Blessed by the Potato

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.

It’s been a recurring theme here, but it bears repeating: I have no idea what to do about hosting. Something that would go a long way towards helping me make my decision would be an idea of how many people use this site; a census of sorts. So I’m asking everyone who hasn’t already left a comment to please leave me one just so I know how many unique users there are. If you’re shy, you can email me at holypotato at gmail instead. Or, you can leave a comment with 3 or more URLs in it, which will then cause it to be caught by my spam filter. I can from there delete it without anyone seeing it.

To encourage you, I’m going to offer a cookie to anyone who leaves a comment to this post. I’m assuming, of course, that right now I’ve only got a small handful of readers located in a small geographic area (that is, friends of mine, or friends of friends). If it’s not feasible to get a cookie to you (or if you wish to remain pseudoanonymous, which I totally understand), then perhaps we can work out some other form of cheap-as-free incentive.

Edit: yes, a real sugary cookie, not some truly worthless tracking file in your web browser.

On to other matters: Kraft Dinner.

It really deserves it’s very own post, but I’ve been wondering lately why I like it so much, and couldn’t wait to author a proper post. It’s so artificial, and it’s not even all that cheap any more (the logs now run at just about a dollar, and the fancy white cheese, spirals, and three cheese flavours all top $1.50). But I love it any way. Not a month goes by where I don’t have a pot, and usually more like once a week. My cat likes it, too, which only strikes me as a little bit strange. What’s really weird though, is that I hate macaroni and cheese, by which I’m referring to that casserole stuff with real macaroni noodles and honest-to-goodness cheddar cheese baked on top.

I’ve had a strange error in Windows XP for several months now. It’s intermittent and as far as I can tell, random. I’ve had no luck searching the web for solutions, so any advice would be greatly valued.

What happens is basically folders will stop responding. I can open up one folder, and then a few seconds later if I try to open another folder file within that folder, there will be no response. No error message, nothing. Right-clicking a file to try to get properties also yields no information. During this error opening subfolders never works, but sometimes I can open files (though I can’t right-click for properties, and if files do open, there’s always a 20 second or so delay).

Usually the last folder I successfully open won’t have a menu bar, just a white space with the windows logo (see the image below). In case you don’t see the distinction, that space usually contains “File, Edit, View…” etc.

If I wait long enough (usually 10 minutes or more), functionality comes back. If it happened once though, it will likely happen again within a few hours, and every few hours until I reset. It very rarely happens within a day of a reset.

In other news, another record number of hits yesterday: a whopping 79. It’s enough to make me wonder if there’s someone out there hitting refresh a million times a day (or if my own testing of the RSS capabilities did the same… I don’t think they would, but it’s possible). Hardly anyone’s leaving comments, so I’m inclined to think that this isn’t real traffic. If it is though, it might be time to look into a new web host to handle that sort of load. I’ve had suggestions for blacksun.ca, hostgator.com, and lunarpages.com. If anyone has any other suggestions, or more importantly, if you get any sort of kickback for referring me, leave a comment! (All else being equal, I might as well go with the host who’ll give my friends a free month, eh?)

I’ve been a long-time fan of Mozilla (now known as SeaMonkey). Except for those few sites that have poor HTML compatability or use ActiveX (or just don’t work for no reason at all, like Yahoo Launchcast), it works really well. I love tabbed browsing, since even in the Netscape 3.0 days I had a billion windows open, usually flowing over into the second level of my start menu (how my 486 handled it, I’ll never know).

Things I love about Mozilla:

1. Tabbed browsing. ‘Nuff said.
2. Tabbed bookmarks: I can open a bunch of tabs, and bookmark them all together. This is handy first off for essentially saving your session if you need to shutdown and reset, but also for streamlining daily browsing. Every day, I read Dilbert, check the weather, check the space weather, check the news, some other comics, etc. Rather than going through my bookmarks one at a time, I simply click on the tabbed bookmark and it opens all of them at once in separate tabs.
3. Not having to always second guess what I’m opening. True, you have to have some modicum of common sense when surfing, since no platform is invulnerable, but it’s nice not having the software compeletly riddled with security holes, and moreover, not having it so intimately tied into the operating system.
4. A decent email client. It does everything I want it to, and again, I don’t have to worry quite so much about what viruses I might get sent, since it’s not outlook.
5. Password/form saves that are protected by a master password.

Oddly enough, despite being such a big fan of the full Mozilla suite, I’ve never quite made the shift to Firefox. The minor differences in Firefox never really appealed to me. For example, since it’s more of a browser for the masses, the configuration options are more limited (at least the ones through the menu: you can still tweak everything by going into the prefs.js file). One thing that really irks me is that when I bookmark a group of tabs, I have to do one more step to get them all to open up (previously it was simply bookmarks->morning_reading now it’s bookmarks->morning_reading->open in tabs). It does have some things not present in the old suite, such as live bookmarks (which don’t work for my own site due to the way I tried to ensure I could survive a change in IP — the live bookmark requires some absolute URLs where I have relative ones). They’re kind of neat: you access a site’s RSS feed to see what’s new so you can tell if it’s been updated before you even open the link.

It’s also a bit leaner, so it loads faster. But other than that, I’m not hugely impressed with Firefox vs. the full Mozilla suite. Sadly, they’re no longer maintaining the full suite (at least not to the same degree, from what I understand the SeaMonkey project, aside from a horrible new name, doesn’t have the same resources as before).

For email, I’m using Thunderbird. I find it’s actually an improvment over the mail package of the full suite, largely in the ability to search messages (not just by sender or subject or within current message, but you can do full-text searches of all your messages when looking for that one archived email). However, I miss having them integrated. True, it makes those rare browser crashes a little more graceful, but I miss being able to right-click on a link in my email and choosing whether to open it in the current window, a new one, or bookmark it. Ah, well, I suppose I’ll learn to live with it.

Both of these packages are highly expandable with add-ons, which is handy. One that is hilarious and completely useless is Bork Bork Bork! an extension to view webpages as though read by the Swedish Chef. One that I’m fond of is the calendar extension… for the old Mozilla suite. Unfortunately, it doesn’t seem to work with the current Firefox or Thunderbird, and has somehow perversely spun off into its own stand-alone program Sunbird. One sad downside of this spin-off is that since it no longer has a bundled email client, the email reminders no longer work. These were great for using my calendar at home to email me reminders while I was at work. The only problem was when I forgot to put my meetings in the calendar in the first place.

Correction: If you search for the calendar on its own, rather than from the Thunderbird extensions, you’ll find the days-old update that does work with the current version of Thunderbird. Sadly, it didn’t automagically import the events from my old calendar install. Everything else seems to work just fine, though. Another disappointment is that in the old Mozilla Suite, the calendar had a start menu icon of a calendar, now it shares the same icon as Thunderbird.

So I don’t really know what I’m going to do now. Tonight I installed Firefox & Thunderbird, and this is the first blog post I’m writing on it. These are all minor problems, and I still prefer this over IE/OE, but I have a feeling I might slip back towards SeaMonkey. Of course, I can see how for many people, the stand-alone Firefox is better. After all, many people only have webmail accounts now, and so have no need for a POP/IMAP client like Thunderbird. Plus, separate programs (even though they are incestually related in their rich content message rendering) is the way Micro$oft does things, so why shouldn’t Mozilla follow that lead?

Some quick tips for new Firefox/Mozilla users:

• F11 will get rid of the title bar and status bar, making your viewable page area as large as possible. F11 again to bring it all back.
• CTRL-T opens a new tab; CTRL-N for a new window.
• CTRL-click a link to open it in a new tab.
• The bookmarks toolbar is a handy way to keep those most essential dozen or so bookmarks readily available. If you don’t really need it though, then you might as well uncheck it from the “view” menu and give yourself another line of viewable page space.
• You can use Thunderbird to subscribe to blogs and get them automagically downloaded to your computer just like an email message. It’s not as pretty, but it can be faster. Note that this does work for my site, unlike the live bookmarks. I’m in the process of writing a quick tutorial on it, watch the page pane on the right for more.

Oh, I’m scheduled to have my cytoscope procedure < shudder > on the 23rd, which is election day, so I’m going to go to the advanced polls to cast my ballot.

Unfortunately, that means I can’t wait for the last-minute estimates to come up so I can decide which way to vote. While I don’t savor strategic voting, it is unfortunately necessary sometimes in our first-past-the-post system.

Here’s my thinking: I’m a fairly left-of-centre guy, so for me the choice is really between the NDP and the Greens. I don’t want the conservatives to get any sort of power, and I’d like the liberals to get a minority or less again. So basically, if the NDP have a decent shot at getting a seat in my riding (say 30% or more support), I’ll probably vote for them. If not, I’ll vote Green and give them the $1.75 for the next election.

The only concern for myself really is getting reasonably accurate polling numbers to determine that over a week before the election.

For others, I’m worried that fears over conservative insanity will lead to another liberal dynasty (Wayfare, for example, is considering voting for them just because she thinks they’re the only party that has a chance against the conservatives, despite thinking that they’re rotten to the core and just need to go). It’s unforunately a fallacy of perception: if many people believe they’re the only ones with a shot, then they’re the only ones who’ll get enough votes. Any party can keep the nutjo–conservatives out of power, as long as enough people believe they can and actually vote for them.

Sadly, I can’t reach quite enough people through my webpage to really get that message out, but I encourage you all to vote your conscience (even if it is for the liberals or conservatives). At the very least, the wide vote-split might encourge the parties to actually go through with some form of election reform so that we’re not faced with this again next year.