Epigenetics - Blurring the Line Between Phenotype and Genotype

I caught a fascinating segment on Nova last night about a field of study called epigenetics. As I understand it, epigenetics is the study of how DNA is expressed in an individual. All of the DNA in your body is the same, but you have bone cells, hair cells, lung cells, etc. The differentiation between cell types is regulated by chemicals that attach to the DNA and turn on or off various portions of the DNA. This is how epigenetics work - specific chemicals turn on or off various portions of the DNA, allowing expression of the DNA to change.

But what's really fascinating is that they're finding through studies that what you do with your body (your phenotype) can actually affect the expression of genes in your offspring. This breaks a cardinal rule in Biology - that your phenotype does not affect your genotype. For example, if you cut off your arm, then have children, you aren't going to have one-armed children.

Strictly speaking, that rule stands, but functionally what the studies they were talking about in the program are showing is that genetically identical rats with different gene expression pass their flavor of gene expression on to their children. They also showed a cat clones with completely different fur pattern and color and eye color. Even the faces looked different, but they were genetically identical cats.

Is that fascinating or what? It's always just seemed intuitively obvious to me that the choices you make regarding your body could affect your offspring, but the biology textbooks have always told me I was wrong. As usual, the biology textbook writers did the best it could with incomplete data, but where they completely failed was by laying down as hard and fast law that your offspring were unaffected by your phenotype, rather than explaining that was the best understanding we had at the time.

I've noticed this trend increasing as I've grown up - scientists have become continuously more bold about proclaiming supposedly irrefutable facts. What is it about the priesthood of scientists that so often interferes with intellectual honesty? Why do they say "DNA is absolutely the only way you can pass anything on to your children." (The passage in my biology textbook was pretty close to that.) Instead, perhaps they should say "DNA is the only known method for passing information between generations, but theories abound and research continues to uncover new and exciting information."

The link at the top of the article to the Nova page has tons of good information including the complete video of the segment, slideshows, resources, etc.

Product Labels & Advertising - Part 1

As a generally logical and sensible person I naturally loathe product labels and most advertising. I will probably make small posts now and again about this topic. It's related to my utter disdain for redundancies in the English language (ATM machine, PIN number, LCD display) which I'll also post about once in a while.

So I'm sitting here eating my lunch and drinking a can of V8. This is what the product label says:

V8
100%
VEGETABLE JUICE
FROM CONCENTRATE WITH ADDED INGREDIENTS

So which is it? 100% vegetable juice, or does it have added ingredients? It makes no sense.

Checkers Solved - Are All Games Deterministic?

BBC News reports that the game Americans call checkers has been "solved" by brute force by computers. It is now not possible for the computer to lose at checkers, and if the human opponent plays perfectly the result would always be a draw.

One thing I sorely missed out on in college and have not allowed myself the time to get up to speed on is game theory, so be forewarned that the below may be a naive/easy question:

Are all games based on logic (i.e. a rigid set of rules) necessarily deterministic? The article mentioned above explains at the end how much harder it will be to solve chess, so obviously someone has done the work to decide that chess is solvable. But is it possible to create a game similar to checkers or chess that is not solvable?

My suspicion is the answer to that question is already known and straightforward, and I've just missed a whole vein of interesting topics in my education. If anyone out there knows - please enlighten me.

More on The Long Tail: Welcome to the Microculture Era

I was thinking more about the long tail idea and its relation to Western culture. I came across this article from CNN Money: The Extinction of Mass Culture.

While I was extolling the virtues of the long tail as it relates to culture, the author of that article makes the case for this being a bad thing:

The interesting question is whether all this choice along The Long Tail is an unalloyed good. "I think it's a net positive, but there are definite tradeoffs," Anderson told me, when I called to ask him. "Do we lose something as a society if we have less in common? How do we define ourselves as Americans if we are not sharing the same culture impacts?"

This is a really important question, and one which I hadn't considered. I'm big on culture and tradition. I believe that we all lose something when we don't work together as a whole, and history has shown that the intermixing of culture inevitably leads to the decline of an empire.

But isn't this inevitable? By definition the only nations at risk of overtaking the US are the same ones who have the level of industrialization that might cause the very problem we're discussing (the fragmentation of core culture), which would (in time at least) have the same effect on them.

The Hive and The Return of the Tribe

I see two things happening here. The first is the advent of the hive culture. Yes, we may all decide to listen to disparate music and favor niche entertainment, but we progressively cleave tighter and tighter to population centers, where jobs are available and entertainment is plentiful. Wal-Mart and Starbucks pop up everywhere while Ma & Pa coffee shops struggle to turn a profit and Jack Handy hardware shops go under. A continually greater percentage of the population is online, and those who are online are spending more time online. (I promise a whole blog post soon on the nature of the internet as it relates to the hive culture. Yay - lucky you.) The point is that while we fragment in proclivities we are actually coming together physically and starting to share the same modes of communication.

The other thing I see happening here is the return of the tribe. Most Americans are so dissociated from their roots that they just call whatever concrete and chipboard apartment they find themselves in "home." We live thousands of miles away from the people we grew up with, and our slightly mitigated freedom allows us to prosper without the support of our elders and peers. But human nature is implicit in our lives; we can strain against it like the sea kelp against the tide, but it will always push us the way it wills. Most of us feel happiest and most secure in a tribe; be it your little family and close circle of friends or your clan of Warcraft players or the IM buddies you met at the furry convention. So we find online clans of game players, communities of regulars on the messageboards popular sites like Slashdot, Fark, and Kuro5hin.

These are our new tribes, and I believe they will become an increasingly important part of our post-industrial information age lives. It is natural for us to want to cleave the the safety and enrichment of the hive; it is also natural for us to seek out individuals like us who we can scheme and commiserate and laugh with. A mass of niches indeed.

The Long Tail

In my first post I mentioned and linked to the mathematical concept of the long tail. The simplified explanation of which, as I understand it, is a statistical distribution where the less frequent events make up a greater portion of the distribution than the high frequency events.

So that may not have made sense within the context of my post. To laypeople like myself, the long tail concept is immediately recognizable in many areas common to modern life. The Google search engine is an obvious example: the top sites represent a large allocation of hits, but the long tail of less popular sites, in aggregate, are a greater portion of the whole.

In some circles the long tail concept has taken on a life of its own and usually refers to the fragmentation of modern culture. In his oft-cited article "The Long Tail" for Wired, Chris Anderson speculates that "the emerging digital entertainment economy is going to be radically different from today's mass market." Because we now have a seemingly infinite variety of choice, we develop niche tastes, which give rise to a statistically significant portion of the economy driven by niche markets.

This is more the meaning I intended in my blog post. I see myself as one of the billions, swimming around aimlessly in the long tail, terabytes of information at my beck and call 24 hours a day, simultaneously developing and discarding tastes, desires, memes.

Once you begin to think about the long tail concept, it makes you wonder how the big businesses of the world will adapt. The music industry certainly seems to be thrashing about in mostly misguided and stupid attempts to deal with the new economy. From Chris Anderson's article:

For too long we've been suffering the tyranny of lowest-common-denominator fare, subjected to brain-dead summer blockbusters and manufactured pop. Why? Economics. Many of our assumptions about popular taste are actually artifacts of poor supply-and-demand matching - a market response to inefficient distribution.

That is at once obvious and prescient. In the digital economy scarcity is mostly artificial (and will be purely artificial once big-pipe bandwidth is both free and ubiquitous), and distribution costs are negligible. It costs a few cents of bandwidth for most people in the US to transfer an entire modern production music CD, including high-resolution scans of the liner notes and bit-for-bit identical compressed audio to another entity.

And if having it in digital form is not good enough for you, all you need to do is conjure a physical manifestation of this work of art: burn the music to CD, print out the liner notes, and pop it all in an empty jewel case, and for less than $2 you have a product functionally identical to the $17 version the music store wants you to buy.

Compare this to the times when the best way to hear new music was to listen to the AM radio station broadcasting in your town. You now have the opportunity to become exposed to all different kinds of music. The same goes for literature, technical documentation, video, etc. We're all different, and we no longer have to listen to what the top 40 station is playing if we don't want to.

So the long tail develops.

For further reading: Accelerando! by Charles Stross. (digital version available for free)

Hi My Name Is

This will serve as the introduction/orientation for my blog. I don't intend for this blog to be as narcissistic as most, but I figure some readers might like to know a little about me.

I am just your average WASP drone in the tech sector. The point of this blog is for me to have a place to post my ideas and reflections (and yes, I'm sure occasionally rants too) usually concerning topics related to science (especially around the edges), philosophy, writing and the future.

Ideas are what tickle me. Philosophy and engineering courses were always my favorite in college. I like to think in terms of concepts and logic. My challenge is usually following through on those ideas and working to give them form in reality. My ideal job would be one where I come up with great ideas and concepts and someone else implements them.

Please don't judge my writing potential by what I post here... my opinion is this is an informal venue and the writing style I will employ here will typically be loose and casual.

Since I obviously do have interests and I am not completely apathetic, the obvious question is, "why the blog title?" The answer is that I am not enthusiastic about work and life in general most of the time. I don't see that my efforts up to this point in my life have really amounted to what I'd hoped for, and I am realistic that I am a single voice among six and a half billion others. I am the very case study of the individual swimming aimlessly in the long tail.

This is your life, and it's ending one second at a time.