Biology 103; Fall, 1998
BIOLOGY: BASIC CONCEPTS
LECTURE/DISCUSSION NOTES
Science? ..... Life?
Science = Life
Science?
- specialized activity done by highly trained congential nerds?
- privileged access to Truth?
- irrelevant to common human concerns?
- a body of (difficult to understand) "facts"?
Scientific method: hypothesis -> experiment -> proof or disproof ...?
hypothesis = summary of observations
experiment = new observation
hypotheses not provable, only disprovable
process infinitely recursive
Hence:
- Science is not Truth
- Cannot be evaluated by increasing proximity to Truth
- Progresses as summaries of ever greater bodies of observations (unification)
- Depends on combinations of diverse perspectives, necessarily social/communication dependent
Start from where one is, do what one knows how to do, accept value of (ideally enjoy) being wrong
"Common sense" but taken SERIOUSLY
- Check understanding (hypothesis=summary of observations) by prediction/test instead of using authority, fit to expectations/standards/esthetics as criteria
- Create summaries, striving for most general ones (check for consistencies among summaries)
- Accept permanent uncertainty
Summaries of observations critical:
- Constitute useful (but always tentative) models of world ("best guess", "starting point", but also "preconceptions")
- Serve to motivate new observations
- Necessarily include both personal and social influences
- Necessarily include creative (random?) element
- Must have predictive value and be falsifiable.
Science = a long standing, ongoing (infinitely recursive), and apparently quite successful effort to make sense of the world, an effort
- for which everyone is equipped from birth,
- in which everyone is inevitably involved,
- from which comes insights of significance to everyone
- which is creative/surprising/fun (if one likes novelty/change).
Life .... ?
Living organism? How tell? Start with preconceptions ....
Practical problem .... life elsewhere in universe? ... how recognize?
A living organism is a ...
- semi-homeostatic
- semi-autonomous
- reproducing with variance
- energy-dependent
- varying and variable
- bounded
- highly improbable assembly .... of physical elements
- (history dependent, summary of observations)
And if see just one ... in space suit, like self?
LIFE is an interacting and interdependent array of diverse living organisms
at multiple scales
- interacting boxes each made up of interacting boxes each made up of ...
- requires study at multiple levels of organization ranging from atoms through molecules, molecular assemblies, cells, cellular assemblies, organisms, populations, ecosystems
with substantial "fit" to its surroundings
and substantial variation both at any given time and over time.
Where does "fit" come from? Why persisting variability and change? Accident ...imperfection?
LIFE is an ongoing process of exploration, of generating and testing hypotheses about the surroundings.
Evolution: - dependent on prior observations and random change ("creativity"?!), selection ("experiment")
- no perfect organism ("Truth")
- no "mistakes", only hypotheses, which influence one another
Ergo:
LIFE=SCIENCE
and:
seek to account for characteristics of life in terms of interactions of elements at multiple levels of scale over varying periods of time.
Patterns in space?
Diversity and Scale
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
- protons, neutrons - 10-15 meters (1 fermi)
- atoms - 10-10 meters (angstroms)
- smaller molecules - 10-9 meters (1 nanometer, 10 angstroms)
- macromolecular assemblies - 10-7 meters
- cell membrane thickness (lipid bilayer) - 10-7 meters (100 nanometers)
- bacterium, cell component (mitochondrion) - 10-6 meters (1,000 nanometers, 1 micron)
- "typical" cell - 10-5 meters (10 microns)
- sand grain, nerve - 10-3 meters (millimeters)
- human, yard stick - ~ 1 meter
- blue whale, large playing field - 102 meters
- a little more than a half mile - 103 meters (kilometer)
- Earth's diameter - 107 meters
- Earth to Sun - 1011 meters (1 astronomical unit, ~5 light minutes)
- solar system - 1013 meters (~8 light hours)
- light year - 1016 meters (v=186,000 miles/second, 3 x 108 meters/second)
- Milky Way diameter - 1021 meters, 105 light years
- current universe diameter - ~1026 meters, 1010 light years
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. There exist lower and upper(?) bounds for living organisms ... as we currently know them
5. Existing observations are greater than in past, but clearly incomplete
6. Can distinguish smaller, single-celled from larger, multicellular organisms (Why no big unicellular organisms? - need for communication/integration?)
Have size, multicell versus single cell - other ways of making sense of diversity?
Back to preconceptions: what things LOOK like and do
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 "clumpiness" (improbable assembly)(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:
- Monera (plus) - single cell, prokaryotic, auto or heterotroph
- Protists (plus) - single cell, eukaryotic, auto or heterotroph
- Plants - multicell, eukaryotic, autotrophs
- Fungi - multicell, eukaryotic, heterotrophs, cell wall
- Animals - multicell, eukaryotic, heterotrophs, no cell wall
- ?Viruses?
Why "clumpiness"? Things like small number of other things, some kinds of things absent?
Look more carefully at animals (metazoans)
More 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
Other ways of making sense of diversity?
Great chain of being - ordering of organisms along some scale?
Evolution as way of making sense of diversity?
- Makes sense of things being similar to other things, but also raises questions:
- Why the PARTICULAR set of organisms we see, and not others?
- Progression?
- Time/history as part of explanatory framework? Life identical elsewhere?
Patterns in time
Scale and Evolution
Time scales?
Human - seconds to years, perhaps three generations (100 years)
Shorter important - milliseconds, nanoseconds (change where not aware of it)
Longer also important (there too change where not aware of it):
- universe - ~15 billion years
- earth (and life?) - ~5 billion years (150 million human generations)
- humans - ~100,000 years (?) (3,000 human generations)
- recorded human history - ~10,000 years (300 human generations)
Humans young, as yet restricted experience, small part of life
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
- Things similar because of common ancestry
- Non-existing things because didn't/can't work? because not tried?
Evolution includes both slow, continuous change and rapid change
- The latter because exploring some possibilities depends on having explored prior possibilities?
- Would help explain how highly improbable things come into existence.
- Indicates very strong history dependence in accounting for life.
Evolution involves "chance", and hence likely to proceed somewhat differently elsewhere or if repeated
- meteor collisions (and the like)
- dependence on random variation within biological systems
Evolution does include some directionality, but is not toward "perfection" or "better" but rather toward having explored more (increased "complexity"?)
- All existing organisms (including ones that have long evolutionary histories) equally adapted ("successful").
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
- protons, neutrons, electrons
- assembly rules
Periodic table - another related remarkable generalization
Vastly more possible different molecules than numbers of different atoms - diversity by combinatorial expansion
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"
- consequences of polar properties ("hydrogen bonds")
- pH, further flux, important for higher level assemblies
- origins of boundedness in polar, non-polar interactions
combinations of simple parts (atoms, elements) yield in assemblies (molecules) new properties
- diversity
- beginnings of autonomy, homeostasis, boundedness
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 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
From hydrocarbons to lipids
Carbohydrates: monomers (saccharides) to polymers (polysaccharides)
Nucleic acids, from nucleotides
- improbable assemblies of matter, energy content, play variety of roles
- Linear polymers (simpler than carbohydrates)
- DNA: information as concept, relation to history dependence of life
- double helix: intergenerational transmission of information
- significant but limited variations in 3-D structure
- where/how the read out (translation) of genetic information?
Proteins, from amino acids
- improbable, matter, energy, lots of roles
- more subunits, of greater variety, so more variable 3-D structure (primary, secondary, tertiary)
- provides understanding of life's ability to discriminate 3-D structures
- enzymes: control mechanisms on flux by facilitating some chemical reactions as opposed to others
- explains temperature, pH sensitivity of living organisms
- remember hydrogen bonding, ability to change shape
Molecules, macromolecules as smallest boxes, relevant properties, rudiments of life properties from interactions
Macromolecules as clumpy diversity (like organisms)
Why these? How come into existence?
Highly improbable, energy dependent, need cells? (chicken and egg problem?)
Lipids, carbohydrates from proteins
Proteins from nucleic acids
Nucleic acids from evolution?
Clearly history dependent
How get macromolecules? Improbable assemblies? Flux/energy/information?
Assembly rules define possible things that can be, not what IS, nor what leads to change from one thing to another ...
First Law of Thermodynamics - energy remains constant
- Organisms don't "use" energy, they transform it
Second Law of Thermodynamics - change is from less probable to more probable states
- life depends on coupling of that change to other changes
Diffusion as the archetype of life - improbability and flux (increasing disorder) driving increasing improbability (increasing order)
- movement from less probable to more probable (less organized), over varying time courses
- dynamic stabilization (homeostasis), with fluctuations - "equilibrium"
- energy flows (things going from improbable to probable) can create improbable assemblies
- improbable assemblies themselves (high "free energy") can be used to create improbable asemblies (order)
Sun (plus?) as source of driving improbability
Need to capture, use improbablity to make improbability
- 6 CO2 + 6 H2O + light -> C6H12O6 + 6 O2
- "endergonic"
- Note increase of electrons shared by carbon and not shared with oxygen
Take advantage of "quasi-stable" improbability, "energy" in chemical bonds
- C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O + 32-34 ATP
- "exergonic"
Carbohydrates (all macromolecules) high order/improbability/free energy
Why can't eat cellulose? Why doesn't cellulose fall apart?
Enzymes as regulatable rate regulators in flux
- Activation energy (increased improbability) barrier for exergonic reactions
- catalysis - affect only reaction rate, unaffected by reaction
- specificity - selective effects ("lock and key"), due to three dimensionality
- regulatability - ("allostery"), due to variable 3-D structure
Enzymes as exergonic/endergonic couplers
"Energy flows" (improbability increases and decreases) - metabolism
Catabolism - more to less improbable ("energy yielding")
Coupled to anabolism - less to more improbable ("energy requring")
The driving force: second law, random movement
The constraint: assembly rules plus surroundings
Enzymes as flux organizers
Cells as energy-dependent, semi-autonomous, semi-homeostatic, reproducing, bounded improbable assemblies (scale: microns, tens of microns, a minimum size?)
- Free-living single cells, cell as parts of multicellular organisms (need for coordination)
- Cell components - need for coordination
- Who's in charge? The role of the nucleus
- Cells as three dimensional flux regulators in flux (matter, energy, information)
- Look both back toward macromolecules and forward toward multicellular organisms - interdependence, distributed control, the new insight
Prelude: The "cell theory", cell size limitations?
Cell components
The role of the nucleus
Matter and energy flux - energy dependent and energy independent processes
Movement - of cell, within cell
Chloroplasts- photosynthesis - half of life's energy flow cycle
Mitochondria - cellular respiration - the other half
Cell reproduction -
Amoeba
Cells as bounded semi-etc improbable assemblies of different interacting molecules
Multi-cellular organisms as bounded semi-etc assemblies of different interacting cells
Similar as well in having internal bounded spaces
Tissues as intermediate levels of organization
Functions of parts of cells served by assemblies of specialized cells
LOTS of different specialized cells in specific, complex three dimensional arrangement (tissues, organs, organ systems)
How get that way (development)? How both work as individual cells, and work together (physiology)?
How get reproduction with variability (genetics)?
Reproduction in multicellular organsims
- single cell to multicell cycle, why?
- chicken and egg problem, revisited
- specialized cell assemblies, cells (female, male)
- special cell division to enhance variability, meiosis
Meiosis
Relation of meiosis to Mendelian genetics
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