our genes/diet/chemical reactions determine our behavior? From a biological standpont, where does free will enter the picture? Can free will be explained bio-chemically? ... Charlotte Ford

Which is more likely: That the sun will "burn out" or that we will in one way or another create our own extinction? ... Sarah Sterling

I also find it interesting and enlightening that all earthly objects are made of the same matter. In fact, I think that this is such an important idea that it should get more publicity! If everyone were aware of all of our similarities and commonalities, perhaps the history of mankind would be different. The future still can be different if we use science to promote these good ideas. There are little discoveries by science every day that abolish stereotypes that we have lived with for centuries ... Samantha Carney

we know that the human population is growing at an increasing rate.(exponentially?) this increase is then adding to the number of highly ordered cells or organized systems in our universe thereby, to some extent, decreasing entropy. At the same time an increasing population also spells an increase in conversions of usable energy to heat released into the universe. clearly, for the second law of thermodynamics to hold, more of the second is occurring than the first. what i find intriguing or think should be considered is the rate at which entropy is increasing. can the rate be quantified? what kind of impact do increasingly organized systems have on the rate at which the entropy or disorder of their surroundings increases? could disorder be increasing alongside our population at a faster and faster rate? ... Viv Bishay

This idea is still kind of rough in my mind so bear with me, but: in class we've talked about patterns of movement: how life seems to be moving towards more and more "improbable" assemblies and how all the energy in the universe is moving towards more "probable" states. All this movement appears to be linear in some way and (to me at least) implies a finite end (either theoretically or in reality). My question is then: can the progression of life, energy, the universe, or even time itself ever be considered cyclic rather than linear? ... A.B.

In the last few classes we have been learning how all matter,including living systems are in constant random motion and states of fluctuation.In that sense,nothing appears to be stable or fixed,but a continuous flow of breaking up and rebuilding(???) to create improbabilites which in turn create more improbabilties.Does that mean nothing is stable??? If so,why do we humans crave so much to cling to things(living and non lving) and desire permanence and stability? ... Savithri Sekanayake

The topics of discussion in our class are becoming increasingly detailed. Now, we are in the process of describing complex proteins and the structures of our own life forms: DNA and RNA. Even this would require more detail, i would appreciate it if we discussed the physical aspects of how all of these items actually work together. Otherwise a complex protein does not really relate that much to my life ... Joelle Web

Fit enzymes into picture, as regulatable chemical reaction controllers and couplers
Why doesn't cellulose fall apart?

Enzymes and reaction rate

Enzymes don't CAUSE chemical reactions, they PERMIT/ACCLERATE/CONTROL them, and are themselves controllable

Catabolic/Anabolic coupling

Metabolism - life as linked/controlled creation, destruction of molecules

5 November

Have some explanations of diversity, boundedness, reproduction, energy dependence, change at levels of molecules, macromolecules but ... are they alive?

We've investigated all of these ideas about atoms up to macromolecules ... However, we've still have so far to go until it all makes sense. Even with all of this new understanding, I still can't necessarily find where life comes in--at what point do all of these reactions combine to make a LIVING cell. How do these cells interact to make up a person? How are emotions, ideas, and personality accounted for with these chemical reactions? Any ideas? ... Emi Arima

Sometimes I find that when thinking about cells and macromolecules it is easy to break it down into very small components ... I'm sure that we are starting to explain (or already have???)how one gets from neurons firing to modern art, but I'm not sure if I understand it. It seems to be a rather touchy subject; the idea that one's thoughts, feelings, and unique mental traits could be considered to be just chemical reactions. ... Rianna Rouelette

"Molecular docking is a serious challenge for bio-chemists. There are many ways to fit molecules together but only a few juxtapositions that bring them close enough to bond. On a molecular level success may mean discovering what synthetic structure, what chemical, will form a union with, say the protein shape on a tumour cell. If you make this high-risk jigsaw work you may have found a cure for carcinoma. But molecules and the human beings they are a part of exist in a universe of possibility. We touch one another, bond and break, drift away on force-fields we don't understand."
-Jeanette Winterson, Written on the Body ... from Kat Fallon

The "cell theory" - All living organisms are either cells or assemblies of cells
What are cells? Why needed fundamental level of organization for life? Why minimum/maxium size?

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

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

Movement ... understandable in terms of proteins

9 November

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

This whole idea that we start out at a highly improbable state and from then on begin to become more and more probable until we can no longer be distinguished from non living things, is really intruguing when considered next to all of the social and cultural discourses on getting old, aging, dying. Why are we programed to be mortal and where does the left over energy go at the end of the living process? ... Tua Chaudhuri

Need to go on to talking about energy in cells ... and will ...

12 November

Responsiveness/autonomy depend on energy - Where/how does that get in game?

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

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

General principles, beyond energy per se

19 November

Cellular reproduction - mitosis

Lessons from cells about life:

Bonus topic - color

26 November

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

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

I feel that cloning might add to a greater understanding of genetics. It could be used for couples who risk passing a genetic defect to their child.
On the other hand, cloning might be used to create the 'perfect' individual. How would we react to this? What about the children knowing that they came from a clone? Could cloning interfere with evolution? ,,, Rebecca Roth

As far as the cloning issue goes, I find it noteworthy that the embryos developed to a point of only 6 cells according to one of the news reports posted on our class webpage. 6 cells, while impressive, is a long way from a human being. Not only that, but the purpose should be considered; i.e., cloning for new organs, or cloning for new humans. ... Rianna Oulette

One can see parallels between cloning and nuclear technology in that both have extremely positive and extremely negative possibilities. The effort to restrict nuclear technology to a privileged group of 5 countries was a futile endeavor and we must understand that if an individual/nation possesses the capabilities to clone, it will happen. We just have to learn to deal with it. ... Neema Saran

I’m still thinking about Emi Arima’s posting about the mortality of cells. She mentions the idea of how cells die and brings up what implications this occurrence has on how we perceive our own identities. Emi’s idea, that on a cellular level we have died and been recreated multiple times (and because of that we can actually say that we’re not the same person anymore), is something that definitely makes me think about conceptions of identity in both non living and living systems. If you have a wooden boat and each year you replace a plank until one by one all of the planks that were originally present are no longer part of the boat, do you still have the same boat? Some people would say no, that the essence of the boat was contained in the planks that it was built with then it was first made and when they are replaced you’re left with an entirely new boat. Can we consider human life in the same way? If not, what makes it different? One could also argue that we should forget about the body and look toward the brain to find out more about identity. It used to be popular belief that cells in the brain did not regenerate, but a recent study at the Salk institute shows that adult humans generate new neurons in their hippocampus. If brain cells are also regenerating, then isn’t your brain constantly changing too? I do not think that we die as soon as all of our original cells do. Our cellular structure is constantly changing, but I don’t know if that means that we are constantly dying and being reborn. What if we are always changing and emerging and in a way in which we’re never quite the same or distinctly different? ... Heather Shelton

The cloning issue: Where does zygote come from?

Fusion of two genetically different cells, themselves the product of improbable assemblies of specialized cells

Meiosis - an "adaptive" biological diversity generator

Importance of diversity generation - "sex" independent of reproduction - practical considerations: antibiotic resistance

10 December

Have dealt with improbable assembly, boundeness, reproduction with variance in multicellular organisms ...

Energy-dependence?

We're NOT going to get through all this stuff. Not with one week left. Oh well, life is ... a process of learning about life. So, what shall we focus on in our last week? How about the self ... and the place of the self in a larger biosphere? Maybe homeostasis, autonomy, the brain, and evolution?
Semi-autonomy, homeostasis, adaptiveness and ... the self? Coordinating systems

12 December

Nature of "self" - interacting autonomous parts
Of
brain

Individual multicellular organisms (humans) made up of complex, interacting set of components - And are themselves components of still larger interacting improbable assemblies
Are both result of and influence on our components, can both be influenced by and influence the larger assemblies

AND SO ...

To be continued


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