![[dr. bob]](/dr-bob-sm.gif)
Dr. Bob is Robert Hsiung, MD,
bob@dr-bob.orgShown: posts 101 to 125 of 126. Go back in thread:
Posted by Bob on November 22, 1999, at 16:59:31
In reply to Re: calculus; monkeys (Scott), posted by Scott L. Schofield on November 20, 1999, at 8:20:54
> I remember hearing of an instance of speciation documented in the southwest. A population of gray coyotes became separated by a canyon as they migrated southward. After several years, a mere nanosecond relative to geological time, one of the populations had begun to show a trend towards having a red coat. Red or tan coloring made for better camouflage in that locale. Perhaps sexual-selection was the driving force. Regardless of the dynamics, this thing was actually observed with human eyes. Fact.
Thus, the fact was that one population had a higher percentage of red-coated individuals than the other. That is the only demonstrable truth. You say it yourself -- "regardless of the dynamics" -- I could just as easily state that since the sky is blue and the sky is made of nitrogen, mostly, that nitrogen must therefore be blue.
Evolution, as a theory, consists of a number of mechanisms that describe how species today may have derived from species in the past (and please note, folks, that evolution applies to species and not to individuals ... particularly if you want to talk about genetic mechanisms of evolution). There are number of possible explanations as to the difference in the groups. Better camouflage for the area is one. That does not necessarily lead to females choosing mates with redder coats. It might mean that males with grayer coats are less successful at hunting and, therefore, are too weakened from starvation or nutritional deprivation to successfully compete for mates with red coats. Alternately, if the area was at all populated by humans, the graycoats may have become easy targets, thus being thinned off through a more direct means. Given that coyotes also have a rather nasty competitor for their spot in the niche -- wolves (the increase in the wolf population in Yellowstone has led to a dramatic decrease in the coyote population, for example)-- this natural predation may have also led to the demise of the graycoats as well.
So, many potential mechanisms, all similar but not identical dynamics, and all support the general notions that are held in common as the THEORY of evolution. Again, tho, the only FACT is the measurable population density of red vs. gray coated coyotes in each group.
> As for the monkeys, there are some things that can be conceptualized that are excluded from existence because of the laws governing the Cosmos. Bob's analogy sound like one of them.
DOH! Positivism rears its ugly head once again!! My application of the Infinite Monkey Hypothesis here may be excluded from YOUR existence, but since you cannot ascertain the nature of all possible existences -- not for a moment, not during your life -- you cannot exclude my Monkey-produced copy of Leon Uris' Trinity (with scribble on the inside cover that looks suspiciously like a dedication from Leon to me) from existing SOMEWHERE in the Cosmos. Even if the Cosmos is bounded, it can still be infinite ... and I have quite an over-healthy sense of the immensitude of both time and space, thank you very much! ;^) =^PBob
(Devoted follower of Dr. Science ... that should explain some things....)
Posted by Bob on November 22, 1999, at 17:15:40
In reply to Re: Zheezh! You turn your back for a second ..., posted by CC on November 18, 1999, at 16:22:58
> "technically speaking, it's a hypothesis that is refuted by one
> negative instance"
>
> Then how did it ever get past being a hypothesis??Oops! General reference there. The sentence would have been more clearly stated as "The scientific 'entity' that can be demonstrated as being false through a single negative case is a hypothesis, not a theory." Just because a hypothesis has not yet been shown to be false does not entitled it to the grandiose label of Theory. Theories, in practice, are collections of supportable hypotheses and models which, as a whole, provide some explanation of some natural phenomena.
Sorry,
Bob
Posted by Adam on November 22, 1999, at 23:05:30
In reply to Re: "positivist-empiricist?", posted by Bob on November 22, 1999, at 16:25:42
>Empiricism is one of the philosophic cornerstones of the natural sciences, something truly held as axiomatic.
There are many philosophical “cornerstones” to the natural sciences, which could be described as “axiomatic”
during their periods of greatest popularity; don’t forget there were always rival camps. If there were ever
bitter fights that the empiricists fought, it might be with Descartes and the other European rationalists,
who valued deductive reasoning informed by intuition (not to be mistaken with instinct), a concept the
empiricists firmly rejected. I guess for the most part the empiricists won out, but one might find in modern
physics a hint of rationalism. I can think of no better example than what Steven Weinberg describes as the
need for scientific theories, especially the unifying theories of physics, to be “beautiful”. This “beauty”
is a quality of successful fundamental theories, and it is the apprehension of beauty that guides many in their
quest for the finest mathematical expression of the “final theory.” Weinberg argues for such an aesthetic
judgement because, as a guiding principle, it works. One might debate that the concept of “beauty” in this
context is more inductive than deductive, that clever minds well-versed in the most complex mathematics become
so wired as to feel the presence of “beauty” when exposed to the best equations for the particular application,
and hence Weinberg is still an empiricist. I don’t know. All such arguments demonstrate to me is the uselessness
of old philosophy, except to provide modern philosophers with examples of what tautological arguments not to
repeat, or whatever. If there is any axiomatic underlying priniciple that endures, it is the scientific principle:
Observe, hypothesize, test, report. Repeat until dead, or at least until tenured. Whether this falls under the
catagory of empiricism I can’t say, and I can’t see why any scientist should think about it.>it fit quite well with the natural sciences (except for when you start figuring in chaos, probability, and
>other quantum weirdness) -- but worst of all, it totally hijacked American psychology and was the perfect tool
>for the behaviorists. In the mean time, Sir Karl Popper came along and pointed out that scientists do NOT verify,
>they falsify -- something that just about killed positivism.As for what did in positivism, I think it may have been the work of Hempel (who just died a few years ago, I
guess) that contributed as much as anything. Logical Positivism didn’t really clash with probability or its
implications. Where the positivists went wrong was not so much, as Hemple pointed out, in their trust in
scientific “truths” but in their innapropriate use of the word. The idea that theories could be proven true or
false through observation in a positivist sense struck Hempel as wrong because any expression of a new theory was
dependant not on the observation but on old theoretical terms. These terms must then be seen as “true”. But
such a reliance on old theory is unscientific, because all scientific theories are, by definition, falsifiable,
and therefore contain no “truth”. Positivism relies on the idea that theories have observational content. Hempel
denies the existence of theory based on observation.Maybe Hempel was right in his criticism of positivists. I don’t know. Maybe Popper is right in his criticism of
positivism by saying that all scientists do is refute the theories of old scientists and thus don’t prove anything,
they just disprove.I say, from a scientific perspective, who the hell cares? The positivists and rationalists and empiracists and
mechanists and atomists and monists can keep debating for all I’m concerned. Maybe I resemble one or the other
sometimes, maybe not. If I spent time thinking epistemologically about my education and ontologically about my next
experiment I’d get nothing done (gee, I put some restriction enzyme in a tube of DNA, but I can’t actually SEE them,
I’m just supposing they are based on what someone told me, and how do they know? Anyway, even if they’re there,
in the end I’m just observing a glowing band of something on a gel, and my theory that this band is the product of an
enzymatic reaction is based only on some other theories, and those on other theories before that in a long line of
theories which just use observations to justfy their a priori veracity so what on Earth is it that I’m REALLY doing
anyway and maybe I should just go home and THINK real hard about this surrogate religion science I’m bowing to and
make no assumptions at all about anything...)>I have a healthy amount of skepticism and a willingness to suspend disbelief when warranted, but I accept nothing
>purported to be scientific on faith.I can think of no useful philisophical argument for or against the appropriateness of science as a guiding principle
and a worthy pursuit. I can think of all sorts of useful things that scientists do on a daily basis by practicing the
scientific method. Leave “truth” to the metaphysicists. How about “realiability”, “reproducibility”, “consistency with
observation”, “applicability to known phenomena”. If some better theory comes along, why shouldn’t someone still have
confidence in the process? And why equate that confidence with “faith”? Confidence gives scientists the ability to do
work without having to prove every underlying principle themselves. It does not make them less skeptical. If scientists
practiced faith, they’d cling to old theories despite all evidence of their unreliability. I guess some scientists do
this, but as soon as they walk that path, they cease to be relevant.>positivism's cult-like, covert adherence in the social sciences is what Stephen Jay Gould calls "physics envy".
Well, leaving positivism, what’s wrong with “physics envy”? I have it all the time as a biologist, and I think this is
healthy. It means you hold yourself to a certain standard of confidence; black boxes should only be allowed to exist if you
do not have the time or the money to probe them further at this very moment. Why accept an id or superego or collective
unconscious or animus if you can’t break it down to the observable interplay of physiology, biochemistry, and environment?
Why favor a notion, say, that there is some inscrutable gestalt of the mind, that “physics envy” couldn’t lead one to discover
the basic principles of consciousness and describe them in physical terms, no more special than a hurricane or a speck of dust?
Oops, I’m being a reductionist.
Posted by Elizabeth on November 22, 1999, at 23:30:23
In reply to Re: "positivist-empiricist?", posted by Bob on November 22, 1999, at 16:25:42
> Positivism is an epistemilogical/ontological (how we know/what exists) stance steeped in empiricism and attempting to make philosophy and other social sciences as rigorous and empirically-based as the natural, "hard" sciences.
Thank you, Bob. I now have enough information to answer your q: heck no. (He quoted Gould's physics envy joke to me once -- the context was particularly amusing since he was referring to a particular psychologist who was clearly of the cognitive-behavioral persuasion. One thing I like about the analytic types: at least they admit that they're doing literature, not science.)
> Which, by the way to CC, is exactly why I have no faith in science.
"Faith in science" seems like an oxymoron to me. :-)
> Nothing like a nice hard, uh, FACT to get you all hot and bothered, is there? ;^)
Oooh baby.
> Bob (heading back to the mounds of paper ... happy T-day to all my fellow yanks out there ... and yes, you canadians can celebrate a second thanksgiving if you want....)
Happy T-day to you too, and good luck wading through all that work.
Posted by Adam on November 22, 1999, at 23:57:54
In reply to fact?, posted by Bob on November 22, 1999, at 16:59:31
>
>one population had a higher percentage of red-coated individuals than the other. That is the only demonstrable truth. You say it yourself -- "regardless of the dynamics"
>-- I could just as easily state that since the sky is blue and the sky is made of nitrogen, mostly, that nitrogen must therefore be blue.
>
You could hypothesize that nitrogen is blue. Then you could test that hypothesis. Then you could conclude "it's blue". Maybe somebody hypothesized red-coated wolves
are there because of a particular evolutionary process. Why assume they put this forth as "truth?" And even if someone did, why does this necessarily speak against the
theory of evolution in science?> Evolution, as a theory, consists of a number of mechanisms that describe how species today may have derived from species in the past (and please note, folks, that
>evolution applies to species and not to individuals ... particularly if you want to talk about genetic mechanisms of evolution). There are number of possible explanations
>as to the difference in the groups...many potential mechanisms, all similar but not identical dynamics, and all support the general notions that are held in common as the
>THEORY of evolution. Again, tho, the only FACT is the measurable population density of red vs. gray coated coyotes in each group.
The point being? I suppose if I just left it at that I wouldn't be doing much to test evolution. I could observe the wolves over a long time and narrow down the list
of selective pressures. A person, when they hypothesize something, is under some obligation to test this hypothesis. If they don't, they're not practicing science.
Why would I use the latter example to talk about science and evolution? And what does such an example tell us about theory? I think you are proposing people use hypotheses
to support theories. They don't, or they shouldn't. They ought to use theories to come up with good hypotheses which they then test by gathering more factual information.
Of course theories have origins. All ideas do. Then they get tested. What's the problem with evolution, then? What's the problem with "THEORY"?
Posted by CC on November 23, 1999, at 1:02:51
In reply to Re: fact?, posted by Adam on November 22, 1999, at 23:57:54
Can anyone give a mechanism for the "evolution" from one species to another? It seem to me that the accumulation of favorable or viable random mutations is unlikely from a mathematical point of view. Excuse me, I have to cast a demon out of my web browser.
Posted by Adam on November 23, 1999, at 9:19:51
In reply to To anybody, posted by CC on November 23, 1999, at 1:02:51
> Can anyone give a mechanism for the "evolution" from one species to another? It seem to me that the accumulation of favorable or viable random mutations is unlikely from a mathematical point of view. Excuse me, I have to cast a demon out of my web browser.
Accumulation of favorable mutations isn't very likely, but given enough time, it makes a difference.
There really isn't much more to it than that. The cellular machinery that replicates DNA is pretty high
fidelity, but it's not perfect. And there are always mutations caused by chemicals or radiation. So
mutations are always occuring, and it is hypothesised at a fairly constant rate. Most of them are "silent"
in that they fall on a sequence of DNA that doesn't code for anything, or, because of the degeneracy of the
genetic code, the amino acid sequence of the final product isn't altered. Of the few that do make a real
difference, most of those are deleterius. Then, very rarely, there is a
mutation that confers a selective advantage. If that individual carrying the mutation reproduces, then
it gets handed down to a new generation, conferring a selective advantage on them, and so forth. When two
or more subgroups of a species are isolated somehow (usually by geography), their divergent accumulation
of genetic change (genetic drift) becomes so significant that they are no longer genetically compatible
from a reproductive standpoint. They are now genetically isolated from one another, and are now referred
to in scientific terminology as separate species. This is a bit of an oversimplification from a taxonomical
point of view, and is skewed toward sexual reproduction, but you get the idea. So you take the constant of
genetic change, plus a large number of individuals in a species, plus millions of years, plus physical
isolation of a subgroup, plus selective pressures, and you get the origin of species.
Posted by Scott L. Schofield on November 23, 1999, at 13:48:40
In reply to Re: "positivist-empiricist?", posted by Adam on November 22, 1999, at 23:05:30
I don't know anything about all this intellectual stuff, but it seems like one hell of a forest to have to navigate through.
> >Empiricism is one of the philosophic cornerstones of the natural sciences, something truly held as axiomatic.
>
> There are many philosophical “cornerstones” to the natural sciences, which could be described as “axiomatic”
> during their periods of greatest popularity; don’t forget there were always rival camps. If there were ever
> bitter fights that the empiricists fought, it might be with Descartes and the other European rationalists,
> who valued deductive reasoning informed by intuition (not to be mistaken with instinct), a concept the
> empiricists firmly rejected. I guess for the most part the empiricists won out, but one might find in modern
> physics a hint of rationalism. I can think of no better example than what Steven Weinberg describes as the
> need for scientific theories, especially the unifying theories of physics, to be “beautiful”. This “beauty”
> is a quality of successful fundamental theories, and it is the apprehension of beauty that guides many in their
> quest for the finest mathematical expression of the “final theory.” Weinberg argues for such an aesthetic
> judgement because, as a guiding principle, it works. One might debate that the concept of “beauty” in this
> context is more inductive than deductive, that clever minds well-versed in the most complex mathematics become
> so wired as to feel the presence of “beauty” when exposed to the best equations for the particular application,
> and hence Weinberg is still an empiricist. I don’t know. All such arguments demonstrate to me is the uselessness
> of old philosophy, except to provide modern philosophers with examples of what tautological arguments not to
> repeat, or whatever. If there is any axiomatic underlying priniciple that endures, it is the scientific principle:
> Observe, hypothesize, test, report. Repeat until dead, or at least until tenured. Whether this falls under the
> catagory of empiricism I can’t say, and I can’t see why any scientist should think about it.
>
> >it fit quite well with the natural sciences (except for when you start figuring in chaos, probability, and
> >other quantum weirdness) -- but worst of all, it totally hijacked American psychology and was the perfect tool
> >for the behaviorists. In the mean time, Sir Karl Popper came along and pointed out that scientists do NOT verify,
> >they falsify -- something that just about killed positivism.
>
> As for what did in positivism, I think it may have been the work of Hempel (who just died a few years ago, I
> guess) that contributed as much as anything. Logical Positivism didn’t really clash with probability or its
> implications. Where the positivists went wrong was not so much, as Hemple pointed out, in their trust in
> scientific “truths” but in their innapropriate use of the word. The idea that theories could be proven true or
> false through observation in a positivist sense struck Hempel as wrong because any expression of a new theory was
> dependant not on the observation but on old theoretical terms. These terms must then be seen as “true”. But
> such a reliance on old theory is unscientific, because all scientific theories are, by definition, falsifiable,
> and therefore contain no “truth”. Positivism relies on the idea that theories have observational content. Hempel
> denies the existence of theory based on observation.
>
> Maybe Hempel was right in his criticism of positivists. I don’t know. Maybe Popper is right in his criticism of
> positivism by saying that all scientists do is refute the theories of old scientists and thus don’t prove anything,
> they just disprove.
>
> I say, from a scientific perspective, who the hell cares? The positivists and rationalists and empiracists and
> mechanists and atomists and monists can keep debating for all I’m concerned. Maybe I resemble one or the other
> sometimes, maybe not. If I spent time thinking epistemologically about my education and ontologically about my next
> experiment I’d get nothing done (gee, I put some restriction enzyme in a tube of DNA, but I can’t actually SEE them,
> I’m just supposing they are based on what someone told me, and how do they know? Anyway, even if they’re there,
> in the end I’m just observing a glowing band of something on a gel, and my theory that this band is the product of an
> enzymatic reaction is based only on some other theories, and those on other theories before that in a long line of
> theories which just use observations to justfy their a priori veracity so what on Earth is it that I’m REALLY doing
> anyway and maybe I should just go home and THINK real hard about this surrogate religion science I’m bowing to and
> make no assumptions at all about anything...)
>
> >I have a healthy amount of skepticism and a willingness to suspend disbelief when warranted, but I accept nothing
> >purported to be scientific on faith.
>
> I can think of no useful philisophical argument for or against the appropriateness of science as a guiding principle
> and a worthy pursuit. I can think of all sorts of useful things that scientists do on a daily basis by practicing the
> scientific method. Leave “truth” to the metaphysicists. How about “realiability”, “reproducibility”, “consistency with
> observation”, “applicability to known phenomena”. If some better theory comes along, why shouldn’t someone still have
> confidence in the process? And why equate that confidence with “faith”? Confidence gives scientists the ability to do
> work without having to prove every underlying principle themselves. It does not make them less skeptical. If scientists
> practiced faith, they’d cling to old theories despite all evidence of their unreliability. I guess some scientists do
> this, but as soon as they walk that path, they cease to be relevant.
>
> >positivism's cult-like, covert adherence in the social sciences is what Stephen Jay Gould calls "physics envy".
>
> Well, leaving positivism, what’s wrong with “physics envy”? I have it all the time as a biologist, and I think this is
> healthy. It means you hold yourself to a certain standard of confidence; black boxes should only be allowed to exist if you
> do not have the time or the money to probe them further at this very moment. Why accept an id or superego or collective
> unconscious or animus if you can’t break it down to the observable interplay of physiology, biochemistry, and environment?
> Why favor a notion, say, that there is some inscrutable gestalt of the mind, that “physics envy” couldn’t lead one to discover
> the basic principles of consciousness and describe them in physical terms, no more special than a hurricane or a speck of dust?
> Oops, I’m being a reductionist.
Posted by Morrigane on November 23, 1999, at 17:22:51
In reply to Re: To anybody, posted by Adam on November 23, 1999, at 9:19:51
You've done an excellent job explaining speciation. I was going to jump right onto the question, but now it seems unecessary.
Pardon me for getting personal, but are you married?
Posted by Adam on November 23, 1999, at 17:36:33
In reply to Re: To Adam, posted by Morrigane on November 23, 1999, at 17:23:01
> Pardon me for getting personal, but are you married?Nope. I think, given some recent events, I'm going to do the single thing for a while. But, you know,
someday, maybe. :)Well, have a happy Thanksgiving, all. My best to a truly unique and wonderful group of people.
-Me
Posted by saint james on November 23, 1999, at 23:55:18
In reply to Re: To anybody, posted by Adam on November 23, 1999, at 9:19:51
> > Can anyone give a mechanism for the "evolution" from one species to another? It seem to me that the accumulation of favorable or viable random mutations is unlikely from a mathematical point of view. Excuse me, I have to cast a demon out of my web browser.
>
> Accumulation of favorable mutations isn't very likely, but given enough time, it makes a difference.
> There really isn't much more to it than that. The cellular machinery that replicates DNA is pretty high
> fidelity, but it's not perfect. And there are always mutations caused by chemicals or radiation.James here....
Another source for mutations are the copies of DNA
men make. Women have X number of eggs, and they are produced very early on while in the womb. Biology gets it right to a high degree at this stage. Men make gazillions of copies throughout their life so by the sheer numbers some errors are made. Cosmic rays and radition from minerals are very important to supply the random chance of mutation.In my study of science I can't help miss how important random chance is. Mutation is a good example. When I look beyond a single random event
to a bigger picture order does come out of randomness. At the moment of the big bang when
our universe winked into existance it was lucky there was exactually the right amount of energy and matter so our universe did not explode or implode in a wink. The frequency at which every atom vibrates was set at the instant of creation, had it been slightly different we could of gotten space but no time of vise versa; out physical laws whould of been very different. Reality is not an illusion but level in Quantum Mechanics.Please take this only as my view, I realize that no one's view can hope to answer all the questions. I think it is more important to find what works for you and allow others to do the same.
j
Posted by Bob (check the email add. if you can't tell which) on November 26, 1999, at 9:30:25
In reply to Re: To anybody, posted by saint james on November 23, 1999, at 23:55:18
I knew I was asking for it staying away so long....
Scott -- best reply yet. Forget Occam's Razor, more like we need McCullough's Chainsaw to get through this forest.
Now I have to try to remember all the points Adam made that I wanted to agree with or redirect ... should have wrote them down... lessee...
"Physics envy" -- well, as a biologist, maybe such a standard is appropriate, since there's a lot of biology that can conform to such a hard empiricist stance. Until we finally connected what happens on a neurological/-chemical basis with actual memories or behaviors or meanings, it remains a BIG problem for psychologists. Sure, those research and clinical psychologists who must remain closely tied to the biological underpinings of behavior and thought can use physics envy as a test for their outcomes, but people in more social, applied fields like me (as an educational psychologist ... no, I don't go into schools and help troubled kids--more like I *cause* trouble for them by asking all sorts of brain-twisting questions to figure out how they learn) physics envy is a counterproductive distraction. Particularly in the area of motivation, what people perceive and believe is far more important than what "is". Sure, I could follow a rather common protocol of examining the correlation between belief and behavior, but this does little to explain why people aren't more objectivist in pursuing courses of action.
Getting back to "fact", hypothesis, and theory, we're in more agreement than it seems from my reading of your post on that. Yes, hypotheses are often made within the constraints of a theory, particularly to provide more support for that theory. And hypotheses, since when constructed appropriately limit their concern to highly controlled situations (one outcome and one cause, unless you're using some multivariate procedure to examine multiple causes), can be rather forcefully demonstrated to be false or a better alternative than anything else to date (the closest thing to "truth" in the falsification paradigm). Theories are far more adaptive mental organisms, being built upon supported hypotheses and capable of generating new ones. One negative case ruins a hypothesis -- but theories tend to adapt to include the negative case as a positive case instead, rather than collapsing. It takes a more systemic failure to knock a theory out for good.
Adam, maybe you could fill me (and the rest of us) in on something else here.
That was a great description of the traditional view of evolution*. The thing about it, tho, is that it suggests a rather gradual change in species over the course of millions of years. I guess there's evidence that sometimes evolution makes great leaps over the course of rather short periods (in the geoligical sense of terms ... thousands or years, perhaps only hundreds, but certainly not millions). How does that notion of "punctuated equilibrium" fit in theoretically?
*One thing I would add is a point about what makes a "good" mutation. It's a very common lay-conception that nature somehow produces the mutations an organism needs to survive, meaning that "survival of the fittest" is somehow a purposeful process and ascribing to Nature some sort of will or intelligence. Traditionally, tho, this is horse hockey. Mutations are produced randomly and (over time and across an entire species) rather prolifically. Think of the high end of a bell curve--very few of those mutations will have a much better fit with the environment than what is ordinary. If it wasn't for time and numbers, if life remained a rather constrained phenomenon, then we wouldn't see much speciation. In a traditional sense, there is no such thing as a good mutation, only random ones that on quite rare occasions wind up conveying an ecological advantage.
Then again, I guess there is evidence against a purely randomized process of mutation as well.
bob
Posted by Scott L. Schofield on November 27, 1999, at 16:40:26
In reply to gack!, posted by Bob (check the email add. if you can't tell which) on November 26, 1999, at 9:30:25
>
> Adam, maybe you could fill me (and the rest of us) in on something else here.
>
> That was a great description of the traditional view of evolution*. The thing about it, tho, is that it suggests a rather gradual change in species over the course of millions of years. I guess there's evidence that sometimes evolution makes great leaps over the course of rather short periods (in the geoligical sense of terms ... thousands or years, perhaps only hundreds, but certainly not millions). How does that notion of "punctuated equilibrium" fit in theoretically?
>
I really do regret using the word "fact" regarding "evolution", if for no other reason than to have avoided the Wrath of Bob. I guess the word evolution may need to be defined first before any discussion can proceed. I'll leave that to greater minds than my own.I once saw a PBS interview with Stephen Jay Gould, whose name has been mentioned here a few times. After his requisite description of his undying love for the New York Yankees, he began to address evolution along with other topics. Perhaps he was purposely overstating to make a point, but he kept referring to evolution as being a "fact". What remained as theory, he said, was not if, but how.
Are the appearances of antibiotic-resistant strains of bacteria an example of evolution or not? If not, then the hell with it. If so, it certainly happened rather quickly. It might even qualify as an example of punctuated-equilibrium.
Monkey business. I was forced to re-examine Bob's infinite monkey (chimpanzee?) scenario, seeing as how I've been wrong about everything else this week. Interesting. I'm beginning to appreciate some of its points. I think what set me off was his choice of the monkeys over the appearance of life. Don't get me wrong - I thought of ways in which the monkeys could do it.
Although I didn't spend too long at it, I found that most of them (the ones *I* thought of) required evolution and/or God. The King James Bible bit really threw a monkey-wrench into the works.Others I came up with while writing this:
(These may not necessarily depend on evolution/God - I haven't thought them through).1. Extraterrestrial beings invoking mental telepathy/telekinesis
2. Time machine/paradox
3. Transport of individuals from one of the other "Many Worlds"
4. A clone of P. T. Barnum tricking the world into believing itAs far as truth is concerned - that there may be more than one truth, or that the truth may be unknowable, or that there may be no truth at all, still all represent one Truth?
Just a question.
- Scott
Posted by Bob on November 28, 1999, at 17:23:11
In reply to Re: gack!, posted by Scott L. Schofield on November 27, 1999, at 16:40:26
> Are the appearances of antibiotic-resistant strains of bacteria an example of evolution or not? If not, then the hell with it. If so, it certainly happened rather quickly. It might even qualify as an example of punctuated-equilibrium.
I guess that could be a good example of punctuated equilibrium. Of course, there's one aspect of bacteria's environment (humanity and the mass bacteria extinctions it keeps causing thru anti-biotics) that in combination with short reproduction cycles makes it all that much more visible a phenomenon (unfortunately).
>... Although I didn't spend too long at it, I found that most of them (the ones *I* thought of) required evolution and/or God. The King James Bible bit really threw a monkey-wrench into the works.
But the Infinite Monkey Hypothesis has nothing really to do with evolution or God, but exists only as an amusing metaphor for "perfect" random generator -- one that produces every possible combination of letter-strings from one letter in length to whatever. I could have easily said that I could produce War and Peace by closing my eyes and poking randomly at my keyboard, given enough time (an infinite amount being certainly enough), but that's not so silly a metaphor.
> 1. Extraterrestrial beings invoking mental telepathy/telekinesis
> 2. Time machine/paradox
> 3. Transport of individuals from one of the other "Many Worlds"
> 4. A clone of P. T. Barnum tricking the world into believing itI vote for 1&4 being possible thru evolution only, given our understanding of nature.
> As far as truth is concerned - that there may be more than one truth, or that the truth may be unknowable, or that there may be no truth at all, still all represent one Truth?
Well, that is the crux of the matter, isn't it? This is where some say the positivists led us wrong. By asserting that scientific understanding (whether derived at thru empirical research or rational argument) identifies what is True Knowledge, they mix up the issues of being and knowing. As a result, western philosophy (since the time of Locke or so) has made next to no progress on ontological issues and has some screwed up epistemological issues by assuming that coming to know the Truth included being able to identify what is True.
Geez, I hope that made sense. Seems perfectly sensible to me, and that's what worries me ;^).
Bob
Posted by Adam on November 28, 1999, at 22:14:54
In reply to gack!, posted by Bob (check the email add. if you can't tell which) on November 26, 1999, at 9:30:25
> Adam, maybe you could fill me (and the rest of us) in on something else here.
>
> That was a great description of the traditional view of evolution*. The thing about it, tho, is that it suggests a rather gradual change in species over the course of millions of years. I guess there's evidence that sometimes evolution makes great leaps over the course of rather short periods (in the geoligical sense of terms ... thousands or years, perhaps only hundreds, but certainly not millions). How does that notion of "punctuated equilibrium" fit in theoretically?
>
> *One thing I would add is a point about what makes a "good" mutation. It's a very common lay-conception that nature somehow produces the mutations an organism needs to survive, meaning that "survival of the fittest" is somehow a purposeful process and ascribing to Nature some sort of will or intelligence. Traditionally, tho, this is horse hockey. Mutations are produced randomly and (over time and across an entire species) rather prolifically. Think of the high end of a bell curve--very few of those mutations will have a much better fit with the environment than what is ordinary. If it wasn't for time and numbers, if life remained a rather constrained phenomenon, then we wouldn't see much speciation. In a traditional sense, there is no such thing as a good mutation, only random ones that on quite rare occasions wind up conveying an ecological advantage.
>
> Then again, I guess there is evidence against a purely randomized process of mutation as well.
>
> bob
Hey,Hmm. Well, speaking teleologically, I was always under the impression that all mutations were random in
nature. I would be interested to know what the evidence is against a "purely randomized process". I
assume this doesn't imply a plan, but may refer to some environmental factors affecting specific loci?
One example of that I can think of off the top of my head is is dimethylbenzamine, a nasty carcinogen that
always causes mutations at codon 61 of the Ras oncogene, constituatively activating it.As for punctated equilibrium vs. my example, as I implied, it was a simplification. There aren't many rules
in evolution, it would seem, and for every species, there is a different story. The main factors are mutation,
genetic drift, and selection. Mutation is a given. Drift and selection may play more or less important roles
depending on the circumstances. A good way to envision what goes on in "punctate equilibrium" is to look at a
population as a bell curve. Draw a line down the middle of the curve. Think of that curve as representing
the genetic makeup of the population, and the line as the environment. So, the average individual in the
population is ideally adapted to that environment. Remember, the breadth of the curve represents genetic
drift, the random deviation from the norm through mutation.Now, move that line over near either end of the curve. The environment has changed (say a big meteorite hit
the Yucatan or something). If you move the line too far left or right you're either out of the curve (nothing
can cope or survive, extinction) or so far towards the edge that you're left with too few well-adapted individuals
(inbreeding leads eventually to extinction). But say your line isn't too far one way or the other. Selective
pressures now favor a new sub-population. The curve quickly shifts to center itself about that new line. You
haven't got a new species in strictest sense, but there is a new norm. Time passes, drift continues, speciation
occurs.To really mix things up, the shifting "environment line" might cut the curve in more than one place...the norm
not only shifts, but fractures. Different subpopulations compete. Which might prevail? One, both, neither?Depending on the circumstances, almost anything could happen.
Posted by Bob on November 29, 1999, at 15:23:19
In reply to Re: gack!, posted by Adam on November 28, 1999, at 22:14:54
Adam ... cool, thanks!
Bob
Posted by CC on November 29, 1999, at 23:04:11
In reply to evolution addenda, posted by Bob on November 29, 1999, at 15:23:19
I still don't see how you could ever hope to accumulate favorable mutations. If one mutation in a thousand is beneficial, then there are 999 that aren't. With the bacteria developing antibiotic resistance, if there is one resistant individual in a million that one individual can repopulate the growing medium in ~24 hours. Plus bacteria have means of exchanging genetic material that higher animals don't and have you ever heard of someone developing a different species of bacteria starting with a known one? There are of course biological processes that can correct mutations but how could they tell a good one from a bad one? So if you had a million monkeys and they each accumulated a thousand mutations only one of which was favorable during the period they are able to breed, and they each have ten offspring to ten different mates, how many offspring have accumulated more favorable mutations than bad?
Posted by Adam on November 30, 1999, at 0:18:04
In reply to Evolution doesn't add up., posted by CC on November 29, 1999, at 23:04:11
>Plus bacteria have means of exchanging genetic material that higher animals don't and have
Are you referring to conjugation? That's a bit like a primative form of sexual reproduction.
Mostly all that gets exchanged are little circular bits of DNA (plasmids) that normally carry
only a couple or maybe just one gene, often a gene that confers resistance to something.Anyway, when you stack the kind of genetic recombination that can happen during the various
processes of sexual reproduction, eukaryotes have it big over prokaryotes. Crossing-over
during meiosis alone can lead to enormous exchanges of genetic material from chromosomes
derived from different parents. Sexuality mixes everything up really well.Bacteria have a doubling time of about 30 minutes. People, for example, take a lot longer.
So you can see bacteria evolving, in the human perception of time, very quickly relative to
us poor primates. But if it takes a million years to get humans as far as bacteria can go
in a decade, it doesn't mean that humans won't evolve. It just takes longer.P.S. In my last post, I guess I said dimethylbenzamine. That's wrong. I'm pretty sure it's
dimethylbenzanthracene. Icky stuff.
> I still don't see how you could ever hope to accumulate favorable mutations. If one mutation in a thousand is beneficial, then there are 999 that aren't. With the bacteria developing antibiotic resistance, if there is one resistant individual in a million that one individual can repopulate the growing medium in ~24 hours. Plus bacteria have means of exchanging genetic material that higher animals don't and have you ever heard of someone developing a different species of bacteria starting with a known one? There are of course biological processes that can correct mutations but how could they tell a good one from a bad one? So if you had a million monkeys and they each accumulated a thousand mutations only one of which was favorable during the period they are able to breed, and they each have ten offspring to ten different mates, how many offspring have accumulated more favorable mutations than bad?
Posted by Scott L. Schofield on November 30, 1999, at 12:26:39
In reply to Re: gack!, posted by Bob on November 28, 1999, at 17:23:11
> But the Infinite Monkey Hypothesis has nothing really to do with evolution or God, but exists only as an amusing metaphor for "perfect" random generator -- one that produces every possible combination of letter-strings from one letter in length to whatever. I could have easily said that I could produce War and Peace by closing my eyes and poking randomly at my keyboard, given enough time (an infinite amount being certainly enough), but that's not so silly a metaphor.
Got ya'
> > As far as truth is concerned - that there may be more than one truth, or that the truth may be unknowable, or that there may be no truth at all, still all represent one Truth?> Well, that is the crux of the matter, isn't it? This is where some say the positivists led us wrong. By asserting that scientific understanding (whether derived at thru empirical research or rational argument) identifies what is True Knowledge, they mix up the issues of being and knowing. As a result, western philosophy (since the time of Locke or so) has made next to no progress on ontological issues and has some screwed up epistemological issues by assuming that coming to know the Truth included being able to identify what is True.
>
> Geez, I hope that made sense.It did.
> Seems perfectly sensible to me, and that's what worries me ;^).
Posted by Bob on December 2, 1999, at 20:14:45
In reply to Evolution doesn't add up., posted by CC on November 29, 1999, at 23:04:11
> I still don't see how you could ever hope to accumulate favorable mutations....
There is no such thing as a favorable mutation withthe spin you're putting on it. Mutations simply are.
There certainly are deleterious mutations ... such as those that produce cancer or, in the case of reproduction, mutations which result in a non-viable offspring. But "favorable" mutations result through a better organism/environment fit. Go back to the coyote example. I can't remember the details well enough, but it involved genetic drift in coat coloring. The difference in coloring comes from a rather common genetic variation that, when placed in context with some environmental factor such as protective coloration as (1) an aid for hunting or (2) better concealment from predators, the "mutation" hasn't done anything "good" for those who become dominant -- it simply is and, in this case, what it *is* is a better fit with environmental conditions conducive to survival and, even if you base it solely on statistics and not on any "instinctual" mechanism to seek out "good" mates, conducive to replication in following generations.
It's a purely mechanical process brought about by brute empiricism. Don't anthropomorphise it by saying that somehow some mechanism in nature picks out what is good and what is bad before it even gets filtered against survival within an environmental context.
Bob
(oops! drop my interpretive trousers for a moment and I get caught with my empirical boxers on...)
Posted by CC on December 3, 1999, at 16:45:53
In reply to We're not dealing with addition ..., posted by Bob on December 2, 1999, at 20:14:45
"There is no such thing as a favorable mutation withthe spin you're putting on it.
Mutations simply are."Mutations can increase the ability of a species to survive although it would be a rare event. I am looking at a possible mechanism for the transistion from one species to another. Would it not take an accumulation of mutations for this transistion? The genetic differences within a species are limited or it would not be considered a "species". For example, chimpanzees and humans are 98% genetically similiar. How many genes do humans have, ~10^100? So approximately 2*(10^98) genes would be this 2% difference. So how would this genetic difference come about if not by mutation? Given the size of this number (2*10^98), does it seem reasonable that this much genetic change could occur through random events, with or without biological selection, within the time frame generally accepted?
Posted by CC on December 3, 1999, at 17:04:50
In reply to Be fruitful and multiply., posted by CC on December 3, 1999, at 16:45:53
> "There is no such thing as a favorable mutation withthe spin you're putting on it.
> Mutations simply are."
>
> Mutations can increase the ability of a species to survive although it would be a rare event. I am looking at a possible mechanism for the transistion from one species to another. Would it not take an accumulation of mutations for this transistion? The genetic differences within a species are limited or it would not be considered a "species". For example, chimpanzees and humans are 98% genetically similiar. How many base pairs do humans have, ~10^100? So approximately 2*(10^98) base pairs would be this 2% difference. So how would this genetic difference come about if not by mutation? Given the size of this number (2*10^98), does it seem reasonable that this much genetic change could occur through random events, with or without biological selection, within the time frame generally accepted?
Posted by Bob on December 5, 1999, at 9:31:35
In reply to Be fruitful and multiply., posted by CC on December 3, 1999, at 16:45:53
> Mutations can increase the ability of a species to survive although it would be a rare event.
I don't think you're taking it far enough here. It would be an exceedingly rare event, but we're talking about rare in terms of probability. For example, an "exceedingly rare" event may have a 1 in 1 billion (0.0000001%) chance of occuring. Just like playing Lotto -- if all you've got is one shot (or five or some other low number in comparison to the P-value of the event), then the Law of Probability is going to kick your arse in all likelihood. However, if instead of one shot at producing a particular result you have more like a number of shots equal to several orders of magnitude larger than the entire "population" of events (1 billion, for comparison to the 1 in a billion shot) then the Law of Large Numbers starts coming into play, providing some assurance that that one in a billion event WILL happen. I'm not talking about a billion events ... more like a billion of a billion events.
> For example, chimpanzees and humans are 98% genetically similiar.
... but don't forget that it's not humans who have been drifting apart from chimps, but rather its both chimps and humans who have been drifting apart from some common ancestor -- two more complex genomes from one common, simpler genome. And are chimps even our closest relative? If not, you have to reach even further back in our genetic history to a less-evolved common ancestor.
> How many genes do humans have, ~10^100?
One googol of genes?! Now there's a number I haven't seen used in quite some time....
No, humans have less than 10^5 (100,000) genes. In terms of base pairs, it's more like 3 billion in the human genome. So, even though matters are 2^(10^93) times less complex than you suggest, the odds are still pretty daunting ... particularly since the more complex aspects of our functioning are prboably determined by, to be conservative, more than one gene.
OTOH, Toss into the mix that adult humans have *trillions* of cells in their bodies. Toss in again how many cell divisions happen to those trillions of cells over the average lifespan of an individual. Now take into account that we are not talking about my genome or your genome, but the HUMAN genome. For all individuals alive at this moment in time -- how many opportunities for mutation are there? 5.5 billion individuals times several trillion cells times some probably large number of cell divisions over a lifetime. Toss into that mix the variety that can be produced not by cell division but, instead, by sexual reproduction. And now toss in all the individuals that we can consider to be homo sapians over the last, what?, twenty thousand years ... or is it more or less?
Are you getting some idea of just how staggeringly high the number of events are compared to the chance for any one given mutation?
If we're going to throw in googols, turn the numbers around. It's more like there have been one googol (give or take a dozen orders of magnitude) of possible events to produce mutations, rather than that being the chance of getting one (and I'm being generous here by not *raising* the stakes to a geometric (power of 2) level).
Now, the real kicker is this. The genome isn't looking for that one mutation, nor is Mother Nature or any other mystical force trying to add a sense of direction to what might be complete chaos. Any given gene may mutate. Maybe someone out there can tell me, with a ballpark figure, how many ways any individual gene CAN mutatue ... I doubt there's only one path for mutation per gene. So, we're not looking for one single event and how many times it gets reproduced in all those possible events listed three paragraphs above ... we must talk about ALL mutations that occur in those events. Again, there is no way of telling a priori, given our knowledge of how the genome produces us, whether one particular mutation is going to produce, say, a digestive system better able to handle a diet of processed foods laced with BGH-like chemicals and pesticides or a brain capable of faster speeds in addition to all the parallel processing it already does.
Heck, somedays I'm just happy to have an opposable thumb (one genetic point I like to torment cats about whenever possible ... just imagine how much more mischief they could cause with opposable thumbs!)
(Source for my figures: http://www.lbl.gov/Publications/TKO/03_introducing.html, a Lawrence Berkeley National Lab publication for the Human Genome Project)
> ... does it seem reasonable that this much genetic change could occur through random events, with or without biological selection, within the time frame generally accepted?
I fint it reasonable that there should be far more variation that there is. I also find it a gift from God that there is so little genetic variation within our species ... we have such a hard time, given our level of "civilization" and "humanity", dealing with difference as it is.
Bob
Posted by lizzy cunningham on March 23, 2000, at 17:03:24
In reply to Re: Philosophy 101 or God & depression etc..., posted by Bob on November 6, 1999, at 21:46:30
> wow. even after years of trying, i have never been able to express my thoughts like that, but i think that you have done it perfectly. thank you, bob.
Posted by CC on March 28, 2000, at 1:00:26
In reply to Re: Philosophy 101 or God depression etc..., posted by lizzy cunningham on March 23, 2000, at 17:03:24
Darwin is dead.
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