BIOLOGY 103
Fall, 2005
Fall, 2005
|
Fall, 2005 |
Biology -> Science of life
Science as process ... of Story Telling and Story Revision
| Linear science | Seriously loopy science |
 | |
| Science as body of facts established by specialized fact-generating people and process
Science as successive approximations to Truth
| 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 |
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
|
Which of the following stories do you prefer?
Life as ... process?
(starting where one is, telling a story, getting it less wrong)
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:
|
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 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
|
|
"Is this kind of thought a waste of our time?" " ... the answer lies within the eye of the beholder?"
|
| Diversity "neither incidental nor detrimental ... instead essential" | ||
|---|---|---|
| 
|  |
|
| 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
Lessons from working up in scale from human ...
|
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
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
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
|
And from working down in scale ...
(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?).
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:Look more carefully at animals (metazoans)
 |
More patterns within patterns (level of
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?
|
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
Longer time scales important for biological systems (change where not aware of it):
Evolution helps to account for diversity/clumpiness, also for ... ordering?
Long, slow, inexorable, inevitable continuous change, progressive improvement? (Evoution as a progressive tree?)
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?
Images of evolution - "getting it less wrong"?
|
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
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"
Shorter time scales ALSO important for biological systems - milliseconds, nanoseconds (change where not aware of it)
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?
And ... ?
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
| Element | Symbol | Atomic number | Percent in universe | Percent in earth | Percent in human (typical of living organisms) |
|---|---|---|---|---|---|
| hydrogen | H | 1 | 91 | 0.14 | 9.5 |
| helium | He | 2 | 9 | trace | trace |
| carbon | C | 6 | 0.02 | 0.03 | 18.5 |
| nitrogen | N | 7 | 0.04 | trace | 3.3 |
| oxygen | O | 8 | 0.06 | 47 | 65 |
| sodium | Na | 11 | trace | 2.8 | 0.2 |
| magnesium | Mg | 12 | trace | 2.1 | 0.1 |
| phophorus | P | 15 | trace | 0.07 | 1 |
| sulfur | S | 16 | trace | 0.03 | 0.3 |
| chlorine | Cl | 17 | trace | 0.01 | 0.2 |
| potassium | K | 19 | trace | 2.6 | 0.4 |
| calcium | Ca | 20 | trace | 3.6 | 1.5 |
| iron | Fe | 26 | trace | 5 | trace |
| Dennis Drayna, Founder Mutations, Scientific American, October 2005
(Trico access from Scientific American archive) |
What are atoms? How get more from less?
|
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 |
|
Assembly rules:
|
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
"Inorganic" versus "organic" molecules?
|
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"?
|
Nucleic acids , from nucleotides
|
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 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 |
From hydrocarbons to lipids
Molecules, macromolecules constantly in flux, serve variety of roles, Intermediary metabolism
|
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:
For Newton's Laws of Motion For Thermodynamics: |
Diffusion as the archetype of life - improbability and flux (increasing disorder) driving increasing improbability (increasing order)
|
Can "trap" improbability in chemical bonds ("potential energy")
Carbohydrates (all macromolecules) high order/improbability/"free energy" -
How do enzymes fit into this picture?
Life as
|
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 |
|
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
|
Cells as energy-dependent, semi-autonomous, semi-homeostatic, reproducing, bounded improbable assemblies of molecules/macromolecules
The matter of boundedness
Membranes the key to boundedness, both of cell and within cell (are also important framework elements, organizing other macromolecules)
|
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
|
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.
|
Responsiveness/autonomy depend on energy (transformation of improbability) - Where/how does that get in game?
| Or ... on "what's another reason why sugar doesn't fall from the sky?" |
Cellular respiration the link to metabolism and the return part of life cycle ......C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O + 32-34 ATP
|
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
|
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:
|
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 ...
|
A noteworth exception, the immune system ... making productive use of randomness (continued)
|
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
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
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
| Biology 103
| Course Forum Area | Biology | Serendip Home |
