Sunday, November 21, 2010

Am I Getting Smaller Or the Universe Larger?

I can vividly recall laying on a gurney starring at the ceiling of a hospital with a strange aplomb accepting my simian ancestry. Raised in a conservative Christian environment I had long "fought the good fight" against the liberal scientists that tried to teach people that they were nothing more than monkeys who came from grown up germs. My kind valiantly battled the scientific community who were in our estimation little more than the ideological progeny of the Nazi eugenicists. But, there I was. Starring at the ceiling. Recovering from massive surgery after an appendix explosion gone wrong. As my body was repairing itself I was repairing my thinking. Cooly, calmly I realized that the presence of this vestigial organ that nearly took my life was proof that I am a descendant of the great apes.

Right there I got a little smaller. My dimensions didn't change, nor the room's, but my size in relation to my ancestry, time scale, and universe had vastly changed. It was much akin to the sensation of looking out a plane and seeing, perhaps, not my own house, but the tens of thousands like it and feeling, well, like jack-crap, puny, insignificant and somewhat humiliated that I ever thought otherwise.

It isn't the first time one of these revolutions has happened.

Eratosthenes noticed the differing angles of shadows at high noon in wells and measuring rods. From that he calculated that the world was round. There was a whole other side to it that he knew nothing of! Was there anything there or was it completely void since everything would fall off? Eratosthenes, too, got a little bit smaller.

Galileo, as is familiar to many, noticed the moons of other planets orbiting something other than the earth - Jupiter. Could it be that not everything revolved around the earth? Could it be, in fact, quite the opposite? Perhaps we were the revolving one. The solar system got a little bigger and Galileo got a little bit tinier.

Columbus was headed for the Orient when something got in his way--the "West Indies." There were two whole continents that had previously been unaccounted for. We were quite a bit smaller than had been anticipated.

Darwin, after circumnavigating the entire globe sampling from seemingly every corner of the world, realized that everything living today came from very different living things in the past. Things change. We change. We changed. Like climbing altitude in a plane we can trace the unbroken chain of life all the way back to simple enzymes and RNA trapped in a lipid bubble.

And we get smaller.

Or, does our world just get larger?

Sitting in that hospital room I don't think I got smaller. The universe got bigger. With every discovery, with every unanswered question answered, with each intrepid person that will dare to question, seek and ask our universe gets a little bit more amazing and grandiose. So, the next time you feel puny and insignificant looking out the window of a plane or standing before some personal existential truth remember that crushing insignificance is only one perspective change away from awe, wonder and worship.

Friday, November 19, 2010

Darwin Regrets Not Enjoying the Finer Things in Life

Excerpt from his autobiography:

"My mind seems to have become a kind of machine for grinding the general laws out of large collections of facts. ..If I had to live my life again I would have made a rule to read some poetry and listen to some music at least once every week...The loss of these tastes is a loss of happiness, and may possibly be injurious to the intellect, and more probably to the moral character, by enfeebling the emotional part of our nature."

Saturday, November 13, 2010

Science is Gospel

I don’t watch much news. It isn’t that I don’t care. It’s just depressing. It makes me feel powerless. I have no power to change any of the awful things that are happening in the world and I know it. Furthermore it’s nearly completely one sided - only the awful, the apocalyptic, the disastrous, the crises. They hardly cover any of the beautiful, the inspiring, the moving, the touching. That doesn’t sell. It doesn’t titillate.


One genre of news - science and technology. I read that quite closely. Why? Because there’s always something exciting, new, innovative, revolutionary. It’s a perpetual dawn! You can read the science/tech section of the news and come away saying, “YES!”

Science is gospel.

As many of you from a Christian background may know, ‘gospel’ means ‘good news’ (In Greek it’s euangelion. We get the word ‘angel’ from the same root as the last part of that word. So, I always see a glorious angel trumpeting good news when I think of that word.).  The fact of the matter is that there is great, glorious, good news happening in the sciences everyday - the Large Hadron Collider, genetic mapping and engineering, clean energy, steps closer to fusion, new species constantly being found, stretches of the universe seen for the first time, new fossils exposing our and our relative's past, medical breakthroughs, computer innovations, technological advancements...The list goes on!!!

Bottom line, read more science and technology news. It’s gospel and it’s good for your soul.

Intelligent Design and Falsifiability

Here's the difference between science and Intelligent Design: one is falsifiable and one isn't.

"I believe gravity causes things to become attracted to each other."
"No, it doesn't."
"Fine, let's put it to the test!"
[Apple is let go and suspends in mid-air]

That's preposterous, but at least it's falsifiable.

Here's how the other conversation would go:

"I believe Poseidon created the seas and all that is in them."
"No, he didn't!"
"O, ya?! Prove that he didn't!!"

Do you see the difference?

That's yet another reason why many scientists cry fowl when religion tries to take a foot hold in science. It doesn't follow the same rules as everything else. Science by its very nature has to be falsifiable. Intelligent Design may be a perfectly reasonable personal explanation of how the universe came to be and life and complexity within it, but religion in sheep's clothes can be a dangerous thing scientifically.

Thursday, November 11, 2010

Science is...Childlike Questions

Heather, my wonderful sister and exemplar scientific thinker, has told me a story of discussing with her her grad school advisor about what good science is. He said that good science is good questions.

Good questions are...
  • Focused - neither too broad nor too narrow.
  • Valuable- after having answered the question will our lives be any more enriched? If not, scrap it.
  • Answerable - will you actually be able to answer the question?
  • Insightful - I view getting a bachelors in biology as studying for years to ask one really good graduate school thesis question. All that study for one question. It takes alot of knowledge to ask good questions.
  • Narrow in asking, broad in implication - Heather also spoke of her sage of an advisor stating that a good question is one that may be small, but answers a larger question. For example, a researcher doesn't study planaria reproduction because they want to only know more about planaria. They want to use that knowledge to know something about the whole tree of life, like how species evolve. One doesn't study aphids, one studies a branch in the ecological web as a whole. One doesn't study whale digestion, but how animals convert chemical energy into biological energy. Et cetera.
By implication, science is being curious. It's wanting to know how the world around you works, why it works and what we can do with that knowledge.  

It's wide eyed wonder about the truly ineffably amazing state of the universe around us.  It's mystery.  It's intrigue. It's the excitement of discovery. It's adventure.

Science is being unsettled. Unsettled by not knowing 'why', 'how'. It's not being okay with standard myths, theories, explanations.

Science is being hungry for answers. It's insatiability.

Science is argument. It's caring enough about reality to debate, to confront, to challenge.

Science is holding reality in reverence above all else - popular opinion, dogma, authority, tradition.

That's difficult business, though. Easier said than done. Life is distracting.  
How can we keep ourselves curious? Vested in the nature of reality?  

By staying childlike.
How do children think?
  • With New Eyes - Everyone remembers their first kiss. There is something impactful about doing something for the first time. Children experience that all the time. You've heard it many times (so much so that its lost its impact, haha, how ironic) that familiarity breeds contempt. The opposite can be just as true, new eyes breed wonder. How can you get new eyes again? One way is to study widely. I've learned the most about English by studying other languages. I've only realized my Americanness by traveling to China. Read fringe thinkers. Learn about other fields of inquiry. You may be surprised at the insights you'll gain.
  • Tabla Rasa - kids don't come with baggage. They have no expectations, no preconceptions. They aren't going to look for something a certain way, they just look.
  • Relating It Back to Yourself - I've read Richard Dawkins talk about how personally kids can sometimes answer science questions like, why are flowers pretty? "So I can enjoy them!" the child might respond. While that in and of itself isn't the most model scientific thinking, it does show how that kids naturally have a way of making it about themselves. That can be a good thing. It can be a powerful motivator. If we could empower that same young thinker's mind with knowledge she/he might say something more along the lines of, "Flowers are beautiful to attract insects to carry their pollen to reproduce and I can't help but enjoy how incredibly ingenious, creative, beautiful that mutualistic symbiosis is!!!"  Studying biology for me has been an unbelievable journey of self discovery. Every fossil I read about, every biological mechanism and processy I learn about tells me something about myself by teaching me how I work, where I came from or about the processes that made me. It's personal. And, that is powerfully motivating to keep learning.
  • They Get Dirty - Kids love gross. Why don't adults? Kids love mud. Why don't adults? Kids want to explore more than they want to be proper, to experience more than stay presentable, to satiate their curiosity over their desire to be accepted, adventure over safety. Bottom line, get dirty! You just might remember how good the cool embrace of mud can feel again!!

  • Kids Take Time to Do Absolutely Nothing - You should, too. Remember having summer off? Think about when you have your best thoughts: while driving, while showering, while running, while meditating, while praying, while quiet, while relaxed, while letting your thoughts wander, meander, explore - unguided, unimposed, borderless, unfettered, natural, freeflow thoughts and inquiries. Figure out a way to maximize your time doing those activities. Nothing may be the most important thing you do all day.
  • Kids Keep Asking and Asking and Asking... - I recently went to a presentation on butterflies. The local expert blew me away by how much he knew about species identification, diet, range, migration patterns, ecology, population threats, how to start a butterfly garden, etc. His knowledge was truly prodigious. I was taken aback by how easily he was stumped by the simplest of questions, though: why do butterfly wings have scales? I mean, the most obvious part of a butterfly is its wings and the most obvious part of their wings are the colored scales. So, why hadn't he thought of it? Well, I should be so hard on him. His interests were elsewhere. But, I did learn something that day from that question. Sometimes the best camouflage is obviousness. The most obvious place to look is often the last. One of the keys to exposing these cloaked blatants is to keep pushing the questions. Force yourself to question.  Don’t let it stop at the surface.  Keeping on pushing it and asking ‘why’ one more time and then one more time and then one more time...

This is my life's message. One of the major things that I want my life to represent right now is that it’s okay to question, to change your mind, to go a different direction, change your path. No, no, scratch that. It's essential to question. Questioning is a holy, sacred activity, integral to truly living, truly experiencing, truly seeing. We must not tell reality what she is, only listen by questioning.

Monday, November 8, 2010

Why the World (Probably) Won't Die from a Pandemic

Bird flu, swine flu, H1N1, flu of 1918, SARS, we've had our share of pandemic scares.  All of them are very serious.  Each life lost is one too many.  Each was grave, but somehow they've pretty much faded away.  Why is that?  The triumph of modern medicine?  Well, I'd be remiss to completely discount that but it's not the only explanation.  We can thank evolution, too.

Basically, viruses don't want to kill the hand that feeds them.

They need us to exist.  If we're dead, they're dead (So to speak. Viruses aren't technically living).  Parasites, viruses, colds, bacteria, pathogens, infections only want to be virulent enough to cause us to transmit them, not off us completely.

Have you ever wondered why the heck our nose runs and we cough when we're sick?

Mucous is supposed to be a defense against a cold by filtering out airborne pathogens.  So, when we're sick already, isn't that a little bit too late to start the water works?  It does seem odd, doesn't it?  Well, yes, apparently there is a boost to antiseptic enzymes and immunoglobulins with mucous production, but the real fight is in the blood by white blood cells, not in your nose.

So, could there be an underlying insidious explanation?  YES!  Our nose runs, coughing, sneezing ensues because we've been hijacked by viruses to become giant virus distribution headquarters!  More mucous means we're literally coughing, sneezing and dripping with the pathogen and constantly spreading it.  The most effective at spreading (the most effective at hijacking our respiration system) will survive.  They don't want to kill us; just use us for their bidding.

How does this respiratory means of transmittance cause the pathogen to evolve?  Towards mildness.  Healthy people go out in public and spread the virus more.   Truly sick (or dead) people don't spread the virus effectively.

Cholera is a perfect example of how virulence (potency) of a virus can evolve.  In the 1990s there was a devastating outbreak of cholera in South America that killed more than 10,000 people.  While working to cure the victims, smart scientists were also watching the evolution of the virus to see if anything could be learned to prevent or ameliorate another possible outbreak in the future.  Turns out some incredibly valuable lessons could be learned from doing this.

Cholera is transmitted by two main means: drinking water and food handling.  In countries that had poor water supplies that were contaminated with human waste the cholera evolved to be increasingly virulent to give the person severe diarrhea to reenter the water supply.  In countries with clean water supplies the cholera was forced to be transmitted by food handling.  Guess what?  Only healthy (or at least moderately healthy) people have enough energy to prepare food for other people.  In those countries the strain became milder.

Great 4 minute video on this:

Maybe that's what happened with the Black Death.  Its deadliness killed itself.  We'll never really know. (Other hypotheses exist, like resistance was developed, which may actually confer resistance to HIV/AIDS today in some eurasians."

It's possible the same could happen with AIDS given enough time.  Typically only the healthy pass on the disease.  Only the more innocuous versions of the virus make healthy people.  Only the wimpy version of the virus survive (Hopefully.  Well, if there is a 'hopefully' talking about something so awful.).

Bottom line is, airborne pathogens tend to evolve towards mildness and the world's water supply is becoming cleaner every day which will help with the water borne pathogens.  Hence, we probably won't die from a pandemic epidemic.

...I wish I could say the same for medicine resistant bacteria like MRSA...well, even that if it goes apocalyptic it will eventually have the same evolutionary constraints..."hopefully"...

Works Sighted [sic]:

Sunday, November 7, 2010

Species Cliques

It's hard not to make the comparison to high school.  Cliques most definitely have ways of 'being different just like everyone else' - goth, prep, grunge, rock, American Eagle, hip hop, gangsta, etc.  Organisms do this, too, and the how and why I find intriguing.

Have you ever looked in a bird identification book (maybe that's asking too much) and thought, sheesh there sure are a lot of not just species but different looking birds?  Reds, yellows, greens, browns, blacks, whites, oranges, plumes, streaks, spots, dots, crests, ridges...The shapes and shades are endless.  Why?  Well, one reason you're probably familiar with - males like to strut their stuff.  You got to look good if you want to get the date.  Dress to impress.

But, there's more.  Say you have a bird's brain, i.e. you're a bird brain, how do you easily tell one species from another to know if you can/should mate with them?  Like in the jungle of a high school cafeteria, animals need to know where they fit in.

What's at stake if you make a mistake and mate with another species?  Well, let's take one classic example - the Darwin finches of the Galapagos islands.  Different islands have different foods.  Different beaks are good at different foods.  Therefore, different islands evolve birds with different beaks, each optimized for its diet, be it seeds, insects or cacti.  Spear like is great for insects, plier like is great for cacti and nut cracker like, unsurprisingly, is good for nuts.

Important: each beak is relatively optimized and any deviation from that is a disadvantage (usually speaking).  So, any hybrid cross breading would only take the evolution of that bird down a blind alley that would hurt and not benefit the long term prospects of that species.

So, how to guard against that?

Species have evolved ways to prevent unevolution.  Make yourself different.  Special.  Unique.  Outstanding.  Cliquish.  Mark your kind as different from others.

In the case of Darwin finches, sound different.  Below is a graph from this article that shows the different species unique vocalizations.

Next example: cichlids.

These cute little African fishies come in a kaleidescope of hues.  Experiments have been done to demonstrate this rainbow of colors isn't just for the pet trade, but is an ingrained programing and color coding system to keep it within the family so to speak  (conspecific mating).  Why?  Remember, to hold on to advantageous adaptations and not have them watered down.

Don't think this is limited to visual cues.  Olfaction is a big player for insects (like butterflies that can often be similarly colored - especially in mimicry where non-poisonous species try to look like poisonous species like the Monarch and Viceroy butterflies) and cave dwelling fish (even some cichlids!) and the visually easy to confuse Coral and Milk snakes (also mimicry).

There is another side of the coin.  It's common knowledge that inbreeding can fix diseases and mutations in a population.  It, like everything, needs to be a balance.  Too much of a good thing gets nasty.

Example 1 of this: humans!  Social taboos keep us from mating with our siblings and relatives.  It's also been shown that we tend to not find the smells of close relatives sexually attractive.

Example 2: petunias (click on for article).

These cute, common garden plants have molecular markers (antigens) attached their their pollen that make it possible to distinguish their own pollen from that of another petunias.  Because they want genetically diverse offspring they have evolved ways to give preferential treatment and position the foreign pollen to the front of the fertilization line.

It's an interesting thought to think about how these two forces play an evolutionary tug-of-war within species. Species both want to maintain their identity and specific adaptations as well as maintain genetic diversity to avoid genetic stagnation and inbreeding.

Maybe this is why some birds continue to acquire new displays.  Maybe elaborate displays like plumage aren't just the handicap principle.  Maybe it's females constantly trying to make sure their little youngins have fresh genes.   Take for example the Mandarin duck, the craziest duck you've ever seen (Please take your time examining the detail in the plumage.  Truly an evolutionary marvel).  They don't just have one really spectacular feature.  They have dozens.  Each display being maintained to distinguish from other species, but added to in order to show genetic diversity to potential mates.

You might think of it like a bullseye.  The female is the center of the bullseye and doesn't want to mate with males also in the center, i.e. very close to here genetically, nor males hardly related to her at all.  It's the in between sweet spot that evolution seems to shoot for (unintended pun).

Works Sighted [sic]:

Monday, November 1, 2010

You Are Bacteria

Endosymbiosis is the theory that eukaryotic cells (advanced life, like our own) evolved by the combination of simpler prokaryotic cells (bacteria and archaea).  For example, our mitchondria have their own DNA, they have ribosomes similar to bacteria, their walls and cristae look like they're bacterial and they divide like bacteria.  Ergo, they were once bacteria.

It doesn't end there.  This theory may also explain a number of other organelles like flagella, cilia, peroxisomes, centrioles, etc.

Really put into imaginary motion what that means.

You aren't one thing.

You're a host of organisms working together.

You aren't a human.

You're a collective of bacteria.

It gets worse.

If you were to count out all the cells in your body you'd get about 10 trillion or so (I've seen varying estimations of this and the next number).  If you were to count out all the bacteria cells in your gut, on your skin and every where else you'd get...drum roll...about 100 trillion.

Let me spell out what that means.

You're 10 times more bacteria than you are human (which is already a bunch of bacteria!!)

Let me say it another way.

You're about 90% bacteria.

I hope that messes with your head some.  It has mine. :)