Blessed by the Potato

So despite spending so much time on my MSc thesis — and suffering so much because of it — I’ve actually put some thought into what I might want to do for my PhD thesis. And I think I know what it is that demands my attention. It’s a grand question that has plagued the world for too long now, causing needless suffering and loss of life. The matter is a little outside my area of expertise, perhaps you could even describe it as a humanities subject, rather than science, but I still think I’m qualified to study it. Two factions, seemingly at each others’ throats since time immortal, who just can’t seem to find common ground for peace.

I’m speaking of course, of the epic battle between Pirates and Ninjas. What is it about Pirates that Ninjas just can’t leave them alone? Why must they fight incessantly? Could not a graduate student, with enough free time and caffeine find some common ground for peace between these great people to flourish? And what of the people who don’t easily fit into either camp? Those parrot-loving, verbal ticking (Yarr!) people who have a penchant for black pyjamas? Or the more flamboyant one-eyed ninjas, trained to be deadly weapons stalking the night, but who also enjoy a liesurely saturday afternoon cruise? Can we not bring them all together to have peace in our time?

I intend to start at the beginning, and research the source of the great pirate-ninja feud. Such things often turn out to be caused by a minor, often accidental, slight by one group, that is then escalated out of all proportion by stubborn hotheads on both sides. Then, after these wars rage for the long enough, simple momentum keeps them fighting, though no one knows why. The middle chapter of the thesis will focus on the modern pirates and ninjas, contrasting them both with their historical versions, and also with each other, as a basis for finding some common ground. The final phase of the research will be more hands-on, as I attempt to apply what I’ve learned to the real world, by bringing together various groups of pirates and ninjas and acting as an arbitrator. We shall see if my skills will be enough to bring about a truce in our time.

Yarr.

Well, I have some ambiguous news for a change. Talked with my supervisor, and he says that the grant he applied for was trimmed back a fair bit from the budget they asked for, but that’s to be expected usually. It’s still approved, so there’s money there for experiments when I go on to my PhD. I still haven’t heard from the rest of my committee about my thesis drafts, but he says that’s to be expected: they want me & my supervisors to do all the nitty gritty million draft revisions work, and won’t even look at it until my supervisors sign off on it as being done.

Orson Scott Card recently wrote an opinion piece on Intelligent Design vs. Darwinism. He made some good points, but I also think that he skimmed over some of the issues in reaching his conclusion.

First off, he did a good job of distinguishing Creationism, Intelligent Design, and Darwinism. Creationism is not quite the same as Intelligent Design: while they both contain appeals to a Higher Being to explain gaps in the evidence, Creationism is significantly more dogmatic and, well, silly. Creationism essentially says that the story of creation in genesis is literal truth. God really did create the earth out of nothing in 6 days, and all the species were placed there in their final, complete, and perfect forms. Any fossils or extinct species we may find today (such as dinosaurs) were simply those species that were not carried by Noah on the arc, and saw mass extinction in the Flood, or alternatively, placed there on purpose by God when He created the world to, as proclaimed by the (non-canonical) prophet Biff, “Fuck with our heads.”

Intelligent Design, by contrast, is… somewhat… scientific. It agrees with Darwinism on a number of important points, including that evolution occurs (species change and diverge over time), and that natural selection may, in some cases, be involved. But where it differs is in the nitty-gritty: rather than relying on the mechanics of random chance and mutation to generate the differences upon which natural selection acts, ID instead invokes the actions of the “Designer” (generally, the Christian/Judaic God). ID (and OSC) argue that the appeals to a Designer are only made in the areas of the Theory of Evolution that are not fully understood, and so are no more religious than the Darwanist appeals to fortune and chance. By that argument, both theories break down into dogma at some point, and so neither should be taught in the schools. Instead, the Theory of Evolution should be taught, but only up to the point where it is well-supported by the evidence (namely, that species change over time, and that selection of the fittest and descent of traits over time is invovled. No mention of why these changes occur, what generates the variance for selection to act on, nor what else might be involved in addition to natural selection).

I’d like to make a few points of my own though (realizing the danger of trying to debate someone as talented as OSC, I’m not going to post a copy of this on his forums :)

He says that ID only exists because it explains the “holes” in Darwinism. I’m not sure that there are holes in Darwinism.

Let’s start with a few quick definitions and some common ground. We agree that evolution occurs, and that natural selection plays a role. This is the basis of the Theory of Evolution — notice that I capitalized Theory, this is because I wish to distinguish it from the word “theory”. You see, we have “theories”, which are our best guesses as to what is going on, stories that explain the facts as we know them, but which aren’t necessarily solid yet. Then we have Theories, where I’ve reserved the capitalization for those special theories that have been proven over and over and which form a fairly fundamental basis of our body of knowledge. So by this, I mean things like the Theory of Gravity, the Theory of Evolution, etc.

So, the Theory of Evolution covers the fact that species change over time, and that natural selection is the engine of that change. If, for example, two subpopulations of a species have different traits, the one with the trait that is more advantageous to survival will survive longer to breed more, and in the next generation that subpopulation will make up a larger portion of the species as a whole, until virtually the entire species has changed to contain the trait.

I would say that it also covers other important aspects of the process, tying into the inheritance of traits (the theory doesn’t work very well if those who survive due to their traits can’t pass them on), which ties into genetics. It doesn’t strictly rely upon another theory explaining where the variance that natural selection acts on comes from (mutation, or divine fiddling), and it doesn’t necessarily get into explaining other problems that I’ll get into (rather, the theories explaining those problems are based on the Theory of Evolution).

First off, we have the “problem” of explaining where the variance comes from that natural selection acts on to cause evolution. We know that inheritance occurs via genes encoded in DNA, and we know about copying errors and other mutations that can change those genes, which produces variation. The problem, as the ID people see it, is that by far most of the mutations we’ve observed have been harmful. Our bodies appear to be finely tuned organic machines, and futzing with the blueprint, even in relatively minor ways, can have disastrous results. So, they cite this as a shortcoming of the theory, and make their first call to the Designer, to put in beneficial mutations on purpose (for how else could something with such a low probability get in there?).

My response to this is that it’s not really necessary. True, getting hit by a cosmic ray and mutating in such a way to improve your odds of survival is like winning the lottery (or even worse!), but we have two things that make this system work. The first is sheer numbers. When dealing with whole populations as long as any one member gets a beneficial mutation and survives to pass it on, it’s gravy, even if millions of others suffered negative mutations and were culled (or even failed to gestate). The other is time. Evolution, particularly drastic speciation, can take place on very long timescales, which gives us lots of opportunities for a beneficial mutation to come along. Keep in mind that the whole time natural selection is also acting on the deleterious mutations, preventing them from becoming too problematic.

Closely related to this is that mutation rates for different genes vary. The genes that are critical to survival, such as the ones that encode the proteins that digest sugar or heat shock proteins (my own topic of study), hardly change at all over billions of years, with just a few trivial basepair substitutions accrued in the divergence of yeast to humans. While other less critical genes, such as those for various pigments, are more open to variation. The arguments over this are difficult for both sides. One one hand, it seems like exactly the sort of thing a Designer who did not wish to meddle too much would put in place, while at the same time, since it offers such a high increase to survival, it would be “strongly selected for” by natural selection. How it got there may be something we may never be able to answer one way or the other, but in my opinion, since it’s there now, it gives a mechanism for “undirected” Darwinism to take place.

The next argument, and perhaps the strongest in the ID arsenal, is the issue of complexity. There are two facets of the argument. The first one, and in my opinion the only valid one, concerns the intermediate steps. A valuable adaptation, such as an eye, or a bat wing, does not spring out of whole cloth in a single generation (though if it did, that would practically scream out the existence of a Designer!), there’s a lot of complexity involved there, and the intermediate steps on the way might not necessarily confer an evolutionary advantage. So if we consider a “fitness quotient”, the base organism might have a value of 100, and the “evolved” organism (with a complete wing or eye) might have a value of 125, but in-between, it has to pass through the “half-finished” stage, where it might be less survivable, with say a value of only 80. Our Theory tells us, then, that barring the outside influence of a Designer, the less-survivable “half-finished” version sould be selected against in favour of keeping the original.

There are a few responses to this. It’s not necessarily true to assume that the intermediate steps hold no value. This has been demonstrated with the eye: if you break it down into more logical steps, you wouldn’t start with an unseeing globe on your face, you’d start with a simple light receptor. All it could do is sense the presence or absence of light. And you can immediately see the use in that: you can more reliably determine what time of day it is, or if the weather is really terrible out (blocking out the sun). If you’re a pond-dwelling organism, you can then decide when to move out into the sun, or when to move away from the fresh-water slick formed on the surface during the rain. Then you can proceed to the next step: an array of photoreceptors to determine direction of light as well. From there, you can enclose them in a globe behind an aperature like a pin-hole camera. Useful both for protection and forming images on the photoreceptor array. Then, you can develop a lens that allows you to better focus the image, to look at specific things in detail. I tried to do the same for the bat wing as a school project, and it was a little harder to go through each step, but there I was helped by the fact that it requires fewer steps. If, for instance, you want to start with something like a flying squirrel (so you already have the soaring behaviour and the flaps of skin), it only takes a single mutation to make one finger freaky long to really stretch the skin out and glide like crazy. One other complication is that selection pressure is not equal through time. Selection pressures change depending on the climate, the relationship with other species and other factors. While unlikely, it is possible that a species could experience next to no selection pressure for a time. For example, let’s say that a group of rats swam to a previously uninhabited island. There would be abundant food for several generations before they had to compete amongst themselves, and predators were completely absent for a time. In those sorts of conditions, all sorts of “experimental” evolutionary off-shoots could take place, regardless of their usual survival value. A few generations of these sorts of conditions could allow a new change (like a bat wing) to progress through those poorly adaptive intermediate stages to form the basis of a fully-functional subspecies.

So this is an area where Darwinism has difficulty explaining the evidence, and where the theories become small-t ones, but I really don’t think it’s a “shortcoming” that requires an alternative explanation like Intelligent Design.

The other part of the complexity argument is that for each of the simple changes I’ve described above, there are fairly large biochemical changes. There’s just so much that has to change, that surely it requires divine intervention? This one, I think, is merely a misunderstanding of the problem. True, there are tens of thousands of genes with millions of amino acids, but the thing about our bodies is that they’re based on a very modular blueprint, and the genetic code is not necessarily on a one-to-one basis with phenotype. You can make minor changes to certain genes and get huge changes in body design, while big changes to other genes make very little difference. And because everything is so modular, it’s very easy to just copy a gene and make minor changes. For example, if you wanted to have 4 arms like Goro in Mortal Kombat, you wouldn’t need to find, copy, and alter all of the genes involved in arm construction, such as the ones that encode the nerves, the muscles, the vasculature, the skeletal basis, etc.; all you would need to do is find the protein that during embryogenesis directs all those other genes to form an arm, and alter it so that it instead called for two arms to be made. The already-established set of genes that direct arm formation would handle the rest. (Though if you wanted to use the arms, you might also need to alter the genes that make shoulders).

Far less complexity than one would think…

Anyway, I’ll wrap up my diatribe here. I agree that definitely the Theory of Evolution should be taught in schools, but I don’t think that it is so deficient in certain aspects of the how and why that appeals to a Designer need to be made. While those parts may not deserve a capital-t Theory (yet), I think they have a good enough probability of being true that they should be taught in schools (and that they’re not quite as religious as OSC makes them out to be). While Orson doesn’t think either ID or this extension of Darwinism should be taught in schools since they’re both based on faith at the moment, I’d have to disagree. While we may not know it to be scientific truth yet, these theories on how evolution occurs represent the best idea we have so far, and teaching them to our kids will give them the best foundations to discover what the real story is in the future.

Moreover, this theory has some predictive value, and is useful in that way. Whereas Intelligent Design won’t ever give you predictive powers unless you can speak to the Designer in some meaningful way — and if we could do that, the debate would be over!

Finally, I don’t mean to say in any of this that science or evolution deny the existence of God. It’s just that invoking Him isn’t necessary to make our theories work, and to explain the world around us. However, if it suits your belief pattern any better, God can happily influence any random process, from your rolls at the craps table in Vegas to the pattern of mutations underlying evolution, without ever impacting the science of your theory. Randomness is and perhaps always will remain beyond our control and understanding. It’s in this domain that God can potentially carry out His divine machinations without overtly revealing Himself and thus denying Faith. It is perhaps for this reason that fundamentalist religious types don’t like science. They don’t like the idea that they may just be praying to pure dumb random chance.

Edit 1: Too many “first offs” :)
Edit 2: Last paragraph.

I miss just sitting down and writing sometimes. I often consider it as a backup profession, since science really really hasn’t been doing so well for me. I might just be able to go off and write, either fiction or as a science reporter or something, if it weren’t for the 15-page brick wall. You see, look through my archives, or worse yet, my hard drive. You’ll find that I almost never finish my longer more-involved stories, despite thinking about them often and playing out different plotlines in my head. They just get to a certain length and that’s it. I even had the same problem with my thesis. I got to about 13 pages in relatively short order (well, not really – I’m a FURIOUSLY slow writer, especially for my thesis), and then just really got bogged down with writer’s block and the like. So I can’t really consider writing as a viable way to make a living if I can’t actually write anything of substantial length.

After all, at 2 cents a word (that was the going rate in 1998 when I published my one and only story for $25) you need to write a lot to make even as much as a grad student.

The website’s been down a long time while I sorted out some issues in real life (c.f.: Thesis), but it’s good to write completely open-ended again. Which is possibly where some of my 15-page issues come from: you get to a point in a story where it can’t go anywhere anymore: you have to bring the threads together and wrap it up. And I’m just lousy at that.

I much prefer writing just train-of-thought, or since I don’t necessarily follow any sort of linear progression most of the time, the off-road vehicle of thought. So it’s good to have the website back.

Oddly enough, I enjoy just writing sometimes. Even when it makes no sense and gets deleted right away. Just writing this has made me realize how incredibly stupid I’ve been lately.

You see, I had this whole thesis thing going, right? And I was feeling some measure of guilt whenever I would write anything else (such as this) while my thesis made no progress. So I made a resolution with myself not to do any work on my website until my thesis was done. But I’m coming to realize that I need to start off getting all the random thought threads out of my head to properly focus on my thesis. Or, at the very least, this doesn’t seem to interfere with the thesis, since for the year I laid off superfluous writing I didn’t make any better progress.

It’s just such a piss-off, since I can churn out a post like this in under an hour. I wrote a 10-page (yes, ten!) introductory guide to curling before the departmental curling fun night, and it took me all of two hours. Two hours would barely buy me 5 sentences in my thesis. Of course, the writing is completely different – this is irrelevant, errant, entropic writing where the main points are to give my fingers something to do and to possibly entertain my miniscule audience, whereas my thesis has to be informative and correct (and referenced).

Remind me to post that curling guide at some point.

So anyhow, that brings us to the bottom of the screen, and this page. As you can see in what was essentially my test post below, I decided to make a blog. It’s essentially what I was doing all along on Blessed by the Potato, only without wearing out the <> keys on my keyboard. It’s hideous at the moment while I learn CSS and whatnot by trial-and-error. I’ve also got to photoshop all my graphics and stuff. I’m also sorting out how to integrate some of the old material into this. Right now I have a front page where you can choose between the old site or the blog; I think soon I’ll integrate the old submenu with the links on the right. I’ll probably ditch a lot of the old subsections (like the science games and model building (Heavy Gear)) and just have the separate rants, advice, and short stories section. I might even get around to converting those to have a style that meshes better with the blog section (or vice-versa).

Hopefully this will be updated somewhat regularly.

Oh, and Rez won the “first” contest. Please, no more.