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Issues with the microcosm (Merged)
Posted: 28 July 2007 11:20 PM   [ Ignore ]
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I don’t know about you, but I can’t stand being taught models and fancy words without seeing with my own eyes the thing that the word or model is signifying.  Right now I’m taking a hormones and behavior course at school, and the massive quantity of scientific terms that have been thrown at me in the past two days, I find quite stultifying to the potential of human intelligence.  In my opinion, one should never try to impart words or models without using those words to point to the actual perceivable topography that the words or models are supposed to refer to.  Use words to point to the sensed phenomena first, and only then should you expect the student to be interested in memorizing words. Immediately get the student using his right brain by visualizing what must be named, and then the student will be able to appreciate the name or model for that phenomena.  Right brain first (visual spatial), then left brain(language).  Don’t go the other way around and indulge in the superficial sensations that can be derived by fancy language.  In my experience learning from people, whether from a friend who tries to teach me the biology or geology he thinks he has learned, or during the times I’ve taken a course in school myself, whether it was in electric circuits or endocrinology, I always find myself bombarded with large quantities of fancy words and dinky 2-dimensional models before my so called teacher makes an effort to correspond his words and models with perceivable phenomena.  It almost makes the teacher or knower seem like he doesn’t really understand anything, but has merely made a lucrative career for himself, or attained some psychological security and self esteem, by merely memorizing a bunch of words which he has attached to some really flimsy, dinky models.  I think that’s the problem with academics.  They are often ignorant people who think they know, which is much worse than simply being aware of your ignorance.

I find that mainstream secular-scientific people (a great deal of university professors) love to jack off with big scientific words and simplistic models.  It doesn’t impress me at all.  Science, when it is used to merely explain (rather than carefully ‘point’) only dulls peoples minds and makes them idiots who think they understand something when they only know empty words and simplistic models.  They are hardly different from theologians.  Superstring theorists exemplify the crassness that I’m referring to here. 
Here is a great example of an intellectually lopsided imbecile:

The Amino Acid photo collection

Don’t get me wrong, the photos of amino acids on the site I just linked are amazing, I’m very happy I found them.  But the piece of writing above that links to the photos was obviously written by someone whose brain is very lopsided and silly.

Consider the first paragraph:

Amino acids are very small biomolecules with an average molecular weight of about 135 daltons. These organic acids exist naturally in a zwitterion state where the carboxylic acid moiety is ionized and the basic amino group is protonated. The entire class of amino acids has a common backbone of an organic carboxylic acid group and an amino group attached to a saturated carbon atom. The simplest member of this group is glycine, where the saturated carbon atom is unsubstituted, rendering it optically inactive.

What makes the above so silly, is that it is aimed at the layman, as the website is trying to sell posters, screensavers, calenders, etc. 

Idiots. 

It wouldn’t be quite so bad if the piece of writing was aimed at a colleague who has worked with his fellow chemist quite a bit and has gone over some actual photographs of amino acids and agreed upon what names to give certain distinctions perceived in the topography.

I’m guessing that they think they are educating people with their eagerness to display fancy scientific words, but it’s really quite ridiculous.

Also, consider this model of an amino acid or this one, and now compare those simplistic models to the actual phenomena, sensed through a microscope, and here’s another one.

If you’re someone who values truth, the models really aren’t that helpful, are they? 

Pretty awesome pics of the amino acids though.

[ Edited: 29 July 2007 12:06 AM by CoryDuchesne ]
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Posted: 29 July 2007 12:19 AM   [ Ignore ]   [ # 1 ]
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I have to say I disagree with your implication that there is a right way to teach concepts. I happen to be a very verbal/auditory learner, and the spoken word is the way I best grapple with difficult concepts. Images are helpful, but secondary. My wife, on the other hand, needs something visual on the page in front of her. I think there are different styles and ways of conceptualizing, and while some may be better suited to certain material than others, in general I don’t think there is a single best way to teach of learn.

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Posted: 29 July 2007 12:54 AM   [ Ignore ]   [ # 2 ]
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mckenzievmd - 29 July 2007 12:19 AM

I have to say I disagree with your implication that there is a right way to teach concepts. I happen to be a very verbal/auditory learner, and the spoken word is the way I best grapple with difficult concepts.

Interestingly, those difficult concepts have been produced by scientists carefully observing empirically, and using their brain visual/spatially.  The concept that the scientist produces, functions as a sign pointing to a visual reality.  The concept and words themselves, which the scientists produces by being right brained, are secondary.  So, you may prefer people to be very verbal and auditory when they teach you, but if you aren’t able to take the words given to you and use them like maps to navigate over visual terrain, then I dare say that your knowing is at a level hardly different from a theologian.

Images are helpful, but secondary.

The phenomena perceivable by the senses is most important, and then there is the model of that phenomena, which can be very helpful.  The least important thing is the mere word.  Although it too is a very helpful tool.

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Posted: 29 July 2007 09:50 AM   [ Ignore ]   [ # 3 ]
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I still dn’t agree. Some concepts are much clearer when expressed mathematically than visually. You can say “mere” words as if language were somehow incidental to the process of complex thought, but I think it is integral to this process in many cases, and certainly to the communication about concepts necessary to do science. I think this is a case of taking one’s own bias and assuming it is fundamental to reality instead of simple how one tends to think about things. As for left brain/right brain, that dichotomy is significantly less meaningful than the popular imagination has come to believe, and is itself a bit misleading.

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Posted: 29 July 2007 11:41 AM   [ Ignore ]   [ # 4 ]
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I was wondering if one of you could tell me about whether or not attempts have been made at photographing atoms, and can I access those photos?  Have people attempted it?  Or, given our present technology, is it even logically possible?
I just wrote an email to Michael W. Davidson, a research scientist who has been involved with various aspects of microscopy for the past 25 years.  I asked him if he had any desire (or if I could inspire him to desire) to take an actual photo of an amino acid, and superimpose on top of that photo, arrows that point to certain distinctions in the picture, naming those distinctions.
For instance, consider this highly simplistic model of an amino acid:
AminoAcidLG.gif
And then compare that simplistic model to what an amino acid actually looks like (photograph apparently taken by Michael Davidson himself):

arginineheader.jpg

What I said to Davidson, was my impression that it is difficult to make good use, or even trust the standard models we have of things like amino acids, as there seems to be an awful lot of distinctions to be named in that actual photo of an amino acid and that, in fact, the actual photo the amino acid, and the standard model, look nothing alike.  With that being said, I asked Davidson if he thought it was reasonable for anyone to try using our present model of an amino acid as a map to navigate an actual photo of an amino acid.  Shouldn’t we be able to do that?  Isn’t that what models are for?  I think it would be a very noble goal for someone to bring to the masses a more coherent way of making sense of the actual photographs we have of the microcosm.  Our present simplistic models just don’t seem adequate for making sense of the actual photos.  On top of that, I feel that education should introduce children to the actual photos of the microscopic first, and then we should use models, but these models should be introduced very carefully and should leave students in a position where they can use the models as maps to navigate and understand the actual topography seen in the photographs of things like amino acids, proteins, neurons, etc.
I’m particularly interested in being able to take an actual photo of an amino acid, and identify the two major parts that are said to comprise the amino acid (e.g., NH2 and COOH) 

My question is, are scientists personally able to perceive such distinctions when they look at an amino acid via photo?  Or have they empirically detected these differentiations in topography by some other means?  (I know Rutherford detected the atom by noting incidental scintillations, rather than perceiving the atom directly - so god knows the sort of techniques physicists and chemists use these days)

[ Edited: 29 July 2007 12:11 PM by CoryDuchesne ]
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Posted: 29 July 2007 01:42 PM   [ Ignore ]   [ # 5 ]
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You can’t photograph atoms.  Photons of visible light have too long a wavelength and electrons (whilst having a short enough wavelength in theory, burn through any specimens that are thin enough to obtain an atomic reolution image (and can only give a black and white image in anycase).  You can see the topography if you look at STM micrographs or AFM micrographs.  However, these are produced by draging an atomically sharp needle across a tiny area of a specimen and a 3D image is produced from the up and down movements of the catilever on which the needle is mounted.  A computer takes the measurements of these movements and makes the image from them.

The micrograph you have shown of “what an amino acid looks like” is what crystals (not a molecule) looks like, and then only between crossed polarisers as seen through an optical microscope.  There are billions of molecules in each of these isotropic crystals and there are a lot of crystals there hence the different colours depending on the orientation of symettry space groups relative to the plane of the sample.

This proably seems unnecessarily complicated to a lot of people also, but science is quite a complicated subject and the forefront of it is difficult to explain in simple terms.

[ Edited: 29 July 2007 05:11 PM by narwhol ]
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Posted: 29 July 2007 02:04 PM   [ Ignore ]   [ # 6 ]
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narwhol - 29 July 2007 01:42 PM

You can’t photograph atoms.  Photons of visible light have too long a wavelength and electrons (whilst having a short enough wavelength in theory, burn through any specimens that are thin enough to obtain an atomic reolution image (and can only give a black and white image in anycase).  You can see the topography if you look at STM micrographs or AFM micrographs.  However, these are produced by draging an atomically sharp needle across a tiny area of a specimen and a 3D image is produced from the up and down movements of the catilever on which the needle is mounted.  A computer takes the measurements of these movements and makes the image from them.

An example: http://www-03.ibm.com/ibm/history/exhibits/vintage/vintage_4506VV1003.html

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Posted: 29 July 2007 08:05 PM   [ Ignore ]   [ # 7 ]
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Cory I think I agree with you about reading long dissertations in text books and accepting them by authority rather than doing the work yourself to understand the concepts.  However, we have only limited lifetimes so we have to “stand on the shoulders of giants”.  As miserable as learning is, once we’ve bucked through it, we can understand far more and far more easily.  Although I’m not a biochemist, I worked as an organic and polymer chemist for over 50 years so your quotation of the first paragraph of “the amino acid photo collection” made perfect sense to me, and I was able, as necessary to envision the structure as a zwitterion and recognize the reason only glycine isn’t optically active. 

Occam

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Posted: 29 July 2007 10:05 PM   [ Ignore ]   [ # 8 ]
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mckenzievmd - 29 July 2007 09:50 AM

I still dn’t agree. Some concepts are much clearer when expressed mathematically than visually.

All you seem to be saying here is that sometimes you find that it’s better to visualize (whether it’s the trajectory of a space shuttle launching, or the statistics of human behavior over many years) phenomena using mathematical concepts, rather than the concepts of nouns animated by verbs and analogies.  That’s fine, but my point here is that the most important part of the human brain is the ability to use concepts, whether mathematical or linguistic, to visualize action in space/time. 

Here is an example:

Consider this list of words.  Each word will be followed by a question, and all you have to do is answer yes or no.

1)  POTATO “Is the word in capital letters?”

2)  horse “Does the word rhyme with course?”

3)  TABLE “Does the word fit the sentence, “the man peeled the ______?”


Each question above requires effort, but each differs in an important way.  The first question requires the most superficial kind of processing, given that you only have to notice how the word looks.  In my view, this is totally left brained stuff, with no right brain involved.

Question 2 requires a bit deeper processing, because you must process the information phonologically, meaning you must sound out the word to yourself and then judge whether it matches the sound of another word.

Question 3 requires the deepest processing, because you must pay attention to the meaning of words, corresponding the words to phenomena in action in space/time.  Recollecting what you know about tables, peeling a table may seem absurd at first, but then on the other hand, you may imagine peeling the paint off a table.  The question, relative to the others, a deeper one, as it involves the right brain the most.

You can say “mere” words as if language were somehow incidental to the process of complex thought

Complex thought doesn’t impress me unless those thoughts are about the phenomena I have experienced.  If I am introduced a massive amount of complicated words or mathematics, and none of it is organized to reflect phenomena that I’ve experienced, then to me, it’s garbage.  It’s a waste of my time. 

As for left brain/right brain, that dichotomy is significantly less meaningful than the popular imagination has come to believe, and is itself a bit misleading.

The subject of right brain, left brain stuff is worthy of a new thread.  I’ll start one soon.

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Posted: 29 July 2007 10:38 PM   [ Ignore ]   [ # 9 ]
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Occam - 29 July 2007 08:05 PM

Cory I think I agree with you about reading long dissertations in text books and accepting them by authority rather than doing the work yourself to understand the concepts.  However, we have only limited lifetimes so we have to “stand on the shoulders of giants”.

There is a big difference between learning from a teacher who finds out what you already know and points out relationships between what you already know and new phenomena that you probably wouldn’t have discovered on your own, and having a so called teacher who neglects what you already know and proceeds to impose some isolated fragments of abstraction that have no relationship to what you already know and thus have no meaning to you personally.

As miserable as learning is, once we’ve bucked through it, we can understand far more and far more easily.

But I don’t think learning has to be as miserable as we have made it.  Humans have made it much harder than it has to be.

Although I’m not a biochemist, I worked as an organic and polymer chemist for over 50 years so your quotation of the first paragraph of “the amino acid photo collection” made perfect sense to me, and I was able, as necessary to envision the structure as a zwitterion and recognize the reason only glycine isn’t optically active.

That’s right, ‘envision’.  If concepts, words and models do not correspond to envisionable phenomena that you have experienced, then they should not be introduced.  Experience should come first, then knowledge.  Or at least receive knowledge, and then test it out, experience it. 

The worst thing you can do, is receive knowledge, and then receive more knowledge, and more and more and more.  This has been my experience of university.  People just filling their head with stuff, destroying their natural inclination to learn, and replacing it with pretense or just plain obliviousness.

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Posted: 29 July 2007 11:30 PM   [ Ignore ]   [ # 10 ]
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I still dn’t agree. Some concepts are much clearer when expressed mathematically than visually.

All you seem to be saying here is that sometimes you find that it’s better to visualize (whether it’s the trajectory of a space shuttle launching, or the statistics of human behavior over many years) phenomena using mathematical concepts, rather than the concepts of nouns animated by verbs and analogies.

No, what I’m saying is that the best way to undertand some concepts is NOT by visualizing them, but via math or language or movement, or whatever. The point is that I don’t accept the primacy you give visualization for understanding or teaching.

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Posted: 30 July 2007 12:29 AM   [ Ignore ]   [ # 11 ]
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mckenzievmd - 29 July 2007 11:30 PM

I still don’t agree.  Some concepts are much clearer when expressed mathematically than visually.

All you seem to be saying here is that sometimes you find that it’s better to visualize (whether it’s the trajectory of a space shuttle launching, or the statistics of human behavior over many years) phenomena using mathematical concepts, rather than the concepts of nouns animated by verbs and analogies.

No, what I’m saying is that the best way to undertand some concepts is NOT by visualizing them, but via math or language or movement, or whatever.

I find what you are saying here very contradictory.  For instance, math is a concept.  Language is a concept.  Movement?  What are you referring to when you say movement?  Sounds pretty visual. 

The point is that I don’t accept the primacy you give visualization for understanding or teaching.

Well that’s not a very good point, in my view.  It seems as if you have missed the whole point of why we have concepts to begin with, which is to rationally account for perceived phenomena.

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Posted: 30 July 2007 02:02 PM   [ Ignore ]   [ # 12 ]
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However, what you have done here:

Complex thought doesn’t impress me unless those thoughts are about the phenomena I have experienced.  If I am introduced a massive amount of complicated words or mathematics, and none of it is organized to reflect phenomena that I’ve experienced, then to me, it’s garbage.  It’s a waste of my time.

Is to dismiss a lot of complex thought that is useful to a large section of society, and to you personally. As I understand it, you are studying amino acids and to pass your exams, you will have to learn and be able to recall some very complex thoughts about them.  For instance, you will probably have to explain the optical activity as mentioned by another poster on this thread in terms of the chirality (handedness, if you will of the tetrahedral carbon’s (these have four bonds coming off of them to other atoms such as the bonded atoms form the corners of a four sided solid shape called a tetrahedron if you join them up).  You will hopefully never experience the effects of the handedness of these molecules, but it can have devastating consequences for those who do.  Diseases like Human CJD and BSE in cattle are caused by just one carbon atom in a very large molecule (with loads of chiral carbon atoms in it) having the wrong handedness.  And it makes big holes in the victims brain until eventually they die.  This is a very complex thought.  I mean, imagine: one amino acid group having the wrong handedness in one protein molecule can cause a disease that kills people; no bacterium involved, no virus, no fungus just one a protein that has slightly the wrong kind of optical activity!  And no, you will probably never get to shake hands with one of these molecules.  But they are important.  And it is important for you to learn about them in order to pass your course.  And it is very coneptual; but that’s just the way science is, I’m afraid.

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Posted: 02 August 2007 11:43 PM   [ Ignore ]   [ # 13 ]
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I tend to agree with CoryDuchesne about this.  I think that people sometimes think they understand something because they can spout some jargon, but really do not have any firm or profound grasp of what the jargon ought to be representing.  But that does not necessarily mean that the jargon is meaningless - the meaning may escape you, but that might mean that you should think a little more, learn a little more, experience a little more, so that you really do understand the reality underlying the words and ideas and models.  But that is rarely done, and people tend to take what is presented as something concretely real even when they do not really understand it.

Switch from biochemistry to postmodern criticism and you can see quite easily how jargon can be made into something like an axiomatic system, so that people can seem to make sense with it without actually knowing what it is that they’re saying, because it is all, in a sense, a kind of algebra where it doesn’t matter what x is when you say that x + x = 2x.  The famous case of Alan Sokal’s joke paper, which was peer reviewed and published despite being nonsense, is one way that you can see how jargon need not make sense in order to appear to make sense, and need only appear to make sense to be assumed to make sense, because the people using that jargon often do not have a firm grasp of the concepts behind the terms they are using.

Words in scientific disciplines usually have a very specific meaning (and it is up to the reader to discover them), but that does not mean that they are treated as such by people who are used to more malleable words.  A word like “information” means something so different in physics than in biology, and in both the meaning is nothing like the everyday meaning, that communicating with that word from the sciences to the everyday is very difficult.

Here’s a good passage from Alan Watts:

The root of the difficulty is that we have developed the power of thinking so rapidly and one-sidedly that we have forgotten the proper relation between thoughts and events, words and things.  Conscious thinking has gone ahead and created its own world, and, when this is found to conflict with the real world, we have the sense of a profound discord between “I”, the conscious thinker, and nature.  This one-sided development of man is not peculiar to intellectuals and “brainy” people, who are only extreme examples of a tendency which has affected our entire civilization.

What we have forgotten is that thoughts and words are conventions, and that it is fatal to take conventions too seriously.  A convention is a social convenience, as, for example, money.  Money gets rid of the inconveniences of barter.  But it is absurd to take money too seriously, to confuse it with real wealth, because it will do you no good to eat it or wear it for clothing.  ... Thus a community may possess all the gold in the world, but if it does not farm its crops it will starve.

In somewhat the same way, thoughts, ideas, and words are “coins” for real things.  They are not those things, and though they represent them, there are many ways in which they do not correspond at all.

...

In the beginning, the power of words must have seemed magical, and, indeed, the miracles which verbal thinking has wrought have justified the impression.  What a marvel it must have been to get rid of the nuisances of sign-language and summon a friend simply by making a short noise—his name!  It is no wonder that names have been considered uncanny manifestations of supernatural power, and that men have identified their names with their souls or used them to invoke spiritual forces.  Indeed, the power of words has gone to man’s head in more than one way.  To define has come to mean almost the same thing as to understand…

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Posted: 03 August 2007 12:02 AM   [ Ignore ]   [ # 14 ]
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Well, I think the topic has drifted far from what Cory originally said or my response. He started the thread by saying that he didn’t find verbal descriptions or explanations meaningful in learning somehting but only visualization. I merely pointed out that there are different routes to understanding, and though some concepts lend themselves to visual representations best (e.g. geometrical concepts), others are best expressed in mathematical temrs (e.g. the relationship between mass and velocity, which makes no intuitive sense but is obvious from the relations expressed in certain equations), and others are best expressed in words. Likewise, some people think better in words, others in images, and this is largely a matter of learning style.  I hardly think it is sensible to adopt the idea that language is all but irrelevant to human thought or communication, as some seem to be suggesting here. There is plenty of room for miscommunication and confusion in language, but it is by far the most effective and efficient arrangement yet for communication, including communication of scientific ideas. Reification of abstract concepts and miscontruction of symbols for thing things they represent are certainly real problems, but the basic point is that language is still the best and primary method for communicating about ideas, facts, concepts, what have you. It is not likley to be replaced by visual modalities, pure mathematics, interpretive dance, or anything else any time soon. Direct sensory experience of a phenomenon is NOT required for an understanding of it, or all science would have to be rediscovered by every generation. Language allows understanding by proxy to some extant, and the accretive process of scientific progress would be impossible if this weren’t the case.

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Posted: 03 August 2007 04:33 AM   [ Ignore ]   [ # 15 ]
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I think he questioned the meaning of the verbal descriptions, rather than their utility.

I doubt very much that there is a “best” method for communicating concepts.  In some cases, there is absolutely no way that any language can explain a concept: what is “red”?  Tell me what “red” is without showing me.  Tell me what “soft” is without my toughing anything.  What is “salty”?  What is “pain”?

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