Thursday, April 20, 2006

Noci-Notes - 'Skeptics and True Believers' - #3

(First of this Series.)
` It should be clear by now that I revel in my Skeptichood, though I have trouble understanding the True Believer mindset. But don’t think that with all this talk about experimentation and faith that Skeptics are supposed to be more sane and rational than True Believers!

` Raymo begins Chapter Two: Decoding the Mystery of Life:
The difference between Skeptics and True Believers is not that Skeptics believe what is sensible and obvious, while True Believers accept what is fanciful and far-fetched. Often, it is the other way around. Scientific concepts can be extraordinarily bizarre, as strange to our notion of what is a proper landscape as are the mountainous frozen oceans and sulfur fountains of Jupiter’s moons.
` Looking upon an electron microscope photo of DNA in the journal Science, Raymo noted that it appears to be a tangled mess. The author of the article described it as looking like an ‘elaborate fishnet’. “Yet somehow the fishnet manages to reproduce itself.” (Check out Science 247 (feb 23 1990): 913 to see yourself!)
` Yes, because that sounds utterly, barking mad.
` It’s not that hard to understand. As I had written in the previous post, DNA clones itself by splitting down the middle like a spiral-shaped zipper: Because each half is complementary and can only be assembled in one possible way, each half serves as a template for an entire strand which then builds itself out of the surrounding material.
` Simple, yes? Or is it?

If you stretched out the DNA in a single human cell, it would reach from fingertip to fingertip of your outstretched arms. In the trillions of cells in the human body, there is enough DNA, if stretched out, to reach the Sun and back a dozen times!
` Please, take a moment to cast your eyes to the ceiling contemplate just how far-fetched this fact sounds.
The DNA in a cell is tangled into forty-six chromosomes. Replication starts at hundreds or thousands of sites, at precisely defined moments in the cell’s reproductive cycle. Billions of chemical units in the DNA must be copied exactly, exactly once, no more, no less. Any foul-up could be damaging or fatal to the organism.
` And yet, how often do we humans mutate and/or become cancer-ridden? Most of us do not suffer that greatly from mutations, if at all! (This is not to say that some mutations can't be fun!)
The genetic material is active not only during cell division; it is writhing and twisting all the time, zipping and unzipping here and there along the strands, generating fernlike traceries as it spins off RNA and builds proteins – a whirling-dervish dance of life. Look again at that electron microphotograph of the tangled strand of DNA. It is not just lying there, static, like a cast-aside string of pearls. It is a pulsing, undulating farrago of threads, feathers, knobs and whiskers, a microscopic lace maker frenetically making a lace called life.
` That this should happen, minute by minute, hour by hour, in every cell of our bodies, without resulting in a hopeless tangle is – to put it bluntly – unbelievable….
` It is, isn't it? And yet, as far as everything that can possibly be determined, all of that stuff is true. The same goes for the glaciations of the ice ages. Even so, Raymo has a neighbor from his seasonal home in Ireland (on a hillside track they call ‘The Fairies’ Road’) who fears the wee folk said to live under the hill. She said to him; “It is easier to believe in fairies under the hill than ice on top.” Raymo adds; ‘And of course she’s right.’
` Once again, I am stumped at just why he reiterates that it is easier to believe in anthropomorphic beings such as fairies, humanoid gods and gray aliens than it is to accept what is evident in the basic workings of nature. I do not understand how some people could come to expect to see their own species projected into things that do not directly relate to humans!!
` My guess is that it has to do with our instinct to project our own selves into the minds of others, in order to understand, and predict the actions of, other people. (Sadly, mine was not able to develop until I was about nineteen years old, so this is normally a struggle for myself.) We also tend to do the same sort of thing with dogs, pigs, and monkeys, because it is obvious that they have motives and can think and learn. It is therefore not a large step for Homo sapiens to think up the idea that weather and other aspects of nature could also have personalities – that storms and rivers really are temperamental!
` Over the millennia, people have seen conscious beings like themselves everywhere, in everything, probably because we humans only have our own human minds to relate to (and understand) the world. How many people have there been throughout time to say otherwise?
` I suppose that sounds logical enough, and yet I do not know why anyone would want to do such a thing. What is this need for spirits and aliens and personified astronomical bodies that people want to fulfill? Even when I believed in strange and pseudoscientific things, I am not aware of ever having such a need.

` …Tangents aside, the next thing that Raymo writes is; ‘So why do I believe in the unerring fandango dance of the DNA, which I cannot fully imagine no matter how hard I try, and not fairies, which any child can imagine?’
` Well! Perhaps my ability to imagine has something to do with my own inability to understand True Believers! Growing up, the only way that I could remember what something looked like was if I translated the experiences into sentences and then remembered the words I used. I could not remember images directly – only descriptions of them. Visualization had eluded me until my late teens, and I am still struggling with the concept.
` Maybe the reason a lot of people want to believe in supernatural creatures and such is because many of them are so anthropomorphic and therefore more easy to both relate to and picture. And yet, I had a very hard time both picturing things and figuring out what was going on in other people’s heads.
` …Curiously, I have always been capable of drawing pictures of things I wasn’t looking at, and then drawing the same thing again, even when the only thing I could think of were a verbal description and the blank paper in front of me: If I wanted to see something imaginary, from my own mind, I would first have to draw the thing before I could see it!
` Therefore, it never mattered to me whether or not I could see something, or really even relate to or understand it. As long as I had a reason to think it was true.

` Second tangents aside, I think I’m starting to understand why I’m a Skeptic: It’s difficult to believe something you can’t imagine without some form of evidence that surely exists outside of people’s minds.
The physicist-philosopher Henry Margeneau made a point to invent a diagrammatic scheme that shows a distinction between the two.
` It involves a vertical line, and in the left field, circles are placed which represent things that are ‘out there’; the world ‘as it is’ through our senses. To the right, one places circles which represent ‘mental constructs’; the world ‘as we know it’ in our head.
` My ‘lucky’ glass coffee mug, for example (the only one that was not smashed in the ‘Battle of the Shiny, Metal Objects’); how would the mere act of seeing it appear on this map? To the immediate right of the perception plane-line, one would see circles that stand for concepts such as ‘green’, ‘reflective’, ‘transparent’, and ‘ridges’. These would be connected via lines to another circle somewhere a little further to the right, which stands for everything I conceptualize about the coffee mug, including its name.
` And, if we assume that I am overwhelmed by toxic fumes at the moment and am not really sure if it exists or not, picking it up and drumming it with a fingernail would yield the sensations of ‘cool’, ‘smooth’, ‘heavy’, and ‘clinking sound’. (Hopefully.) Those sensations would contribute yet more links to my mental construct of ‘glass coffee mug’, thereby reassuring me that it was really there.
` Not everything is so well-reinforced in this way, however: Fairies can be inferred if one notices that a gardening tool cannot be found, or if one hears a mysterious singing noise, and links these occurrences to the construct ‘fairies’. ‘What is missing from out map are lines connecting the construct “fairy” directly to immediate sensations. No one has actually seen a fairy.’
` On the contrary, I have seen a fairy, and he was so adorable I was almost sad that any attempts of seducing him on my part would be for naught. But, I’m getting off the subject. Raymo! What else do you have to say?

”DNA replication” is a construct far removed from the perception plane. There is almost nothing about the construct that relates to ordinary experience, which is why the construct is so difficult to imagine. The perceptions upon which the construct is based are highly technical – for example, X-ray diffraction photographs and demanding chemical assays.
` The construct “double-helix DNA” is connected with reality by way of many other technical constructs, circles connected to circles in a vast web, by as many paths as we can devise and test, until at last we reach the relevant immediate perceptions – blackened grains in a photographic emulsion, for example, or a reading on a microbalance in the chemical lab – perceptions that mean nothing except in the context of the entire web of constructs.
` The scientist looks for taut and unambiguous connections between constructs and perceptions that can be subjected to quantitative and reproducible experimental tests.
` And yet the construct ‘fairy’ is closer to the plane of perception than DNA. Why does the Skeptic doubt the fairy so?
The noise might just as well be explained by the construct “wind,” with links that are firmer, more reproducible, and more widely acknowledged. The missing tool might be attributed to absentmindedness or human theft, both of which are universally acknowledge parts of our common experience. In other words, “fairy” is connected to immediate sensation by few and arbitrary lines. Snip away the construct “fairy” and the rest of the map stands firm, no sensations go unexplained.
` And just so we’re clear on the fact that I am not making up things about the concept of science, I am giving Mr. Raymo here a large amount of room to explain:
Our understanding of DNA replication, on the other hand, is embedded in a vast and resonant web of interconnected constructs. It is the essence of scientific skepticism to test and retest each link in the web, to try to prove it faulty, to look for more concise patterns of constructs and connections that will adequately explain our immediate sensations – the blackened grains in the photographic emulsion, the results of the chemical assay. If we have succeeded in constructing a resonant web of constructs, then any observer, Skeptic or True Believer, should be able to trace the links back to the perceptional source along vibrant lines of connection.
` It is the firmness of these many connections, based upon tens of thousands of exact, quantitative, reproducible experiments, that anchors the construct “double-helix DNA” to reality. Snip a line of connection here and there – the web still holds. Remove the construct entirely, and sensations go unexplained. And that’s why we [accept] the seemingly impossible dance of the DNA.
` But it isn’t easy. Many of the links in the scientist’s map of the world are highly technical. Only narrow specialists will comprehend some of the connections. Any one scientist must trust the veracity of all other scientists, which is why so much effort goes into quantitative data keeping, citation of relevant prior research, and peer review. A scientist giving a talk to fellow scientists, even to close colleagues, is unlikely to get very far before someone interrupts with “Now wait a minute, about that last step…”
` I have often watched the skeptical engine of science at work – winnowing, pruning testing the resilience of the web. You don’t want to be on the receiving end of this kind of collective scrutiny unless your ducks are well in line.
` Yes, all of that! You didn’t hear it from me, you heard it from Chet Raymo. Once again, that is the tried-and-true process! Though I very well know how to explain the concept of science, I’ve been steering clear as much as possible because I’m just not sure how many people will trust me.
` Must be all the madness and struggling in my life. People have a tendency to misunderstand my ways.
` Anyway, yes, scientists do accept anything to be true as long as it makes sense of many observations. This includes the very fact that a strand of DNA is several feet long, and yet it is tightly wadded into the nucleus of a microscopic cell. It is difficult to imagine, yes? Keep in mind, however, that an animal cell is about fifteen millionths of a meter in diameter, while the double helix is but three billionths of a meter across!
` When Raymo calculated this impossible-sounding size ratio, he found ‘that an arm’s length of DNA is hundreds of times less voluminous than a cell…. Moral: Mathematics can be an indispensable aid to the imagination.’
` Really our scientific concepts are quite difficult to picture if they are not immediately familiar. The fact that DNA works seems only conceivable when one considers that computers – though not nearly as complex – can also function with their hundreds of millions of switches turning on and off at breakneck speed for years without once malfunctioning.
` And just when I thought MAL was invincible, I discovered that one of his components was faulty.
` Thankfully, though those of us granted with life are not invincible, we are not machines: We are so much more complex and much hardier than them. And yet, mechanical metaphors are indispensable to the biologist for describing their own findings – they are just too difficult to describe without some degree of familiarity.
` Such are the limits of the human brain. Personally, though, I think that such things often get in the way of actual ideas. In fact, when I grasp such a concept without first being presented with a familiar analogy, I find that the analogy is what
gets in the way.
` On top of this, I often find that when I grasp a metaphor that I am merely grasping a metaphor rather than what it stands for.

` Sigh… is there not anyone out there who is mentally defective the way I am?

` Ah, okay, that is my off-the-subject conclusion to this post. And if you have any opinions about whether I'm being way too plagiaristic or personal in my essays, please tell me. I have a tendency of constantly analyzing what is going on in my head when I write.
(Next of this series.)


Denny said...

i have to wonder, if so much time is given to analysis of everything that perhaps that maybe the true meanings might get a little fuzzy, skeptic or true beleiver. Thats just me though, I tend to think in more romantic terms of life and such and thats why i like to read your blogs, because i have no concept of how to see things from such and anylitical perspective, but surely makes me appriciate it.

S E E Quine said...

` Really? You like my mental defectiveness? *Bats eyelashes inside of goggles*
` Whatever do you mean, though, in saying that analysis can take away the true meaning of things?
` Since it is my main way of thinking, I find that it adds to everything that is analyzable.

Galtron said...

Oh, you're not mentally defective. You're just a freak of nature. I'm pretty much like that, too! That must be why I'm always reading your blog.
I agree that analysis can really add to things..... though too much can confuse you!

Denny said...

i guess not so much the meaning, but more lets the magic out of the bottle.

Hubba hubba goggles are sooo sexy !

Galtron said...

While I agree that goggles are sexy, I'm not sure if I know what thees 'magic' eez you speak of?

Oh, and,,, nice avatars. Violent deaths by stabbing and combustion are fun!!!

S E E Quine said...

` Grah! I was unceremoniously cut off before I could post my comment at the library! So, I will write it again while eating vegetarian chili at Zippy's (the best way of all!):

` Now, how is it that analysis takes the magic out of the bottle? I don't really understand this idea very well, at least if I read correctly into what you're talking about:
` While I was squaring off in the woods with my favorite superhero, I took some time out to read Richard Feynman's book The Pleasure of Finding Things Out.
` The very first page, as you can see, is a transcript of Richard talking about how an artist friend of his who said that scientists cannot appreciate the beauty of a flower as other people can.
` Yet... flowers are much more than pretty on the outside; there is much more to them than looks. There is cellular activity, and not only that, but the reason flowers are attractive is interesting, too: They look the way they do in order to attract insects! That means that insects, too, can see the colors. (In fact, they can see more colors than we can, and so there are flowers with ultraviolet markings as well!)
` Says Richard:

` All kinds of interesting questions which shows that a science knowledge only adds to the excitement and mystery and awe of a flower. It only adds: I don't understand how it subtracts.

` This, of course, also applies to everything, from the motions of atoms to the motions of the entire universe.
` So... is that the kind of thing you're talking about?

` Now that I think of it, though, I think I understand what you mean considering that nobody can figure out how the universe could have come into being in the first place, and whether or not there are other universes.
` Having only a limited understanding (so far!) of such things certainly does make the universe seem perversely and somewhat horrifyingly mysterious.

Galtron said...

Now, I disagree with you there: I think that the universe seems to be more mysteriously perverse!

But that's just me.

Denny said...

thats exactly what i was getting at and why i was explaining that i enjoy reading about whats in your mind because i think that seeing things from that kind of perspective really gives someone like me who looks at things from well lets say a different angle maybe provokes thoughts that normally arent even considered let alone put in any kind of eloquent or coherent way like you seem to do consistantly

S E E Quine said...

` ...Cool! Thanks! I'm glad that my way of thinking can sometimes inspire neat things in other people's minds!
` It encourages me to keep writing about these things, which is simple, I guess, because I like writing about them, too.

Point of Goodness said...

Is Quine saying that she lacks awe and wonder about the universe? Or is she saying that she doesn't care about ultimate answers? Just APPROXIMATE ones?

Judging from the past couple of posts, she doesn't care if something's completely true or not!!!

Galtron said...

Ummmmmmmm. No!!!!??? What the hell?!?! Why would anyone say that!?!? Who are you!?!?!? Do you have trouble interpreting sentences written in plain English??!

Spoony obviously enjoys thinking about the universe due to its perverse, horrifying mysteriousness (or possibly, mysteriously horrifying perversity) and all that, which she clearly stated many times.


Since we don't have direct contact with reality, the best we can do for the perception of it are approximations. The scientific mechanism is the best way to get the most accurate approximations.

It is best to leave a little "room for error" in one's perception of the universe because as you probably know it is so difficult to get everything exactly right.

Therefore, you cannot ignore the possibility of something being wrong. Even if there appears to be no reason for that at a given point in time. That is the purpose of scientific ideas being fluid and open to change.

Please tell me; that makes some amount of sense to you!!! PLEASE!! I will explode if my attempt has failed!!!

(Hey, I guess you could say I'm Quine's bulldog!)

S E E Quine said...

` Oh, wow!! Thank you, Galtron! I couldn't have put it much better myself! You seem to be fairly knowledgeable in the area of critical thinking.

` You da bulldog.

Galtron said...

Bark, woof!

Point of Goodness said...

Well, if you ALWAYS think that something might not be true, then what does that say about scientific knowledge?

That it's UNSTABLE? I think so.

S E E Quine said...

` To put it in basic terms, anything that seems to be correct stays and anything that turns out to be wrong goes. So, the wrong stuff is unstable, while the rest retains its practical value.