BIOLOGY 103
Fall, 2000

Notes

4 September: What is science? Why can't it "get it right"?

Science = life?

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

6 September:

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"

8 September:

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)

11 September:

A living organism:

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

13 September:

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 ...

Similarities between science and life?

15 September:

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

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

18-22 September:

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 .... ?

25 September:

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):

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

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)

2 October:

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

Remarkable generalization - dissociate ANYTHING, get out elements = atoms

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

Living, non-living assemblies not distinguishable by identity of constituents at atomic level
Nor are different kinds of living things
Living assemblies are distinctive in proportions of atomic constituents (improbable assemblies)
Fewer kinds of constituents than of assemblies


What are atoms? How get more from less?

Atoms -themelves combinations of still smaller and fewer constituents

Periodic table - another related remarkable generalization

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

6 October:

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

"Inorganic" versus "organic" molecules?

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

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

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

Proteins, from amino acids

Nucleic acids , from nucleotides

Carbohydrates, sugars (monosaccharides to polysaccharides)

From hydrocarbons to lipids

27 October:

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

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

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

Second Law of Thermodynamics - in any isolated system (the universe) change is always from less probable to more probable states Diffusion as the archetype of life - improbability and flux (increasing disorder) driving increasing improbability (increasing order) Sun (plus?) as source of driving improbability
Need to capture, use improbablity to make improbability
Take advantage of "quasi-stable" improbability, "energy" in chemical bonds

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

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).

1 November

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

Enzymes and reaction rate

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

Catabolic/Anabolic coupling

6 November

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

Some interesting issues ...
  • Cells in multicellular organisms are "alive" in two sense, first in and of themselves, and second as contributors to "aliveness" of multicellular organism? How does that work?
  • And what about this "alive" versus "sentient" thing? Is it really true that cells are "alive", in the sense of doing things "for internal reasons" ("semi-autonomous", "semi-homeostatic")? And that's different from "sentient" ("thinking", "being aware of")? And "alive" is something one can make observations to establish as so, but "sentient" isn't? Now THAT is something to think more about ...
The "cell theory" - All living organisms are either cells or
assemblies of cells
What are cells? Why needed fundamental level of organization for life?

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

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

Movement ... understandable in terms of proteins

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

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

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?


27 November

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

Where does zygote come from?

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

"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

Meiosis - an "adaptive" biological diversity generator

1 December

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

Energy-dependence?

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"

Experientia 44: 960-971, 1988.

Semi-autonomy, homeostasis, adaptiveness and ... the self? Coordinating systems

13 December

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

Popluaton Ecology

Community and ecosystem dynamics ... and constraints

AND SO ...


To be continued


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