Bio 103, Fall 2007, Lecture/Discussion Notes

Submitted by Paul Grobstein on Sun, 09/02/2007 - 3:28pm.

• biology
• Biology 103 course
• complexity
• diversity
• education
• emergence
• science
• story telling

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Life .... from us to the very large and very small

• As a human being, I tend to think of things as in reference to myself or the people around me ... Sharea
• I had never really thought of how the cosmos related to and affected the Earth. To put it more plainly, I had never really thought of Astronomy and Biology as being connected ... Catrina Mueller
• when things are looked at through different spatial scales, we realize that there is not much difference between anything, and that it is all about the way these small particles are arranged. It made everything in the world seem more beautiful, even a rock. Now the world seems more exciting because of the fact that it is continually expanding, and so we never realy know what can pop up next ... Andrelle (also cmcgown, kendra)
• We basically found out that we are all made of space and eclectrons, and stardust ... kjean, (also ekim)
  
• I simply cannot grasp how space was created from nothing and can continue to expand as we speak ... Andy Kim, (also Samar)
  
• The only thing harder to imagine than an infinite universe is a limited universe ... kharmon (also Ruth Goodlaxson, Jen Bonczar, Shanika, Luisana, eharnett, Lakesha, ekoike, kgould)
• Up until this point, I didn't feel uncomfortable at all with the idea of there being no one "truth," that we can't solve problems and answer questions with one magical idea. But now I've had my first real challenge in accepting that there's something we really don't know (and that I think it's OK not to understand "nothingness"). Hopefully, I'll encounter more of these challenges; having a whole group of them might make me really face the fact that the "truth" is that there isn't a truth ... Rachel Tashjian
• Observations -> Stories -> Questions -> Observations -> ... : Is Space Finite?, Parallel Universes

 

Temporal 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):

• universe - ~15 billion years
• stellar evolution (sun - ~ 5 billion years old, of ~10 billion year life span)
• 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)

Shorter time scales ALSO important for biological systems - milliseconds, nanoseconds (change where not aware of it)

• Time to Think?
• Alkanes in Motion
• Protein Motion
• Schrodinger and quantum physics
  • Its not movement/change that has to be accounted for, its stasis that requires explanation
  • Fundamental randomess, indeterminacy on which all order sites, from which all order derives

At both very large and very small temporal scales, change is the norm rather than the exception. At small scales, have beginnings of some key characteristics of life: sem-autonomy, diversity.

 

Noticing/try to make 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 might they look like, how might they be defined, what would that imply about life?).

Starting with intuitions (as we did with "life", as one always should, in science and elsewhere): what things LOOK like and do
What is similar to what, how similar, how many relevant axes?
Are there "discontinuities" in life's diversity? Is there a "natural" scale?

 

Diversity is "clumpy" - the kinds of existing organisms are not randomly distributed among all possible kinds; instead there are lots of variants of a smaller number of more general kinds of organisms? Some organisms are more "complex" than others? How does it look to a biologist, summarizing LOTS of observations?

Plants versus animals versus fungi(?)

Autotrophs versus heterotrophs (interdependence)
With 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?)

Internal boundedness vs lack of internal boundedness

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?

Discovered some order in diversity: is "clumpy"

• Most things are variants of a small number of things
• Some things that can be imagined (BECAUSE we classified!!!!) don't exist (multicellular autotrophs without a cell wall? multicellular prokaryotes?)

Why "clumpiness"? Things like small number of other things, some kinds of things absent?

Clumpiness in plants

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Last week's lab (with appreciation, see Working Group on Introductory Science Education)

• It was interesting to see how different plants looked similar under the microscope at a smaller scale, thus enabling me to directly experience what we were discussing in class; that there is less diversity at smaller scales ... Jen Bonczar
  
• looking at the microscopes brought back all these tedious memories of grid paper and tables and putting things into arbitrary categories (kind of like the movie "Office Space"). But ... looking at the cells was really interesting it was a bit like watching an iPod commercial, or that sensory-overload "Sgt. Pepper's Lonely Hearts Club Band" movie from the 70s ... what was even more interesting to me was what happened during our oral presentations. We were just kind of discussing things, asking and answering questions, and my lab partner almost offhandedly said, "Maybe cell size is in relation to their stages of development." Then each group seemed to come up with more great ideas as to what cell size could correlate with. I just thought it was so cool that the most interesting observations we made seemed to be stumbled on accidentally ... Rachel Tashjian
• We really got into the topic of how cells may vary for many different reasons including climate/weather, or simply over time changes as their surroundings change. Evolution is all about organisms developing over time, changing as their environment, etc develop ... Sharea (see also kcough, andrelle)
• The lab this week really got me thinking about how we can view the world differently with the use of technology such as a microscope. Things look completely different when viewed in different manners ... It got me thinking a bit about how humanity's views changed over the ages due to improving technolgy. Everything can be revolutionized due to one tiny observation or the invention of a new technolgy that provides a new scope to things. It's funny how quickly things so set in stone can be changed ... Catrina
• I was happy to see that this week's lab posed a question that did not have a set answer to it. We, as scientists had the freedom to choose how to approach and test the prompt. We also had the liberty to make up stories for all of the observations made that day. This kind of thing not only leaves us with questions unanswered but with more questions to think about which I feel like is the most crucial difference between this and all labs I have ever done before entering college ... LuisanaT
• because we were actually trying to create knowledge for ourselves, I think the process of presenting and attacking was actually pretty genuine and helpful ... Ruth Goodlaxson

Last week discussion

• Class was very interesting on Wednesday! It was similar to our trips in lab to the other worlds. It was interesting to see how everyone placed the cards you gave us differently. We all had similar piles in terms of what we put together but where we put them was different. Some grouped mammals, some did seaplants and animals that live in the water together, etc. I feel that because everyone comes from different places and learned science very differently, that we all have our own ideas about how we classify species. I also feel that we can't disagree with what someone else says because their opinions aren't wrong, just different than the other persons ... LaKesha
• Looking at how diversity is organized, it seems like such a daunting task. It also, in some ways, seems like an arbitrary task. I mean, the way we look at science, new observations can always be found. And if new observations can be found, then isn't it possible that plants/animals/everything can be classified in new ways based on those findings? ... MarieSager
• The more we study this, and the more I research my web paper, the more I understand how complex science is. There are no real right answers. Everything is interdependent, including all the information. I'm becoming more comfortable with the idea, though it was nice to have something that I could think of as definitive, but I guess I'll just have to let that go .... kcough
• I think that things in general has several reasons why they are the way they are, and that it's never one clear cut reason. That's why its hard to group things in definitive categories, there are always going to be overlapping ... andrelle
• Although there haven't been any clear boundaries or distinctions about living organisms, I think I have learned a great deal about life and what composes them ... Andy
• i actually like it without sharp boundaries because not everything's black and white...there's always a gray area ... ekim
• what struck me was the idea that there are no living organisms that connect the gap between the two groups ... samar
• I thought it was intersting that, after our discussion on Friday, we "determined" that there is not random variation but rather nested clumps of diversity. Because there are so many similarities between organisms at different levels and scales, it seems like this would make sense. However, according to Darwins Theory of "survival of the fittest", shouldn't part of evolution be random variation? Along the way there must have been some sort of variation that allowed for certain organisms to be "fitter" and reproduce more successfully than others and therefore allow for their genes to be passed on. Maybe I am thinking about this the wrong way, but that was what puzzled me after class-there must of been some type of random variation ... eharnett

Clumpy diversity: Look more carefully at animals (metazoans)

More patterns within patterns (level of internal complexity, embryology)

• Diploblasts vs triploblasts - alternate
• Protostomes vs Deuterostomes
• Invertebrates vs Chordates
• Mammals within Chordates
• Humans within Mammals
• Humans within humans (clumpy diversity at all levels)

More clumpiness. and more "arbitrariness"

• Why no ventral nervous system with endoskeleton?
• Why all humans not the same?

Nested Clumpy Diversity

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?

Classification

• Categories "real", independent of human observers?
• Categories "useful"?
  • Helps to make sense of things, reduce blur
  • Correlations help to predict based on partial information
  • Raises new questions ... no "essential" characteristics?
  • Problems similar to those in defining "life"?
  • Relevance in other cases?

How make sense of diversity at all levels (including human), of nested clumpiness, what's here AND what's missing, of difficulty in defining categories?

• Great chain of being - ordering of organisms along some scale?, no "narrative" character, everything has its place, there is a place for everything, but why clumpy diversity at all levels?

Evolution as an alternate way of making sense of diversity? Time/change/variations essential descriptors of life?

• Descent with variation makes helps to make sense of things being similar to other things, of missing things, of variation at all scales? Add to it natural selection? In turn raises questions ....

   

• Has life changed over time in appropriate ways?
• Was there a first organism? a first organism of each kind?
• Why the PARTICULAR set of organisms we see, and not others?
• Progression? Ranking? Adaptedness? Fitness? Natural selection?
• Time/history as part of explanatory framework? Would it have to come out the same way? Life identical elsewhere? The same here if taped replayed?
• Similarities between life as process and science as process?

What IS evolution? A good summary of observations? What are the observations?

 

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):

• universe - ~15 billion years
• ,stellar evolution (sun - ~ 5 billion years old, of ~10 billion year life span)
• 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 - BUT also have in us record of much of history of universe
LOTS of time for evolution

Evolution helps to account for diversity/clumpiness, also for ... ordering?

Long, slow, inexorable, inevitable continuous change, progressive improvement? (Evoution as a progressive tree?)

Fossil record - Observations

Earliest life (?) - prokaryotes (> 3 billion years, and getting older)

• Cyanobacteria
• Impact on earth - alternate

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

• 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 - more
  • Yucatan Peninsula
• Cenozoic - 65 million years ago to present, radiation of mammals (among other things)

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Thoughts on evolution

• its not a matter of why there is diversity but rather why there isn't homogeneity. The combination of reproduction with variance where there is differential contributuion of genes in the next generation with changes in the environment causes distinctions amongst groups where some will thrive in different ways than others ... Luisana
• Before this class, evolution was always described to me as "survival of the fittest." For some reason this phrase has become the universal phrase associated with evolution and it never really made sense to me ... I like the idea of describing evolution as a combination of descent with variation and natural selection. I think it makes a lot more sense than "survival of the fittest." ... I don't think that there is one characteristic or even a few characteristics that we could use to determine fitness in this sense ... Life will never stop changing and diversity will never stop expanding and branching out. I like this ... cmcgown
• It is interesting to think that simple organisms have evolved into more complex organisms. The concept itself is fascinating because it is hard to grasp the idea that we are all different because we are a product of a system that produces with variation but at the same time it makes a great deal of sense ... Samar
• i like the notion that evolution is a consequence of history 'cause that puts a time dimension to the change which doesn't simply equivocate "change" as necessarily being advancement, which is why there are still the simple living organisms like bacteria and complex living organisms like humans ... but what i don't get is how from simple living organisms...other more complex living organisms came about. are we all essentially related in a sense then? ... ekim
• The idea that prokaryotic organisms were not better or more advanced than eukaryotic ones was a new concept. It makes sense because they do still exist. What really intrigued was when we began to think about humans and how evolution doesnt necessarily stop .... kjean
• Using prokaryotic cells and other bacteria as an example, the specimens that were found millions of years ago were not the same as the ones that exist today. They evolved. So, it would make sense to realize that humans are still evolving ... Kendra
• It is mind boggling to think that 99% of life has gone extinct, and that humans, in all likelihood, will suffer the same fate. What then are the organisms that are still around? Is it just prokaryotes that have survived throughout the ages? If so, why? It seems as though the more complex an organism is, the more difficult a time it has surviving ... kcough
• I have always found evolution to be a process that was very visible in animals but not much in humans. When the question of, how have humans evolved over the past 60,000 years was asked, it made me think ... asavvanah
• I have a problem with the notion that the past is an indictation of the future. It is a bothersome statement when i think of it in the content of "HUMANS" ... Shanika
• i still believe mankind is very special and is at the pinnacle of� living organisms on earth ... Andy
• Evolution does not have one set "goal"-like we discussed in class, it is not necessarily working to make the "perfect being", so this should explain why humans would still be evolving. I'm just intrigued and curious as to what some of the changes will be to humans in the future ... eharnett
• For humans to become extinct like the majority of the fossil record's other organisms, something BETTER would have to come along that would prevent us from thriving. I hate to be arrogant, but can anyone think of anything better than us? Not smarter, not more efficient, not bigger, but better? ... kharmon (see also andrelle)
• An idea that is really controversial is designer babies, or the idea that one day we will be able to pick and choose the best genes for our children. This seems to me like a kind of sped up evolutionary process ... Paige (see also Rachel)
• I think evolution is a useful story which helps us make sense of our current observations; however I do not think it is the be all and end all; for instance, evolution does not help describe why organisms conform to the Golden Ratio. I also do not understand why those who believe in Intelligent Design theory or those who believe that God created the universe must completely dismiss evolution theory as counter to their religious beliefs. For all we know, God could be the author of evolution, or evolution could be one of many tools He used to create the universe ... Jen
• I found the comparison of Intelligent Design and Evolution... interesting. It made me wonder what people were thinking when they decided that Intelligent Design was a "science" and should be taught in schools ... kgould

Evolution = slow progressive improvement ... humans at least?

Nope - diversification and extinction here too (alternate, alternate)

(see more recent article)
Though there are here, as elsewhere, some reasonably slow, continuous changes

Ongoing human evolution?

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?
• Was there a first organism? a first organism of each kind?
• What accounts for appearance of progression? ranking?
• Why does "change" happen? - need both differential survival and randomness to explore.
• Life identical elsewhere?

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 also helps to account for "adaptiveness" and does include some directionality, but is not toward "perfection" or "better" but rather toward having explored more (increased "complexity"?)

• reproduction with variance AND selection
  • Darwin's Finches
  • domestication
  • drug resistance
• Selection forces always changing
• Life itself changes the selection forces
• All existing organisms (including ones that have long evolutionary histories) equally adapted ("successful").
• Genetic randomness ("reproduction with variance") and selection rather than
  • "intelligent design" (see also Intelligent Design and the Story of Evolution: No Need for Drawing Lines in the Sand)
  • transmission of individual experience (Lamarck)
• Relation to cultural evolution, intentionality
  • Brings into existence both?
  Exploration of novelty speeded up by being able to conceive/test possibilities internally?
  
  • Lateral spread of information more in cultural than in biological evolution?

Images of evolution - "getting it less wrong"?

• Evolution as a progressive tree
• Cladograms
• Darwin?!
• Evolution as increased branching, bush
• Evolution as "non-essentialism"
  • species as diverse groups reproductively isolated from other diverse groups
  • themselves continually undergoing change
• additional changes
  • continous change in branches
  • exchange among branches
  • long time course dynamics

Evolution as an "(attempt to) describe places and times outside of human scales"

Random variation (reproduction with variance) and natural selection (differential reproductive success) helps to make sense of

• clustered diversity, geographic variation, interdependence
• "adaptiveness" (without normative judgement or hierarchy)
• practical matters, such as plant/animal domestication, the development of antibiotic resistance, human variations having medical and other significances

Evolution (so defined) also raises new questions

• Was there a first organism? How did it/they come into being?
• Can the same mechanisms that account for small scale clustered diversity (micronevolution) also account for larger scale clustered diversity (macroevolution)? For the progressive appearance of more complex organisms?
• How is one to account for large scale patterns of temporal change (eg repeated episodes of diversification and extinction)?
• How much interaction is there between lineage dependent influences on living systems and non-lineage dependent ones (culture and other "horizontal" interactions, information exchanges)?
• What implications does the story of evolution have for the likelihood and character of life elsewhere in the universe? for our own sense of what who we are and where meaning comes from?
• How should new stories and older ones be handled in science classrooms, in education generally?
  
  Question about evolution is not whether it is "true" but whether it offers new and useful ways to make sense of things

Evolution as undirected, somewhat random, exploration of possible forms of living organisms, lacking purpose/meaning except insofar as we can it those things. is that a good story? Your thoughts?

Life=Science?

• On-going change, exploration
• No perfection or right answer
• Observation-gathering, hypothesis generation, testing, and repeat

  And ... ?

• Periods of relative stasis interspersed with periods of more rapid change?
• Periods of extensive hypothesis generation with relatively little testing interspersed with periods of extensive testing with relatively little hypothesis generation?
• Periods of data collection interspersed with periods of data compression and loss?
• Getting less wrong - in sense of summarizing more and more observations?
• Strong dependence on history?

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Evolution

• driven by random change
• shaped by natural selection (differential reproductive success) - itself somewhat arbitrary, changing, being changed by life, opening new possibilities for life
• no ideal/end state, categories fluid/changing, significant relatedness among all living organisms
• says about humanity?
• Humans are "special"
• Humans are not "special"

Evolution is a way to figure out what works and what doesn't, not necessarily to find the "best" organism. So if single-celled organisms work for what they need to do, and we work for what we need to do, and elephants work for what they need to do, everything is special, in a way ... kcough

Right off the bat my intuition says yes, humans must be special. But the more I think about it the more unsure I am of my position. I don't believe that humans are superior, but that is not what we are discussing in this debate. So I guess I have to think of what makes us unique. And, as the pro-team discussed in the debate, I believe that art, culture and religion seems to make humans unique to other organisms (as far as we can tell). I don't necessarily believe that these characteristics make us superior, but rather just unique and different ... eharnett

no other species is yet know to posses anything even remotely similar to consciousness nor greed ... andy

The idea of humans being the only beings that can reason is obviously a good point. Why can't other animals reason like we can? Is it that they are not capable? Is it possible that in the future other animals could devolop this skill? What are the brain functions that we have that we use for our reasoning that animals do not have? ... Catrina

how are we to know what animals are thinking? and how are we to know what they do is not out of intention or expression of feelings? ... ekim

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), things (including humans) all related but different, building one one another?

Remarkable generalization from small scale looking - dissociate ANYTHING, get out elements = atoms

• Anticipated by Greek atomists (who also inferred life elsewhere in universe)
• Very important advances in 1600's; see Soul Made Flesh by Carl Zimmer, Free Press, 2004 ("life essence" is ... matter)

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

 

• no hand atom, foot atom, human or elephant atom, no "live" atom
• nothing BUT atoms?
• therefore ... life is particular (improbable) assemblies of atoms
• of which there are many fewer kinds than there are living organisms

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
• combinatorial explosion

Periodic table - another related remarkable generalization

 

Game of Life Assembly rules: Each green location must have either three or four red neighbors and no red location has exactly three green neighbors. Construction rules: Start with any distribution of red and green squares Turn red square green if it has exactly three green neighbors Turn green square red if it has fewer than two or greater than three green neighbors Repeat

"Assembly rules" as a concept

Assembly rules = what is allowed, construction rules = how to make allowable things

• Defines possible buildings/organizations
• Can yield pattern, improbability not obvious in the rule
• Can yield infinite but bounded set of possibilities - combinatorial explosion
• Can account for one level of organization, how get more?

Assembly rules for atoms into molecules by covalent bonding (electron sharing), see periodic table

 

Vastly more possible different molecules than numbers of different atoms -
Diversity by combinatorial explosion

• Hydrocarbons ... and on and on
• Begins to help make sense of/support idea of life as assembly of atoms, with molecules as intermediate step ... can at least begin accounting for diversity

Combinatorial rules also create 3-D shapes, central to biological processes

• Stereoisomers (enantiomers, optical isomers) - How distinguished by biological systems? Related to temperature, pH sensitivity?

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 - animation
  • water as contributor to homeostasis - high specific heat
  • cohesive (and adhesive) properties - tall trees, wider striders, capillary action
  • ice floats
• pH, important for higher level assemblies, further flux (the time dimension)
• origins of boundedness in polar, non-polar interactions

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• When we began to incorporate the periodic table and talk of the different molecular bonds in class discussions, I panicked. This was because I decided to take a biology course in order to avoid any chemistry, which was my worst nightmare last year. But now I realize that the two are, of course, interconnected and that studying the periodic table helps us to better understand the molecular diversity of living organisms ... I thought the point that 'there is no atom that makes us alive, rather a group of atoms' is a good one to recognize ... Kendra
• Diversity seems to be a strong factor in many of our class discussions. The idea to actually relate the word diversity with structures of molecules explains that the word diversity can be used in many ways, contexts ... Shanika
• if it's all made of the same thing, doesn't that mean that at the most basic level, the "clumps" we see in, say, species, is not present at the most fundamental level? ... Rachel
• The one thing that I found especially interesting was the when we discussed the 3-D shapes of atoms in relation to diversity. I had never really realized that two things could be made out of the same atoms, yet end up being completely different depending on the order of their assembly. It is intruiging to think that thephysical differences of two things are possibly the result of just one small difference in their biological assembly ... Caitlin
• I was really interested by the statement that elephants and humans consist of the same atoms. I had never thought of it like that, and it brings up the question of how we are different? In class, everywhere really, the answer to that question (of why humans and animals are different) has always been hard to answer. But, according to class this week, the difference lies in assemblies of atoms. And even the differences between a person's hands... it all comes down to differences in composition. And then to think that composition, which implies some kind of order can and does originate out of randomness... and at such a small scale... its all mind boggling ... Marie
• Not having a "human" atom or an "alive" one really struck me. Before, I had thought carbon as being the "alive" atom. Carbon, however, does not make the compound "alive". It just happens to be the things that are/were alive, but it is in other stuff also. Before, I would have said that carbon was the key to "life", but now that I think about it, there cannot be any specific "life atom" ... Catrina
• The fact that all living - non living organisms are created of same atoms and cannot be distinguished provided some comfort to my confused state of mind. Now that we know that living and nonliving things are composed of the same atoms, I would like to find out more about the difference of composition between living and non living things ... Andy
• This week's discussion really fueled interesting conversation in the class that made me fully realize the importance of "improbable assemblies" (on a molecular and minute level) that make up various organisms ... Erin

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?

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

• polor/non-polar
• acidic/basic

 

"Inorganic" versus "organic" molecules?

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

• chemists
• universe
  • Interstellar molecules
  • Illustration

Biological molecules distinctive?: macromolecules

• proteins
• nucleic acids
• carbohydates
• lipids
• not mysterious: generally polymers of smaller molecules

Enzymes: Essence of Life? Speed up breakdown, are not themselves broken down U-shaped temperature, pH senstitivies highly specific in what breakdowns they facilitate little men? something in and of itself, not to be explained? specific catalyst that is sensitive to environment? might also account for distinguishing left and right handed molecules?

Proteins, from amino acids via peptide bonds (alternate)

• improbable, matter, energy, lots of roles
• more "combinatorial explosion": twenty subunits of quite different characters, so LOTS of variety
• 3-D structure (primary, secondary, tertiary) - alternate
  • importance of primary structure - Sick cell anemia (alternate) -HBB: The Gene Associated with Sickle Cell Anemia
• enzymes: control mechanisms on flux by facilitating some chemical reactions as opposed to others
  • Specificity - lock and key, 3 D shape important
    • Shape change may be important for breaking down acceleration - alternate
  • both shape and flexibility/shape change important
    • 3 D structure complex in origin, fragile
  • provides understanding of life's ability to discriminate 3-D structures
  • explains temperature, pH sensitivity of living organisms
  • remember hydrogen bonding, ability to change shape, improbability (polymerization by dehydration, energy source)

Nucleic acids , from nucleotides

• improbable assemblies of matter, energy content, play variety of roles
• Linear polymers (like proteins, but simpler)
• DNA: information as concept, relation to history dependence of life, human genome project
• "explains" sequence of amino acids in proteins - DNA -> RNA -> protein
  • sickle cell anemia
• double helix: intergenerational transmission of information, mutations "explain" reproduction with variance `
• remember also improbability (polymerization be dehydration, energy source)

 

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Macromolecules: proteins, nucleic acids

• The idea of randomness and mutation also intrigued me. It left me with a lot of questions that I thought I knew. For example what does cause a mutation is it interior or exterior? Is it the surrounding atmosphere. I don't know but it intrigues me how random combinations can make so many different people ... kjean (see also kgould, Andy, Luisana)
• It’s amazing to me that with the number of possibilities for genetic defects and disorders that so many people’s genes actually work. Given that it only takes one small change in one tiny base pair for a mutation to occur, and there are so many different reactions that have to happen perfectly, it’s incredible we work at all ... kcough
• I remember learning in ap biology that there are certain mechanisms that could possible correct for these errors (dna polymerases?). what makes some errors able to be corrected, but makes others unable to be corrected ? ... eharnett
• it's incredible how our personality traits, fitness and likelihood of disease can all be determined by how our molecules fit together ... Jen Bonczar
• It's crazy how something as small as a change in a chromosome can cause a person to have fatal disorders later on in life. I was also wondering how much of a role mutations played in evolution? DO mutations help species to evolve? ... LaKesha
• These mutations mean that life is constantly changing and even more, always has the potential to change. I was thinking about this in relation to life, and more specifically in relation to evolution. Maybe mutations are the foundation of evolution and adaptation, in that they occur randomly and create situations and changes that are conducive for life to adapt ... Marie
• Isn't it interesting that something so random (an accident, really) is turned into something that can, potentially, have a somewhat positive effect on someone's life? ... Rachel T
• Randomness is also an active word" played" within our Biology ourse. If many things are random then how can one make sense of things!Is randomness an important Notion in ''Biology"? As of now, I am convinced it is! ... Shanika
• all of this was, apparently, randomness ordered by a set of rules ... It just seems a little hollow to me ... Ruth
• I understand that the bigger the chain of atoms, the less probable that they will come together as such, but clearly they are uniting on a much higher rate in organizims' bodies. I wonder if there is something fueling these strains to come into existance or it is just coincidence ... Catrina
• if macromolecules are organic chemicals that are naturally made and found in living things, then...why do we need to consume more of it (i.e. carbs, protein, lipids/fat) in the food we eat? do we need to consume more macromolecules in order to produce more within our body? ... ekim

 

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?) What one can eat depends on what proteins one has ... see The gastrointestinal system: an introduction and Animal nutrition and digestion for more on ruminants

Carbohydrates, sugars (monosaccharides to polysaccharides) - alternate

• energy storage (though less than lipids), structure, recognition(?)
• water soluble (of course)
• multiple structures from simple elements
• cellulose versus starch versus chitin (alternative, alternative)
  Why can't eat cellulose?

 

 

From hydrocarbons to lipids

• fatty acids to triglycerides
• generally hydrophobic (but also mixed)
• energy rich (improbability plus assembly rules, including oxygen)
• phospholipids central to boundedness of cells
• simple lipids include cholesterol and steroid hormones, important element in sexual identity/behavior
  • Lowering blood cholesterol to prevent heart disease
  • Relationship between blood cholesterol and violent behavior?
  • Cholesterol as a precursor - steroids. possible relation to serotonin
  • Fats/cholesterol in diets - the current story?

Living systems are molecules, macromolecules constantly in flux ...

• Complex web of interdependences - molecules serve multiple roles - transitions and choice points dependent on enzymes - Metabolism (if we consist of macromolecules, why do we need to eat macromolecules?)
  • complexity - alternate - cell/tissue specificity -
  • pyruvate
  • catabolism - breakdown (decreased improbability
  • anabolism - assembly (increased improbability)
  • Cyclic breakdown/assembly
• Change one thing ... likely to change other things, somewhat unpredictably
• At deeper level: why do things change (not change) at all?
  • "improbable", "energy-rich", useable as "food"
  • break down "natural", where/how get assembly, the improbable?
    • Remember ATP, NAD(P)H

Accounting for change ... and stability
(and their relation to order, chaos, etc)

 

• 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)

Some other versions of thermodynamics: You can't win You can't break even You can't get out of the game For Newton's Laws of Motion Newton's Three Laws of Motion Newton's Laws of Motion For Thermodynamics: What is a simple definition of the laws of thermodynamics? Entropy is Simple ... If ... Entropy and th Second Law of Thermodynanics Some wry variants of the three (?) laws

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

• Organisms don't "use" energy, they transform it (ditto for matter)

Second Law of Thermodynamics - in any isolated system (the universe) change is always from less probable to more probable states (entropy increases)

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, things all fall apart but critical thing is rate
• beginnings of "autonomy" and 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)
• chemical reactions have same characteristics as diffusion

• thinking about waterwheels
• life depends on coupling of that change to other changes
• improbable assemblies exist not despite but because of a continuing movement toward probability
• and because of differing rates at which different things move toward higher probability states

Random change underlies all biological organization, with "order" resulting from it "Only in the co-operation of an enormously large number of atoms do statistical laws begin to operate ... All the physical and chemical laws that are known to play an important part in the life of organisms are of this statistical kind". "Order" (improbable assemblies) are forms of stability within flux Things "spontaneously" fall apart, at different rates (probability increases) One set of things falling apart can cause other sets of things to get together (probability decreases) "Order" depends on continuing production of disorder (with more falling apart than getting together) "Stable" order may reflect dynamic equilibria (purely statistical) slower rates of falling apart

• remember also improbability (polymerization be dehydration, energy source)

 

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Macromolecules, genes .... "energy"

 

• the Pandora's box of genetic discrimination ... Andy
• No one's perfect, and no one should be perfect. The idea that someday parents might be poking around their child's genome to make them "better" makes me rather ill ... kgould
• "In DNA Era, New Worries About Prejudice" - NY Times, 11 November 2007 (read for discussion on Friday)
• The way macromolecules are used in the body paralled very well with the way my sister and I use to play with legos. We would first build the legos according to the directions. After a while, however, we would get bored and deconstruct the parts. We would then construct new creations, often combining the legos from many sets to form one large, complex piece ... Catrina
• I never thought of energy and matter as being the same thing and not different entities ... eharnett
• It was interesting how energy is not created, it is just a transformation from one state of energy to another ... Samar
• it was interesting to hear the story that there is no such thing as energy independent from matter and that energy is just a way of describing the organization of matter ... Kendra
• I was relating this notion to my personal experience with gaining energy from another’s action. That is a big difference. If I am playing in a basketball game and I do not have enough energy, my teammates usually say motivational things that affects the way I am feeling. Hold on, so emotions are factors to the way energy is transformed for an individual ... Shanika
• today's class started out okay, until it got to the waterwheel ... ekim
• Our discussion progressed making a lot of sense to me but then the water wheel topic came up ... kjean
• Now the waterwheel example, I'm still a little confused about it ... Sharhea
• I'm not sure I quite understood the water wheel example ... Jen
• Every thing was making sense until we got to the waterwheel analogy ... andrelle
• I really got confused when we began to talk about the water wheel ... Lakesha
• the wheel is moving down (probable), and the bucket is moving up (improbable), so both an improbable and probable assembly is happening at once ... Rachel T

Adding the time/change dimension to life (at the molecular level)

Sun (plus? alternate) as source of driving improbability
Need to capture, use improbablity to make improbability

• 6 CO₂ + 6 H₂O + light -> C₆H₁₂O₆ + 6 O₂
• "endergonic", not "spontaneous", energy "absorbing", moving to less probable, depends on something else moving to greater probability, anabolism
• Note increase of electrons shared by carbon and not shared with oxygen
• autrophy

Take advantage of "quasi-stable" improbability, "energy" in chemical bonds

• C₆H₁₂O₆ + 6 O₂ -> 6 CO₂ + 6 H₂O + 32-34 ATP
• "exergonic", "spontaneous", energy "yielding", moving to more probable, catabolism

   

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

 

How do enzymes fit into this picture?

Enyzmes as regulatable regulators of falling apartness, adjusting the size of the hole

• Why doesn't cellulose/peroxide fall apart?
  • Enzymes and reaction rate
    • Competitive inhibition
    • Non-competitive inhibition
    • Allosteric control
  • Enzymes don't CAUSE chemical reactions, they PERMIT/ACCLERATE/CONTROL them, and are themselves controllable
  • Key is to reduce increased improbabilities needed to get to decreased improbability, 3-D shape important not only for "fit" but also f