On 07/01/2011 10:25 PM, Warp wrote:

>    I think you are confused. The modern banana (that yellow one) is
> only something like 200 years old. It's the product of a mutation of
> a single wild banana plant which suddenly started growing that yellow
> sweet version. The wild banana is much smaller, green, full of seeds
> and almost inedible in raw form.
>
>    The mutation in question is actually so severe that the modern banana
> plant is sterile: It cannot reproduce by itself, requiring human
> intervention for cultivation (this happens mainly by transplanting
> underground stems or tissue cultures).
>
>    (Ironically, the modern banana is so mutated that it can be considered
> by all practical means "unnatural", as without human intervention it would
> have died right from that very first mutated plant 200 years ago, which
> makes it a perfect example of gene manipulation by humans, yet people who
> strongly oppose gene manipulation have usually no problems in eating
> bananas.)

Well, there are plenty of other plants that are so mutated that they are 
now incapable of reproducing for themselves but for some special animal 
that farms them. (I might mention, for example, the fungi that 
leafcutter ants culture, for example.) The natural world is full of 
complex partnerships such as this. I don't think you could call the 
banana "unatural".

As for people who oppose genetic engineering, they will argue that 
bananas are OK, because the gene alteration happened "naturally". If the 
gene alteration had happened because of a man in a white coat, that 
would obviously be "unatural", which is bad. Obviously.

Post a reply to this message

>> So mathematics is not science?
>
> No, math is not science.

I concur with Darren.

Science is the systematic investigation of the real world. Math is the 
systematic investigation of abstract systems of axioms of an arbitrary 
nature. Some of these systems may or may not be related to something 
that happens in the real world, and as such may be "useful". But there 
is no requirement for that in pure math. (Applied math is another 
matter, of course...)

Some have asserted that "mathematics is the language of science" (which 
is not the same as "mathematics *is* science").

On the other hand, more recently some have suggested mathematics 
becoming an experimental discipline. (After, e.g., the fiasco with the 
4-colour map conjecture and its proof.)

Post a reply to this message

On 07/01/2011 04:51 PM, scott wrote:
> For someone with no chemistry or biology education past basic
> school-level, that was really interesting, thanks. It answered some of
> the questions I had, and made me hungry to find out more...

The mark of a well-written piece. ;-)

Yes, I too have little chemistry knowledge, beyond what I could get from 
The Osborne Introduction to Chemistry. In particular, the idea of 
catalysis seems bizarre and inexplicable.

If you read a typical encyclopaedia entry, at best you'll discover that 
DNA makes proteins, and proteins do chemical reactions, and that's how 
cells work. It might even mention that there's an RNA step in between, 
tell you which organelles do all this work, and perhaps even show you 
the table of amino acids and which codons code for them.

The reality of the situation, as I wrote, is far, far more complex (and 
interesting).

If a human being had designed the cellular machinery, they would 
redoubtably have designed it as a set of independent little compartments 
that all do their own thing in an orthogonal way, signalling to each 
other as appropriate. But when you read about how /actual/ living cells 
work, you find a tangled mess of haphazard interactions and fortuitous 
reuses of molecules and structures for multiple simultaneous purposes - 
/exactly/ as evolution would predict. It's really a very striking 
demonstration, to me.

If you read a brick-thick tome like The Molecular Biology of the Gene, 
it talks about Daltons and thermodynamic equilibria and van der Waals 
forces and so forth as if you have any idea what the hell it's talking 
about. Only Behe describes proteins as "the motors, gears, pulleys and 
scaffolding of the cell". This explains what it's all about far more 
vividly than any discussion of activation energy levels.

Still, not being an expert chemist, I find myself lacking an intuition 
for how individual molecules of a substance behave. You can sort of 
imagine an amino acid chains as being like a string of beads on a 
necklace. The books tell us that some of these beads are watery, some 
are oily, some electrically changed negative or positive, some are 
acidic or basic, the beads are all different sizes... but it's difficult 
to really visualise exactly how that makes them move. Or, for that 
matter, how some RNA molecules can fold up and edit themselves, chopping 
out introns automatically.

Basically, I lack an intuition for how these molecules float around in 
their environment.

Then again, protein folding is one of the great problems of this decade. 
(Remember folding@home, anyone?) So maybe the chemists don't yet 
understand it either...

Post a reply to this message

> Amazing to see how molecular biology uncovers how the operating
> mechanisms of living cells are not so much chemical as they are
> nano-mechanical.
>
> The "nanobots" are out there already.

The wheel? Nature did it first.
Explosives? Nature did it first.
Powered flight? Nature did it first.
Sonar? Nature did it first.
Electricity? Nature did it first.
Turing-complete computers? Nature did it first.

...and you're surprised that nature has already done nanobots? ;-)

Post a reply to this message

>> The more I read about molecular biology, the more interesting it becomes.
>
> Really incredible stuff goes on. I'm never sure whether I'm more amazed
> that it works like this, or that we can figure out that it works like this.

Indeed. It's not surprising that people win Nobel prises for this kind 
of work.

Take a look at the paper I linked to. Just look at how much statistics 
went into merely checking whether human opioid receptors have changed at 
all, and if so whether it's by chance or due to selection pressure.

(The idea of the human brain containing receptors for opium has always 
bothered me. Opium is a foreign substance that doesn't belong there; why 
the hell would every single walking human have receptors for responding 
to it? The answer, of course, is that they aren't *opium* receptors at 
all! They're endorphin receptors. They respond to the endorphins that 
the human brain itself naturally produces. And yet, even the word 
"endorphin" means "endogenous morphine". How backwards can you get?)

>> Mutations that are fatal are vigorously eliminated by natural
>> selection. And indeed, you can find genes that have barely changed for
>> billions of years. These are the so-called "highly conserved sequences".
>
> I remember reading somewhere that there's a gene that controls how many
> fingers you have *and* something about the reproductive system, so any
> mutation in that gene tends to keep you from reproducing for entirely
> unrelated reasons. Hence the reason why everything from fish to bats to
> birds to people have five finger bones.

Actually I think you'll find it's that all tetrapods are descendants of 
a single fish ancestor, which just happened to have 5 digits. By now it 
would be far too difficult to change it.

Incidentally, you may have heard about the theory that embryos retrace 
their ancestry as they develop. For example, a human embryo initially 
looks not unlike some kind of bizarre fish. Similarly, baleen whales 
initially grow teeth before later reabsorbing them (since their 
ancestors had teeth, but they do not).

Actually this theory is wrong. Embryos do not /literally/ retrace their 
evolutionary history. What /is/ true is that alterations to the early 
parts of embryology tend to bugger up more things than do alterations to 
the later parts of embryology. Not as an absolute rule, just a general 
tendency. The net result is that typically animals change their final 
body plan by changing the later stages of their embryology rather than 
the early ones.

In short, I suspect that tetrapods all have 5 digits because there are 
now highly complex, well-developed and extensively inter-dependent 
systems of gene regulation for building 5 digits. You'd have to change a 
hell of a lot of stuff to make it, say, 6. If you just changed one 
chemical gradient, for example, you'd break so much stuff... it just 
wouldn't work.

If you look at things that aren't tetrapods, you find that 5 isn't so 
special.

>> Speaking of which, here's a thing: Every single living cell in the
>> human body (with a few exceptions) has the exact same genome.
>
> Every single *human* cell. About half (or more) of the cells in your
> body aren't human, tho.

Humans are eukaryotes. Eukaryote cells are apparently *way* bigger than 
bacterial cells. So it's not difficult for bacterial cells to outnumber 
human cells; they're smaller. And while we're on the subject, everybody 
thinks of bacteria as "those things that make you ill". But the vast 
majority of bacterial species have no effect on human health at all. And 
a large number of them are /beneficial/.

(For example, E. coli is well-known for making people ill. But it's a 
normal resident of the human body, and it even "communicates" with the 
human digestive system, telling it for example how much nutrients it 
needs. The human digestive system then absorbs all but that amount, 
leaving enough behind for E. coli (and friends) to stay fed. They are 
symbionts.)

Then of course, there's the theory (presented by Richard Dawkins as if 
it's an accepted scientific /fact/) that most of the organelles of the 
eukaryote cell are actually symbiotic bacteria which have become reduced 
almost to nothing, retaining only their key chemical processes that 
benefit the cell. If it were true, it would mean that basically the 
entire chemistry of visible life is possible due to bacteria.

> I'm not sure why you have a job in IT instead of a job in teaching.

I'm not sure why I have an honours degree in computer science, and yet 
my sister actually gets paid to write computer programs. o_O

Then again, she works in London, so...

Post a reply to this message

Invisible <voi### [at] devnull> wrote:
> Well, there are plenty of other plants that are so mutated that they are 
> now incapable of reproducing for themselves but for some special animal 
> that farms them. (I might mention, for example, the fungi that 
> leafcutter ants culture, for example.) The natural world is full of 
> complex partnerships such as this. I don't think you could call the 
> banana "unatural".

  Well, many people seem to think that anything that is man-made (or only
possible because of human intervetion) is by definition artificial and
unnatural (and hence obviously harmful).

  There seems to be this notion that "mother nature" protects people from
harm as long as humans don't tamper with her ways. In other words, as
long as something is deemed as "natural" (the product of natural processes
without human intervention) it's good and harmless, while anything that is
deemed as "artficial" is harmful (to both people and nature).

-- 
                                                          - Warp

Post a reply to this message

Invisible <voi### [at] devnull> wrote:
> >> So mathematics is not science?
> >
> > No, math is not science.

> I concur with Darren.

> Science is the systematic investigation of the real world. Math is the 
> systematic investigation of abstract systems of axioms of an arbitrary 
> nature.

  Aren't you confusing "science" with "natural sciences"? Natural sciences
study the natural world, but "science" in general can encompass more than
that.

  As for math, would you say that, for example, the branch of mathematics
called geometry studies how the real world works or not?

-- 
                                                          - Warp

Post a reply to this message

On 10/01/2011 12:16 PM, Warp wrote:

>    There seems to be this notion that "mother nature" protects people from
> harm as long as humans don't tamper with her ways. In other words, as
> long as something is deemed as "natural" (the product of natural processes
> without human intervention) it's good and harmless, while anything that is
> deemed as "artificial" is harmful (to both people and nature).

But of course. It's not as if millions of lives around the world have 
been saved by the synthetic compound Tamiflu, not that every year people 
are killed by toxic mushrooms, spiders, snakes and jellyfish.

In fact, you know what? Mankind has spent decades trying to perfect more 
and more powerful nerve toxins. And after years of creating such 
deliberately poisonous artificial chemicals, the most toxic nerve poison 
known to man is /still/ 100% natural. It's called botox. It isn't even 
hard to find.

Post a reply to this message

>> I concur with Darren.
>
>> Science is the systematic investigation of the real world. Math is the
>> systematic investigation of abstract systems of axioms of an arbitrary
>> nature.
>
>    Aren't you confusing "science" with "natural sciences"? Natural sciences
> study the natural world, but "science" in general can encompass more than
> that.

Well, I suppose if you wanted to be really pedantic about it, science is 
the study of that which can be experimentally verified (or falsified). 
Mathematics is /usually/ about what can be logically proven, which isn't 
exactly the same, but... there's perhaps some overlap there.

>    As for math, would you say that, for example, the branch of mathematics
> called geometry studies how the real world works or not?

Which geometry? Euclidean geometry? Elliptic geometry? Hyperbolic 
geometry? Some sort of non-homogeneous geometry?

Pure mathematics studies these geometries purely for their own sake. One 
or other of them /may/ correspond to the real world.

(For example, Euclid presumably proposed Euclidean geometry because he 
thought it corresponded to real figures drawn on real flat surfaces. But 
of course today we know that the universe actually has negative 
curvature, so hyperbolic geometry is probably a better match.)

Post a reply to this message

Invisible <voi### [at] devnull> wrote:
> >    As for math, would you say that, for example, the branch of mathematics
> > called geometry studies how the real world works or not?

> Which geometry? Euclidean geometry? Elliptic geometry? Hyperbolic 
> geometry? Some sort of non-homogeneous geometry?

> Pure mathematics studies these geometries purely for their own sake. One 
> or other of them /may/ correspond to the real world.

  The very word "geometry" means "measuring land" (from ancient greek
geo = earth/land, metri = measurement). Geometry is one of the oldest
branches of mathematics (probably only preceded by elementary arithmetic)
and was, indeed, motivated by real-world applications (such as measuring
the area of a piece of land and dividing land into equal parts by area).

  If that's not science, I don't know what is.

-- 
                                                          - Warp

Post a reply to this message