BIOLOGY 103
Fall, 2003

Notes


1, 3, 5 September

Biology -> Science of life

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

Science = life?

Science as "summary of observations", "getting it less wrong"
has predictive value?
  • accounts for lots of observations (is pragmatically "useful")
  • motivates new observation, rather than "falsifiable"? (new observation may lead to change in story/hypothesis w/o falsifying)

Name:  Nomi Kaim
Username:  nkaim@brynmawr.edu
Subject:  How is Science like Life?
Date:  2003-09-03 13:42:26
Message Id:  6312
Comments:
How is the process of science similar to life itself? Well ...

- Neither provides clear or objective "answers"
- Both strive for (but cannot attain) objectivity
- Both often take you to a place other than your predicted end-point
- Both sidetrack (and annoy) you with unforeseen things, information, events, various blockades than hinder or change your path
- Both are easier understood when reduced, divided up, compartmentalized
- Aspects of both seem more meaningful to us when we assign them labels
- Just when you think you've got it under control and figured out, it often appears the world / destiny has other plans in store
- You're never quite sure of what questions you're supposed to ask at least, not until you've already got some answers
- In retrospect, the proper questions, steps, actions seem so much more clear
- Sometimes, things you think you can "finish" / "solve" quickly end up dragging on and on, never quite finishing, perhaps not even seeming to progress at all
- Other times, you've only just begun something difficult when progress, change, solutions you never would have conceived of pop out in front of you
- There are long, dry periods in which little changes
- This lack of change can be extremely frustrating
- Nothing is ever quite certain; there are always infinite more questions
- The more you learn / find out, the more questions you develop, and the more you perceive the extent of your own ignorance and tininess in the universe
- You're constantly afraid of missing out, being in the "wrong" place at the "wrong" time
- It's always much easier to explain the "what" than the "why" (you can never quite be sure of the why)
- We strike out with ideas in mind of what we are looking for, and do not notice much of what exists that we are not looking for.
- Even if you seem to be "right," do "well" (which is exciting), you still have to dive right back into the same old game (scientific inquiry, life) you've been playing all along
- Others can see / experience the same thing and interpret / respond to it entirely differently
- The unknown is intimidating and, sometimes, threatening; we struggle to know
- Life as continuous repetitions / readjustments of the scientific method of inquiry
- The drive to be right, fear of controversy
- The desire to assign everything we encounter a subjective moral "value judgment," and the struggle against this desire


Life is ... ?

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


8, 10, 12 September

From Forum 1

Does science understand the individual emotions or likes and dislikes that characterize a person? How come one person may cry when they see a film and another won't ? Why is orange one persons favorite color and blue somebody elses? ... Elisabeth

The second definition of life, "the subject matter of the course", would be the view from a biologist's window. It is necessarily limited by the recognition that there are only so many hours in the day... so the biologist, like the psychologist and the anthropologist, asks certain types of questions about certain topics. This understanding of life is a point of view, in that it doesn't capture all the aspects of the experience of living. It is thus a summary of observations, exactly like the more general practice of science.

But the experience of being is also a summary of observations: of those we are capable of making unaided. Scientists and their quest to define life have helped to expand this experience. We were oblivious to genes, viruses and hormones (though not to their effects) before the different branches of science developed. Yet we have also been shown that our experience is not the be all and end all of existence. The concept of evolution drastically changed our views, as have studies that show consciousness is not unique to us, nor the possibility of life to planet Earth

As the base of knowledge grows, and once the foundation has been laid, the configuration of factors that are considered constant or variable will change, and science can begin to tackle issues that arise at a higher level of organization. ... Su-Lyn

I'm somewhat unconfortable with the idea that science doesn't have all the answers. I understand that knowing everything would make life (as in human life) completely pointless, but for me, thinking that *someone* knows or will some day know what is going on and what life is all about is comforting. Su-Lyn's idea of science as biology, neuroscience, psychology, sociology, and anthropology is helping me to get over this discomfort. Now, instead of thinking that there is one way of "scientific thinking" and that it doesn't work, I am able to think that there are many ways of thinking that *do* work, and it is just *what it is that works* that keeps changing ... Adina

A living organism ... ? "walks/talks"?

What IS "energy"?

Alison: What about fire?

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

Have to think about not only here/now but also there/then:
Interdependent diversity, change over time




Beyond "alive/livingness" to "life" (ie is life something more than those things that have a particular "essence" (Melissa); is there an "essence" at all?)
  • Interdependent diversity
  • Change over time
  • Both make sense in terms of evolution?
Similarities between science and life?

How "make sense" of diversity? patterns of order in improbable assemblies or random distribution?

Arrange in order of .... ?

Arrange in order of size?

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


15 September

From Forum 2

Is life more than those stated (highly improbable assembly, bounded, energy dependent, semi-homeostatic, semi-autonomous, reproduces with variation)? The question is in fact quite philosophical. Is an unborn child (a fetus) a life? At what point does it become life? ... Talia

An example of how technology changes our observations and therefore our stories...
      When did abortion and euthanasia become ethical issues? Why not stillbirth and old age? Where does contraception stand? And at the opposite end of the spectrum, what about artificial insemination? Cloning?
      Notice that it's the extremes of life and death that are being negotiated. Thanks to technology, "life" can now start earlier and end later than it would naturally ... Su-Lyn

Isn't a characteristic of a living thing that it is made up of cells? would that be something that should be added to our list of characteristics that make up a living thing? ... Melissa

belated thinking about the whole science relating to life issue... exploration is a good thing. sometimes discarding the status quo and being creative is a must! ... Shafiqah

INTERESTING ISSUE: do definitions need to change as available observations increase?

I wonder what drives us to decide which animals deserves which value ... So when we are looking at "Life," and the process of studying and grouping life, I just wonder what our biases are. And how that has effected our study of biology. The world around us? ... Patricia

I wonder if humans can ever really be trusted to observe or analyze and come to conclusions about the unfamiliar without attaching value judgments that stem from highly subjective personal values and experiences ... Maria

INTERESTING ISSUE: can one organize/categorize without using "value"? without being understood to imply value?

In addition to these mechanics with which we were presented in class, I feel there is also a certain amount we allocate to the "essence" of something which we deem alive ... Melissa

essence : the indispensable quality or element identifying a thing or determining its character; fundamental nature or inherent characteristics.

life essence as the potential capacity of fulfilling given capacities or individual traits?

does life essence exist before the actual birth of a plant or human? ... Elisabeth

Is there a certain "essense" or style that makes us accept some things as literature and reject others? What about a grocery list - what makes that different from a poem? I think this is very pertinent to our Biology discussion, because it's all about how we see things ... In English we read an article called "Rhizome vs. Trees"; it basically says that instead of trying to force literature into a tree-like category, with roots, branches and leaves (a begining and end for every part) we need to think of it more as a rhizome formation, a horizontal root with sprouts and growths spurting in all directions, with no one beginning point and no ending (hypothetically) everything is connected, and part of the whole ... Laura

Going on the theory of evolution, at some point when life was first starting on Earth, there were just a few little microbes or whatnot. Because the first little creepycrawly that we want to say was living made more like itself, and for a while they must have all been of the same species, until enough generations had gone by that there were seperate species. But I think that even if there was only one species at that point, I would still gasp and consider there to be "life" on Earth ... Julia

I'm not really one to compartmentalize things; I hated putting plant life into different categories in our lab just as I hated the arbitrary divisions of classes in high school ... Lindsay

If there is no life essence, then how are we to classify life at all? If no essence is needed to qualify something as living, then what was the point of the list made in class a few days ago that was meant to be used as a general guideline for identifying something as living? Saying that life essence is nonexistent is extremely problematic; such a statement suggests that any qualifications made to distinguish between living and non-living things are arbitrary ... Alison

INTERESTING ISSUES: Must there be "essences" in order for there to be "categories"? Can we have "categories" without them meaning SOMETHING? Must categories be fixed and eternal?

Galaxies have highly improbable assemblies. Our brains are similarly organized in highly complex ways, processing information in a way that seeks order. I wonder if the way in which I'm struck by the Milky Way indicates the way in which order recognizes order... is that the most fundamental aesthetic appeal? Are we responding to the beauty of the galaxy because we're responding to the same order that exists within us? ... Su-Lyn

"life" as we know it is a term completely dependent upon individual perception. It's all semantics. For example, what if---and I know this sounds a little silly, but humor me here---rocks had some sort of sentience that we weren't able to identify with our limited technology? Suppose those little chunks of malachite sitting in the glass cases in Park were studying *us*? It's less a matter of how *advanced* our technology is than in what *area.* Despite our attempts to look at "life" objectively, we're still biased in that we can only view the term from our perspective, i.e. a Sol-stranded collection of energy-dependent, semi-autonomous, bounded, etc. etc. organisms. There could be a whole other level of "life" that remains invisible to us because of our natural biases ... Brittany

in bio 103, we are asked to define life and the living for ourselves. its hard not to draw from earlier conceptions of evolutionary processes or religious beliefs. can a biological view, an anthropological view, and a religious view all mesh to form one theory? ... Megan

there just has to be something that screams "life" to us. Maybe this is something that humans, despite their fervent search to compartmentalize and catagorize, cannot bottle up and sell as truth. Perhaps we will never be able to understand life ... Nancy INTERESTING ISSUE: Can we transcend our "biases"? our brains? How? Do we want to?

Is it "evil" (wrong, inappropriate, unfair, "unscientific", poor teaching practice) to invest time in trying to define something one way, and then turn around and suggest that maybe that something needs to be defined in a different way?

Lessons from working up in scale from human ...

And from working down in scale ...

1. Larger things are improbable assemblies of smaller things
2. Improbable assemblies exist at a most scales (though see Alvarez)
3. Different features apparent at different scales; at larger scales, smaller wholes become invisible parts
4. Both very small and very large scales are important for understanding life.
5. There exist lower and upper(?) bounds for living organisms ... as we currently know them
6. Existing observations are greater than in past, but clearly incomplete
7. Can distinguish smaller, single-celled from larger, multicellular organisms
(Why no big unicellular organisms? - need for communication/integration?) 8. Size is not, in general, a good way to classify ... no natural divisions (gaps, spaces, clumps)

Have sense of spatial scale, existence/potential of life, size (not so good for categorizing), multicell versus single cell (better, why?) Are there other ways of making sense of diversity? Is categorization/classification totally arbitrary, simply a "social construction", or does it reflect to some extent characteristics of what is under investigation? are there "natural" categories? and, if so, what does that imply about life?).

Starting with intuitions (as we did with "life", as one always should, in science and elsewhere): what things LOOK like and do
Are there "discontinuities" (is there "clumpiness"?) in life's diversity?

Plants versus animals versus fungi(?)

Autotrophs versus heterotrophs (interdependence)
With correlates (e.g. cell wall versus no cell wall)
Fungi have cell walls, but different molecular constituents (chitin versus cellulose), are heterotrophs but with external digestion
Can use molecules, like any other feature, to evaluate similarities/differences
Get discontinuities/"clumpiness" (diversity itself an "improbable assembly", not either all possibilities of improbable assemblies nor random assortment of them but lots of variants one some kinds of improbable assemblies, none of others)
(Why no autotrophs without cell walls?)

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

Anna: "alienate yourself from the experience ... let the familiar become strange and uncanny"

Abby: "... presents itself to me to be nearly impossible ... [unless] we are trying to categorize on a level that deals more with internal structures and makeup"

Five (or six, or more) Kingdoms:


22 September

From Forum 3

Before the discussion I thought it was obviously easy to tell whether something is living or not. However, the discussion led me to question the meaning of life ... Ramatu

This problem of determining what is alive/ what is not alive is really bugging me--and maybe it's just the English Nerd in me coming out but isn't "alive" just a word someone came up with to describe what most people generally think of when they hear it? ... Lindsay

A CURIOUSLY CHALLENGING QUESTION?

I have actually been thinking of the question of life. teachers always tell you, think about this over the weekend, and students never do. however, this topic actually has me thinking ... in bio 103, we are asked to define life and the living for ourselves. its hard not to draw from earlier conceptions of evolutionary processes or religious beliefs. can a biological view, an anthropological view, and a religious view all mesh to form one theory?Megan

Ironically, now that I have come to understand that there is no definite conclusions when it comes to science - this non-conclusiveness brings a possible answer to the age old question of where faith and religion meets science. While evolution is a theory, it is just that. As is religion. While each may have evidentiary support, neither are right or wrong. They each hold a place in our lives - whether or not we feel convinced by their defenses ... Enor

Imagine your doing Brecht theory. The next time you go outside Park Science to look at trees and shrubs, which seems like a pretty familiar thing, alienate yourself from the experience. Take on a new kind of spectatorship. Let the familiar become strange and uncannily, an un-at-home-like experience. Your critical attachment will amazingly, provoke you to action ... Anna

Even though it's hard to let go of biases, we can still try to look past them a little by using imagination ... Laura

SCIENCE AS PSYCHOANALYSIS?

does life essence exist before the actual birth of a plant or human? ... Elisabeth

Madeline L'Engle included a farandola in a human cell as a sentient character with a soul in A Wind in the Door. I think the existance of any such soul or essence is impossible to prove scientifically - you can either believe it or not, which I guess is the definition of religion ... Julia

And because our observations are always changing, our beliefs and our definitions are always changing. Therefore it is hard for us to pinpoint the "correct" definition of science and of life because there is none. I thought that this meant that we would never learn anything about what we were trying to define. However, as Professor Grobstein pointed out, the object is not to use what observations we have to find a "right" definition, but to use them to formulate a theory that is "less wrong" ... Flicka

Is science really a human construction? If all babies are scientists from birth, why not all organisms? Is the process of scientific inquiry innate in all life? ... does the pursuit of science have to be conscious? Because that's the major difference between human inquiry and the reactions of a cell ... Nomi

SCIENCE AS LIFE?

Discovered some order in diversity: is "clumpy" Why "clumpiness"? Things like small number of other things, some kinds of things absent?

Clumpiness in plants

Look more carefully at animals (metazoans)

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

Why no ventral nervous system with endoskeleton?

Humans a small part of life, as life (as we know it) a small part of universe (but humans also steadily, perhaps even explosively, experiencing more and more of universe - is that distinctive of humans?

How make sense of diversity, clumpiness?
Great chain of being - ordering of organisms along some scale?
Evolution ... ? Go on to time, and its scales.

Evolution as way of making sense of diversity? Time as an essential descriptor of life?


29 September

From Forum 4

RELIGION?

I believe there is a heaven and a hell and one is *conscious* is both. I believe there is a realm that the human eye nor science can detect and I believe there is life there ... Michelle

so if I truely believe that my soul is what gives me life and if my soul still exists just in a different world not seen by humans, .....then do I ever really die? ... La Toiya

Religion permits us the liberty to believe in the souls and essences and other things so sacred and mysterious they can not be uttered, AND THAT IS SUFFICIENT! As budding academics we are searching for sanity, whether we peer through the microscopes or pour over scriptures ... J'London

I am in agreeance with at least some of the "stories" about the universe that exist today, but i also believe in God, and what interests me about science and even philosophy is the brain busting effort people put into disproving the existance of God ... Shafiqah

If there are no "truths" in science, no sets of definitive answers, then how will there ever be a final and complete definition of what is living? ... Elizabeth B.

Are we just born with the hidden obsession to be right? In addition, although we may learn that it's ok to be wrong in this class it's actually unapplicable to real-life on-the-job scenarios. In the corporate world, the pay you to be right - the first time. What I like about what we learn and discuss in this classroom is that no one is teling us what is right and wrong, what is truth and what isn't; regardless of what the rest of the Earth's inhabitants may say... Michelle

CONSCIOUSNESS? CULTURE?

So, in conclusion, I believe that "consciousness" is the ability to communicate with other organisms and the ability to feel something outside of a natural instinct to survive ... Flicka

I've always thought of consciousness as the realization or knowledge that one exists, is ALIVE. And maybe, also, an understanding of where one stands in space, an ability to perceive other things outside of oneself. (How would I define this? I don't know!) ... Nomi

Which leads back, of course, to the idea that it is possible for other organisms to be alive but unconscious (as we humans sometimes are) ... Su-Lyn

I also think that consciousness is heavily tied to language, as is history, and then the connection between language and culture... AAAAH, this is getting to complicated ... Manuela

BIOLOGY?

Our talk today about the origin of the universe and the movement of the galaxies has left me feeling uncomfortable and almost sad. I think that movement and change are great, but I did not like the data saying that we are all moving away from each other. I think it is super that all points of the universe no matter how small can be at the center. But the space between all the galaxies and stars is so big, it makes me anxious. So much distance and emptiness ... Elisabeth

an ordered entity is defined by the process by which it was assembled, and not the thing in and of itself ... Would it be beneficial ... to develop ... a definition by participation in a set of characteristic processes? ... This approach might be helpful in resolving some of our artificially-constructed polarities. Imagine applying this to the 'definition' of gender! ... Su-Lyn

we are coming closer and closer to the conclusion that being 'alive' isn't about an essence that you put in or take out, but rather the sum of smaller bits and pieces that are not by themselves alive, but when put together in a sufficiently complex manner result in something that is. I think people often don't like this conclusion because it seems to take away some of the mystery and awe that has surronded the concept of 'life' and life 'essence' and made it this almost sacred thing. Yet, if you think about all the interactions and complex activities that the ''smaller parts'' of us must undergo in order to result in making us 'alive', it's really just as impressive and just as fascinating as any idea of a 'life essence' ... Maria

the story behind the organism stays the same until these two organisms are "born". For example, I have the same story as my sister, up through the parts about my parents, but when it gets to the part where each of us are born, the stories diverge. It's kind of like those books for grade school kids where you chose what happens next, and that determines the next thing that happens, and so forth. If you chose one option very early on in the book, things will end up a lot different to if you chose another option. There's nowhere that the two stories once again combine. You're on a very different course ... Adina

Scale and Evolution: Time Scales

Human natural time scale - seconds to years, perhaps three generations (100 years)

Longer time scales important for biological systems (change where not aware of it):

Humans young, as yet restricted experience, small part of life - BUT also have in us record of much of history of universe
LOTS of time for evolution

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)

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

Well then ... humans at least?

Nope - diversification and extinction here too
(see more recent article)
Though there are here, as elsewhere, some reasonably slow, continuous changes

Different time scales reveal different patterns, just as different space scales do
Clumpiness understandable in terms of evolution, but (and) raises new questions

Evolution includes both slow, continuous change and rapid change Evolution involves "chance", and hence likely to proceed somewhat differently elsewhere or if repeated Evolution does include some directionality, but is not toward "perfection" or "better" but rather toward having explored more (increased "complexity"?) Images of evolution - "getting it less wrong"?

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

Why do things change? At small scales, in space and in time, change is fundamental.

Have at small scales, beginnings of an explanation of one fundamental characteristic of life: change, exploration? Have also, at large time scales, some explanation of "adaptiveness", and of "clumpiness"/diversity


Have also sense of life as increasing complexity, improbable assemblies of improbable assemblies .... Need to underestand origins of improbable assemblies, of diversity, as well as boundedness, energy dependence, reproduction with variance, homeostasis, autonomy

Will work our way from small scales to large, seeing how much we can account for at each level of organization (improbable assembly)


6 October

From Forum 5

RELIGION? (see also Forum 4

I just wanted to give a high five forum style to the girl in class on wed who had the guts to say that she beleived in creation in the midst of an intense evolution discussion in biology ... After all - doesn't it sometimes feel a bit too perfect an explanation? ... Enor

I liked Enor's comment that we are depending too heavily on evolution as a theory. One of my favorite things the teacher ever said to my high school bio class was "The theory of evolution is just that - a theory. Statistically, most theories the scientific community has come up with in the last few thousand years have been wrong. So statistically, someday we'll probably realize that this theory is wrong and replace it with another one. But that one will quite probably be wrong too." ... Julia

I'll admit, the theory of creation is put into a fun story, where as the theory of evolution would make me rather poke my eyes out than read. The stories of the Bible, the earliest ones that is, were set down more than 3500 years ago and the new testament being written around 100 AD. The theory of evolution? Darwin put it down in 1859. Which of these has the lasting power? ... Megan

I think there is some purpose to recognizing that the story offered by the bible has been more widely accepted for a longer period of time. I wonder, however, how much this has to do with who has control of institutions of education - while this was left up to the church for many years, and all "learned" people had a religious background, that is not necessarily so today. As scientists continue to take over the system, will people change their views? I don't think so, partially because one of things that I believe causes people to gravitate towards creationism is the openess of the story. It allows you to believe in God and the story it presents but still believe in other stories ... Katherine

Is our search for a creator/creation driven by the same feeling that causes orphans to try to track down one of their unknown parents? And if we found an answer to the question, would our lives change even a little bit because we knew the details of a five-million-year-old story? ... Lindsay

I think that knowing or coming close to finding out where we come from would change everything ... Knowledge always creates a reaction, and that engenders, necessarily, change ... Manuela

from an earlier conversation on evolution with K-12 teachers: I don't "believe" in stories ... ... PG

from an email to Serendip commenting on a student paper: "I would rather place my trust in God rather than a few introverted scientists who come up with theories they can never prove ... "

EVOLUTION: PAST, PRESENT, FUTURE?

Professor Grobstein said that evolution does not produce organisms that are better-adapted to their environment than those that came before them, and cited as an example that humans are not better adapted to earth's environment than bacteria ... but we are still better-adapted to life on earth than all of the species that have gone extinct during the period of our existance, aren't we? ... Natalya

A re-phrase to make sure I understand your point: Being around the longest doesn't necessarily mean that you're the best adapted, only that you have been adaptable in the past. Adaptations are not fool-proof as they are highly context-dependent (if the environment changes, adaptations can become useless at best, deadly at worst) ... Su-Lyn

PS: In spite of the emphasis placed on the idea of "evolution as process", and the ease with which this is applied to the past leading up to the present, I still find it difficult to think of the here & now as part of a process ... Su-Lyn

Still, I couldn't help thinking about how provocative the topic is, even for those of us who believe in evolution. It's so scary to think of the limited span of time for which we humans as a species will exist, even though that's potentially thousands (millions?) more years in the future. Or just tomorrow! It really makes me feel my own mortality and think about the impact that I make on the world ... Kathryn

Populations of single-celled organisms were once considered "life", but now, grouped within single multicellular organisms, the definition has been wrested from them. So too might multicellular organisms some day find themselves defined as mere 'parts' to a truly "living" superorganism. There goes the definition of life again, and imagine what this will do to the classification scheme as we know it ... Su-Lyn

An ant may think of itself as a vital and unique being and not recognize the whole structured community in which it plays only a tiny part. If cells could think, maybe they, too, would be incredulous to discover they were only useful in conjuction with so many billions of others! ... Nomi

MOTION AND CHANGE

I guess it just troubles me that with all the chaos in the world, these is even turbulence where there should be tranquility. And yet, it also interests me to know that the world would not exist without the turmoil, and constant movement everywhere ... Talia

Motion is something which in my realm of understanding predicated life. We are many times able to identify the dead among us by the fact that these organism cease to "move". Can we successfully add "movingness" or "the ability to move" to our list of something that a living organism possesses? ... J'London

I don't think that motion is at all a property of life. But I think that all things in life, and all their particles, are unstable. And so everything moves, no matter how tightly bound. There can never be anything without space to exist around it. Existance requires space. Which may not seem that fascinating to anyone else, but has always really set me back ... Patty

I'm wondering......You know how Professor Grobstein is always testing us in ways that boggle our minds? Well, I wonder if at the end of the semester he's gonna say that the whole class was just a big test ... The things that make you go HMMMMM.... La Toiya

Usefulness of story of evolution Need to account for patterns in space and time at multiple scales
Improbable assemblies, adaptiveness, diversity, change, as well as boundedness, energy dependence, reproduction with variance, homeostasis, autonomy
Can get that from improbable assemblies of physical elements (atoms)?

Remarkable generalization - dissociate ANYTHING, get out elements = atoms

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

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


What are atoms? How get more from less?

Atoms -themelves combinations of still smaller and fewer constituents

Periodic table - another related remarkable generalization

"Assembly rules" as a concept


20 October

From Forum 6
CREATION AND EVOLUTION

I beleive that creationism is the way in which man came into being, but I can also accept evolution as a theory based on scientific observations we have now. That way, I don't have to say that one is "true", but i can accept both as being possible theories. Some people may not be able to look at it this way based on how religious or non-religious they are, but it all depends on the person. As long as you're not searching for the "truth", you can believe whatever you want to believe ... Flicka

[this course] ... forces me to think of life and existence in a new way. Although, I have to admit it is at times mind boggling and scary, I have learned that scientists and people in general are not always right in their discoveries and observation; this I can now accept ... Ramatu

What I'm inclined to do then, personally, is not to attempt to reinterpret what the Bible says to align perfectly with the observations from this (vastly different) day & age, but rather to use what still 'fits' and to incorporate those aspects into a new and on-going story. ... I found Prof. Grobstein's quote particularly helpful in this respect: "I don't 'believe' in stories, wherever they come from. I listen to them, learn from them, and make use of them when I find them useful. To 'believe' in a story is, for me, to end the ongoing process of discovery, of 'getting it less wrong', and that's not something I'm inclined to do. I'd rather go on changing/evolving/emerging." ... Just for the record, I do believe in God, but my next question relates to what I feel are more grounded matters: Is religion allowed to change? Does it evolve?... Su-Lyn

EVOLUTION AND HUMANITY

I find it comes more naturally to me to think of individualism as the pinnacle of human achievement, as a trait that will not evolve, and it is only when I force the thought beyond this limited frame of reference that I can begin thinking about humans as parts of a larger entity, how evolution in that respect is still possible (even probable?) ... Su-Lyn

It reflects on society as a whole, past and present, that maybe we're just a little...well, full of ourselves! ... Sarah

I was wondering how humans will look in the future ... Manuela

It's funny to think about what traits we're breeding into the species by our choices, too, not just how the environment is acting on us ... Julia

when my ancestor people came over from Ireland back in the day they all had like 10 kids apiece but as each generation was able to get a better education and to have more "successful" lives in terms of employment and quality of life, the number of offspring they had dropped ... Maria

No other life form requires such a narrow temperature range in which to live, depends so heavily, for its health, upon both fire and ice. Only human beings could stick themselves out in the wild -- with some "basic" human inventions, no less -- and call it "Survivor." Other organisms call it "Life." ... By protecting ourselves and making life easier and more convenient, we are, essentially, grinding down the tougher fibers of our beings ... Nomi

We are only better adapted to the world as we have changed it, not to its original form ... Megan

yes, I think studying evolution does affect our present-day decisions. For instance, knowing the natural process of extinction certainly influenced our attitude toward currently-disappearing species. Understanding how old, and how durable, our planet is has diminished our fears that we "all-powerful humans" ... On the other hand, I understand the need to deal with present issues and conflicts ... The question then becomes: how far back can you dig and still have your findings be relevant to the here and now? Perhaps the answer is: infinitely ... Nomi

LIFE AND ITS PARTS

i loved it, isotopes and protons isn't it incredible that there is so much diversity in the world that it took about 50,000 years for the human race to pull it together in a single chart, and there may be more out there too! imagine about a hundred elements making up the whole world. whooooa ... Shafiqah

I just find it interesting that everything is made up of the same things. I guess I always realized this but if differences just come about because of structural organization is it possible that if we could figure out how to control the organziation we can create life? ... I know we discussed life essence and how it really does not exist but it just seems weird to me that if you stack enought objects you'll get a dog and that there is nothing that makes it a dog ... Justine

Could we really turn Professor Grobstein into an elephant or a rock if we knew how to manipulate these particles? ... Brittany

Things we need to make sense of

Things we have to work with

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

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

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

Electron, electron affinities key to many biological processes

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

combinations of simple parts (atoms, elements) yield in assemblies (molecules) new properties

keep eyes on electrons, oxygen, charge
on polar vs. non polar
on water
remember three-dimensionality, flux


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

"Inorganic" versus "organic" molecules?

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

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

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


20 October

From Forum 7

Could we really turn Professor Grobstein into an elephant or a rock if we knew how to manipulate these particles? ... Brittany

This whole thing abut "Life Essence" is troubling to me. How can we say there is no essence to life? How is that scientifically proven? It seems to me that a days, with science being so unpredicable, it is hard to tell what is truth and what is not. ... Ramatu

Someone commented that they could conceive of a dog being formed without barking - a dead dog, essentially. Although this notion sounds physically possible, I still can't help but feel that there is a reason that dogs exist in nature rather than as human products and that structuring them chemically would only yeild a human product that did not work in terms of the same components as a dog in nature ... Enor

Why is it that we could imagine a dead dog being formed and not a barking dog? In my view, evolution helped to combine many characteristics that caused dogs to be able to bark. It was some time during this process that this thing that we call "life essence" came into existance, but maybe if someone had put all these atoms together in their exact positions with all of those protein chains and things in exactly the right places, dogs would still exist and they would still bark, even if they had not evolved at all ... Adina

it seems to me that perhaps we just arn't able to concieve of all the tiny complex interaction that go on at an atomic and then cellular level that we don't think of as being the cause of a tail wagging, but which in fact are. That if we don't think of a dog's tail wagging as simply that but rather as the visible culmination of bunches and bunches of smaller things doing thier jobs then it seems less absurd to think that it is, perhaps, possible ... Maria

I say we should not dismiss the notion of "life essence," but rather entertain the possibility that it arises from the combining of pieces, that the whole is always more than the sum of its parts ... Nomi You can take the molecules in a dog, dump them on the ground, and they won't make a dog. You have to infuse them with a complex organization---give them *order*. And for your experiment to work, your order must adhere to the laws of evolution, the "rules" of the periodic table, the laws of genetics, and the exterior environment. Otherwise you just have a bunch of random carbon, oxygen, and water molecules lying in a heap on the ground. Life is an essence; we just call that essence "order." ... Brittany

What makes a person alive is all these parts together, which creates something MORE than just the sum of the parts. Because each of the parts affects every other part, and these interactions are limitless ... Sarah

The problem with making a Frankenstein-dog out of single molecules seems to be that we don't have any way to keep stuff in living condition long enough to put it all together ... Julia

INTERESTING ISSUE: is the creation of life not a conceptual problem at all but rather simply a practical one? Does that make it less difficult or more so?

Su-Lyn, that's a really fascinating idea---that consciousness requires more than one individual to exist ... Brittany

Brittany, "mosaic" - magic word:
Imagine pieces A through E (the series that you suggested in your post) in a theoretical 'space' that includes all possible types of organization. The circular form should help us get away from the idea of hierarchy/ linearity/ predetermination. By putting the origin (A) in the center, we can imagine the evolution of forms of life more as a process of exploration rather than purpose ... The major implication of this diagram, if it is actually applicable for our purposes, is that the series we are familiar with is not inevitable. It is not the only possible outcome of all the interactions around us and even before us ... Su-Lyn


Proteins, from amino acids

Nucleic acids , from nucleotides

Carbohydrates, sugars (monosaccharides to polysaccharides)

From hydrocarbons to lipids

Molecules, macromolecules constantly in flux, serve variety of roles, Intermediary metabolism


3 November

From Forum 8

In order to be aware of what you're thinking or what you're doing, you need someone else to *make* you aware of it. The only way humanity has a knowledge of the unconscious and the conscious is because interactions with other people have made their thoughts about the subject conscious ... Flicka

Wonder if one needs others to be conscious? or to be aware of unconscious? ... PG

I believe that we all want quality children for the sake of our own pride and joy, and being able to alter his or her DNA structure is simply a preventitive measure for the childs own good ... Some of us would be BURBERRY and others a moomoo from walmart. And i guess we could throw out the notion of "all men being created equal" because that would not be the case... and so we would be able to assert that some people deserve certain rights while others are not entitled to them because they are less perfect human beings ... rrrrrrrr... I hate it when i contradict myself... J'London

J'London, you raise some really great points, and I think the contradictions point to some crucial issues that we're facing in deciding what to do with the power that science has given us ... Su-Lyn

On the other hand, if we could correct everyone's "shortcomings", even those termed diseases, such as depression, or alcoholism, what would become of art? ...Natalya

is anyone just simply afraid of a lack of diversity? I feel that from the many people I have met in my life, it has been the things about themselves that they considered to be their worst traits, that have built the most defining strengths about them. People truely are made stronger by having their own individual weaknesses. ... I think the most similar we become, the more we all lose out. Our greatest oppositions serve as the best reasons for introspective thinking and strengthening of our own beliefs and traits. The world would lose so much more than art if we genetically improved ourselves ... Patricia

All life is diverse and experiences diverse physical and psychical conditions. All of life responds to varying external and internal environments. And if those environments did not vary? If we got rid of our differences, and squashed this diversity of experience, what would we have left? Would it even be accurrate to call us alive? ... Another strange thing I thought of is that by manipulating the genome, the science of medicine will be going in the OPPOSITE direction from where it has always gone before: toward sameness, rather than toward diversity ... Nomi

I was wondering if there are genes for race? I'm sure there are genes that are associated with certain traits of people of diffrent races. Would people change there race if they could? ... Patty

It seems silly to me that with all the technology we have, we can genetically engineer bone for bone graphs, but we have no way of knowing if HIV has infected a bone from a cadaver before using it in a living human ... Anna

the virus load would be too small for even our "advanced" technology to locate the virus in its earlier stages. It would be like searching for a needle in a haystack. I also don't think that the technology for engineering the bone, and for locating the virus are really comparable either ... Stefanie

It's so strange that the mysterious processes of thought and emotion could be quantified in time and space - in chemical reactions. I wonder if you could chemically construct a thought or belief the same way you could hypothetically take Professor Grobstein's atoms and turn him into a dog ... Natalya

This is in response to J'London's comments about thoughts being chemically constructed ... I think anyone who uses drugs (legal or illegal), lusts after chocolate, binges, has PMS, or a variety of other things can say that it is quitely likely that our thoughts are chemically constructed because they can be chemically altered. I think that we have to remember that our minds do not exist independently of our bodies ... Katy

I don't agree with the mechanical way in which consciousness is being prescribed, with the idea that thoughts can be engineered. While there is probably a set of reactions that take place in our body whenever we process a thought and its associated emotions, etc., I doubt that inducing those same reactions will produce that same thought. It's the same objection to the assertion that genes correspond with traits in a simplistic one-to-one relationship ... Su-Lyn

Any study of psychology will show that environment and experience have a huge impact on how a person will feel in/react to a given situation. There is also much variation in personality, but there is no saying that the nature part of the nature vs nurture debate is not biological. I'm just saying that the biological processes that cause thoughts occur in the body ... Adina

My gripe is not about your point, but about the notion that floats around in the forum (and that you countered) that biology is deterministic ... Su-Lyn

Also, like a hypothesis, a thesis isn't really good unless there's a possibility that it's not true. A blanket statement is meaningless, the more room there is for opposition and controversy, the better the thesis, really ... Natalya

It would be hard enough to organize the I don't know HOW many molecules to make a dog. But, then add in the instability of all of those molecules and we have quite a mess! It just makes me realize more and more how complicated living organisms are. The instability of the molecules within us somehow creates a stable, functioning, complex organism ... Abby

Large macromolecules, improbable assemblies ("energy rich"), useable as "food" ("combustible" ... proteins, carbohydrates, lipids) - How get created? Why don't fall apart? .... cellulose? starch? hydrogen peroxide?

Macromolecules: Beginning to account for change, diversity, reproduction with variance, improbable assemblies. Assembly rules define possible things that can be, not what IS, nor what leads to change from one thing to another ... For that, need to take about energy, energy dependence

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

Re Su-Lyn (above): There ARE things added in going from genes to traits (hormones, experiences, randomness?, etc), so genes demonstrably do not correspond to traits in a "one to one relationship". I'm less certain about the proposed parallel to thinking about "reactions" and "thoughts", at least if by "reactions" one means the entire complex of events going on in the nervous system which potentially constitutes a "thought". Is there any reason in this case to believe there is anything "added in"? Unless there is, one has to reason to doubt there is a "one to one relationship" in this situation.

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

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

Second Law of Thermodynamics - in any isolated system (the universe) change is always from less probable to more probable states (entropy increases) Diffusion as the archetype of life - improbability and flux (increasing disorder) driving increasing improbability (increasing order)

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

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

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


10 November

From Forum 9

I have always thought athletes like Michael Jordan and Joe Montana and Marion Jones were just not.....human? They seem to posess superhero powers, and really, be freaks of nature, not in a bad way, but just in a mutated sense. I feel cheated to think that their abilities are not real and authentic, but aided by some drug ... it's wild to think that there might be a predisposition to super height, or super quickness, or super jumping ability ... Anna

I think life just IS imperfect (and this more than anything I HATE to accept), and I think that imperfection is due to, as well as the source of, life's variation and diversity ... Nomi

Basically, I feel like it's easy to say that somebody is more "predisposed" to something than another person might be--but what, exactly, is meant when it is said that somebody has a biological predisposition? ... Alison

If no gene can cause things such as osteoporosis, why are certain groups of people more subceptible to different things? For example, Asians and African Americans are more likely to have osteoporosis. If its not hereditary, or coming from a gene, then why is it more common in some than in others? I guess it goes back to the age old controversy over whether or n ot there is biological race. Also, why are people with parents who had cancer more likely to have cancer, if its not in their genes? ... Megan

Dawkins proposes that the gene, the basis of heredity, is a fundamental entity of selectivity. Only the "strong" genes, which serve their own self-interest, replicate themselves from generation to generation ... why do such maladies exist? Is it to strengthen mankind, leaving , excuse the cliche, only the strong to survive? ... Melissa

regarding the "cuplet" of things moving from a highly improbable organization and things that are moving to a highly improbable organization. It's such an interesting concept, and it sounds so abstract when you first hear it but when you really look at it you find that it's true, that it makes sense ... Maria S-W

Cars, for example, are pretty highly organized machines, but they create disorder in the form of ozone-eating polution. (Is this an appropriate analogy?) ... As Americans improve their quality of life more people around the globe (and even in America) are plunging into poverty, political chaos, and suffering. Can anything be done? Or would any solution only pose greater problems? ... Natalya

*why* is Life's counterpart "move towards disorder" the sun? I know life depends on the sun, but why choose *that* particular entity as Life's partner in the thermodynamic tango? It implies a relationship between the two that may not actually exist. I'd like to see biologists/physicists *prove* that the reason Life can develop order is that the sun is devolving into disorder... Brittany

Seeing the sun as a large, improbable entity which is giving itself away piece by piece to allow the earth to become more complex and improbable is actually a lot more comforting to me than the thought of our sun as a gigantic yellow ball of energry. I find it hard to imagine "energy" as some abstract thing that magically makes life. But to think of the actual light and heat being physically used in plants and other molecules (and letting off APT) is much easier to imagine ... I feel like it's a metaphore for anything - it's more improbable to have lots of knowledge, because of all the many circumstances necessary to create that knowledge. It's the same as culture and art, and music - these are all extremely improbable assemblies and without maintaining them they could all potentially move towards a more probable state ...Laura

Anabolic and catabolic processes coupled, break things down to build things up, always create "waste"

Can do same thing in the absence of light (Alexis Hilts), which also raises an interesting issue with regard to circadian rhythms (Susanna Jones).

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

*/*: in the presence of light AND organized spatial arrays of other molecules

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

*/* in the presence of organized spatial arrays of other 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
  • Organized spatial arrays of molecules are essential
  • Enzymes and their shape changes are critical
    • for facilitating spontaneous reactions
    • for linking spontaneous and non-spontaneous reactions
Why doesn't sugar fall from sky? Why doesn't cellulose fall apart?

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

Enzymes and reaction rate

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

Catabolic/Anabolic coupling

Metabolism - life as linked/controlled creation, destruction of molecules

Why doesn't sugar fall from the sky?

The "cell theory" - All living organisms are either cells or assemblies of cells
What are cells? Why needed fundamental level of organization for life?

Enzymes can only enhance the rate of chemical reactions that spontaneously occur more slowly.

Is there any way that life can slow down things that spontaneously occur more rapidly?

Why minimum/maxium size?

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


17 November

From Forum 10

When people first spread out over the world we got isolated into little clumps, so it makes sense that people from the same clumps would've shared traits. If you have kids with someone who has the same facial structure, skin color, etc (i.e. race) it makes sense that you might also share the same predisposition for sickle cell anemia because your ancestors came from the same clump, and your kids will have the same traits ... Julia

My point is, there *is* a specific gene (or at the very least, specific part of a gene) that causes disorders like sickle-cell. The fact that the gene wasn't created to cause sickle-cell is irrelevant; if it's shaped a certain way, it inevitably leads to the disorder ... Brittany

it is NOT a specific gene that codes for a disorder, and the series of genes that does code for it can be taken in many combinations, all of which result in different proteins and different physiological manfestations. There is not, ever, just one "button," and that is why a simple trace-back from protein up to gene doesn't always work ... The variations initiated by biological environments -- recombination, mutation, forms of "imperfectification," if you will -- are then supported and perpetuated by the ecological environments to which they are best suited. ...So natural selection's movement toward homogeneity is bound to fail because of the changing nature of living being's environments ... life is NOT the only thing that is diverse, and, in fact, in order to BE and remain diverse, living things depend upon the great diversity of their environments ... Nomi

These disorders, and others, *are* "boxes with buttons." Sure, not *all* disorders function this way. But sickle-cell, Down syndrome, and several others (especially sex-linked disorders!) definitely do. I guess my point is that, while in some cases you're right and you *can't* specifically link a gene to a disorder, in other cases, the relationship is crystal-clear, cause-and-effect, a single bullet from a single gun ... I also have to disagree with your discussion of the biological trend towards sameness. A single environment will never reduce its occupants to a single species. Life just can't exist that way---organisms feed off one another, utilize one another, form symbiotic relationships with one another. And say earth *did* have only one environment; that environment would still have "niches" that different organisms could fill. Look at the Sahara. You can't get a more homogenous environment than that, right? And yet the Sahara supports a wide variety of organisms, all exploiting different aspects of the Sahara's harsh environment. Diversity is as inherent to environment as it is to life. Even in an environment that *appears* to be the same throughout, organisms adapt to different aspects of that environment in their quest for survival.

because each environment imposes a variety of pressures on each organism (in our Sahara example, high day time temperatures, freezing night time temperatures, locomotion over soft sand, etc.), adaptations are always a result of compromise. Because of this element of compromise, there exist multiple forms and multiple 'lifestyles' that work equally well. That is what accounts for the diversity that Brittany points out ... Su-Lyn

we, as a society, seem to be moving towards a scientific explanations for things we don't tolerate well. The obvious example I am thinking of is homosexuality. There is constant talk of finding the "gay gene", as if finding a gene for something that is hard for society to digest will make people feel better. I think it would be interesting to locate such a gene, but the motives seem to be to use genetics to explain the behavior. Another example is obesity. The media overly valorizes thinness, and everyone knows the benefits of a healthy diet and exercise, yet the percentage of americans who can be classified as obese is constantly on the rise? My fear is that if we find a gene for an unhealthy condidtion such as obesity, people will feel as though they shoudlnt work to prevent it since it is genetically predispositioned ... Nancy

We need, of course, to accept homosexuality and obesity, as well as any other characteristics, and to stop judging them. Judging does nothing. It's never a matter of "fault!" I think people are correct in looking for "the gene" behind these characteristics if they do so in an attempt to erase the concept of fault ... Nomi

I also think that if we do find a major contributing factor to obesity, it will be easier to treat severe cases of it medically ... Adina

At the same time we sort of have to face up to the fact that our genes do determine, to a large extent, who we are, and we are limited by them ... Natalya

This concept of genetic "predisposition" has been plaguing my thoughts recently ... it leads me to wonder if these "explanations" presented to society are simply nothing more than an "myth" for our own understanding. This might be somewhat odd, but following the reasoning that for generations culture have used "creation myths" and other myths of sorts to explain the "unexplainable", it leads me to wonder this might just be a way to pacificy society with a short-term, easily accessible reasoning ... The explanation for predispositions is often sorted into one of two schools-- environment or genetic ... Here the example of identical twins seperated at birth becomes an interesting issue. While environment is often viewed as a formative force in the development of a child's personality and traits, many examples of identical twins, raised in opposite environments, show that despite differences in childhood and lifestyle, certain characteristics and preferences are identical ... It leaves me wondering if identity is really environmental or genetic ... Melissa

Genes influence, they do not determine

Genes are not, in themselves, either "bad" or "good"; their significance depends entirely on the context of other genes and the "environment"

Genes reflect past experience

Genes are an important source of diversity

Good question for next part of course:

WHY are genes NOT determining things?

It is a little frightening to think that who you are and what you are depends on things that you cannot control... like your genes or your environment, and that between one or the other, there lies nothing that leaves room for something our society values so highly: individual expression. Are we not responsible for our own actions because we are responding to biological predispositions or because we cannot help but reflect our upbringing? ... Manuela

my answer to the question about why cells have lower-limits for size. I think that, just as with upper limits, it is a practical, spatial reason. In this case, however, I think it has to do not with surface area but with molecular complexity. The smallest atom must still take up a certain amount of space. In order to perform the complex biological tasks for which they are responsible, the molecules within cells must contain a certain minimum number of atoms. Along the same lines, the proteins composed of these molecules must be a certain minimum size to hold up to their complex, varied jobs. Same goes for the lipids and carbohydrates, not to mention the highly complex cell organelles themselves ... Nomi

Cells assemblies of macromolecules, arranged in such a way as to couple naturally occuring breakdown with assembly ... can not only speed up break down but also slow it down - boundedness

Size limitations at upper end:

Size limitations at lower end ... see Nomi

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

Movement ... understandable in terms of proteins


24 November

From Forum 11

Genes influence, they do not determine

Genes are not, in themselves, either "bad" or "good"; their significance depends entirely on the context of other genes and the "environment"

Genes reflect past experience

Genes are an important source of diversity

Good question for next part of course:

WHY are genes NOT determining things?
I see science to be very subjective. For example, with all of the talk lately about finding genes for things such as being gay and being obese. Though it is possible that the study that goes into it is unbiased, just the questions of what we research and what we don't is a matter of bias. Why do people care whether or not there is a gay gene? Because it will help people to understand what the do not understand - psychologically and socially ... Talia

If there is a gene related to obesity, it most likely codes for fat retention, not for a dangerously high weight. We don't live in the environment we evolved in - we live in one full of refined sugars, desk jobs, cars, and high-fat snack foods. A gene that may have been adventageous several hundred years ago could result in life-threatening conditons today. I guess this sort of plays into Talia's point about objectivity. A gene that codes for fat retention would be a good thing in the environment humans used to live in, and would be considered a bad thing today. I guess this sort of plays into Talia's point about objectivity ... Katie

objectivity = non context-dependence?

Genes don't determine who you are as a person; they determine how you look physically ... Flicka

In response to Flicka's comment that genes influence only our physical appearance and not the way we act, I profoundly disagree. Behavioral patterns like depression, mental illness, and even eating patterns are extremely heritable on a genetic basis ... Natalya

I don't think it's fair to say that scientists and researchers today simply "blame" everything on genetics. With new technology, they have been able to gather that genetics DO in fact play a very large role in determining many of a person's traits (both internal and external). Therefore, it is legitimate to form hypotheses that revolve around genetics as the "cause" of something ... Christina

We are clearly dealing with Nature AND Nurture. People may be predisposed to become or suffer with any number of things. People are also often in control of the onset, extent, severity, and overall effect that these "things" have on their life. It's so stressful to have two rationales for one occurrence (i.e. obesity, homosexuality, etc.) that are both equally important to the discussion. We have SOME say over our lives, but not complete ... Accepting a stance that satisfies both the nature and nurture arguments and does not force them to oppose each other is a quicker way to find solutions that suit our lives ... Patty

Something that occurred to me in considering the Nature vs. Nuture and Nature AND Nurture arguments is that it is all about the extent of our personal control over our lives ... Our genes may control our destiny to some extent, but to what extent can we master our gene and/or genetic defects, and control our own destiny ... ? ... Natalya

I agree that this whole Nature and Nurture, Free Will / Responsibility and Predetermination discussion is really complicated! I have always wondered, for example, what role the SELF plays in the Nature-Nurture debate. Are we a part of Nature because we are, at bottom, genetically constructed beings? Or do we constitute a piece of the Nurture, of our environment, because our feelings and actions inevitably influence our later feelings and actions? ... Nomi

A very important trait in determining a person's level of stress is locus of control/chance. This is basically whether the person thinks they can control the situation or not. People who have a belief that they can influence their internal states and behavior and influence their environment and bring about desired outcomes are much less susceptible to stress than those who simply give up and think that they have no control over the situation ... Sarah

I still maintain that responibility and biology are relateable as well, even if it does involve the brain ... Enor

If we regard genes simply as coding for proteins, doesnt that kind of flush the whole idea of nature vs. nuture down the tube? ... Megan

I find that there are 2 conflicting messages in dealing with biology and what this class discusses. First biology is based on diversity or so I think we stated in class. Second we also say that there are certain fundamental things associated with certain species types of people whatever. So does that mean that diversity only derives from a fluke a that creature's/ object's genetic make up? Does diversity only come about because of some mistake or can it be influenced by how that certain creature grows up? ... Justine


1 December

From Forum 12
(temporarily in course forum)

Su-Lyn

Prof. Grobstein, in response to your thoughts on the New York Times article:

"The distinctive role that science has played in our culture... is to be the embodiment of permanent skepticism, of a persistant doubt about the validity of any given set of understandings reached by whatever means (including those of science itself). It is the insistence on doubting existing understandings, not the wish to eliminate humans ills nor to find 'answers'..." -- Prof. Grobstein

I have represented the views that you express in class - about the noble skepticism of science - as those of the scientific community at large. Now I sense my own naivety in having done so.

I feel there is a strong dichotomy between the doers and the thinkers, and it the thinking minority that allows science to remain, in large part, unaccountable for what it has brought about.

Finally, if science is truly about this greatly exulted skepticism, how can science make claims (as Reagan's science advisor, George Keyworth II, does in the article) to knowing that no God exists? Spontaneous generation was once dismissed as religious rubbish, and yet science eventually returned to it to explain the origins of life.

Katie

it was sort of neat to see what other people's concept of "science" is:

http://objective.jesussave.us/creationsciencefair.html

Nomi

If everything exists somewhere in some state, it follows that there should be no absolute truths but also no absolute untruths. No absolute lies! When Prof. Grobstein talks about our "getting it less wrong," I think he needs to realize that, just as one is never absolutely right in science or in life, nor is one ever absolutely wrong. *

*I'm speaking in the universal sense, of course, which is fun but not very practical. Practically -- as it applies to use human beings -- there ARE rights and wrongs, things that can exist and things that cannot. But all of these things are relative in the greater scheme.

Grobstein ...

I don't "believe" in stories, wherever they come from. I listen to them learn from them, and make use of them when I find them useful. To "believe" in a story is, for me, to end the ongoing process of discovery, of "getting it less wrong", and that's not something I'm inclined to do. I'd rather go on changing/emerging/evolving.

If science is actually going to become a common property of humanity, scientists themselves are going to need to learn to transcend their own tribal inclinations, to not only entertain the possibility that the observations and stories of people outside the community are relevant but to begin actively valuing them, to genuinely open the "scientific community" to all comers ... Science ... Everybody Getting It Less Wrong Together

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

Responsiveness/autonomy depend on energy - Where/how does that get in game?

Looking back and forward - link(s) between life and the second law

Or ... on "why doesn't sugar fall from the sky?"
Bonus lecture: Color
OR "ANOTHER use of photopigments"
OR "Why a tree falling in the forest DOESN'T make a sound unless ..."
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

General principles, beyond energy per se

Cellular reproduction - mitosis


8 December

From Forum 13

The question of science and the existence of God continually plagues me ... the question of religion (NOT FAITH) is something I believe science should play a vital role in "unpacking" so to speak ... Science has a DUTY to try to uncover the mystery of life, where we came from, how the world was created ... It is science's duty to see that the separation of Church and State is CLEARLY DRAWN, ... and to show that the space of the world is a mystical place-- it allows for the possibility of anything ... The Zen Master said "There is no answer; seek it lovingly." ... Anna

I don't think Nomi was supporting the "existence" of God in a religious sense, or at least, in a sense you need to contradict so vehemently. She was simply saying that if the universe is infinite, and if all of those sci-fi writers are right and parallel universes *do* exist, and those universes *do* represent the breadth of reality, then somewhere, on some alternate universe, in some remote nook or cranny of the dimensional plane, a God (or Gods) do(es) exist ... Brittany

LIFE is about getting it less bad, less wrong ... Nomi

I think it is part of the wonderous nature of science to not disprove or prove the *existence* of God, but more so, to add some sort of *factual* grounding from which people can spring from in understanding and interpreting stories within themselves ... Anna

No one needs proof or support. That is not what this is ever about. We all have much to offer. Anyone who feels that they have more to offer than another person needs to be more honest with themselves ... Patricia

Perhaps it is best to be agnostic with regards to both science and religion ... Melissa

As tiny citizens of a much greater universe, each catering and basing opinions through our own experiences, a tolerance should be reached through this reality ... Enor

PG ... Interesting conversation. Some perhaps relevant contributions:

Lessons from cells about life:

Multicellular organisms as improbable assemblies of cells having three-dimensional structure, boundaries, internal boundaries/spaces, energy dependence, autonomous/homostatic properties, reproduction with variance

Key points:
  • Lots of different sets of organized cells, lots of different cells
  • Sets and cells all themselves alive, as well as being parts of living thing
  • Need "differentiation" (specialization), organization (coordination)
  • Where get lots of different cells? in organized form?

Making sense of diversity - morphological tissues as intermediate level of organization between cells and organs/organ systems

How get elaborate, three-dimensional assemblies of diverse elements? Development as guide, further insight into diversity, background for "cloning" issues ... see also Cloning: Past, Present, and ..."

The cloning issue: The diversity issue - development as a magnifier of variation

Where does zygote come from?

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

Meiosis - an "adaptive" biological diversity generator

Importance of diversity generation - "sex" independent of reproduction - practical considerations: antibiotic resistance Playful exploration as an adaptation/characteristic of life and ... science

Bottom line (for now) ...

To be continued


| Biology 103 | Course Forum Area | Biology | Serendip Home |

Send us your comments at Serendip

© by Serendip 1994- - Last Modified: Wednesday, 04-Feb-2004 11:14:02 EST