word of the day

spannungsbogen:

A Fremen word (from Frank Herbert's Dune) used to denote the self-imposed delay between desire for a thing and the act of reaching out to grasp that thing.

how i got my book of mormon

I was walking home from work the other day when a couple of older teenage boys wearing white dress shirts and black dress pants approached me. They asked me my name, asked me about how my day was going, and about where I worked and went to school. I already had them pegged for Mormons on first glance, so it was no surprise to me when they told me their names and mentioned that they were from the Church of Jesus Christ of Latter Day Saints.

Now, I'm sure some people dislike being interrupted by proselytizers, and some probably get downright rude with them, but personally, I enjoy talking to them. Besides, they seemed real nice (as most proselytizers do). They asked me if I knew anything about their church, and I mentioned that I watched a lengthy PBS documentary about them on TV. I added that it most likely misrepresented them in certain regards, as many TV documentaries do with controversial topics. They asked me what I remembered from watching the program and I replied that I knew the story about Joseph Smith being given some kind of vision to go to a hill in America and dig up some golden tablets that had been put there by ancient people or angels or something. Once Smith found the tablets, he translated them, and they became known as the Book of Mormon.

At this point they seemed impressed that I actually knew something about their history, and started talking to me about the Book of Mormon and how it was inspired by God or Jesus or whatever. The funny thing is, I have actually been trying to get myself a copy of the Book of Mormon for the last year or so, but never got around to arranging a house-call from them. This really seemed to take them aback. So far, I must have appeared very interested in what they had to say. In fact, I'm interested in pretty much every religious belief, but the bottom line is that I think they're all just as crazy.

Anyways, they told me they could arrange to stop by my apartment later on and provide me with a copy of the book. This is when the discussion got interesting, as they finally popped me a question that I had been anticipating:

Mormon #1 (currently smiling): "So which religious belief do you hold?"

Me: "Actually, I'm an atheist. I don't hold to any religious beliefs or faith in gods."

Mormon #2 (smiling as well, but a bit puzzled): "You don't believe in a divine being?"

Me: "I think it's possible that one exists, but for all practical purposes I don't think it's very likely. I don't believe in a divine being any more than you believe in Zeus or Thor. Every religious group believes that their particular god exists, and rejects the gods of other religions. I reject all of them."

Mormon #2 (very concerned now): "So what is your belief about how all of this beautiful stuff around us came to be?"

Me: "I believe in a gradual, step-wise evolution of life on Earth, based on natural principles, as being the only real explanation for complexity. It's not really a belief though; I just accept it as the best available explanation, as I do with any other scientific theory."

OK, so far the conversation was proceeding pretty much how I figured it would have. It's probably not very often (although perhaps more often than it used to be?) that these two run into an atheist who is willing to stop and talk with them about god and beliefs. But back to the conversation...which continued pretty much exactly as I figured it would:

Mormon #2 (pitying me?): "So you believe that all this stuff around us came about by accident?"

Me: "No, I told you that I accept evolutionary theory as the best explanation. Raw mutations may be random or accidental, but natural selection most definitely isn't."

Mormon #2: "So you think it's possible that cars parked along the street over here could have popped into existence out of the ground?"

Me: "You're probably thinking of the 747 argument, where junk in a scrapyard gets hit by a tornado and randomly arranges itself into a Boeing 747. But that's not a good argument against evolution because it isn't how evolution works. Evolution is gradual, starting with small, simple things, and slowing tinkering with them over 3.7 billion years...and counting. The 747 argument is actually a better analogy of how creationism works, with stuff just randomly popping into existence based on the whim of some kind of creator."

Mormon #2: "I've taken some classes on evolution, but when I look at the complexity of the human body, I can't believe that a random process can give rise to such intricacy and coordination."

Me: "But that complexity didn't happen all at once. It happened gradually over 3.7 billion years. Just like how these cars along the street are more complex than the cars that were first churned out on production lines...humans have tinkered with them over time, selected good ideas, good designs, and the result is a higher level of complexity."

Mormon #2: "But what about the big bang? Since energy cannot be created or destroyed, the universe must be infinite."

This part really threw me for a loop. I had no idea where he was going with this infinite universe thing, as it actually supports my argument of no god more than it supports his argument of a loving god. Oh well.

Me: "Well, I don't think the universe had a beginning either. The big bang was likely just one of many that have occurred throughout the history of our universe."

Mormon #2: "I believe that the big bang theory is false, and that god created all matter in the universe."

Me: "Umm, OK?"

Mormon #1: "So you really think that that car over there could have descended from a smaller car or toy car of some sort?"

Me: "That's not how evolution works! You're still starting off with a car, but in reality, it would be more like a wheel or a ball rolling down a hill. The point is lost though because you can't use non-living examples as evidence against an idea that only works on living organisms."

At this point they appeared to give up, and I could tell that they wanted to get rid of me and move on to someone else. They were extremely nice about it though, and changed the subject back to my earlier request for a Book of Mormon. I think they wanted to find out why exactly I was interested in getting a copy of it, now that they knew I was an atheist. I explained to them that I like to read up on different religious beliefs, and that I have a rather large library of religious books at home that I study from time to time. Mormon #1 offered me his personal copy of the Book of Mormon, as well as a card with a phone number and a website where I could get more information and arrange for a house-call.

I'm actually thinking about calling them up and having them stop by my apartment. I enjoyed discussing god, religion, and science with them, even though they were totally ignorant about evolutionary theory and a lot of science in general. I was surprised that Mormon #1 knew about the first law of thermodynamics (aka the conservation of energy), although he apparently didn't know that even though energy cannot be created or destroyed, it can be transformed into other forms, i.e. matter. From my understanding of the big bang theory (which I will admit is fairly limited, as I am more interested in evolution and abiogenesis), at T=0 (time equals zero) of the big bang there was only a singularity, which had an insane amount of mass. When the bang occurred, it exploded and released matter and energy out into space. None of this implies, or requires, the existence of a creator. Right now we don't know what things were like before the singularity, which is itself simply a theoretical limitation in our current understanding, not a physical beginning. An infinite number of universes may have been in existence before the big bang, or they may even exist all around us.

Anyways, that's how I got my Book of Mormon.

the emergence of life

On this blog (and as much as possible in my day to day life) I often try to emphasize the importance of evolutionary theory; chiefly as a valid explanation for how all forms of extant life came to exist, but also as a mechanism creating many different kinds of complex systems. To a large extent, evolutionary theory has entangled itself into my worldview and changed the way in which I view myself and the world around me.

One important aspect of evolutionary theory that I do not focus on as much is the origin of life. Or rather - as Sidney Fox would have me say - the emergence of life. The difference between "origin" and "emergence" is an important one that I will elaborate on further down in this post. In order to rectify this problem, I have recently started research into the history of our understanding of origins.

First off, I should refer to what is commonly taught as the definition of "life" in modern biology classes: life is a form of matter that can reproduce, metabolize, grow, and respond to stimuli. Special emphasis is sometimes given to the ability of life to replicate itself without relying on external processes for help, e.g. a cell is alive because it can divide without needing direct assistance from outside sources, while a virus (see below) is not technically alive because it must hijack existing cellular machinery in order to reproduce.

While many people would claim that the origin/emergence of life (abiogenesis) is a discipline outside of evolutionary theory, I think it is quite definitely an integral part of it. I have come to understand that the origin of life relies quite heavily upon natural selection and other evolutionary forces. Perhaps the reason many try to separate the two is because creationists often attack what they believe to be flaws in our understanding of abiogenesis and throw the whole evolutionary "baby" out with the bath water. Efforts to teach others of the importance and validity of evolutionary theory should not resort to cutting out the controversial parts, i.e. abiogenesis, in order to shoe-horn people into accepting other aspects of the theory. The fact is that most of the controversy over abiogenesis lay amongst conservative religious types who let their presuppositions, rather than the evidence, dictate what ideas they accept. Of course there is controversy among scientists who do origins of life research on how exactly life may have emerged, but there is a consensus that it did emerge via natural processes discoverable by scientific methods. It is like any other scientific theory, resting both on a factual premise and ideas about how exactly it works.

As for the difference between the "origin" and the "emergence" of life, it is largely required because of our tendency towards discontinuous thinking. We would prefer that there was some kind of grand Origin Of Life point, a discrete point in time where life on Earth began. This kind of origin story is not very likely, but it may be the one that most people envision in their mind's eye when asking big questions about life on Earth, and it may be why many don't buy into the whole abiogenesis idea.

To make my point more clear, let me state something that I believe to be truly ridiculous (and most origin of life scientists would probably agree with me): Life on Earth originated at 2:05 PM on a Wednesday afternoon, 3.7 billion years ago. This statement makes it sound like there was no life at 2:04 PM, and then suddenly at 2:05 there was. It is as though something magical happened at 2:05 that breathed life into something.

What is more likely is this statement: At 2:05 PM on a Wednesday afternoon 3.7 billion years ago, life on Earth emerged. Life, being a term most difficult to acceptably define, is not a binary quality, whereby one minute it does not exist and the next it does. Life emerges from existing matter, but only because of our shaky definitions of life. In order for our definitions of life to mean anything in day-to-day conversations, we have to give it some discrete values that separate living matter from nonliving matter. But the difference between living and nonliving is a fairly grey area, a kind of step-wise increase in properties from what we define as nonliving "towards" what we define as living.* To put it another way, while inanimate matter was emerging into animate matter over millions of years it was not doing so with the goal of becoming alive. It was not sitting there, evolving, hoping that one day advanced living organisms could look back at pick out some point in time where living matter first arose. Our opinions about life's origins tend to be skewed due to hindsight and our always-present anthropocentricity (wow, I actually go to use that word!).

As in any other case of evolution, life on Earth probably began as a very simple form that may have had one or some of the properties that we now give to living objects, but this form was not something that we would call alive. In the 1950s, Sidney Fox did a number of experiments on proteinoid microspheres, which were simple protein-like amino-acid chains with a very basic membrane that spontaneously formed when placed in a solution of aspartic and/or glutamic acid and given a moderate amount of heat. Many of these proteins had properties of modern enzymes, although their catalytic abilities were nowhere near their modern "descendents", which have evolved much higher efficiency over 3.7 billion years. Fox suggested that these microspheres became the building block upon which life eventually emerged after they evolved the additional properties that we give to living organisms.

In his book The Emergence of Life: Darwinian Evolution from the Inside, Fox stresses the importance of constructionism; that is, the scientific value of postulating possible starting points and then moving forward from there (the "Back to the Future" approach), rather than attempting to move backwards from what already exists. It is extremely unlikely that life emerged from molecules with modern counterparts. Instead, there was probably a gradual transition from inanimate to animate via very primitive molecules. The molecules upon which life was built may not even exist today!

In more recent studies, RNA has become the focus of much origin of life research. RNA (a single-stranded nucleic acid) used to be known purely as a molecule involved in intermediate information transfer between DNA and proteins. That is, RNA is transcribed from DNA, transported out of the nucleus in prokaryotes, and is then translated into protein by cellular
machinery. This is the "central dogma" of modern biology. However, it has been discovered that, in fact, RNA has many catalytic properties, which was previously believed to be something unique to proteins. RNA can not only transfer information, but it can actively assist in cellular activity like translation (ribosomes, the cellular translation machines, are composed largely of catalytic RNA). These kinds of RNA molecules are known as ribozymes.

Ribozymes are important because of one of the properties that humans have assigned to living forms - the ability to reproduce. Although RNA is single stranded, it will often fold back on itself in a kind of hairpin formation and hydrogen bonds will form between complimentary nucleotide sequences. The ribozyme may then cleave itself, emitting a "child" template that can form more complimentary copies and reproduce further via self-cleaving.

Studies into the emergence of life have shown us a number of possible paths which early nonliving molecules may have taken, eventually evolving the array of properties that we use to describe living forms. Whether it was via primitive ribozymes, proteinoid microspheres, or some other yet undiscovered type of molecule, the mere fact that a number of viable natural solutions to the problem of life's origins exist gives support to the idea that life in fact began this way. We do not need to invoke a supernatural creation in order to explain how life began, nor is a supernatural explanation of any use to us - it ultimately explains nothing, and creates an unnecessary dead-end in the search for understanding.



* For an example of the fuzziness of our definitions of life, look to the example of viruses. Viruses do not meet all of the accepted requirements for what we define as life, but they are often included in modern biology textbooks as special cases of near-living organisms and taught alongside sections on bacteria and other more ancient forms of life.

this is how you pull in heroic ramparts

If you're a nerd like me (and I hope you are), you might find this slightly interesting. I was playing World of Warcraft yesterday and ran a heroic ramparts with an awesome group. The paladin tank was especially good. Our healer suggested that we try pulling the entire next room just to see if we could do it. By my count, we had around eight epic humanoids on us and a couple dogs as well.

Of course, because I am a super-nerd, I Frapsed the whole thing and made a little video late last night with music and the whole nine yards.

a little bit of self-exorcism

When I was growing up, my dad used to read the bible with me all the time. I would ask him questions that I had about what we had read, and he would answer them as best he could. My upbringing involved a lot of bible study and prayer, supplemented by countless hours of listening to my father talk about God, the purpose of life, the sacrifice Jesus had made for humanity, and the usual stream of Christian beliefs.

The thing about my father is that he is a master of the English language; he can say things that drill deep down into the core of your thoughts. Because he genuinely sounds like he knows what he's talking about, you are inclined to believe what he says without thinking too much. He is a quiet and unassuming man at times, but always has just the right words to say when they are required, and can make you feel very small indeed.

I don't speak to my father very much these days. Ultimately I made decisions about reality that strongly conflict with his worldview. Whenever we do talk, it gets ugly real fast. He is one of those people you cannot reason with, because in order to accept even a smidgen of what I say as being at all close to reality, he would have to admit that decades of his own life have been wasted on nonsense. There is a wall built around his beliefs, and it's covered in barbed-wire.

However, there's numerous things that I'm still grateful to him for; some of them even having to do with religion. During those readings from the bible, he would make certain events "magically" come to life. He made me feel like I was a Jew trapped in Jerusalem in 70 C.E. when the Roman armies had it under siege. Other times, I felt like I was carrying the Ark of the Covenant around the walls of Jericho while trumpets blared, or walking on dry soil across the middle of the Red Sea while the Pharaoh's armies chased us. Every child should have such an education in biblical literature.

Although I no longer believe that many of these biblical events ever occurred, it was still a nice mental exercise. My ability to empathize with characters in books that I read largely comes from those times I spent reading the bible with my dad.

So thanks, dad. All those hours you spent trying to indoctrinate me weren't a complete waste of time.

emiliana torrini & chemical party

I first heard the voice of Emiliana Torrini in a couple of Thievery Corporation songs. Since then, I've become a huge fan of hers - I highly recommend her album Fisherman's Woman. One of my favorite songs off the album is Serenade, which someone has mashed together with some anime on YouTube:

Also, check out this awesome science/music video that I found the other day. Besides being entertaining, it's educational as well!