BIOLOGY 103
Fall, 2000
Fall, 2000
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Fall, 2000 |
Science = life?
Science as "summary of observations", "getting it less wrong"
What is science? Why can't it "get it right"?
From the forum:
| Science, like life, is a matter of trial and error, of overcoming adversity, of striving toward something "better." -- Jakki Rowlett |
| ... science is comparable to mythology ... Just as we now believe the ancient myths to be untrue, so we discover that science is also sometimes just as inexact -- Katie Kaczmarek |
| ... science is that constant pursuit of understanding which runs just behind life’s fast paced evolution -- Caroline Dyar |
"Scientific method"?
| Hmmm, is he serious about this? Science isn't Truth ... its always tentative, by its very nature? No "laws", only summaries of observations? Critical thing isn't being right, but getting it less wrong? That isn't the way I've heard the story before, and can't be what MOST scientists think? Maybe I need to think about this some more ... |
Now, what is life?
Practical issue related to really major "getting it less wrong"
What is science? Why can't it "get it right"?
From the forum (VERY rich, Check it out):
| I think one of the deeper reasons behind society wanting to find, or wanting science to find, the "truth," would be the psychic need for stability. -- Jill McCain |
| ... while "trained" scientists see ever-changing science as a beautiful and wonderful aspect of their field of study, many others without this great insight may feel very insecure by the statement. -- Jess Hayes-Conroy |
| When I was in school I hated Science, and Math for that matter, for exactly the opposite reason - because they were so rigid. -- Jakki Rowlett |
| So, in some ways, I suspect we're returning to an understanding of both the value and the limitations of science which is more open/honest than that provided during (and used to justify) an explosive expansion. -- Paul Grobstein |
| Science became, and will continue to become, ever more part of our lives. There's nothing dangerous about it. The danger comes when it is not carried out completely, or thoroughly; when people try to make money instead of discover knowledge; when a premium is placed on fast results, and when the public cries out for a solution to a problem... and the scientist, in a hurry for fame or under pressure from a funder, caves in and hands over something he's been working on -- Joe Santini |
| Is it possible that by making new observations about arcane phenomena, important new "summaries of observations" could be made? -- Rachel Hochberg |
So ... NOW what is life? (see links at end of 6 September)
A living organism:
Interdependent diversity, change over time
| Hmmm, need to think more about this autonomy/homeostasis business; its confusing, and not at all the way I've heard these terms used before (is it?). Got the dog scratching a flea versus the dog waking up when nothing happened distinction, but, if you think more about it, are homeostasis and autonomy related to one another or not?
Boy, and what about that question of whether there was or wasn't a first living organism? That's a doozy. There MUST have been a first living organism, that's only logical. Or is it? Maybe ... |
And ... ?
How "make sense" of diversity?
Arrange in order of size
Human perspective relevant: Technology dependence of observations
Limited range of observations? of sizes of organisms?
Size scales
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?).
Leila: "because science is a social construct ... one must beware of molding categories"
vs?
Robin: "Science is .. imply the acts of observing, making mistakes, trying again, and learning. If we didn't do this, we would sit in one place and die of starvation". Hence (PG), categorization not only necessary but desireable? if one presumes categories may well change as more observations are made?
Starting with intuitions (as we did with "life", as one always should, in science and elsewhere): what things LOOK like and do
Are there "discontinuities" (is there "clumpiness"?) in life's diversity?
Plants versus animals versus fungi(?)
Autotrophs versus heterotrophs (interdependence)
With correlates (e.g. cell wall versus no cell wall)
Fungi have cell walls, but different molecular constituents (chitin versus cellulose), are heterotrophs but with external digestion
Can use molecules, like any other feature, to evaluate similarities/differences
Get discontinuities/"clumpiness" (diversity itself an "improbable assembly", not either all possibilities of improbable assemblies nor random assortment of them but lots of variants one some kinds of improbable assemblies, none of others)(Why no autotrophs without cell walls?)
Taking advantage of technology: Eukaryotes (Protists) vs Prokaryotes (Monerans: eubacteria and archaea) (Why no multicellular prokaryotes?)
Five (or six, or more) Kingdoms:
Why "clumpiness"? Things like small number of other things, some kinds of things absent?
Look more carefully at animals (metazoans)
More patterns within patterns (level of internal complexity, embryology)
More clumpiness
Why no ventral nervous system with endoskeleton?
Humans a small part of life, as life (as we know it) a small part of universe (but humans also steadily, perhaps even explosively, experiencing more and more of universe - is that distinctive of humans?
Other ways of making sense of diversity?
Great chain of being - ordering of organisms along some scale? Not "better or worser" (more evidence to follow) but .... ?
Evolution as way of making sense of diversity?
Scale and Evolution: Time Scales
Human natural time scale - seconds to years, perhaps three generations (100 years)
Longer time scales important for biological systems (change where not aware of it):
Long, slow, inexorable, inevitable continuous change, progressive improvement?
Earliest life (?) - prokaryotes (> 3 billion years, and getting older)
Plenty of time for subsequent development of improbable assemblies, but ...?
Consistent with progression, but changing what adapted to, and persisting
Next steps? How soon?
Eukaryotes - 1-2 billion years ago (last quarter of life's history to date)
much more improbable than prokaryotes?
Multicellular Organisms - ~600 million years ago (last sixteenth of life's history to date)
VERY improbable?
Stasis and change - THEN slow progressive improvement?
Nope, continued fits and starts
Well then ... humans at least?
Nope - diversification and extinction here too
Though there are here, as elsewhere, some reasonably slow, continuous changes
Different time scales reveal different patterns, just as different space scales do
Clumpiness understandable in terms of evolution, but (and) raises new questions
Evolution includes both slow, continuous change and rapid change
Evolution involves "chance", and hence likely to proceed somewhat differently elsewhere or if repeated
Evolution does include some directionality, but is not toward "perfection" or "better" but rather toward having explored more (increased "complexity"?)
Shorter time scales ALSO important for biological systems - milliseconds, nanoseconds (change where not aware of it) Why do things change? At small scales, in space and in time, change is fundamental.
Have at small scales, beginnings of an explanation of one fundamental characteristic of life: change, exploration? Have also, at large time scales, some explanation of "adaptiveness", and of "clumpiness"/diversity
Have also sense of life as increasing complexity, improbable assemblies of improbable assemblies .... Need to underestand origins of improbable assemblies, of diversity, as well as boundedness, energy dependence, reproduction with variance, homeostasis, autonomy
Will work our way from small scales to large, seeing how much we can account for at each level of organization (improbable assembly)
Need to account for patterns in space and time at multiple scales
Improbable assemblies, adaptiveness, diversity, change
Can get that from improbable assemblies of physical elements (atoms)?
Remarkable generalization - dissociate ANYTHING, get out elements = atoms
| Element | Symbol | Atomic number | Percent in universe | Percent in earth | Percent in human |
|---|---|---|---|---|---|
| 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 |
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
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
Overwhelming diversity of molecules (like life)
Any way to make sense of it? Any other useful things to learn at this level?
"Inorganic" versus "organic" molecules?
Carbon based versus non-carbon based, but no longer a good distinction for small molecules (large?)
Functional groups help to make sense of both small and large molecules
Classes of biological(?) macromolecules (and related constituents): lipids, carbohydrates, nucleic acids, proteins ... polymerization, dehydration reactions
Proteins, from amino acids
Nucleic acids , from nucleotides
Carbohydrates, sugars (monosaccharides to polysaccharides)
From hydrocarbons to lipids
Have diversity, improbable assemblies of parts, macromolecules. Assembly rules define possible things that can be, not what IS, nor what leads to change from one thing to another ... For that, need to take about energy, energy dependence
Matter: what one can feel/touch, what IS (down to levels of atoms, molecules)
Energy: everything else (almost), including what accounts for change
Energy = motion/change (kinetic energy), capacity to cause motion/change (potential energy)
First Law of Thermodynamics - in any isolated sytem (the universe) energy remains constant
Second Law of Thermodynamics - in any isolated system (the universe) change is always from less probable to more probable states
Diffusion as the archetype of life - improbability and flux (increasing disorder) driving increasing improbability (increasing order)
Sun (plus?) as source of driving improbability
Need to capture, use improbablity to make improbability
Take advantage of "quasi-stable" improbability, "energy" in chemical bonds
Can "trap" improbability in chemical bonds ("potential energy")
Carbohydrates (all macromolecules) high order/improbability/"free energy"
Anabolic and catabolic processes coupled, break things down to build things up, always create "waste"
Can do same thing in the absence of light (Alexis Hilts), which also raises an interesting issue with regard to circadian rhythms (Susanna Jones).
Fit enzymes into picture, as regulatable chemical reaction controllers and couplers
Why doesn't cellulose fall apart?
Enzymes don't CAUSE chemical reactions, they PERMIT/ACCLERATE/CONTROL them, and are themselves controllable
Catabolic/Anabolic couplingSome interesting issues ...
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Cells as energy-dependent, semi-autonomous, semi-homeostatic, reproducing, bounded improbable assemblies of molecules/macromolecules
Membranes the key to boundedness, both of cell and within cell (are also important framework elements, organizing other macromolecules)
13 November
Gene regulation - More on responsiveness/autonomy at the single cell level
15 November
Responsiveness/autonomy depend on energy - Where/how does that get in game?
Looking back and forward - link(s) between life and the second law
Photosynthesis the starting point ....... 6 CO2 + 6 H2O + light -> C6H12O6 + 6 O2
21 November
Cellular reproduction - mitosis
Lessons from cells about life:
Have a good thanksgiving ... then on to multicellular organisms ... what sense do you think we can now make of them?
Multicellular organisms as improbable assemblies of cells having three-dimensional structure, boundaries, internal boundaries/spaces, energy dependence, autonomous/homostatic properties, reproduction with variance
Making sense of diversity - morphological tissues as intermediate level of organization between cells and organs/organ systems
How get elaborate, three-dimensional assemblies of diverse elements? Development as guide, further insight into diversity
Fusion of two genetically different cells, themselves the product of improbable assemblies of specialized cells
Cellular respiration the link to metabolism and the return part of life cycle ......C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O + 32-34 ATP
Where does zygote come from?
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"But none of these things can begin to explain who I am or you are or who that woman was" - Debbie Plotnick "... superior consciousness ... can learn from a situation without having to go through it ... somewhat prepared to deal with different encounters" - Katie Kaczmarek "... wouldn't give humans so much credit ... is stupidity rather than adaptation ... do not realize (or choose not to realize) their dependence on the natural systems of earth" - Jessica Hayes-Conroy "... capability of self-consciousness ... Can a line be drawn? and can it be drawn purely on biological grounds?" - Allison Hayes-Conroy " ... the vast majority of humans live a life guided by blind faith ... will this utter lack of comprehension for the things that surround us have any repercussions?" - Susy Jones "... we humans are specialized" - Jeanne Braha |
Have dealt with improbable assembly, boundeness, reproduction with variance in multicellular organisms ...
Energy-dependence?
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Matter (stuff), energy, and .... information? (with thanks to Jakki) Information = organization (improbable assembly) of mass/energy Can have same "information" in different mass/energy assemblages Is "information" (disturbance of mass/energy) rather than mass/energy itself that moves from one place to another, has effects (on other mass/energy assemblages) Information, unlike mass/energy, depends for its significance/reality on "sender" and "receiver" |
Individual multicellular organisms (humans) made up of complex, interacting set of components - And are themselves components of still larger interacting improbable assemblies
Are both result of and influence on our components, can both be influenced by and influence the larger assemblies - Need to understand them, ecology/environmental sciences the new biological frontier
Community and ecosystem dynamics ... and constraints
AND SO ...
To be continued
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