BIOLOGY 103
Fall, 2005

Discussion Notes


29 August

Bio 103 as process ... making sense of life

Biology -> Science of life

Interesting/relevant Raises further interesting/relevant questions, both specific and general ...

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

Linear scienceSeriously loopy science
  
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 making of observations, summarizing, making new observations, making new summaries

Science as skepticism usable by and empowering anyone at any time about any thing for any purpose

Science as Practical Tool, Continually Being Adapted
"The Crack" as Feature Rather than Bug (multiple possible summaries)

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

Which of the following stories do you prefer?

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

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

Life is ... ?

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

Characteristics of a living thing?

What's alive here?Is Langton's ant alive?
from Sahara Meteorite Prospecting from The World of Langton's Ant:
Thinking About "Purpose"

For the forum:

Your initial thoughts about


5 September

From the Forum: Thoughts About Science

science is no longer a field comprised of absolutes but is rather a methodology for interpreting and understanding the world ...One patient science teacher explained to me that science, like religion, requires a 'leap of faith'; like the acceptance of God as an absolute force, one must accept the (already-tested and established) facts of science as absolute truths. This 'leap of faith' idea unsettled me ... But ... if it is to be a process of 'story-telling' then there does not appear to be any end in sight. Who gets to contribute to this story-telling? Whose words carry the most weight? And while I see the advantages of redefining science as an inclusive rather than exclusive activity, I wonder if this if this inclusiveness is realistic. If there were such a scientific world community would it not (just like the global community of the web) be riddled by misinformation, indecisiveness, even fraud? ... Keti

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

what we are learning in this course is ... to think outside the bubble, to observe and to wonder. What I myself wonder, however, is if through this process we are training ourselves to be skeptics, or to work too hard to see possibilities, rather than accept some of the simpler facts of life ... Is this kind of thought a waste of our time? ... Lizzy

Science can be, and has been, extraordinarily useful, and there is an undeniably practical element to the Western conception of science which, in my opinion, legitimizes it. The relativist approach to science should not overrule its ultimate usefulness ... Nick

our list of characteristics for what is considered alive may change over time. Currently we are taught that all organisms fall under living or nonliving and that living organisms have common characteristics, which include: eating, growing and reproducing. However, these are current observations and it may turn out that what we consider non-living may actually be a living thing in mars ... Iris

What is a living thing?, con.
I find the definition of life that I learned way back in High School bio difficult to get away from; the basic gist of our first semester was that an object was living if it respired ... Magda

It would be very hard to determine whether or not something is living simply by looking at it for a few seconds ... Stephanie

How can we decide what is living? If there are once again no "Truths" where do we get our authority? ... Sara

we are trying to create our own definitive version, isn't this what we are trying to avoid, or is the process of coming to our own definition of life the important part? ... Brom

  • highly improbable assembly
  • bounded
  • energy dependent
  • semi-homeostatic
  • semi-autonomous
  • reproduces with variation
Defining "life" collectively: Is it worth it? And if so, why?

"Is this kind of thought a waste of our time?" " ... the answer lies within the eye of the beholder?"
Yes, but ...

  • Curiosity, the wish to see beyond ...
  • The practical issue of life elsewhere in the universe
  • The past lesson of the consequences of too narrow a definition of humanity
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?) ... maybe life is not something things have (no elan vital) but instead ... ? 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


Change over time

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

An Overview: Spatial Scale and Diversity

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

Lessons from working up in scale from human ...


12 September

From the Forum: Thoughts About Life


Despite my attempts to free my mind from all school-related matters Friday ... In the vastness of this universe, can Earth really be the only place that sustains life? ... So, where am I in this dot, a dot inside of the dot? ... Katie

That itself got me thinking about how we as humans process things; the human brain, a squishy, grey mixture of cells, is capable of performing all of these intensely complex functions, and it's so tiny in relation to everything else ... Magda
  • The Brain - is Wider than the Sky
    For - put the side by side -
    The one the other will contain
    With ease - and You - beside.
        Emily Dickinson, 1820-1886

I think the sheer size of the universe must be pointed to by many who believe in other forms of life, I would think the odds are in favor of there being life elsewhere. Has any mathematician tried to figure out the odds of life elsewhere in the universe? ... The carbon present in our solar system is the product of a supernova. Even if their was only one supernova in the history of the universe there would have to be carbon somewhere else besides here ... so it seems likely to me that somewhere in the universe there is another carbon-based life form wandering around ... Lastly if the life is not carbon-based, what are other possibilities give serious consideration? ... Brom

the conditions on Earth are just right for life (as we know it). Its distance from the sun, the character of the atmosphere, the presence of tons and tons of water - all of this lends itself, at least in the case of Earth, to the creation and sustenance of life. As we moved back from the Earth a bit during class, I had an idea. If Earth is the ideal planet for life in our tiny solar system, maybe our solar system is an ideal system in the galactic sense. If the sustenance of life is primarily based on the Earth's distance from the sun, then maybe the same can be said for our solar system with respect to the center of the galaxy ... Maybe, if/when we get out of our solar system in the search for life, a good starting place may be to plot a circle around the galactic center which includes our system, and (if this is at all possible) search in this general area before moving in or out any farther ... Nick
  • "Granted, then, that empty space extends without limit in every direction and that seeds innumerable are rushing on countless courses through an unfathomable universe ... It is in the highest degree unlikely that this earth and sky is the only one to have been created ... So we must realize that there are other worlds in other parts of the universe, with races of different men and different animals" ... Lucretius, 99-55 BCE.
  • Extrasolar Planets Encyclopedia
  • SETI
  • Drake Equation
  • Galactic habitable zone
  • Habitable zone ?

I'm trying to look at this one feature at a time. (highly improbable assembly, bounded, energy dependent) seems like the most fundamental set of features to me, although clearly this set includes much that is not life (stars, for example.) Semi-autonomous seems like the next really useful criterion, even though I'm not entirely comfortable with it. Do sea sponges have any semi-autonomous features? And reproduction, while it seems like a no-brainer, has problems we've already discussed. How about mules? And thinking back to the dawn of life, does it seem reasonable that the first billion or so organisms to be formed out of the primordial ooze might have lacked reproductive capabilities, and only later did one form that happened to have that capability? Were those first organisms life? If not, why not? ... Where I really become uncomfortable, however, is when we start defining diversity and interdependence into the meaning of "life." These are phenomena of great importance and worthy of study, but I feel that the real question raised is "why does (insert definition of life here) invariably live in diverse interdependent communities". You basically kill the whole subject of study if you just assume that as part of the definition ... Zach

life anywhere would need to be an improbably assembly. Perhaps boundedness may not be a property of life on other planets. I could imagine a scenario where there was something quite large and unbounded which ended up being alive. Also, being energy dependent could be different on other planets and we would have to come up with a definition of energy that fits other planets as well as our own. It may be a criteria on Earth for life to be semi-homeostatic and autonomous, but it could differ somewhere else. Of course, I cannot get out of my 'earthy' way of thinking and cannot even begin to imagine what type of creatures might exist on another planet ... Stephanie

Seeing the differences in the planets of our galaxies it seems that organisms in planet X will have differences because organisms adapt to our environments for survival. These differences may have changed them in such a way that they do not need each other to live ... While posting I was also thinking about our periodic table and how we discover new elements. Can there be an element that we haven't discovered? And if so maybe this element can be sustaining life in another planet ... Iris

What I am arguing is that our particular classification is so evidently random because it is characterizing the results of one 'Petri dish' (The Earth) when there are millions of other Petri dishes ... We are still stuck in the old mindset where we presuppose that we have an idea of what life is, when we are just drawing random lines in the sand. Maybe rocks are pods that protect aliens who are existing on a different plane of existence before our very eyes, but they experience time a billion faster than we do and they communicate through auratic telepathy ... I know this idea sounds crazy, but honestly if we're talking about the universe and infinite then the craziest possibilities are exactly what we should be talking about. We must humble ourselves and realize that we are so isolated, so ignorant, and the definition of life we create is only useful on a social and political level. As far as truth, we shouldn't even tempt ourselves with the word definition. Limited inference is more like it ... Scott

despite the breadth of possibilities our imaginations allow us ... a few things (to the best of my knowledge) are pretty universally true .... We know enough to conclude that everything in the universe is matter and energy, correct? That is to say, isn't everything in the universe is made up of protons, neutrons, and electrons, and the energy that makes them interact? ... So if life exists on some other planet, it's going to be composed of atoms and elements the way we are, and moreover, from the same basic collection of atoms and elements ... This, it would seem, cuts down pretty drastically the number of possible forms extraterrestrial life may take. More specifically, it appears to demand that life would take a form Nearer to life on earth rather than Farther. Given this, our ability to distinguish something living from something nonliving would be pretty serviceable in our interstellar travels ... Matt

What is life? The American Heritage dictionary defines it as 'the quality which distinguishes living organisms from dead organisms' ... My roommate defines it as 'everything that's not rocks' While the first is an authoritative definition, the second is actually more helpful. It reminds me of a class in which everyone was asked to define modernity. Nobody was able to offer a definitive answer but could only say what modernity was not. In a sense, this mode of classification (defining by opposition) might be more useful in our discussion of the nature of life ... it seems to go along with the idea of science as a process of getting it less wrong ... a way to recognize and classify patterns of life without essentializing the observations made ... Keti

In general, I am not one to automatically realize/make connections between science and some of my other interests, specifically art and politics. Sometimes certain statements, however, stand out and help me to realize just how integral science (particularly biology) is in every day life. The definition of alive which Keti provided was one such statement ... If an organisms symbiotic relationship with a living being (i.e. a fetus connected to its mother by an umbilical cord) could serve as justification for calling that organism a living being itself, then abortion would be, for a fact, the termination of a life. I realize now that just the basic definiton of the word "life" also defines concepts far beyond the realm of science and biology ... Lizzy

And from working down in scale ...

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 vs Prokaryotes (Monerans: eubacteria and archaea) (Why no multicellular prokaryotes?)

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

Clumpiness in plants

Look more carefully at animals (metazoans)

Nested Clumpy Diversity

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?, no "narrative" character

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


19 September

From the Forum: Thoughts About Life

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

the human way of categorizing the world has worked thus far, which would lend evidence to the point that this diversity naturally divides and organizes the world. My point, though, is that the idea of "naturalness", ie what the world would look like to a non-human observer or if no humans were present, is a pretty pointless line of questioning. There is no way to know, and, even if we did know, the world wouldn't look or feel any different to us ... Nick

I agree with Zach that there inherently exists some sort of "natural clumpiness." ... However, I think that we often get "category-happy" by trying to force things into categories that may not really fit. For example, let's say there are only 6 categories of plants. If we discover a plant species that does not fit into one of these categories I think that people do not know what to do. Do we create a new category? ... Katie

Categorization then, is a useful tool. Attempts to find similarity between species can lead to discoveries far beyond new arbitrary distinctions. Also, creating categories allows us to get started on our massive project of sorting through this mess of life on the planet ... Zach

Sure, classifying organisms is useful, but only so useful. What is more interesting is this idea that an ordered force appeared despite the disorder and, at least on Earth, proved to find a relationship with the disorder. Things are here because at some point it did them better to be the way they were, and as we see, at times things could evolve because it was better for them to change, or if the changing wasn't "better" it at least did not bring about their immediate destruction ... Scott

I've come to fear categories, and class this week has made me think again about why ... Essentializing members of a racial or religious group has obvious negative implication for how we see perceive particulars and treat individuals ... as the Great Chain of Being that we saw in class shows, it is difficult for the framework we use for categorizing plants and non-human animals to be seperate from our approaches to other sources of information and understanding of the universe ... I'll be interested to see how crucial evolution is in diversity. Last week, we seemed to place it at the center of modern biology's categories. Can organisms that evolve from different sources independantly develop significant common characteristics, to the point where they have more in common than species with the same ancestor? ... Norma

What makes one category better than another?? That it causes each clump to be small. So how far do we go in categorizing organisms? Until there's one left or maybe two?? I was reminded of the movement by the multicultural students at Haverford to have a different box on the application for admission, which took into account that an individual could have more than one race. In their case, human categorization was limiting their choice to only one group and a new category needed to be created ... Iris

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

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

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):

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

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

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

Fossil record - Observations

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

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

Next steps? How soon?

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

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

Stasis and change - THEN slow progressive improvement?

Nope, continued fits and starts

Well then ... humans at least?

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


26 September

From the Forum: Thoughts About Evolution

Just as it is impossible for us to see tiny objects without a microscope it is also impossible to imagine the world billions of years ago without the aid of science. Science can actually take the place of the human eye and (attempt to) describe places and times outside of human scales ... Ketie

When scientists break down life into species, orders, etc, do they begin with observable differences or their understanding of evolution? ... I'm trying to imagine a classification system based on the final image you showed us in class, and having trouble ... Norma

See new image

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

I wonder if we are slowing or even stopping the process of evolution through our use of modern science and technology to create a race that strives to make people "fit in."If a child is born with webbed toes, the webbing is usually cut. Why do we do this? What if we were supposed to have this "mutation" as part of the evolutionary process? I'm curious as to who has the authority to say what is a mutation, and what is the norm ... Kate

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

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

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

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

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

Life=Science?

Have sense of life as increasing complexity, improbable assemblies of improbable assemblies .... Need to underestand origins of improbable assemblies, of diversity, as well as boundedness, energy dependence, reproduction with variance, homeostasis, autonomy

Will work our way from small scales to large, seeing how much we can account for at each level of organization (improbable assembly)

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

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

Dennis Drayna, Founder Mutations, Scientific American, October 2005 Is it useful to recognize that humans are assemblies of atoms? Medically? Culturally? What new understandings/questions can/do follow from such recognitions? What scales/architectures do we need to appreciate to achieve such understandings/questions?

(Trico access from Scientific American archive)

For background on haplotypes
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
3 October

From the Forum:
Atoms and ...

This atom thing is pretty intense ... Maybe I am so used to the biological heirarchy and thats why it is so hard to understand that we are all the same. With such a limited amount of building blocks could we play with atoms and predict what other living things would look like? ... Sara

So, we're all the same, huh? People and monkeys and ants and plants and rocks and trees and stars? Well, that's hard to get your head around... but it's not a new idea ... The first time I saw this formally presented in an academic setting was in a class on Buddhist Philosophy. The fundamental unity of everything is pretty much the basis of the whole religion. Whoever said that science and religion are opposed clearly hasn't spent too much time around either of them ... Zach

One of the questions I had after the Sept 28 class was "where do other religions fit in the discussion of intelligent design vs. evolution? polytheist?" so I was glad when Zach mentioned the Buddhist religion in his comment. When I first found out we are all composed of atoms, I became ecstatic ... given my environment and witnessing people continuously ridiculing each other, being able to say that we are all made up of the same thing was something I clung to. I still find it difficult to look at a table and think about it being made up of atoms ... I guess it's harder to think of non-living things being similar to us. ... Iris

I want to be willing to accept that everything is made of atoms, just more or less of them. But then I look at the room around me, and think "How can that be possible?" ... if I'm made up of atoms, and the desk is made up of atoms...why am I living, and its just a desk? ... Please tell me that there is more to it than this ... Lizzy

The possible creation or appearance of new organisms lies in the possible assembly of a limited set of atoms. This leads us back to our discussion of clumpy diversity- namely how the gaps between clumps represent either species which once lived but did not survive or organisms which have not yet appeared. Do the rules governing the assembly/proportion of atoms dictate certain possibilities? In other words, is it possible to predict what life forms may come to exist in some distant future? ... Keti

given the number of random combinations that could be made from these few atoms, it seems nearly impossible to predict what the future will hold, especially because the environment, which is unpredictable in and of itself, plays such a huge role in the way molecules are formed... Kate

Game of Life

Assembly rules:

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

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

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

Electron, electron affinities key to many biological processes

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

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

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

"Inorganic" versus "organic" molecules?

Carbon based versus non-carbon based, but inorganic/organic no longer a good distinction for small molecules (large?) Size and functional groups help to make sense of both small and large molecules Biological macromolecules distinctive?: lipids, carbohydrates, nucleic acids, proteins ... polymerization, dehydration reactions
17 October

From the Forum

As I wrote my lab report, I realized that I had trouble evaluating when a hypothesis is testable. I know that testable hypotheses have to be disprovable, but I'm having trouble figuring out exactly what this means. Professor Grobstein said in lab two weeks ago that the hypothesis "cell size and organism size are linearly correlated" is not testable ... How, more generally, should one think about whether a hypothesis is testable? ... Norma

I think/hope I'm being misremembered/misquoted. A "testable" hypothesis is one for which there are, in principle, future observations that will DISprove it. What I suggested was NOT a "testable" hypothesis was "there is some relation between cell size and organism size". Since there are an infinite number of conceivable "relations", one could never make a set of observations that would exclude all of them. "Cell size is proportional to organism size" is a more "testable" hypothesis in the sense that there is a well-defined relationship to be evaluated and a give set of observations could in fact show that that relationship does not exist ... Could a more extensive set of observations show subsequently that that relationship does in fact exist? ie that the initial sample was, for example. poorly chosen or too noisy, and that a relationship it doesn't show appears with a larger sample? Yep, I guess that could indeed happen and so one might prematurely reject a "testable" hypothesis. Still, though, it is the ability to make observatiions that falsify the hypothesis rather than to support it that is key to the "testable" idea ... PG

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

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

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

I made the (potentially?) obvious connection between the electric charges of hydrocarbons and their role in the lipid bilayer. This was the first time that the whole point of discussing electric charges in a bio class honestly made sense ... I can't remember if it came up in discussion, but I was just wondering where the charge came from. Are all atoms present in the universe charged either negatively or positively? Are there any neutral atoms? Does it have anything at all to do with the earth's magnetic orientation? Just wondering ... Magda

Last week we began to touch upon the role of enzymes in biology. I was surfing the web, looking at some of the links on serendip, and saw this cool website (http://bio.winona.edu/berg/ANIMTNS/allostan.gif) that showed how some enzymes need to be activated by something before it is able to perform its function. It got me thinking: How many enzymes in our body are not functioning because they have not been activated? Or, how many enzymes are activated a day? ... After looking at the website it also got me thinking about the level of difficulty of finding the component that is the perfect fit to activate an enzyme. On the website it looks like all you need is the special key or the magic password to activate an enzyme, but somehow I fear that it is a bit more complicated ... Kate

Does this mean that certain nutrients/ ingredients which we ingest activate enzymes, or certain actions. When we exercise, aren't some enzymes activated? Does energy in the body activate enzymes? ... Lizzy

Do enzymes have the properties they have because they are "alive"?
or
Do living things have the properties they do because they have enzymes as a basic constituent?
  • ability to facilitate change without themselves being changed
  • U-shaped temperature and pH sensitivity
  • distinguishing between mirror images
Proteins, from amino acids via peptide bonds

Nucleic acids , from nucleotides


24 October

From the Forum

All known life is DNA-and-protein based, correct? That seems even more improbable than the fact that such complicated macromolecules could have come into being by random processes in the first place. It simply seems mind-boggling that only these very specific types of macromolecules are capable of producing the characteristics we attribute to "life". But if that were not the case, why would we not see "life" based on much simpler molecular structures ... Zach W

Macromolecules help account for how organism have many of the properties of life that we laid out at the beginning of the course, but how much has what we've studied shed light on why organisms have these features? ... Mutations in nucleic acids contribute to variations in reproduction - again, one can speculate about why reproducing with variation might facilitate survival, but examining macromolecules doesn't provide clues. As far as I can tell, what we've studied about macromolecules so far doesn't shed light on three other properties of life: that organisms are bounded, semi-autonomous and energy dependent ... Norma

my problem lies with the assertion that the explanation of all life can be reduced to improbable assemblies of atoms. If this is true, how do environmental factors outside the body affect the workings of macromolecules within it? ... In studies done on identical twins in which one twin is affected by MS, it is 50% more likely that the second twin will develop the disease. But this leaves us with another 50% unaccounted for by genetics. So then how are environmental factors outside the body accounted for by improbable assemblies of atoms within it? ... Keti

Why would textbooks and lectures phrase things as if that was always the case, when in reality there is the possibility of one base connecting with another to which it normally doesn't? ... Magda

The more I think about macromolecules, the more astonished I grow ... This is especially true considering the fragility of living systems (ie one misplaced amino acid -> potentially lethal situation). I guess we have however many years of evolution on our side to make sure that things run pretty well, but it's hard for me to think that more disastrous things don't happen to living systems on a more regular basis, with so many proteins being created at all times. Even if such an occurence were one in a million, this would mean that most living things would fall apart within a fraction of their lifespan ... Nick

Are these mistakes what causes some cancers? because many doctors state that some cancers are passed down. Can we tell if an error occurred within ourselves or if it came like that? ... Iris

(see "Founder Mutations" in October Scientific American, Trico access from Scientific American Archive)

I just finished reading an article in the New York Times about the building of "nanocars" and "nanotrucks" that are capable of carrying molecules to a specific location ... Assuming certain genetic disorders are caused by point mutations, a vehicle that could deliver the correct nucleic acid to the point on the DNA where the mutation has occurred would be invaluable in fixing the problem ... another idea would be to replace the incorrect nucleic acids on the RNA before it is read by the ribosome and proteins are manufactured ... Brom

by creating enormous amounts of infinitesimal bots that can reproduce we are giving them the opportunity to evolve and become dominant, destructive organism ... DNA seems to work so well not because it is a flawless system, but because replication and translation are happening on such a small scale thousands of times over in different parts of the body that the counterproductive errors will have little success in perpetuating themselves if they are not helping the body that depends on their regeneration. Kind of like a biting the hand that feeds you. What we have to question with nanotechnology is how soon will the "dog" be big enough that he can make the humans his dinner - bypass the hand and go straight for the heart ... Scott

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?)

All scientific descriptions should be given as probabilities

The "environment", like organisms, is atoms/molecules

Are there "errors", "mistakes" that humans should correct?

Can't (usefully) drink gasoline because of lack of enzymes, shouldn't drink gasoline because of boundary violations?

Proteins as both enzymes and receptors

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

Carbohydrates, sugars (monosaccharides to polysaccharides) - alternate

From hydrocarbons to lipids

Molecules, macromolecules constantly in flux, serve variety of roles, Intermediary metabolism


24 October

From the Forum

If we did not impose "order", ie. rules, laws, norms, etc. would our society be moving towards an increased state of chaos? How similar is this "isolated system"referred to in the Second Law of Thermodynamics to human nature and the human system? It is interesting that "order" is not a natural state, and that it is forced on systems to limit the chaos/disorder. It leads to me to question if introducing "order" into systems is really improving it any way, or if we are losing an essential part of that system by inhibiting its natural flow towards chaos ... Kate

putting someone in a box with a sandwich would be isolation but is there a natural isolated system (earth, galaxy & universe)? This is relevant to the discussion we had earlier in the semester, when looking at larger scales, about the black hole sucking in matter. Doesn't this go against the 1st law of thermodynamics because matter is being consumed? Or is it believed that the black hole has transformed the matter? ... Iris

some political theorists would argue that the world structure is one of anarchy, necessitating governments to combat the anarchic tendencies. While this is all very fascinating, I think it is much more interesting that this movement towards chaos in isolated systems occurs through very ordered processes. Chemical reactions which take place are precise enough that we have equations and formulas to describe them. If change is from less probable assemblies to more probable ones, this change occurs through ordered interactions ... Keti

In light of Keti's comment that rules so precise that we can describe them by formula govern increasing order: do these rules ever develop? If so, we could view the development of these rules as part of the process of creating order. Keti talked about political systems; humans are part of these systems and are responsible for the imposition of order. Similarly, could rules that increase order develop within an organism, or are they simply derived on pre-existing laws of physics? ... I don't understand why entropy, or disorder, increases when a system moves from a less probable to more probable state. When something becomes more probable it is less chaotic, right?... Norma

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

Life is not an exception to a rule--just an example of a rule that doesn't apply to most situations. And, seeing as how life involves transformations of energy and matter, who is to say that a greater kind of organization will not evolve? Why not think that the more life grows and varies, the more it changes its situation so that the former "improbable assemblies" are now the probable ones? ... Zach G

The argument that "order" is unnatural I think is a flawed one. Order is an improbable element within the closed system that is the universe, but nonetheless order has always been a part of the system ... Brom

if you have an egg, it is likely that the egg will break, thus fulfilling the second law of thermodynamics. The egg is in an improbable state, but after it is broken, it is in an probably state. But how did the egg come to be in the improbable state of being an egg? At some point in time, it must have gotten larger and gained matter from its surroundings, becoming more and more improbable of an assembly. How should this be accounted for? ... Stephanie

I like the idea within the Second Law of Thermodynamics, but I would like to see a few examples of things generally rolling towards a stop. If the natural state of things is inclined towards reaching inertia, why does life continue to function? Why does matter continue to be converted rather than just stopping? ... Magda

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

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

For Newton's Laws of Motion

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

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

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

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

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

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

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

Life as

is not entirely fantasy.


7 November

From the Forum

It seems that throughout this entire course, we have been learning to indentify improbabilities in life, in nature, in science. Are we then, in fact, learning that to make any sense of science, we should understand that things do not really make sense? How have we been teaching students facts and equations, if life is really just...random? ... Lizzy If there is always an overall loss of organization, does this means that all processes which sustain life invariably create waste? Furthermore, if one of the links in the chain disappeared or was made to disappear, all life would cease to exist. But if we are saying that it takes spontaneous processes to create improbable assemblies, what's to prevent one such spontaneous process to occur which does just this- that is, break the chain. I am very troubled by this ... Keti

Since we are improbable, it seems more probable for something to stop working (like the lungs) then us being healthy. We are constantly battling against the probable ... Iris

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

Going back to my example of the human system, if we were to apply this concept it would mean that order is being created because of the constant disorder of society. This seems to fit because if the world weren't disorderly there would be no need for our imposed "order", ie. rules, laws, etc. I also find it interesting that "stable" order may reflect slower rates of falling apart. This too I think can be applied to the human system, in which a law or certain social construction is created to maintain "order" but upon closer observation the society is slowly falling apart, as crime rates increase ... Kate

This discussion takes us back to our very early discussions of truth and science (ie getting it less wrong, yet using our "knowledge" practically). Macromolecules and "lower" levels of organization are undeniably important to any proper discussion of life, but the discussion of lower levels cannot overshadow the bigger picture, as it were. Macromolecules become useful to living systems only insofar as they function as a part of a larger organization, as in specialized cells ... Cells, and organs, and living entities are what give meaning to macromolecules for us, and macromolecules, though important, should only concern us insofar as they help describe cells, organs, and living systems ... Nick

even if some macromolecules contribute little or nothing to our understanding of life, they may be interesting in their own right - because of other affects, or for their own sake. While life certainly seems like a more interesting line of inquiry to me, I don't think we should close off others... Norma

I'm not sure exactly what is going on, but the properties of oxygen are such that the plant structure can use these properties to separate oxygen from its probable molecular configurations, forcing hydrogen and carbon to improbably "hook up", and the result is pretty hot and sweet ... Scott

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

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

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

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

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

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

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

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

The matter of boundedness

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

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

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

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

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

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

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

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


14 November

From the Forum

there are all kinds of questions that we must do more to be able to answer. Just thinking about the human digestive system, say: how do we break down food? How does food translate into energy? Why do I need green vegetables? We need to talk more about how cells and organs interact within an organism ... Norma

While I think it is important to look at macromolecules as they fit into larger structures, we then have to look at how organisms themselves fit into larger structures. In other words, this presents us with the question of how humans fit into society. To go back to the diagram linking life and the second law of thermodynamics, at the level of biology, the term "culture" is included. How then do the properties we have discussed account for such a thing as culture, given that we have discussed these features in terms of lipids and protein shape ... Keti

I think that there is a difference between molecules, genes and humans in terms of "being influenced by and deriving significance from the bigger picture they are part of." I think that molecules and genes seem to be influenced by more mechanical, biology, chemistry and physics while individuals seem to be affected by more intangible concepts like societal norms, values and morals. So, is it easier to identify how molecules and genes are influenced by the bigger picture in comparison to individuals? How do we compare all of these things on the same level? ... Kate

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

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

"The full importance of Darwin's theory can be better understood by realizing that modern biology is guided by two overwhelmingly powerful and creative ideas. The first is that all biological processes are ultimately obedient to, even though far from fully explained by, the laws of physics and chemistry. The second is that all biological processes arose through evolution of those physicochemical process through natural selection. The first principle is concerned with the how of biology. The second is concerned with the ways the ways the systems adapted in the environment over periods of time long enough for evolution to occur - in other words the why of biology" ... Edward O. Wilson, from an introduction in From So Simple a Beginning - The Four Great Books of Charles Darwin, edited by E.O. Wilson, W.W. Norton, 2005.

Want more on how eggplant becomes Norma or more on "the bigger picture"? Or both? And why? (see The Emergence and (continuing) Evolution of the Story of Story Telling)

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

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

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

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


21 November

From the Forum

Life and/or the bigger picture

A few classes ago, we were asked whether we would rather learn about how eggplant turns into Norma, or more about the cultural significance of everything we have learned about over the course of the semester. I personally wonder why we can't do both ... Lizzy

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

I think it is misconception that we can dis-aggregate the question of eggplant becoming Norma from the question of the place of humans within the "bigger picture." ... the purpose of scientific enquiry lies in its ability to propose new questions and not in its ability to provide definitive answers ... a discussion of processes at the level of the macromolecule cannot be separated from the processes occurring at the cultural level. The relation between humans and society/culture is an issue implicit in, not exogenous to, the study of biology ... Keti

we are biological creatures. There are reasons we interact with other humans in specific ways tied directly to our evolution and place in the food chain. Exploring both the biology and psychology behind that would give us a fuller understanding of people in general ... Magda

there has to be some point where the discussion will lose whatever ground it has in what we as a society have come to call biology ... it seems like these bigger picture questions are more suited to classes in other academic disciplines. For example, I'm not quite sure how essential an understanding of macromolecules is to an understanding of the rise of a society. I think the trajectory of the course at the moment is giving us as a class an interesting biological perspective on the functioning of living systems and their relation to their surroundings, and I'm not sure if broadening our perspective would necessarily make our biological knowledge any more complete ... Nick

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

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

In order to create new stories about biology that are "less wrong" we must apply science to society and culture. Furthermore, if there are no Truths in science what is the point of learning all of the science without applying it to the "bigger picture" if we don't even know what are learning is really fact. The links are too strong to be broken and therefore cannot be ignored. We need to know more about the cultural implications of Norma and why and how eggplant becoming Norma is important in the "bigger picture." Without the "bigger picture" we only have part of the story ... Kate

I'm interested in how society shapes the way we understand how I become eggplant ... and in examining how useful biological methods are in other disciplines ... I hope, however, that we maintain the ability to distance ourselves in certain circumstances. For example, in debates about gender differences biological findings about possibilities are important, but we should be wary of what is "natural" and look to what is possible, and to what we want. As humans we have the ability, to a degree, to define society and ourselves - we should look towards what we want to value rather than towards what biology tells us is "natural" ... Norma

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

Cellular reproduction - mitosis


28 November

From the Forum

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

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

Lessons from cells about life:

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 (alternate) as guide, further insight into diversity, background for "cloning" issues ... see also Cloning: Past, Present, and ..."

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

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


5 December

From the Forum

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

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

See The Brain: Insights into Individuals and Complex Organization
and
Biology 202 and Biology 202 Evolving
and ... come back Wednesday

Pay one last visit to course forum area ... What has/has not changed in how you think about science and life?

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

The nervous system as an additional novelty generator

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

The "story" from biology (so far)

Thanks all for participation in this process this semester. Keep learning, thinking, acting, imagining, "getting it less wrong". Visit the forum area once more. Keep in touch.

To be continued


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