Wordjumble and Tennyson

Midway through

Stephen Jay Gould's

 "Dinosaur in a Haystack",

I reached his essay 

on Lord Alfred Tennyson.

unfortunately, 

due to the epic 

(really; sans hyperbole) 

nature of the work, 

the broad flavor of the piece

 is impossible to communicate

 without direct experience 

(like anything worth anything).

However,

if you're either an English major,

or you've read Gould's bit,

the following should make some sense.

If that's not the case, let it at least rouse your curiosity

for a poet in deep (by modern reckoning) time.

*you can generate these remarkably useful arrays here.

Sapolsky (egads part 2)

"Egads!" A more qualified voice 

has been found to elaborate on

the tiny bit of 

sociobiology and evo-psych 

mentioned last time unit.

Aside from being an all-around awesome scientist/writer, 

Robert Sapolsky (paired with Stanford University) 

has brought his 

"Human Behavioral Biology" course to Youtube.

As if there were not already 

enough things to admire 

about his  communication M.O..

he is explicitly careful, 

from the start of things, 

to provide a cautionary  warning 

about "categorical thinking": 

that is, the danger of being stuck 

in so-called 'buckets' (or "-isms")

of interpretation.

Why might this be useful, and how does it tie in?

Don't be alarmed by the length, 

the part we're interested in (albeit myopically) 

starts at just past the one-hour mark.

However, the whole video (series) is unequivocally worth watching: 

it's extremely helpful to note 

that this course was designed so that 

individuals don't necessarily need to come from 

a canonical science background, 

which amounts to a friendly 

(rather than blistering) 

rate of introduction to the material.

A couple quick notes:

Sapolsky's commentary on

contemporary refinements of "group selection" theories

 seems roughly parallel  to the 

"Lamarckian evolution"/epigenetic inheritance controversy.

Why bother to try the analogy? 

Well, it helps to illustrate a trend in biology to 

develop a theory which may be false 

as a dominant mode or mechanism, 

but one that may accurately predict an outcome 

of some other theory when 

a special set of circumstances are applied. 

In a very loose analogy to physics,

the dynamic is akin to the 

seemingly dichotomous relationship 

between classical "Newtonian" models 

and Special Relativity.

The first model, when applied over the whole range,

fails to accurately explain certain phenomena, but 

can be fully accounted for 

by the predictions of the second theory.

The most abstracted way 

to summarize the importance 

of such a review is the following:

"assumptions about evolutionary hypotheses 

cannot be made from within an absolutist standpoint, 

(such as the notion that every trait is adaptive) 

but must be accountable to 

empirical scrutiny at all levels, 

such as genetics or population mathematics."

Another great point that was highlighted described Gould's "spandrels", 

which ties in perfectly to the anthropocentric fallacies of the Cabbages post. 

Once again, it seems there is a nearly irresistible tendency 

to believe that evolution somehow strives for/achieves "perfection" 

as opposed to "just good enough".

Tremendously complicated arguments,

but absolutely critical to an understanding of evolution.

Hopefully, this post was a fair treatment that sparked your curiosity.

If it didn't, SPARK.

Readers who are still interested:

Let's meet here at some point in time, but only when entropy has increased.

Footnote to Cabbages!

A few posts ago, 
i threw out the term 
"junk DNA" 


which linked to a wikipedia page titled "noncoding dna", 
with the full intention of returning 
to flush out the controversy and nuances of the term
when qualified to do so the time provided itself.

[Farnsworth] Good news everyone! [/Farnsworth]

As it turns out,

the [adjective for unspeakably vile] ID propaganda whores 

over at the Discovery Institute

have provoked an excellent opportunity for science education.

(as opposed, of course, to their usual mis-education)

Boy, if i had a nickel ...

How'd we find out about this?

It just so happens that fellow truth crusader scientist Larry Moran over at Sandwalk

has done a fantastic job of dissecting the junk (science, that is) 

while at the same time providing a wonderful exposition

 on the whole non-coding 

paradox 

(as in, mystifying but resolvable problem).

And by dissect, i of course mean: 

torn apart bit by bit 

with the white hot intensity of a thousand suns 

and the precision of optical tweezers 

paired with photothermal nanoblades. 

The discussion is well underway (multiple parts already posted), 

so this link will take you to the most recent aggregation of the posts. 

[Pause for breath]

Embedded in the earliest post, 

Larry included this gem of a link from

evolutionary biologist  T. Ryan Gregory 

over at Genomicron...

...whom we can thank for transmitting this excellent quote into the blogosphere:

"If we take the simplistic assumption that the number of genes contained is proportional to the genome size, we would have to conclude that 3 million or so genes are contained in our genome. The falseness of such an assumption becomes clear when we realize that the genome of the lowly lungfish and salamanders can be 36 times greater than our own."

*Attributed to Susumu Ohno 

Needless to say, i was ecstatic 

to find this in my interweb wanderings, 

and hopefully now i've given the topic 

a more rigorous appraisal.

Tune in next time for tuna!

Egads! new stuff....

Taking advantage of the full capabilities of Google Reader, it has become painfully clear that this blog can offer very little original content in the way of scientific discoveries, ideological controversy, or dazzling images that frequently decorate the portion of the blogosphere represented to the right of this post (sort of).

However, that's no reason to stop trying.

But certainly, in terms of format,

there may be some modifications.

Today, let's tackle a few bits of

controversy 

(pronounced with British syllabic emphasis, Attenborough style) 

from the "softer" science of anthropology/sociology. 

[yes, separate but overlapping fields]

Why those two fields? Well, a few of the topics deal with culture, so naturally, it falls into certain realms. What gives me the right to intrude into such academic territory? Not a damn thing, save curiosity and access to Google, but why limit discussions to ivory towers?

With that being said, 

i'll try to be mindful of 

the usual cliched bunk science 

that floats around far too often

Like "evolutionary psychology" theories that seem to
carry their merit in persuasiveness as opposed to empiricism:

Cue the following: "Evolutionary theory says”
Tsk, tsk Tim.
That should read "evolutionary theorists..."

Or, put in a slightly more serious tone

the work of  Jon Wilkins' webcomic character

Guillame (the adaptationist goat)

who has more explicitly pointed out problems with this approach.

A stupendous analysis of the fundamental controversy can be found both here and here

The second link, while admittedly more dense, is the most thorough elaboration I've yet come across.

Then, of course, 

we also have to be careful 

to avoid the faintest whiff of 

any scientific racism

(a hot and happening phenomena in the Victorian era).

The typical arguments (ran) run along the following lines

"We [observer group] note

a set of conspicuously absent features in

you [less "us-like” successful group]

and can only conclude that this absence

left you crippled in some critical way/and or elevates us to superiority”

Or, less abstractly and suitably scathingly:

"Well sir, we didn't notice the local tribe* performing any Shakespeare or Judeo-Christian rites, so naturally, we assumed they were only fit for plantation labor."

(It's a perversely well-rooted argument,

in that it crops up frequently

and resists attempts at eradication.)

Speaking of asterisks, this brings us to the next point.

While I'm vaguely familiarized with 

the idea of certain vocabulary 

in anthropology/etc being specifically defined

(think of words like tribe, group, etc),

satisfying the necessary pedanticism is counterproductive.

The goal is to start asking questions, not censor language prior to asking.

There is, of course, one important exception to 

this otherwise blatant disregard for academic nuances:

the idea of "race".

The views of the author, strictly for discussion purposes, are as follows:

"biological variation acknowledged, discontinuous cultural categories discarded".

With this absurdly long introduction out of the way,

the next posts can cut right into the thick of the ideas,

namely:

cultural relativism and diversity, ethics and paradoxes of globalization, 

and science-based rationalizations 

shoring up an ethnocentric condemnation 

of  certain Japanese gastronomical practices.

Join me next time,

in my endeavor to be a not-racist explorer

in these infinitely tricky questions.

Or...don't. 

It's your choice.

DNA and complexity: terribly sorry, cabbages might have us beat...

*not part four of the consciousness thread, but something else entirely mostly*

Astute readers 
may have picked up on the 
superficially counter-intuitive
commentary on complexity
in last [time unit]'s post:

"So, it could be something as 'simple' as a bacteria, a virus, or fruit-fly?"

The reasoning for the quotation

(aside from an acknowledgement 

that the term has a fairly loaded 

and non-universal set of connotations)

was meant to hint at the enormously challenging problem

of reconciling our views of  the "complex"

with what actually exists.

Ah, hang on now, mate, 

you've lost me with 

your seemingly pointless 

abstraction...

Well, starting with the premise that 

the use of the word "simple" in the previous post

met with no intuitive objections

(unless you're in the field and know the hook to be baited),

let's ask the question:

"Why is it that we can easily imagine [bacteria/viruses/fruit-flies] as simple?"

Ah! you're sneaking up on word-mongering...

Why are we asking this "why" question?

Given that we, 

either as a species or as a culture,

(let anthropologists decide)

seem so keen on the idea of... 

...flaunting our complexity, IE;

"Ah, but you see a monkey could never have written Shakespeare" or 

"A computer will never be able to write a great symphony!"
[or perhaps more unnervingly, the following image]

and... 

...given that this blog has

 managed to blunder about 

haphazardly

 in topics that concern

 human "human-ness",

...we'd better be damn sure what we mean when we talk about complexity or it's funny little complement, simplicity.

So, to the why question!

Yes, why is it so easy to think of these things as simple?

Well, perhaps we encode values for "complexity" 

based on the functions 

we have observed about an object...

In this case, it might be very easy to dismiss 

the microbial world as somehow simpler

 than we naked apes,

but only because we get by

by imagining them as little black boxes,

with their inner workings obscured 

nearly permanently

 from us 

throughout all our encounters with them (the microbes).

So where are we going with this?

Part of the inspiration 

for this post

was a remark by the geneticist Steve Jones

on a BBC Radio 4 program called the

"Infinite Monkey Cage", which went something like the following:

"I think the biggest question [in biology] is 'Why are there so few genes?' As everybody knows, we've sequenced the human genome, and we can now do it with extraordinary speed...
...now that we've read it off, it turns out that there are remarkably few genes
-when I was a student some years ago, around I'd say...the origin of the universe more or less, we used to believe (and we were told) that there were hundreds of thousands of genes, possibly millions of genes to make anything as beautiful and elegant and generally marvelous as, for example, me. That seems reasonable.  

It now turns out that there's only about 24,000 genes...to make a human, and that's less genes than it takes to make a cabbage."

So, at first this may strike you as an affront to our human special-ness (read: complexity) -and it may well be- but consider the question "Why are we surprised that a cabbage has a larger genome?" which ties in quite nicely into the early bit on complexity.

I suspect,

posited the blogger boldly,

that our surprise has to deal with ideas like 

intelligent design being special special-beings,

which have been particularly difficult 

to completely eradicate.

Now, I could talk about the really messy (and wonderful!) intricacies of 

DNA, information theory, and (formally defined) complexity...

...except that I am not qualified to do so.

Instead, I'll throw out leads like "junk DNA", "irreducible complexity", and "neutral evolution" 

to whet your appetites for a more thorough and rigorous treatment of the topic. 

(For those of you who protest the use of Wikipedia, sod off, it is only Wittgenstein's ladder a tool) 

If you're relatively familiar with cell biology (and even if you're not),

 Skeptic Wonder has a fantastic defense of neutral evolution that can be found here, 

which jives quite well with the following video (and quote):

"Well, many biologists will tell engineers and others, organisms have millions of years to get it right, they're spectacular, they can do everything wonderfully well. 

So the answer is biomimicry -- just copy nature directly. We know from working on animals that the truth is it's exactly what you don't want to do. 

Because evolution works on the just-good-enough principle, not on a perfecting principle. And the constraints in building any organism when you look at it are really severe. Natural technologies have incredible constraints. Think about it. 

If you were an engineer and I told you that you had to build an automobile but it had to start off to be this big, then it had to grow to be full size and had to work every step along the way. Think about the fact that if you build an automobile I'll tell you that you also inside it have to put a factory that allows you to make another automobile."

So what is this all building towards?

Consider the next hypothesis: 

Is it possible that the reason we're surprised by 

our evident lack of complexity (and things like non-coding DNA) is because

 we still cling, perhaps subconsciously, to the notion that we are exquisitely crafted for existence, 

with each bit and codon fixed perfectly for our lives, 

and not a hair more or less? 

"Left as exercise for the reader" 

For those of you protesting that we've looped back inadvertently on the debate around the anthropic principle (or similar ideas), yes, this is a possibility, but it may have been worth the ride.

See you in the future!

part three...where do we go from here?

Hello again, internet.

Last [time unit], 

we started diving into 

the dizzying array of complexity within

 a generic cell in the human body.

While the beauty of such a system 

might leave you mystified even at the nth glance,

it still might be easy to dismiss the automation

as independent of consciousness.

What are you implying by 'independent'?

Well, in a simplistic nutshell,

imagine David Bolinksy  

hadn't told us

this was a human cell.

So, it could be something as 'simple' as a bacteria, a virus, or fruit-fly?

Exactly! 

[Forgiving the architectural differences

 between eukaryotes, prokaryotes, and viruses]

Ok, so it's hypothetically not a human cell. Why is this relevant?

The relevance of this extra bit of information is all based on 

the audience's range of reactions to the images presented. 

When we might think of a bacteria, fruit-fly, or (especially) a virus, 

we're not surprised at all to imagine they are governed by some 

fixed, instinctual behavior. 

We don't ever have to engage in a debate of free will, 

because we've short circuited the debate by 

not endowing them with any form of consciousness.

 In fact, this jives quite well 

with our understanding of such critters. 

Think about the language we use to describe biological experiments with such species:

terms like "programming", "genetic code", "molecular machinery", et al.

Okay, fine. So little bugs are like robots. 

I'm cool with that.

What does this have to do with consciousness?

Well, here's where it gets complicated(ish).

There are vast expanses of our biology

 that use the same fundamental ideas and terms as

the research tinkering with E. coli etc. 

e.g.;

"Mr. So-and-so, the lab tests came back and we found that 

your body has a genetically-based

 inability to manufacture a certain enzyme..."

Okay, yes, you might say, I'll admit that some parts of my body are automated in a sort of predetermined way. Perhaps it's time for some more powerful examples. 

When you, internet,

woke up this morning,

I'm sure the first thing you thought about was the need to 

change the way your heart beats as you get out of bed. 

When you, internet,

opened your eyes from the darkness of dreamland,

and assaulted your retinas with cascades of photons

from the small whale oil lamp,

I'm sure you remembered

to contract the ring of muscles in your eye

that we call the iris.

When you, internet,

prepared breakfast,

I'm sure you remembered to 

tell your salivary glands to get to to work

pumping out a concoction of enzymes.

I'm sure you also placed careful attention

to making sure your esophagus 

moved in smooth, wavelike oscillations

in an effort to deliver the food effectively

to the roiling pit of hot, frothing hydrochloric acid.

You probably then went on to make sure your stomach 

communicated with the rest of your body 

to suppress your appetite.

Okay, so far this has been far from earth-shattering.

I'm comfortable with the idea that bits of my body are 

beyond my control. 

So what if digesting my food doesn't require conscious thought?

That's an understandable objection.

After all, that was only 

a (staggeringly) brief list

 of bodily functions that

 we're already accustomed to not controlling.

I'm sure that when you last fell asleep

(after carefully telling your brain to shift to the proper mode)

you remembered to keep breathing.

I'm sure that as you drifted off to sleep 

by counting prime numbers,

you reminded yourself to keep the steady pace

of inhaling and exhaling

making absolutely certain to keep the flow of air to your lungs

constant.

I'm sure that when you got out of bed,

stumbling across the room as you shake off the stupor,

you remembered to remind your legs

the perfect sequence for balancing.

After all, you might give a lot of thought to 

the same process while...hiking, or rock climbing, right?

Ok, I see where you're going with this.

But the claims you make implicitly in the examples

are totally uncontroversial.

I mean, hey, can't I walk and talk at the same time?

What about more intimate examples?

I'm sure that you, internet,

while [commuting verb] to [place that's not home]

you reminded your brain and ears

to be on the lookout

for that certain song from [memory lane].

I'm sure you perused the incoming information,

the beats, the tones, the hums,

the snippets of lyrics and fractions of symphonies

diffusing out from the construction crew doing roadwork,

the latest i[device],

or the obnoxious sub-woofer.

I'm sure you then compared all these bits of audio

to the data-bank inside your memory

scanning and analyzing

patterns, genres, reflections,

permutations,

searching for a link across time

to a forgotten musical fingerprint.

I'm sure you then chose to recall said song

in all its glory

replaying inside your mind's eye ear

again for the first time in [x]

and again

and again

 and again.

Okay, yes, this I can deal with. 

Assign some functions to the subconscious, 

that's fine.

But there are still plenty of things

(that are not formally called instincts)

that I know I choose to do.

What about really complicated parts 

of our consciousness,

like...love 

(romantic or otherwise)?

Ah, what an excellent point you bring up.

After all, it does sound a little cheap

to say that something as complex 

as the rush of emotion

you feel

when seeing the face of a loved one

can't possibly be explained 

by a surge of chemicals

or a wild-firing of synapses

deep within the brain.

I'm sure that you, internet,

upon seeing for the first time

your [current significant other],

were reminded of the 

decision you made

 earlier in the day:

to carefully scan the sweep 

of your visual field

searching all the while

for a face (or body) 

you had preconceived as beautiful.

I'm sure that upon seeing 

said significant (other),

you reminded some neurons deep within your brain

(and perhaps elsewhere)

to let loose the love signal!

I'm sure you reminded your eyes,

instead of jumping butterfly-like

from point to point 

at a frenzied pace,

to stop

and smell the roses.

I'm sure you reminded yourself to be 

more mindful of your posture, your smile, 

and set your heart beating, just a little faster.

 Perhaps there was even 

increased sweating involved

...all deliberate, of course.

Aha! Your clever attempt at swaying my opinion has failed.

I, said the internet boldly, am no silly romantic.

I don't believe in this whole "love at first sight" thing.

Fair enough.

Perhaps you'll want to stick around for the future

(you'll be there anyway, if you're lucky).

In the next part, we'll take a stab at

some kinds of takeovers of consciousness

the instances of veritable "body snatchers"

in the lives of mice and hominids.

If you've read this far, stop.

It's okay, the post is done.

Go about your business.

part two...if you're still around

hi there!

I don't know about you, internet, 
but I'm one of the bandwagon riders who ascribes to 
this thing called the "germ theory of disease". 
I know, I know, it so mainstream and all, 
but the quirky thing about science is that 
to be a hipster, you're guaranteed to either
 be a yet-unnoticed revolutionary or a quack
 (these categories can even overlap for a single individual).
 I'm sure the miasma theory still has some adherents, 
mostly the mosquito lobby, certain South African politicians, 
and Jenny McCarthy. 

Hey don't you think  throwing in 

a concerned parent's take on autism is 

a bit hyperbolic given the contents of your list?

No.

"Mistakes are as serious as the results they cause!"

...returning from a potentially caustic diatribe...

So if you're one of those folks who
 openly spits in the face of Pasteur 
-which is fine; science has no gods beyond the reach of criticism- 
this next bit might not jive so well with you. 
Read it anyways. 
Worst case, you find out you're wrong 
(and you're now made smarter for it), 
best case, I'm wrong, and you have further kindling for your debate. 

Part of the cool  thing about our bodies

 is that so much complexity is racing around 

at mind-boggling paces and  reactions,

all hidden enigmatically beyond the veil of our awareness

...or something.

But, to better illustrate this, 

let's scuttle across the interwebs to 

the work of a hominid called David Bolinksy, 

who brought the world this astonishing gem:

(Or, if you're particularly impatient and want to skip over what is really an eloquent prelude to the actual artwork, click here.)

"These are expressions of truth as awe-ful things, 

by meaning, they are things you can worship. 

They are ideals that are powerful, 

they are irreducible, they are unique, they are useful

 - sometimes, often a long time, after the fact."

I've promised to keep the posts on the shorter side for your viewing pleasure, so I'll break this one off here, but the goal is to get you thinking about the weirdness of a cell, the automation, the machine-like beauty of it all. 

And hey,

if you should come out of the experience 

with a sense of awe for the beauty of life,

well

that wouldn't be too bad.

Stay tuned for more, if that's what you're into.