Bio 103, Lecture/Discussion Notes

Paul Grobstein's picture
Biology 103, Fall, 2009, Bryn Mawr College

COMPLEXITY

BIOLOGY: An exploration and conversation

Making Sense of Life


UNPREDICTABILITY

Lecture/Discussion Notes


31 August, 2, 4 September

Bio 103 as shared process ... making sense of life

  • starting places ... Paul Grobstein
    • complexity and unpredictability
    • successive levels of emergent properties, following similar rules?
    • in process
  • And you ... making us collectively
    • diverse interacting entities exploring new terrain
    • with resulting somewhat unpredictable movement beyond current understandings
    • to be shared among ourselves and with others

Biology -> Science of life

Interesting/relevant


What are genes? What is heritability?
Why are some things more affected by genes than others? What else matters?
Should scientists look for an aging gene? a cancer gene? Should scientists try and prevent aging? cancer?
How come "The scientific view ... has swung back and forth"?

  • What is science? Why can't it "get it right"?
  • What is life? Can one get it "right"?
  • Science = life?

Science as process ... of Story Telling and Story Revision

A traditional perspective A loopy story telling perspective
   
Science as body of facts established by specialized fact-generating people and process

Science as successive approximations to Truth


Science as authority about "natural world"

Science as process of getting it less wrong, potentially usable by and contributed to by everyone

Science as ongoing story telling and story revision: repeated making of observations, interpreting and summarizing observations, making new observations, making new summaries ... individually and collectively

Science as skepticism, a style of inquiry that can be used for anything, one which everybody is equipped to to/can get better at/be further empowered by, and contribute to - a way of making sense of what is but even more of exploring what might yet be

 

The crack
 

  • Multiple stories for a given set of observations
    • 3,5,7, .... ?
    • 1+1=2 or 1+1=10?
  • Observations in turn depend on stories
  • Science is as much about creation as about discovery

If science is as much about creation as discovery then the "crack"is a feature, not a bug ... and differences among people are an asset to the process rather than a problem or an indication it isn't working

Science as practical tool, continually being adapted and therefore
  • should be expected to keep evolving rather than to get it "right"
  • is as much about creation as about discovery (multiple possible summaries)
  • the crack is a feature rather than a bug; both "objective" and "subjective play essential roles
  • differences among people are an asset to the process rather than a problem or an indication it isn't working

Trying It Out ...

Science as process

"Generalized" summary of observations, in form that can be disproved by a future observation

Loopy, with subjective element, continually revisable "stories" based on observations

Contextual usefulness, permanent skepticism

 

Which of the following two stories do you prefer?

  1. The earth is flat
  2. The earth is round

Because of ...

  • personal observations?
  • observations made by others (personally verified or not)?
  • social stories (heard from others)?
  • usefulness?

Relevant observations:

Is one or the other story true? Have there been others? Will there be?

Which of the following two stories do you prefer?

  1. The sun goes around the earth
  2. The earth goes around the sun

Because of ...

  • personal observations?
  • observations made by others (personally verified or not)?
  • social stories (heard from others)?
  • other?

Relevant observations:

Is one or the other story true? Have there been others? Will there be others?

Scientific stories are frequently efforts to summarize the widest possible range of observations, always motivate new observations and hence new stories, should never be understood as "authoritative" or "believed in", do not compete with or invalidate other stories. Key issues about scientific stories
  • What observations do they summarize?
  • What new observations do they motivate?

Which of the following stories do you prefer?

  1. Existing life forms (including humans) are as they are because of a previous and ongoing process of evolution consisting of random change and natural selection (differential reproductive success).
  2. Existing life forms (including humans) are as they are because of repeated creative acts of a supernatural being with a plan and intent?
  3. Existing life forms (including humans) are as they are because of an initial creative act with a supernatural being with a plan and intent?
  4. Other?

Because of ...

  • personal observations?
  • observations made by others (personally verified or not)?
  • social stories (heard from others)?
  • other?
  • is one or another story "true"? Have there been others? Will there be? Will this story continue to evolve? (NYTimes Science Times, 26 June 2007)

Relevant observations:

Loopy story telling science is a tool to help one become better at thinking for oneself

at using observations and stories (of one's own and other peope) to make stories that motivate new observations that motivate new stories, to create as well as to discover

Science as process rather than thing

  • commitment to "summary of observations", "getting it less wrong", continuing meaningful story creation/sharing/revision/evolution
  • stories are part of science if they are part of the process, not because of any defining characteristics intrinsic to the stories themselves

Your thoughts? ... science as fact or story telling? evolution as "story"?

Your thoughts? ... science as fact or story telling? evolution as "story"?


9,11 September

Science as .... process (things are "scientific" if they are part of a process of "getting it less wrong"?)

Truth be told, I have in the past thought of science as Truth (capital t). Though I always approach ideas with skepticism, I always assumed that there are Truths in science, and regarding issues we have not come to conclusions about, that there is a Truth out there ... in science there isn't a single right answer to a question or an issue. It is a never-ending process, it is subjective, and it can be interpreted different ways. These are all aspects I love about, say, interpreting literature or considering history. Now I realize can think about science using the same mental tools I use in my humanities classes ... cejensen

Once I heard Professor Grobstein say that science does not deal with creating Truth but creating mistakes and having success failing I thought he was going crazy!  ... The idea that experimenting within the field of science is an ongoing process of simply telling "stories" makes the "natural world" around us a playground full of adventures waiting to be discovered ... paoli.roman

When professor Grobstein said that we were all scientist and that we had been making science since we were babies, that really struck me because is true. I never realized that we do things and try out things just like scientist. Truth is we all have the capacity to do science ... Karina G

I agree with your statement about using science to create better social communities ... if we are all scientists, even without white lab coats, science is much more accessible, which provides greater incentive for the entire community to contribute to it ... dchin

     

Of course there are facts in science but those are because people stop asking questions and whoever has decided that their conclusion makes the most sense and enough people believe them bingo bango bongo you get yourself a $100 bio book.  With that said I really think this whole process is really beautiful although daunting that notion that we will forever be revising our "stories" I think its the reason we are all here in the first place...to ask questions and never completely settle for (T)ruths ... c.k.koech

no human observation is made free of perspective. Furthermore, any observation made without the human touch of perspective would be useless. What good is an observation that does not apply to our actual lives? ... If we conceptualize science as an experiential endeavor specific to the individuals doing it we can begin to forgive ourselves for natural human error; we can begin to better understand and love our humanity ... "Science" could conceivably be defined as "taking charge of one's reality by actively engaging the world around oneself with a healthy skepticism/distrust ." ... drichard

Most importantly, this "loopy process" removes the fear of making mistakes. I no longer fear making mistakes because I know it is integral part of the process; I need to make mistakes in order to modify and improve my summary. I know now that the goal is not be right, but instead to be less wrong ... JPierre

Science (or at least the loopy version) seems to be doomed to be wrong until it is proven such. It's depressing. Can't there be facts? And if there can't be then why are we making "summary of observations?" ... Terrible2s

I think that the idea of science being subjective is a crucial idea to any progression we might have in the scientific world. On a basic level, subjectivity might allow a particular scientist to focus his/her study on a subject that they might have personal experience with, whether it be interest or some connection to that subject. This would drive them to "dig" deeper, creating new observations that could lead to a new(er) story ... JJ

Despite the fact that we have talked in this class about the subjectivity of science, many people look to science as objective fact. Here, this subjectivity is both a cost and a benefit. The drawback is that because of the disconnect between the public conception of science and its reality, a opinion-tainted "fact" will be accepted as truth by the average person, and in that regard, a scientist has a dangerously important role in determining what truth is in a given society ... heather18

by subscribing to this idea that there is a definitive Truth, we are missing out on all the little truths we could be ruling out ... heather18

I think it would be excellent if we could have this class around a table instead of in theater rows. It's hard to have a conversation with my classmates about all this interesting stuff when I can't even see them. Do you think it would be possible to have the class in a different room?? ... Emdoscio

 

Life as ... process?
(starting where one is, telling a story, getting it less wrong)

  • When i think about my stories of what i think life is, I still can not tackle the notion of what it is? Its proably a set of observations that can never be truth.....but ... Why can't I answer the question with confidence, when i experience what it is every day? ... Shanika

 

Life is ... ?

Practical issue related to some really major "getting it less wrong" issues

Characteristics of a living thing?

What's alive here? Is Langton's ant alive?
from Sahara Meteorite Prospecting from The World of Langton's Ant:
Thinking About "Purpose"

 

Mars?

Europa?


Titan?

 Elsewhere?

Defining a living thing: Intuitively obvious but surprisingly difficult to make explicit

  • No single distinguishing characteristic
  • Cluster of characteristics, some more "basic", others building on them ("onion")
  • No sharp border between "alive" and "not alive"
  • Changes over time
  • Depends on purpose of definition

Life, like science, a process? Life is those things involved in a process?

 

 

For most general purposes (life elsewhere?) and to help specify what needs to be explained, a living thing is

 

 


14, 16, 18 September

From the Forum

This past week we talked about defining what we see and define as a living organism. I'm sure most of us didn't think it would be that  difficult. However we usually go by what other people say and have already defined for us. That is why it is so hard to question and go through the thinking process to come up with a definition ... Karina G

the meaning of any given word is arbitrary.  Fortunately, we've all had many experiences with the word "life", and we agree on what is alive and what is not (at a remarkably high rate given the subjective nature of semantics.)  For the purposes of analyzing what life is, we have to work within the construct of what the generally accepted definition of "life" - the real puzzle being figuring out how to translate the shared ideal of the word to an acceptable written definition ... jingber

Perhaps the reason that it is so difficult to pinpoint a definition of what it means to be alive is because this constantly changes as things become more or less significant to us. For example, before the dangers of deforestation were truly in the public eye, people did not consider trees "alive" enough to save from being cut down ... dchin

This subjectivity in science, like you (paoli.roman) said, "makes me feel uneasy." ... dchin

we cannot escape societal prejudices and biases that have been implemented in the very core of our being ... ktan

perhaps there is no method of defining life other than the instinctual, we just have to know what it means to be alive the way in the same way that we believe we know what it means to be a man, or what it means to be a woman ... sophie balis

The religion I was raised with sees abortions as wrong because it says that the soul enters the body at an early stage in the pregnancy. So basically it defines "life" or being "alive" as having a soul ... Terrible2s

not being able to prove something with definite measurements/numbers doesn't mean that thing doesn't exist. I think spirituality and religion exist for a reason-- I don't think spirituality is just made up. My mother claims that new born babies have clear personalities (which would contradict JPierre's statement that fetuses don't have a life) ... Emdoscio

Living signifies molecules, cells or (whatever is needed for that person or thing to function), all working inside to make sure that you as a person or thing function.  Living is a physical aspect, which I feel like everyone or thing can be ... However, life is a little more difficult to achieve. life is about experiences, spirituality, emotions, thoughts, and etc. You can live and never experience something such as a life. A flower is living but will never experience the pain about its first breakup ... JPierre

To me, the key word is function- I see living organisms as having several functions (no matter how basic), such as eating through hunting or scavenging, and reproducing, so to perform these functions the living organism needs to have a system of cells that allow it to go through these behaviors. Whether a plant, the simplest little worm, or a more complex animal, these are living because they need to grow, "eat" (absorb some energy source), and reproduce. No living organism has a static life ... JJ

one important distinction to make when trying to define life is that between life in general and intelligent life ... at what point is something complex enough to be called life? ... cejensen

 

Categorizing/classifying/naming is a way of expressing our current understanding of ourselves and our relation to the world around us.  Useful for

  • quick responses to new, unknown situations
  • sharing knowledge
  • thinking about alternate ways of understanding ourselves and our relation to the world around us

Important to remember that names/categories are human constructions, useful only in particular contexts, subject to change.  See also

a living thing is

Additional defining characteristics of life ... as process

 

Diversity
"neither incidental nor detrimental ... instead essential"
 

Darwin's Voyage Revisited

See also Reviving the lost art of naming the world and the Encyclopedia of Life

made available by Emily Scioscia

Categorizing/classifying/naming is a way of expressing our current understanding of ourselves and our relation to the world around us.  Useful for

  • quick responses to new, unknown situations

  • sharing knowledge

  • thinking about alternate ways of understanding ourselves and our relation to the world around us

Important to remember that names/categories are human constructions, useful only in particular contexts, subject to change.  See also

 

 

Interactivity
 

 

Change over time
 

 

Have to think about not only here/now but also there/then.
Life as process: Interdependent diversity, changing over time

 

Something is "alive" because of a collection of nested characteristics that may differ somewhat from instance to instance, and change over time, rather than because of any single characteristic

  • breathes, has heart beat?
  • conscious? purposeful?

Life is an improbable assembly of clustered, diverse, interdependent  living organisms itself undergoing continual changes

clumpy diversity: smaller categories are subsets of bigger categories - humans at Encyclopedia of Life and humans at Tree of Life

Why?

Something is "alive"because it is a participant in that process?  Similarities between science and life? Good story? Summarizes observations, raises new questions? 

 

To further explore, need overviews in both space and time

In space, improbable assemblies of what?, different amounts of complexity?  levels of organization?

 

 


21, 23, 25 September

From the Forum

Life, science, and education

when the class was trying to select a common definition for "life", it was so difficult because one could always question or deconstruct the hypothesis of another. Although it was exciting to always ask questions, it was also so frustrating and even a bit of a deterrent because no one could ever find or think of a set foundation for the definition of "life". In each try, one was always a little wrong and I wondered how I would ever get through such a class if I could not even conceive basic concepts such as life. I really liked the idea of being "less wrong" in the beginning, but now I wonder if I will ever learn anything that might be a "little right" in this class ... JPierre

I think the main reason why I was initially finding it a bit.. overwhelming to continuously strive for being "less wrong" is because, as high-school science-students, we'd all been accustomed to a certain level of hand-holding and spoon-feeding! It had always been about someone else's experiments/observations/findings. And as a result, atleast for me, my brain had became somewhat.. lazy. I subconsciously knew that I'd always have someone else to do my 'scientific thinking' for me ... what IS subjectivity? Doesn't it ultimately boil down to a matter of perspective? And isn't perspective what makes each of us unique and gives us a sense of individuality? And isn't it chiselled over years of interactions with our culture and society? ... Yashawini

it is human nature to want to seek the truth despite our limitations. But i think that instead of letting certain situations, people, etc reveal themselves to us, we often have a fixed notion of what things ought to be like and project these notions onto these situations, people, etc. I think what I am learning in this class is that Science is not built upon static principles, but rather, Science is an ever changing and ever expanding subject that shapes and is shaped by the people and environment that inhabits the world ... xhan

Though understanding is always relative to some objective, can't that objective be a standard of knowledge? Doesn't that help us avoid the idea that "anything goes"? ... drichard

Classification

(see also Senior Seminar in Biology and Gender and Sexuality Core Course)

In some ways, we don't only have to decide how to classify things, but also when classification works and when it doesn't. I like the idea that we are not just choosing just one system overall, but instead one system at a time. That way, we choose a system each time our needs change.Still, I'm left wondering if that makes any sense at all ... mfmiranda

catergorizing/ classifying/ or naming organisms is a way of expressing our current understanding of ourselves and our relation to the world around us ... paoli.roman

it's interesting to think that maybe all that we notice in life (emotionally or just visually) is simply us figuring out ourselves ... Terrible2s

I was surprised at being in the same category with a fish ... Karina G

Eventually, all living things are going to fall into one big category--will we then be expected to feel a kinship with bacteria? ... heather18

In classification and evolution, the key to understanding what is to come is mastering an understanding of history ... Classification has allowed humans to feel comfortable assigning value to the lives of other organisms (killing a bug is nothing, but killing a dog is unthinkable). But, the Tree of Life would suggest that we shouldn't get too comfortable at the top ... achiles

the idea that all life on earth is related, even if extremely distantly, is one of the reasons I find Biology so fascinating ...All living things (we know of) evolved here on earth. We are all related, if in few other ways, because of that. We have that in common. We only have one earth, one place that supports our type of life, and we need to protect it ... cejensen

Context, in space and time

Improbable assembly?  of what?

An Overview: Spatial Scale 

Spatial scale - at what scales do improbable assemblies exist and how do they relate to one another? alternate

  • protons, neutrons - 10-15 meters (1 fermi)
  • atoms - 10-10 meters (angstroms)
  • smaller molecules - 10-9 meters (1 nanometer, 10 angstroms)
  • macromolecular assemblies - 10-8 meters
  • cell membrane thickness (lipid bilayer), viruses - 10-7 meters (100 nanometers)
  • cell component (mitochondrion, chloroplast), bacterium - 10-6 meters (1,000 nanometers, 1 micron)
  • "typical" cell - 10-5 meters (10 microns) - may be part of multicellular organism or itself a living organism ("cell theory" - a major advance based on new observations from new technology) - 10-5 meters (10 microns)
  • sand grain, blood vessel - 10-3 meters (millimeters)
  • human scale - yard stick, human (female - male) - ~ 1 meter
  • blue whale, large playing field - 102 meters
  • a little more than a half mile - 103 meters (kilometer)
  • distance from BMC to Philadelphia (days walk) - 104 (tens of kilometers)
  • 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

Lessons from working up in scale from human ...

  • Technology important to make new observations
  • Bigger things are assemblies of smaller things
  • Living organisms are limited in size
  • Life is bigger but also limited in size?
  • Improbable assemblies still bigger and relevant for understanding life
  • There's LOTS of room to explore (that's nice?)

 

And from working down in scale ...

  • Scope of observations dependent on technology ... living things smaller than 100 microns
  • Larger things are improbable assemblies of smaller things ... cell theory
    • levels of organization - atoms->molecules-->cells-->multicellular organisms-->ecosystems
  • Improbable assemblies exist at a most scales, though not all
  • Different features apparent at different scales; at larger scales, smaller wholes become invisible parts
  • Both very small and very large scales are important for understanding life.
  • There exist lower and upper(?) bounds for living organisms ... as we currently know them. Why?
  • Existing observations are greater than in past, cover large range of scales, but can be expected to be incomplete in other ways
  • Can distinguish smaller, single-celled from larger, multicellular organisms (Why no big unicellular organisms? - need for communication/integration?)
  • Size is not, in general, a good way to classify ... no natural divisions (gaps, spaces, clumps)
  • At smaller scales, things start looking more similar (less diversity)
    • all organisms consist of cells
      • atoms same in different organisms, same in living organisms, non-living things

Life in spatial context

Improbable assemblies of improbable assemblies of improbable assemblies ...

Need technology to look beyond human scales (10-3 meters (millimeters) to 103 meters)

Improbable assemblies from 10-15 meters to 1026 meters

Living organisms from 10-6 meters (microns) to 102 meters

Life and its products from < 10-8 meters (and expanding? nanotechnology) to > 107 meters (and expanding? space exploration)

 

Temporal Scale

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)

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.

Life in spatial context

Life is ongoing change at human scales (seconds to years)

Need technology to look beyond human scales 

Ongoing change at all scales up to 15 billion years

Ongoing change at all scales down to nanoseconds and below

"The only lasting truth is Change"?

How can we account for changing improbable assemblies at multiple scales?  Your thoughts in the forum ...

 


28, 30 September, 1 October

From the Forum

When we look at the small area in which we live or even at our country, it is hard to relate ourselves to the simplest little organisms (like bacteria). From such a close view of life, all the species seem so different and distinctive. On the other hand, when you look at the Earth as a planet in the much larger universe, that may or may not contain other "life", we seem much more related to other living things ... JJ

As we saw from lab this week, thinking small is important as well. Thinking in a different scale than the one we're used to is what we need to do to see similarities ... cejensen

Our look into classification could be a model for how we look at other issues outside of the classroom. For example, our decision of scale is extremely important; it dictates how similar two different objects/bodies will appear ... if we examine an issue too closely we lose the context of the issue and practicality goes out of the window. If we examine an issue from too great a distance we tend to generalize and, once again, our observations are skewed and our conclusions potentially invalidated. There seems to be an important balance to be struck; our decision of scale proves a very important task. We must ask ourselves what exactly we are looking for and which scale will likely get us the "most right" obseravtions ... drichard

Visualizing our significance in relation to the other planets, stars, suns, galaxies, etc. out there is disorienting ... This reminds me of our discussion about how categories are human constructions that are subject to change and created for a purpose. The subjectivity in creating categories makes me wonder about how categorization might change in the future as technology progresses and we are able to discover more about life on Earth and other planets ... dchin

knowing that I share a kinship to bacteria because of our abilities to store DNA is more reassuring than saying that I am related to bacteria just because everything in this world is related somehow.  Having a context in which to classify organisms or living things reassures me that in this class, I won't be learning that I'm actually related to a wooden table without ample reasoning to support that claim.  Moreover, this mode of thinking is pretty exciting. Thinking about classification in these terms increases my ambitions as I see myself wanting to find or observe the link between me and other organisms. Now that I can see a link between myself and bacteria, an organism that is so anesthetically different from me, I wonder with what I will find a connection to next ... JPierre

I particularly enjoyed the discussion on the "Big Bang" theory on Friday. I feel like it's an abstract concept that everyone hears about, but it was interesting to put it into the context of our scientific method. (as in, here's the observations we have, what story could possibly explain these events?) However, I think it's interesting to note that there's just as much to be discovered at the smallest levels of life (inside and atom) and in the greatest scale of the entire universe. Also, the improbability of all of these things even existing is absolutely astounding. Everything is so incredibly complex, it's absolutely impossible to imagine how it all fits together ... jmstuart

This also made me think of how we've established a sort of heirarchy in the classification system. Despite the heirarchy, however, I believe the classification system is more of a.. horizontal platform, where all creatures are placed at the same level and given the same amount of importance: no creature is superior to another ... Yashawini

More than anything though, thinking about scale and the breakdown of life in last week's classes made me return to an issue that haunted me for awhile. Our bodies are made up of all these other pieces (macro molecules, atoms) that constitute life--they compose us-- but the atoms that make us are not actually ours. The issue is attachment and the whole idea of durability... everything is temporary. So what does it mean to "own" something? Even your hand is not the hand you were born with-- the atoms have all been replaced with new ones over time ... Emdoscio

I think this is sooo much fun like whats really out there???? ... c.k.koech

being in this class that has made me a skeptic, because during most of the classes I kept thinking "how do we know?" ... Terrible2s

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? Missing organisms?

Some organisms are more "complex" than others?

Taking advantage of technology: Eukaryotes vs Prokaryotes (Monerans: eubacteria and archaea) (Why no multicellular prokaryotes?)

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?  Darwin Time/change/variations essential descriptors of life?

 

Biology 103 Evolving

"I have always thought of life as always changing but then I realized I never REALLY thought about it ... we as humans change every day! I can't think of one thing in the world that stays the same, unchanged. Even the solar system is changing! Earth changes daily if not more. Think about it." ... lcorhan

From lab - At very small scales of space and time everything is somewhat randomly changing

What needs to be accounted for is not change but stasis/order

Order at larger scales can come about from the statistics of random change

Diffusion

Order can also be brought about by simple interaction rules within the system

Game of Life

And by interactions of the system with external influences - "natural selection," differential reproductive success, differential persistance

Evolution is ....  random change together with inheritance (reproduction with variation) and differential reproductive success  ("natural selection")?

No plan at outset, no goal, no more and no less than an ongoing exploration of possible forms of life?

Adaptation/fitness a consequence rather than an objective - "Survival of the fittest" is a tautology: what persists is ... what persists, there is no independent measure of adaptation/fitness by which organisms can be compared

Story of evolution still evolving .... Join in wider discussion

Nested, clustered diversity?  Progress?  Value? 

 

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 (variant, variant, variant)?

  • Very different way of thinking, itself still evolving, random exploration with no initial intention and no objective
  • "selection" misleading, is actually "differential persistance"
  • Patterns continually changing, no essences, hence classification problems
  • Randomness underlies order instead of being opposed to it
  • Is there "progress"?  How defined?
  • Similarities between life as process and science as process?

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 now, 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?
  • What IS evolution? A good summary of observations? What are the observations?



5, 7, 9 October

From the Forum

I have always thought of life as always changing but then I realized I never REALLY thought about it. It's just so weird to me to think of it as the opposite ... I can't think of one thing in the world that stays the same, unchanged. Even the solar system is changing! Earth changes daily if not more. Think about it ... lcorhan

our discussions this week were really discussions of constant change at different scales. Evolution represents constant change on a large scale, while the idea that "everything is in constant motion" (even things we perceive as still, or not in motion) represents constant change on a small scale. I am really fascinated by the fact that almost everything we observe is related to the scale at which we observe it. Sort of obvious, I know, but I think the act of finding similarities an differences in the different scales at which we view life will be key in defining it ... cejensen

This reminds me of the first few days of class, when we discussed subjectivity in science and if there could be Truth(s) in scientific study. I think that much of the reason for us not being able to have any definite Truths or one-sided views of a scientific question is because of the issue of scale and thus perspective ... Added to the differences in scale we have the idea that things in general are always changing. This points back to never being able to have Truths- even if a new story appears correct and is verified by many people, it will never be always true because eventually the observed things in the story will change ... JJ

The diversity on Earth that we as humans wish to organize is probably never ending. I think it says more about humanity in terms of our need to find a place for everything and feeling the need to explain it ... Kalyn

couldn't "random movement" just mean that we haven't discovered the purpose behind the movement yet? ... I think that the lab on Wednesday for instance, demonstrated that although there is only one widely accepted scientific explanation for certain things, there are still other stories that are interesting and worth at least thinking about ... heather18

I am still having trouble with the idea that "purely statistically" entities have motion as one of their properties. I struggle with this idea because of the theory that there is "no free lunch." ... this theory means that every action has a cause--nothing happens without it originating from somewhere ... if it call comes down to energy, where does it come from? Is this just like asking the question why are we alive? Does it all get back to the Big Question of creation and god? Why don't we have an answer? How is it possible that energy can just be a property? ... Terrible2s

While having a sense of perspective can be good, at times we really do need to narrow our focus down to one specific level.  Without looking at things through a certain fixed perspective, we'd be paralyzed ... jingber

If the world is in constant motion (and it is increasingly apparent that it is) then we certainly don't notice it. We see a table as a stable object. Indeed, we base our notion of physicality (a large part of our identity) on the relative stability of the world around us. I propose that this sense of stability is a story that originates entirely in the brain so as to facilitate our day to day lives ... This idea speaks to our general aversion to change. Though we exhibit an unparalleled ability to adapt to harsh climates, for example, we strive for continuity and stability within these climates ... drichard

Chance in life and the world

The part that I am most interested in isn't so much the whole constant change/motion part, but more how we're adapting to these changes. I guess what I mean is how we're choosing when to adapt and when to react. How are we choosing when there's a need to recognize change and when we can ignore it? ... mfmiranda

Do we need to recognize change or can we ignore it in studying biology?  Can we live with multiple perspectives or do we need to stick with one?  Can we accept random motion as a first cause or must it itself have a cause?   Are these incompatible stories amongst which we must choose or can we come up with stories that take account of the observations underlying both?  Put results of small group discussions in forum.  Include initials of everyone in the group.  

Biology 103 Evolving

"I have always thought of life as always changing but then I realized I never REALLY thought about it ... we as humans change every day! I can't think of one thing in the world that stays the same, unchanged. Even the solar system is changing! Earth changes daily if not more. Think about it." ... lcorhan

From lab - At very small scales of space and time everything is somewhat randomly changing

What needs to be accounted for is not change but stasis/order

Order at larger scales can come about from the statistics of random change

Diffusion

Order can also be brought about by simple interaction rules within the system

Game of Life

And by interactions of the system with external influences - "natural selection," differential reproductive success, differential persistance

"Missing" organisms?

  • didn't work
  • not tried
  • ??

Evolution is ....  random change together with inheritance (reproduction with variation) and differential reproductive success  ("natural selection")?

No plan at outset, no goal, no more and no less than an ongoing exploration of possible forms of life?

Adaptation/fitness a consequence rather than an objective - "Survival of the fittest" is a tautology: what persists is ... what persists, there is no independent measure of adaptation/fitness by which organisms can be compared

Story of evolution still evolving  .... Join in wider discussion

Nested, clustered diversity?  Progress?  Value?  Relevant?  Still occurring?

evolution has been taught as a slow moving process- and for the most part the occurrences of the past remained in the past, I've never thought how things that happened so long ago effect us now ... sophie balis

Is some kind of pattern and stability the explanation of life or the product of it?  Could our preference for seeing pattern/stability be itself a product of life rather than an inevitability? ... PG

the pattern and stability we see is a result of life. I think it relates to the evolutionary theory of survival of the fittest in that when a species develops and evolves, it tries different ways of doing things. The animals or plants that "discover" the most efficient ways of doing something such as reproducing, finding food, and migrating will be the ones who are ultimately the most successful. They will probably live longer and pass on their genes, creating a pattern of actions and therefore stability within that species' community ... JJ

 

Evolution is a different way of thinking about things, a way that depends fundamentally on randomness/change/time.  Is it useful?  Does it raise new questions?  Implications for looking back in time?  What more can we learn by doing so?

Temporal scales reminder

  • 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)

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

Alternatively, evolution as a "filter" - lots more diversity in past than in present?

Fossil record - Observations

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? evolve from prokaryotes? - Endosymbiosis - illustration

Multicellular Organisms - ~600 million years ago (last sixteenth of life's history to date)
VERY improbable?



19, 21, 23 October

From the Forum

I have been thinking about the idea of constant change a lot over the past week. It both excites me and depresses me. Change makes the world go round, but it also means that nothing stays. As far a science is concerned, constant change is exciting. As far as my life is concerned, it makes me a little sad ... Now that I am more aware of constant change, I sort of feel like I perceive change everywhere; I perceive change in places and people that I wouldn't have previously ... cejensen

My last fortune cookie: The only certainty is that nothing is certain ... Emdoscio

I think one of the great things about being human is we can ask questions and we can seek answers. "What's the point?," you ask. Well that's the beauty of having possibility and being self-aware. Humans posses these qualities which allow everyone to give their life purpose or not ... Kalyn

Evolution: observations in time

 

Images of evolution - "getting it less wrong"?

Additional issues:

In class we were talking about "change" and how evolution doesn't actually make entities more "fit" but rather more complex. We talked about how the process was not only one of filtering, but one which created .... A particular image that was given which I liked was that time "makes door open." I like this idea that time does not make us any better, but rather just expands what was already in existence. It makes me wonder, however, when will these doors stop opening/ when will we run out of doors. In other words, when will we be the most complex, unable to evolve any further? ... What if the more complex we become, the actually less and less suited to our environment we become ... I'm scared ... Terrible2s

Last time in class we were talking about how a spider is not more/better evolved than a human or a whale vs a chimp etc... however, this got me thinking: i feel that we are the only species that could wipe out life if we chose to. Many animals are becoming extinct due to loss of habitat (because of our growth of habitat) and hunting (because we are/encourage poaching); many forests no longer exist due to deforrestation; etc. the only thing i could think of that is alive and could possibly "take us [humans] out" would be bacteria--however--we then would just develope an antibiotic to "take it out".  I can't see any other living organism that can keep us in check. i mean if all of humanity decided that we needed to destroy life, i believe we could. what keeps us in check? our mind? our belief in a higher power? do we have an innate affinity for life that keeps us from doing this? hmmm ... lcorhan

"Pattern pleases us, rewards a mind seduced and yet exhausted by complexity. We crave pattern, and find it all around us, in petals, sand dunes, pine cones, contrails. Our buildings, our symphonies, our clothing, our societies - all declare patterns. Even our actions: habits, rules, codes of honor, sports, traditions - we have many names for patterns of conduct. They reassure us that life is orderly." .... Diane Ackerman (thanks to drichard)

But is the universe, or life, "orderly"?  For another example, see The Nature of Technology: What It Is and How It Evolves

Our problem for the rest of the semester: How to account for

Ongoing exploration of possible forms of bounded, energy-dependent, semi-homeostatic, semi-autonomous, improbable assemblies that reproduce with variance, for past/present/future diversity?

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

Nothing there but atoms

  • Life distinct from non-life because of how atoms put together
  • Small number of atoms, large number of things - diversity
  • New phenomena from putting things together

 

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



26, 28, 30 October

From the Forum

This class does a great job of scaring me ... With all the green movements and environment consciousness, we tend to try to send out the message "save the earth." But as professor grobstein said, the earth is pretty resilient. We're killing ourselves.  I feel like that would be a much better message--"save us!" Yes I care about the environment and all the other species we are killing along the way, but they put the message out like a nagging mother about a dirty room, "save our planet, keep our home clean." I think we need to start thinking about ourselves to maybe make some change ... Terrible2s

life on Earth is interlinked and interdependent, and as much as we would like to believe otherwise, our existence is dependent, if not completely determined, by the existence of other life forms. If we set out to disturb the environmental equilibrium and wipe out various species, we will be courting self-destruction ...  Yashaswini

[Interdependency] although obvious, is a bit profound for me and it draw backs to some of the themes that we spoke of in previous weeks. Nothing in this world is independent of one another and all these organisms need each other to live, even the "great and mighty" humans. This reminds me of the discussion we had concerning evolution and how aspects of current life stem from  other previous and ancient aspects of living organisms ... JPierre

I do believe in the potentially catastrophic effects of global warming--I have witnessed its devastating effects on my own people, my own country just very recently, but I doubt that humanity would go extinct because of it. We're pretty smart and very adaptable. And we can be pretty tough when it comes to survival ... I do know that we will NEVER know what will happen, we can only guess. Along with the idea that we don’t know what is real—human intelligence is SO small and limited that something so completely out of our understanding can interfere with the reality or life, or whatever as we know it. It's pretty exhilarating, actually ... ktan

"Life is a particular assembly of atoms."  It was about time to finally know the difference between an elephant, a human and a desk :)  The difference is the assembly of atoms. However this raises more intriguing questions that we are just beginning to explore. Since there are over 100 atoms there is an infinite number of possible assemblies.  This could mean that there are things/ species or features that we haven't seen and that can pop up all of the sudden. How do these combinations happen? ... So far we can say that some atoms have the need to stabilize and other atoms are willing to help. :) That is how bonds happen. But we also cannot forget the charge of these atoms. How does the net charge of atoms affect life?  ur discussion on polar bonds was not clear to me. What I understood is that oxygen doesn't take away the electron from Hydrogen unlike Cl from Na. The electron becomes more associated with the oxygen. What does this mean and why does it happen?   So many questions .... Karina G

Assembly rules for protons/neutrons/electrons yield atoms

Assembly rules for atoms yields molecules - more stable configurations of atoms

  • electron sharing - covalent bonds
  • electron movement - ionic bonds
  • intemediate sharing - polar bonds

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

  • Stereoisomers (enantiomers, optical isomers) - How distinguished by biological systems? Related to temperature, pH sensitivity?
  • carbon particularly suitable for life, because of diversity of three dimensional molecules it can participate in? 

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"

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?)

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?

Open questions: temperature/pH sensitivity, discrimination of three-dimensional forms, enzymes?

Proteins, from amino acids via peptide bonds



2, 4, 6 November

From the Forum

forumposts103f09

 

 

 

"Biology, like all science, is a social process, one in which the observations and tentative summaries are shared among individuals, so that each can benefit from the ongoing inquiries of others."

 

 

 

 

 

 

"moving on to what we can learn about life starting at small scales and moving progressively to larger ones.  We've moved form atoms to molecules to macromolecules.  What have we been able to account for?"

Progress to date

  • diversity from combinatorial explosion; simple things interacting in simple ways leads to infinite numbers of new things
  • everything is in flux, some things are relatively more stable than other things
  • electrons, three dimensionality of molecules of critical importance
  • proteins, among other things, function as enzymes, alter stability of other molecules, helps make sense of u-shaped temp/pH sensitivities of living organisms
  • suggests living organisms involve variable maintenance of stability of molecules in flux

Proteins long strings of amino acids, complexly folded in 3-D, primary structure critical for 3-D structure and function (Sickle cell anemia -HBB: The Gene Associated with Sickle Cell Anemia, alternate, alternate2), how account for primary structure? 

Proteins, linear polymers which  are (among other things) enzymes, speed up breakdown of other molecules, specificity depends on 3-D structure which in turn reflects (in part) primary structure

 

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
  • double helix: intergenerational transmission of information, mutations "explain" reproduction with variance - external factors, intrinsic "noise"
  • remember also improbability (polymerization, energy source) 

 

Nucleic acids are linear polymers which (among other things) determine the primary sequence of proteins.  Account for inheritance with variation.  What is being transmitted from parents to children is, in large part, information about primary structure of proteins.   The primary structure of nucleic acids reflects evolutionary history. 

 

 

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

 

Carbohydrates are sugars and polymers (linear or branched) which (among other things) serve as energy sources.  They are not "coded" for by DNA but reflect instead ongoing chemical reactions catalyzed by proteins. 

 

From hydrocarbons to lipids

Lipids are relatively non-polar, and hence non-water soluble molecules and polymers that, among other things, create boundries in biological systems.  They also serve as energy sources.  Like carbohydrates, lipids are not "coded for" by DNA but instead reflect ongoing chemical reactions catalyzed by proteins. 

 

 


2, 4, 6 November


From the Forum

I think the real question for this class is how in depth should we be studying atoms and macromolecules? Should we be provided with a general concept that lets us understand their complexity in the grander scales of life? Or is it necessary to learn every minute detail of their function? I think what's happening is for some people the details are necessary and for others its not ... Kalyn

it is not easy to understand how the bonds and associations between them happen. For me it is difficult to study atoms and molecules without fully knowing all there is to know ... Karina G

I know everyone is saying how important it really is to learn about them [molecules and macromolecules] and I generally agree with that. However, I'm just gonna say it, they're boring. I'm bored. But I do think it is very important to learn about them. It's all the little parts that make up the whole ... that's what makes the real difference between us and rocks. An important difference, I think ... Terrible2's

I think that the way cholesterol is viewed in our society sort of highlights a) the way that science can be severely twisted, and why we should question the use of "truths" and b) how science is a highly effective form of hegemony. Cholesterol is a necessary part of our existence that must be monitored, yet because it has been identified by science as a leading cause of heart attacks we view it as an enemy, something that invades and attacks us. Maybe its important for us to study these smaller scales, so we can understand our own inner workings better, and not merely depend on the messages that have been sent to us via cheerio commercials ... Sophie Balis

when one puts simple "things" together (atoms, molecules...) then one will get something completely new with a different structure, function, and role ... I like to think of these las couple of lessons as a big puzzle piece. The more we connect and construct each piece together (atoms, molecules, macromolecules, proteins, carbohydrates, cellulose, etc...) the closer we get to see, analyze, and understand the bigger/final masterpiece! ... Paoli.Roman

I just completed my web paper on taste - it's awe-inspiring the amount of chemical reactions that transpire when you bite into a piece of bread! And yet, all that we experience is a particular taste, maybe tied to a particular memory. In this way, the chemical, physical reality of bread differs greatly from the experience of "bread." ... drichard

we still have not explained why these improbable assemblies occur ... dchin

how could Bio 103 get "less wrong"?  better handle atoms/molecules/macromolecules? ... PG

                 
  • drop the section entirely?
  • spend more time on details?
  • ????

 

 

 

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

Organisms are not "alive" because of having any one particular macromolecule (or any one particular property) but rather because of dynamic interactions among an array of different macromolecules, each performing a different function in a dynamic interactive assembly. 

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

For Thermodynamics:

 

How can there exist improbable assemblies?

Energy is change (kinetic, radiant) or the possibility of producing change (potential)

Spontaneous change is from improbable to probable

Waste is ?

How keep dorm room "neat"?  Why do we eat?

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"
  • chemical reactions have same characteristics as diffusion
  • 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)
  • thinking about waterwheels

Wat is probable? - lcorhan (and yashaswini)

Don't we see lots of people?  Aren't they therefore "probable" instead of improbable?

People are particular assemblies of parts that are very unlikely to occur simply by chance, therefore "improbable" in larger space/time context

What about molecules?  What makes them "improbable"?

Molecules are also assemblies of parts.  They are improbable if those assemblies are spontaneously falling apart more rapidly than they are appearing, ie if they wouldn't occur with a significant frequency by chance, if their concentrations are away from equilibrium. 

What is "waste"?

Kinetic energy having no possibility of producing change on larger scales, equilibria, uniform heat - complete randomness, the least possible improbability, stasis

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" -

 

 


9, 11, 13 November


From the Forum

Even though the concept of everything falling apart from less probable to more probable holds true for most things, I feel it very unsettling to apply this to humans as well ... this would mean, that from the time a baby is born, the journey towards getting "more probable" begins, that from the moment life begins, it is directed towards death. This seems very.. morbidly unsettling ... Yashashwini

Not only do we, as improbable assemblies, depend on things the are breaking down, but also (simultaneously) the things that we depend on that are breaking down are breaking us down. This can also be seen in the food we eat - we depend on it to maintain our improbable state (life), but the food we eat is not always good for us, and can simultaneously break us down ... cejensen

should we begin to explore how to stop things from falling apart? Do we have a right to so blatantly tamper with nature? ... dchin

are our bodies only meant to last for a certain amount of time? And if so, is there any way to artificially extend that time period? ... jmstuart

What interests me most about entropy is the human propensity to deny and fight it ...The best example is modern medicine. Whether it's the administration of life-saving antibiotics or a weekly shot of collagen, we are constantly trying to preserve life, to prolong death. In this way intentionality alters the natural course of the universe. This could have harrowing effects on the balance struck between the sun, plants, and humans ... What exactly could come of this disturbance? And is it really a "disturbance" at all, or is human intentionality itself a "natural" process? ... drichard

Sometime last week, someone said that they were unsettled with the concept of human DNA "falling apart." I disagree--I actually find it pretty cool. Not the act of falling apart, but the phrasing of it ... I have never heard of the act of dying described as "the natural tendency of falling apart." I don't know of anybody who has had "death" explained to them in such a way. I find it kind of refreshing, that dying isn't this big mystical, incomprehensible concept, but rather just the improbable reverting back into the way it always has been ... [this] has really got me thinking about how oxymoronic life is--chaotic and random, yet orderly and purposeful at the same time ...ktan

Although it is morbid to view everything, including ourselves as breaking down I think it almost comforting in a way, it offers us a sense of camaraderie with basically the entire universe  ... We know that nothing in our universe can last forever- not even the sun, which seems eternal. However when we say that life has to end at some point, we basically are saying that the concept of life as we understand it is limited, but other forms of life, other planets and new universes could possibly form. Entropy to me more represents a lack of commitment to our current status, and endless  future possibilities  ... sophie balis

I tried to think of this entire "breaking down process" as a continuous circle ... Kalyn

  scienceloop 

What is "death"?  The end of life or .... ?

What is the relation between death and life?

Should biologists do research to prolong life? prevent death?

An update: the sun falling apart is not the only possible source of improbability

How do enzymes fit into this picture?

6 CO2 + 6 H2O + light -> C6H12O6 + 6 O2

C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O + 32-34 ATP

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

Enzymes as couplers of catabolic and anabolic processes, of falling apart and building - transforming improbability from one state to another

  • Why doesn't sugar fall from the sky? 
  • Catabolic/anabolic coupling
  • Shape change of proteins (cycling between probable and less probable states) essential
  • The falling apart of things can make sugar (macromolecules) available

Life as

is not entirely fantasy.

How does all this relate to (NYTimes 20 November 2009)

This week, the science of medicine bumped up against the foundations of American medical consumerism: that more is better, that saving a life is worth any sacrifice, that health care is a birthright.

many patients — and organizations of doctors and disease specialists — find themselves unready to accept the counterintuitive notion that more testing can be bad for your health.

Thoughts in forum ...

 

 

Can account for various properties of life with molecules, macromolecules, and thermodynamics, but can't yet make a living thing in the laboratory ... Why?

The "cell theory" - All living organisms are either cells or assemblies of cells

What are cells? Why a needed level of organization for life?

 

Why must there be a "cell" to have life? How can cells be both "distinct entities and building blocks"?

 

 


23, 25 November


From the Forum

iDeath is unpleasant, but practical. If organisms did not die, they would overwhelm the Earth, subsequently making life more difficult for everyone. This is, of course, much easier to say when we are discussing death in the abstract. When it comes to the death or impending death of someone that we care about, we are probably more likely to advocate finding ways to preserve life ... It would be trying to fight our very natures if we decided to stop exploring and practicing ways to put off death ... dchin

I believe that there has been a remarkable lack of emotion within our in-class discussion of death. Yes, the emotions conjured up by death are socially constructed, but this does not mean they are not functional! Our discussions have revolved around certain assumptions that I'm just not okay with ... achiles

Sometimes, when I think back to what we have said in class, it makes me feel guilty/ashamed of our insensitivity. But at the same time, I think we should just remember that everyone in class has had their share of experiences with death, all different from one another, and we can't expect everyone to cater to our emotions. Maybe that's why there has been this lack of emotion during discussion--we're not talking about/relating to personal experience, but rather the context of the class ... ktan

I'm extremely afraid of dying. The very thought of not living consumes all my focus and many times I'm unable to think of other topics. I understand that this fate in inevitable and this class has provided some biological reason to support this. Yet it still does not lessen my fear of death ... As for the breast cancer screening discussion, I still believe that this tool has elements of efficiency. It's true that the test has been unable to decrease the amount of people with breast cancer and new methods need to be invented in order to better combat the spread of this disease. Yet knowing that for one more year I had avoided the painful ordeal associated with breast cancer, is enough to qualify the test as effective for me ... anonymous

i think that the fear of death comes from very primal human instincts - to survive and to procreate. In relation to our discussion of cancer screening, those instincts might be reasons someone would want to get checked out his or herself; but that doesn't account for why we would want our friends and loved ones to do so. I'm not sure how to explain that part in any other way, besides in terms of human emotion ... Lili

The unpredictability of death makes people worried and they look for answers to calm their fears. People like having options and death provides none so science seeks to make them ... Kalyn

For a person not enamored my life, for someone who doesn't notice the beauty of everyday things, the warmth of the sun, the chill of the winter breeze etc, for someone not in love with life, death probably wouldn't be that serious an occurrence. We fear death BECAUSE we love life, and we love life BECAUSE we fear death. This again reminds me of the discussion we had.. ages ago, and again today, in class about the cyclic nature of everything in science--from patterns in evolution to the very fundamental question of what science is--everything travels a circular trajectory ... yashashwin

Screening debate reveals culture clash in medicine

Behind cancer guidelines, quest for data

  • In what have your understandings of cancer, death, emotion, medicine, science been altered by the current controversy/our discussions?
  • What should scientists do in the future in relation to cancer, death, emotion, medicine, science itself?

 


30 November, 2, 4 December


Ideas/tools at our disposal to make sense of life ...

  • evolution is a process of trying things out to see what works at any given time, leads to clustered diversity, interdependence
  • living things are improbable assemblies of macromolecules, continually in flux

What additional ideas/tools do we need?  would we like to have?  From papers ...

why do people go on rampages? ... cejensen

Why would many athletes engage in behavior that seems risky based on the potential consequences of playing with a concussion? ... jingber

why are some people ... more susceptible to alcohol abuse? ... jmstuart

why do we human beings have an organ that we can simply do without? ... lcorhan (see also paoli.roman)

Where did the concept of “zombiism” come from to begin with?  ... Lili

I wonder if steatopygia plays a role in the body of today’s black woman ... JPierre

In the next 50 years, we will see tremendous advancement in the study, treatment, and prevention of Venereal Disease ... Anna

The chemical interaction of food molecules with taste receptors would be totally meaningless if the resulting signals were not sent to the brain ... It is essential to realize that we taste with our brains, not with our mouths ... drichard

what is certain is that music does alter our brains by inciting hormonal activity, and this brings us one step closer to unlocking the power of music ... hmarcia

Further development in understanding of cells, genetics and synthesis technology will also be needed to get synthetic biology into larger and more complex projects, but until then it is still an interesting and promising field whose security and ethical implications need to be addressed before it reaches its full potential ... mcasias

It is practical to utilize the knowledge that we gain of life at small scales, but this must be tempered with a commitment to ensuring that the pursuit of progress does not result in the loss of our humanity ... dchin

the real “chemistry” behind the attraction people feel when they fall in love is mainly biologically based ... Kalyn

Though viewing love as merely a drug-induced state of mind a complex interplay of chemicals can provide some balm for a broken heart, could it be really be true that the most wonderful, soaring feeling in the world amounts to no more than a narcotic high, a temporary state of mania? ... Yashashwini

Communication is essential in order to complete the different tasks that the colony needs to function properly ... Karina G

In the end purpose of organic farming is not to improve the nutritional value of our food, but rather to make the overall process of food production better ... sophie ballis

one more thing to be thankful for regarding sex: it adds meaning and excitement (again, jokes aside) to life ... ktan

As previously mentioned, my interest [in lucid dreaming] does not only lie with adventure, although that is a large part. Oh, the freedom of controlling all your surroundings and your life! There is nothing comparable ... vdonely

we are beginning to acknowledge that our inclinations to use fossil fuels-which has harmed national security, the economy and the environment for decades-needs to end ... xhan

knuckle cracking is a personal decision with few risks involved ... Terrible2's

Is everything "biologically based"?

Do we need more than macromolecules to make sense of life?

More than evolution and macromolecules plus some general insights from acquired from thinking about them?

Candidate additional ideas/tools ...

Multiple levels of organization

Cells as interdependent improbable assemblies of macromolecules, multicellular organisms as interdependent improbable assemblies of cells, populations/ecosystems as interdependent assemblies of organisms

Multiple and reciprocal interactions, no simple cause-effect relationships, no gene/environment controversy

Ontogeny/development - evolution within individual lifetimes

Interdependence of individuals and improbable assemblies of of which they are a part

Top down as well as bottom up influences - no individual/culture controversy

 

 Cells as energy-dependent, semi-autonomous, semi-homeostatic, reproducing, bounded improbable assemblies of molecules/macromolecules (One microbe as a group of 200 protein machines)

  • diversity (again) - how account for it? what's its significance?
    • Prokaryotes, eukaryotes ... viruses
    • animals cells vs plant cells
    • common characteristics of cells
      • boundedness
      • ability to transform improbability
      • ability to reproduce (create comparable improbable organization)
      • genetic material
      • semi-autonomy
      • semi-homeostasis (reactivity)
      • eucaryotic cells: internal bounded spaces (compartments)
  • scale: microns, tens of microns, a minimum size for life?, why?
    • macromolecule diameter ~ 10-8 m, so 100 or so across a small cell, need a million macromolecules?
  • a maximum size for cells? why? relations to outside world? ... maintenance of internal improbability
  • nature of inside world? ... internal coordination
  • cell as assemblies of diverse components (and hence themselves can be diverse), creates need for internal (and external) intercommunication/coordination, variable three dimensional structure
  • the new factors: specialization, interdependence, distributed control
  • problems of conflict/cooperation/coordination, of definitions of life (and death)

The matter of boundedness

Life requires not only ways to speed up spontaneously occuring breakdown (enzymes) but also ways to slow it down

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

The energy/improbability matter and boundedness

Looking back and forward -

link(s) between life and the second law

 

Another reason sugar doesn't fall from the sky ....

6 CO2 + 6 H2O --*/*--> C6H12O6 + 6 O2

*/*: in the presence of light, enzymes, and organized spatial arrays of molecules

C6H12O6 + 6 O2 --*/*--> 6 CO2 + 6 H2O

*/* in the presence of organized spatial arrays of molecules, including enzymes AND simultaneously ADP -> ATP

  • As with energy, living systems do not consume matter, they transform it
  • Transformations are cyclical and involve linked transformations
  • Non-spontaneous transformations are driven by spontaneous ones
  • Enzymes and their shape changes are critical
    • for facilitating spontaneous reactions
    • for linking spontaneous and non-spontaneous reactions
  • Organized spatial arrays of molecules are essential

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

 

 

Given spatial arrays of macromolecules that can do the link:

Improbability drives the creation of

  • molecules
  • macromolecules
  • spatial arrays of macromolecules
  • cells, organs (including brains), people, culture, ecosystems, biospheres?

Problem of creating a living cell is problem of assembling intricate architecture of large numbers of molecules, macromolecules?

 

General principles from the discussion of energy at the cellular level, beyond energy per se

  • matter, like energy, is not "used", it is transformed, may be recycled
  • 3-D organization of macromolecules critical (not explicit in genetic information), as are molecules other than proteins (ditto)
  • are at level of cell already talking about complex interactions among complex, semi-specialized, semi-autonomous parts (the cell as symbiotic system) - cooperation at least as important in biology as competition (Lynn Margulis)

Movement, and autonomy ... understandable in terms of proteins

"the discussion of lower levels cannot overshadow the bigger picture"

Molecules ARE important, DO affect the bigger picture, but they in turn are influenced by and derive significance from the bigger picture they are a part of

Genes ARE important, DO affect the bigger picture, but they in turn ...

Individuals ARE important, DO affect the bigger picture, but they in turn ...

Stories ARE important, DO affect the bigger picture, but they in turn ...

 

 

Back to why don't genes (or anything else) determine everything

Responsiveness to environment

Internal changes due to environmental signals - "

learning

"

 

Gene regulation - More on responsiveness/autonomy at the single cell level

Cells as complex (improbable) assemblies of different molecules/macromolecules, with different ones contributing different characteristics

  • Life as interacting different parts
  • No one is in charge !!!!!
  • No sharp border between alive and not alive
  • Difficulty in creating life in laboratory (but .... and)

 

Cellular reproduction - mitosis

 

Lessons from cells about life:

  • Life is not any one thing or any one part but rather an ongoing and coordinated dance among lots of different parts
  • Three dimensional organization and boundaries are essential to the dance
  • Different parts play different roles - are "specialized"
  • Signals are constantly moving back and forth among the parts - coordination key
  • No simple "cause/effect" relations, elements reciprocally influence one another
  • No one is "in charge" - coordination emerges from the semi-autonomous characteristics of the parts and the signals that move among them
  • The problem of building a cell, of creating life?, may be at this point more a problem of properly assembling the components than of determining what the components are. There is more to life than what one sees in cells ...

 

Is everything "biologically based"?

Do we need more than macromolecules to make sense of life?

More than evolution and macromolecules plus some general insights from acquired from thinking about them?

Candidate additional ideas/tools ...

Multiple levels of organization

Cells as interdependent improbable assemblies of macromolecules, multicellular organisms as interdependent improbable assemblies of cells, populations/ecosystems as interdependent assemblies of organisms

Multiple and reciprocal interactions, no simple cause-effect relationships, no gene/environment controversy

Ontogeny/development - evolution within individual lifetimes

Interdependence of individuals and improbable assemblies of of which they are a part

Top down as well as bottom up influences - no individual/culture controversy

 

Cells as assemblies of interacting diverse macromolecules, multicellular organisms as assemblies of interacting diverse cells

Semi-autonomy and semi-homeostasis as properties of interacting macromolecules, as properties of interacting cells/organs

No one is in charge !!!!!

Implications for thinking about "death"?

The gene/environment controversy: there isn't one

  • Genes do not code for phenotypic characteristics; they code for proteins or for molecules that regulate production of proteins; "coding" depends on other proteins/molecules;  phenotypic characteristics reflect, among other things multiple proteins - typically a given gene influences lots of different phenotypic characteristics and a given phenotypic characteristic is influenced by lots of genes
  • Genes are themselves regulatable by, among other things, the environment
  • Genes and environment interact in the production of all phenotypic characteristics (body size, hair color, "intelligence," depression/schizophrenia)

To be continued ...

randomness