mahiwaga

Still reading stuff about multicellular computing.

Not necessarily applicable to software above the level of a single device, but Burbeck gets it wrong with regards to versioning issues in multicellular organisms.

For one thing, there is the key versioning difference between somatic cells and gametes. Somatic cells, the type of cells that become neurons, myocytes, hepatocytes, blood cells, etc., are diploid and always have two copies of a particular code sequence of DNA: two copies of every gene, which are going to be two versions, one from each parent. Gametes are haploid, containing only one copy of every gene. The creation of gametes involves choosing which version of a gene to include. This has been thought to be a completely random process, although as we learn more, it may not be completely random.

More dramatic is the versioning that occurs in cells of the immune system: each cell gets random changes to its DNA—bits/base pairs are spliced out and discarded permanently, allowing each cell to recognize different parts of different foreign organisms—different epitopes. Versioning becomes important because the body has to deactivate versions that react to itself. Versioning also occurs when a B lymphocyte (a specific type of cell in the immune system) class-switches: it dumps entire segments of DNA in order to form different classes of immunoglobulin—different classes of antibody, corresponding to different phases of infection. (IgM and IgD are produced acutely, IgG is produced generally after six weeks or so.)

Another type of versioning occurs with the specialization of stem cells. A pluripotent cell becomes a multipotent cell, which then becomes a stem cell. The stem cell divides so that one daughter cell remains a stem cell, while the other daughter cell goes on to differentiate.

The reason why you can’t use differentiated cells to form other types of cells like you can with stem cells is that there are differences in the resultant DNA. While it doesn’t necessarily mean that actual bits/base pairs are discarded, the histone scaffolding only allows certain genes to be expressed, and we don’t (yet) have a good handle on how to manipulate the scaffolding (although as recent research has shown, we can reverse differentiation to a certain extent.) The problem with non-selective manipulation of the scaffolding is that this is precisely the mechanism that causes cancer: cells that mutate and become malignant tend to de-differentiate.

Yet another example of versioning is what occurs on the X chromosome in women: in each and every somatic cell, one of the two X chromosomes gets randomly deactivated so that there is a proper balance in gene expression. (This process is called lyonization.) Because the two versions are essentially guaranteed to be different (one is from mother and the other from father), it can sometimes result in mosaicism of traits. More interesting is the fact, in some instances, the cells are able to uniformly deactivate the version that has a deleterious mutant gene.

Then there are the sub-organismal transactions of data. Viruses and transposons continually infect cells and their DNA sits in the nucleus, often quiescent until some stress stimulus forces it to manifest itself, which then provokes an immune response and eventually leads to apoptosis. While the viruses we are most familiar with in daily life: rhinoviruses, adenoviruses, rotavirus, etc., infect cells that have limited life cycles, making such infections self-limited, there are other viruses that essentially take up permanent residence in our DNA: varicella, herpes simplex, cytomegalovirus. Also hepatitis B and C. And HIV. These predominantly cause diseases of reactivation. (For example, the primary infection in HIV really just causes flu-like symptoms which eventually subside. The disease doesn’t really progress until much later.) While one can argue that these are foreign, invading DNA/code, it is clear that the packaging, transporting, and integration of pieces of DNA has long been a part of life, and may have a direct hand in evolution.

Again, the similarities between cell biology and computer software became more apparent with the popularization of Open Source. The prime example of DNA versioning is with the Linux kernel. The same source code—the same DNA—is used to generate widely different kinds of kernels. Some are run on desktop computers, others on servers, but even more drastic are the different versions that run mobile phones, PDAs, routers, DVRs, and various other embedded devices.

We are beginning to enter the age where code can become self-sustaining. Mac OS X’s and Windows software update programs are just simple examples of what is likely to become standard fare. Google and Amazon already give suggestions about what other content we might be interested in. We can make DVRs selectively record shows we might be interested in. iTunes has already had rudiments of being able to select songs that you like in your collection, simply by keeping track of the play count. For very specific things, the computer can anticipate your needs.

Imagine if you extrapolated this principle to software—RNA—itself. Obviously there would be enormous security risks. But what if your system anticipated and automatically downloaded software you might be interested in? What if your Linux distro could anticipate which of the cutting edge patches you might be more interested in and it could offer to immediately download and compile it in? What if embedded devices, when connected to the Internet, could detect when a patch relevant to that particular device was released, and it could essentially update itself?

I think it might’ve been Sirius, the dog star, in the southern sky that lit my way tonight, like a beacon, brighter than the ambient glow of the urban sprawl before me, but I only have a faint grasp of celestialography, so I could be wrong.

Ten days until the sun finally halts its retreat and finally stands its ground. Twenty days until the year’s end, leaving me wondering about the future, and whether it’s even worth wondering at all.

The problem with driving down to San Diego with only my iPod as my companion is that I can get lost in the random music that it plays, dragging me through my memories, many of them dark and bitter. The following is not necessarily exact, but it serves as a rough guide.

1. Vienna Tang “Harbor”
   hauntingly echoing my deepest desire, although perhaps something that will never come to pass in this lifetime.
2. Semisonic “Singing in My Sleep”
   on the connector ramp from the Glendale Fwy southbound to the Golden State Fwy southbound, bringing back faint memories of nine years ago after leaving the Bay Area in defeat, and resigning myself to at least a year in limbo in L.A.
3. Hooverphonic “Cinderella”
   past the junction of the Golden State Fwy with the Pasadena Fwy, on the way to the East L.A. Interchange. The rhythm of the song at first makes me think of “Bettie Davis Eyes” by Kim Carnes. Maybe this could be inspiration for a mashup.
4. Amina “Hilli”
   speeding through Irvine, past the El Toro Y, making me think of something that might have been composed by Nobuo Uematsu for the theme of some imaginary town in some as-of-yet undrafted installment of Final Fantasy
5. Aaliyah “Journey to the Past”
   as I wound my way through Laguna Niguel, remembering faint memories of ten Decembers past, and my heart not didn’t so much break, as it did just dry out. And still I dream of home.
6. Hooverphonic “Battersea”
   through San Clemente. The lyrics are faint, leaving haunting traces in my mind.
7. Nelly Furtado “All Good Things (Come to an End)”
   through Camp Pendelton. This song has captured my mind ever since I heard it for the first time this summer, and the answer is quite simple, and quite bitter.
8. Frou Frou “Hear Me Out”
   probably either Oceanside or Carlsbad by this time.
9. Feist “Secret Heart”
   probably Encinitas or Solana Beach. Reminding me of how so many words have died stillborn in my heart, freeze dried by despair, evaporated by helplessness.
10. Sunny Day Real Estate “Song About an Angel”
    going past the merge, heading south on the 805
11. S Club 7 “Never Had A Dream Come True”
    southbound on the 805 past La Jolla, through Clairemont Mesa, to the connector ramp to the southbound 163. This song always kills me, dragging me through the last ten years, and sticking a dagger right in my half-rotting, half-dessicated heart.
12. Anggun “On the Breath of an Angel”
    exiting the 163 to Friar’s Road, remembering that even with the mess I could’ve turned everything into, she still saves me with her friendship.

It was pretty much ten years ago when I realized that my life would definitely not have a “happily ever after” ending. It’s not that I would necessarily live a tragic life, though. I mean, everyone has their regrets and failures that haunt them for the rest of their lives, right? At least that’s what I tell myself whenever I start feeling sorry for myself.

The more that time passes, the more it becomes apparent that the way things went down was inevitable. The moment came, I was tested, and I was found sorely wanting. I wasn’t meant to be the one, and that’s the way the cookie crumbles.

And yet, somehow, everything that has happened since seems to be an echo, a reverberation from that time long gone, and even this far out, I can’t seem to completely break free of my self-destructive patterns. It’s as if from that moment on, I was doomed. I was damned.

For a while, I’ve held out hope that things would change for me, that I would grow, that I would eventually have my chance for happiness someday. Even though I’ve wanted to give up, I’ve kept going, still keeping this ember of hope burning, still somehow hoping for some miracle.

I wonder how many years must go by before I must accept that my hope has run out. How many years must go by before I can just thrown in the towel, call it quits. Some things were never meant to happen.

I think, sometimes, of the curse of The Flying Dutchman, doomed to wander the seas until the end of time, never able to reach the shore. Or of Coleridge’s doomed Ancient Mariner, or perhaps the Wandering Jew. Bill Murray in “Groundhog Day.”

But I’m still hedging my bets. I also think of Schmendrick the Magician, cursed to never age until he learns the secrets of magic, and reaches his full potential. Maybe, still, maybe, I’ll meet a unicorn, and maybe even someone like Molly Grue, and while the story won’t necessarily end happily ever after, maybe I can at least find my way home again, and at least have some sort of peaceful end.