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Biology 103; Fall, 1998
BIOLOGY: BASIC CONCEPTS
LECTURE/DISCUSSION NOTES

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Science? ..... Life?

Science = Life

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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).

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Life .... ?

Living organism? How tell? Start with preconceptions ....
Practical problem .... life elsewhere in universe? ... how recognize?

• Europa, one of Jupiter's moons, from Galileo
• Mars, from Pathfinder
• Life on Mars?, from Earth
• Beyond the solar system?, from the SETI Institute

A living organism is a ...

• semi-homeostatic
• semi-autonomous
• reproducing with variance
• energy-dependent
• varying and variable
• bounded
• highly improbable assembly .... of physical elements
  (Improbable assemblies from simple interactions of simple things? displaying homeostatic, autonomous properties?)
• (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

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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.

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Patterns in space?

Diversity and Scale

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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?

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Patterns in time

Scale and Evolution

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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)

• Cyanobacteria
• Impact on earth

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

• Paleozoic - 540-245 million years ago, Explosion and extinction (Cambrian Explosion and Burgess Shale)
• Mesozoic Era - to 65 million years ago, Extinction (K-T), very probably meteor impact
  • Solar system impact craters
  • Terrestrial impact craters
• Cenozoic - 65 million years ago to present, radiation of mammals (among other things)

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").

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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)?

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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

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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

• assembly rules for atoms into molecules by covalent bonding (electron sharing)

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

• Stereoisomers (How distinguished by biological systems?)

Electron, electron affinities key to many biological processes

• covalent bonds - electron sharing
• ions, ionic bonds
• polar bonds, polar vs. non-polar molecules, (molecules with polar, non-polar regions)

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

• consequences of polar properties ("hydrogen bonds")
  • water as solvent, reaction facilitator
  • water as contributor to homeostasis
  • cohesive (and adhesive) properties
• 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

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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?)

• chemists
• universe

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

• fatty acids to triglycerides
• generally hydrophobic (but also mixed)
• energy rich (improbability plus assembly rules, including oxygen)
• phosphlipids central to boundedness of cells
• simple lipids include steroid hormones

Carbohydrates: monomers (saccharides) to polymers (polysaccharides)

• water soluble (of course)
• ring formation (structural isomers)
• cellulose versus starch (structural isomers at next level)
  Why can't eat cellulose?
• energy storage (though less than lipids), structure, recognition(?)

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

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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
  • competitive inhibition
  • non-competitive, "allosteric" interactions, due to variable 3-D structure
  • regulatory loops, including feedback inhibition

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

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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?

• Relations to outside world - surface to volume considerations
• Organization of inside world

Cell components

• cell membrane, nucleus, "protoplasm","cytoplasm", cytosol
• membrane bound spaces
• membrane bound organelles: mitochondria, chloroplasts
• cytoskeleton - another example of protein shape change
• keep eye on membranes (spaces, structural elements, interfacers)

The role of the nucleus

• Influences on other components
• Mechanisms of influence on other cell components
• Dependence on other cell components
• Influence from outside world, other cell components

Matter and energy flux - energy dependent and energy independent processes

• from outside in - diffusion, facilitated diffusion, active transport, endocytosis (bulk transport)
• from inside out - all the preceding but exocytosis
• internal

Movement - of cell, within cell

Chloroplasts- photosynthesis - half of life's energy flow cycle

• non-cyclic photophosphorylation - light reactions
• Dependence on compartmentalization, three dimensional structure
• Calvin cycle - dark reactions

Mitochondria - cellular respiration - the other half

• Glycolysis - the trade balance
• Fermentation to alcohol
• Fermentation to lactic acid
• The Krebs cycle - the trade balance
• Electron transport and chemiosmotic synthesis of ATP
• Energy yield summary
• Metabolism central
• Organelle autonomy

Cell reproduction - Amoeba

• cell cycle
• mitosis - karyotypes (metaphose chromosomes) - mitosis in action
• chromosome structure
• DNA replication
• cytokinesis - component semi-autonomy
• semi-autonomy - cell cycle regulation
• variability - mutation plus various forms of genetic exchange

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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

• Epithelia as external boundaries and internal boundaries
• Muscle
• nervous tissue
• connective

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)?

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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

• two cell divisions instead of one
• enhancement of variability (independent assortment)
  • in humans, 2²³ possible gametes, 2⁴⁶ possible offspring
• further enhancement by crossing over during first meiotic division

Relation of meiosis to Mendelian genetics

• Random segregation - Punnet square, genotype/phenotype differences
• Independent assortment - Dihybrid cross - but linkage
• Recombination and linkage mapping
• Sex "determination" and linkage
• Strengths and limitations of mendelian genetic approaches to phenotype prediction

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